Student Publications

2023

Silverstein MR, Segrè D, Bhatnagar JM, 2023, Environmental microbiome engineering for the mitigation of climate change, Glob Chang Biol, Jan 20.

2022

Kern JG, Tilston-Lunel AM, Federico ANing B, Mueller A, Peppler GB, Stampouloglou E, Cheng N, Johnson RL, Lenburg ME, Beane JE, Monti S, Varelas X, 2022, Inactivation of LATS1/2 drives luminal-basal plasticity to initiate basal-like mammary carcinomas, Nat Commun, Nov 28;13(1):7198.

Turcinovic J, Schaeffer B, Taylor BP, Bouton TC, Odom-Mabey AR, Weber SE, Lodi S, Ragan EJ, Connor JH, Jacobson KR, Hanage WP, 2022, Understanding Early Pandemic Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in a Medical Center by Incorporating Public Sequencing Databases to Mitigate Bias, J Infect Dis, Nov 11;226(10):1704- 1711.

Rodríguez-Sastre N, Shapiro N, Hawkins DY, Lion AT, Peyreau M, Correa AE, Dionne K, Bradham CA, 2023, Ethanol exposure perturbs sea urchin development and disrupts developmental timing. Dev Biol, Jan;493:89-102. Epub 2022 Nov 8.

Jafari N, Chen A, Kolla M, Pompa IR, Qiu Y, Yu R, Llevenes P, Ennis CS, Mori J, Mahdaviani K, Halpin M, Gignac GA, Heaphy CM, Monti S, Denis GV, 2022, Novel plasma exosome biomarkers for prostate cancer progression in co-morbid metabolic disease, Adv Cancer Biol Metastasis, Dec;6:100073. Epub 2022 Nov 4.

Landaverde L, Turcinovic J, Doucette-Stamm L, Gonzales K, Platt J, Connor JH, Klapperich C, 2022, Comparison of BinaxNOW and SARS-CoV-2 qRT-PCR Detection of the Omicron Variant from Matched Anterior Nares Swabs, Microbiol Spectr, Dec 21;10(6):e0130722. Epub 2022 Oct 18.

Turcinovic J, Kuhfeldt K, Sullivan M, Landaverde L, Platt JT, Doucette-Stamm L, Hanage WP, Hamer DH, Klapperich C, Landsberg HE, Connor JH, 2022, Linking contact tracing with genomic surveillance to deconvolute SARS-CoV-2 transmission on a university campus. iScience, Nov 18;25(11):105337. Epub 2022 Oct 12.

Pacheco AR, Pauvert C, Kishore D, Segrè D, 2022, Toward FAIR Representations of Microbial Interactions. mSystems, Oct 26;7(5):e0065922. Epub 2022 Aug 25.

Becker EJ, Faiz A, van den Berge M, et al, 2022.Bronchial gene expression signature associated with rate of subsequent FEV1 decline in individuals with and at risk of COPD, Thorax,77:31-39. 

R Hong, Y Koga, S Bandyadka, A Leshchyk, Y Wang, V Akavoor, X Cao, I. Sarfraz, Z. Wang, S. Alabdullatif, F. Jansen, M. Yajima, WE Johnson, JD Campbell. Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data. Nat Commun (2022) 13, 1688. 

2021

Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR, Segrè D. 2021. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nat Protoc. 2021 Nov;16(11):5030-5082. doi: 10.1038/s41596-021-00593-3. PMID: 34635859 View in PubMed

Boateng JO, Wachman EM, Turcinovic J, Devera J, Jain M, Jean-Sicard S, Woodard E, Cruikshank A, Sinha B, Bartolome R, Barnett ED, Parker MG, Yarrington C, Connor JH, Taglauer E, Sabharwal V. 2021. SARS-CoV-2 in infant urine and fecal samples after in utero COVID-19 exposure. Pediatr Res. 2021 Oct 30:1-5. doi: 10.1038/s41390-021-01822-x. PMID: 34718351 View in PubMed

Huang X, Qiao Y, Brady SW, Factor RE, Downs-Kelly E, Farrell A, McQuerry JA, Shrestha G, Jenkins D, Johnson WE, Cohen AL, Bild AH, Marth GT. 2021. Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med. 2021 Oct 28;13(1):170. doi: 10.1186/s13073-021-00989-6. PMID: 34711268 View in PubMed

Aaron Chevalier, Shiyi Yang, Zainab Khurshid, Nathan Sahelijo, Tong Tong, Jonathan H Huggins, Masanao Yajima, Joshua D Campbell. 2021. The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the discovery, prediction, and exploration of mutational signatures. Cancer Res. 2021 Oct 8; canres.0899.2021. doi: 10.1158/0008-5472.CAN-21-0899. View in PubMed

Lim, Y., Beane-Ebel, J.E., Tanaka, Y., Ning, Bet al. 2021 Exploration of alcohol use disorder-associated brain miRNA–mRNA regulatory networks. Transl Psychiatry 11, 504

Chang D, Klein JA, Nalehua MR, Hackett WE, Zaia J. 2021. Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein. Anal Bioanal Chem. 2021 Oct 12:1-14. doi: 10.1007/s00216-021-03643-7. PMID: 34635934 View in PubMed

Bouton TC, Lodi S, Turcinovic J, Schaeffer B, Weber SE, Quinn E, Korn C, Steiner J, Schechter-Perkins EM, Duffy E, Ragan EJ, Taylor BP, Miller N, Davidoff R, Hanage WP, Connor J, Pierre C, Jacobson KR. 2021. Coronavirus Disease 2019 Vaccine Impact on Rates of Severe Acute Respiratory Syndrome Coronavirus 2 Cases and Postvaccination Strain Sequences Among Health Care Workers at an Urban Academic Medical Center: A Prospective Cohort Study. Open Forum Infect Dis. 2021 Sep 17;8(10):ofab465. doi: 10.1093/ofid/ofab465. PMID: 34646910 View in PubMed

Maoz A, Merenstein C, Koga Y, Potter A, Gower AC, Liu G, Zhang S, Liu H, Stevenson C, Spira A, Reid ME, Campbell JD, Mazzilli SA, Lenburg ME, Beane J. 2021. Elevated T cell repertoire diversity is associated with progression of lung squamous cell premalignant lesions.  J Immunother Cancer. 2021 Sep;9(9):e002647. doi: 10.1136/jitc-2021-002647.PMID: 34580161  View in PubMed

Hackett WE, Zaia J. 2021. The Need for Community Standards to Enable Accurate Comparison of Glycoproteomics Algorithm Performance. Molecules. 2021 Aug 6;26(16):4757. doi: 10.3390/molecules26164757.PMID: 34443345 View in PubMed

Moyer D, Pacheco AR, Bernstein DB, Segrè D. 2021. Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure. J Mol Evol. 2021 Aug;89(7):472-483. doi: 10.1007/s00239-021-10018-0. PMID: 34230992 View in PubMed

Hicks-Berthet J, Ning BFederico A, Tilston-Lunel A, Matschulat A, Ai X, Lenburg ME, Beane J, Monti S, Varelas X. 2021. Yap/Taz inhibit goblet cell fate to maintain lung epithelial homeostasis. Cell Rep. 2021 Jul 13;36(2):109347. doi: 10.1016/j.celrep.2021.109347.PMID: 34260916 View in PubMed

Sutradhar I, Ching C, Desai D, Suprenant M, Briars E, Heins Z, Khalil AS, Zaman MH. 2021. Computational Model To Quantify the Growth of Antibiotic-Resistant Bacteria in Wastewater. mSystems. 2021 Jun 29;6(3):e0036021. doi: 10.1128/mSystems.00360-21. PMID: 34100640 View in PubMed

Pacheco AR, Segrè D. 2021. An evolutionary algorithm for designing microbial communities via environmental modification. J R Soc Interface. 2021 Jun;18(179):20210348. doi: 10.1098/rsif.2021.0348. PMID: 34157894 View in PubMed

Strampe J, Asogun DA, Speranza E, Pahlmann M, Soucy A, Bockholt S, Pallasch E, Becker-Ziaja B, Duraffour S, Bhadelia N, Ighodalo Y, Oyakhilome J, Omomoh EO, Olokor T, Adomeh DI, Ikponwonsa O, Aire C, Tobin E, Akpede N, Okokhere PO, Okogbenin SA, Akpede GO, Muñoz-Fontela C, Ogbaini-Emovon E, Günther S, Connor JH, Oestereich L. 2021. Factors associated with progression to death in patients with Lassa fever in Nigeria: an observational study. Lancet Infect Dis. 2021 Jun;21(6):876-886. doi: 10.1016/S1473-3099(20)30737-4. PMID: 33484646 View in PubMed

Dela Cruz A, Kartha V, Tilston-Lunel A, Mi R, Reynolds TL, Mingueneau M, Monti S, Jensen JL, Skarstein K, Varelas X, Kukuruzinska MA. 2021. Gene expression alterations in salivary gland epithelia of Sjögren’s syndrome patients are associated with clinical and histopathological manifestations. Sci Rep. 2021 May 27;11(1):11154. doi: 10.1038/s41598-021-90569-w.PMID: 34045583 View in PubMed

Hogan JD, Wu J, Klein JA, Lin C, Carvalho L, Zaia J. 2021. GAGrank: Software for Glycosaminoglycan Sequence Ranking Using a Bipartite Graph Model. Mol Cell Proteomics. 2021 May 14;20:100093. doi: 10.1016/j.mcpro.2021.100093. PMID: 33992776 View in PubMed

Gurinovich A, Song Z, Zhang W, Federico A, Monti S, Andersen SL, Jennings LL, Glass DJ, Barzilai N, Millman S, Perls TT, Sebastiani P. 2021. Effect of longevity genetic variants on the molecular aging rate.Geroscience. 2021 Jun;43(3):1237-1251. doi: 10.1007/s11357-021-00376-4. Epub 2021 May 4. PMID: 33948810 View in PubMed

Goncearenco A, LaBarre BA, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Turner SD, Hayes VM, Elnitski L. 2021. DNA methylation profiles unique to Kalahari KhoeSan individuals. Epigenetics. 2021 May;16(5):537-553. doi: 10.1080/15592294.2020.1809852. PMID: 32892676 View in PubMed

Pacheco AR, Osborne ML, Segrè D. 2021.Non-additive microbial community responses to environmental complexity. Nat Commun. 2021 Apr 22;12(1):2365. doi: 10.1038/s41467-021-22426-3.PMID: 33888697 View in PubMed

Zhao YFederico A, Faits T, Manimaran S, Segrè D, Monti S, Johnson WE. 2021. animalcules: interactive microbiome analytics and visualization in R. Microbiome. 2021 Mar 28;9(1):76. doi: 10.1186/s40168-021-01013-0.PMID: 33775256 View in PubMed

Sebastiani P, Federico A, Morris M, Gurinovich A, Tanaka T, Chandler KB, Andersen SL, Denis G, Costello CE, Ferrucci L, Jennings L, Glass DJ, Monti S, Perls TT. 2021. Protein signatures of centenarians and their offspring suggest centenarians age slower than other humans. Aging Cell. 2021 Feb;20(2):e13290. doi: 10.1111/acel.13290. PMID: 33512769 View in PubMed

Johnson WE, Odom A, Cintron C, Muthaiah M, Knudsen S, Joseph N, Babu S, Lakshminarayanan S, Jenkins DFZhao Y, Nankya E, Horsburgh CR, Roy G, Ellner J, Sarkar S, Salgame P, Hochberg NS. 2021. Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler. BMC Infect Dis. 2021 Jan 22;21(1):106. doi: 10.1186/s12879-020-05598-z.PMID: 33482742 View in PubMed

Hackett WE, Zaia J. 2021. Calculating Glycoprotein Similarities From Mass Spectrometric Data. Mol Cell Proteomics. 2021 Jan 6;20:100028. doi: 10.1074/mcp.R120.002223. PMID: 32883803 View in PubMed

Ryan J. Quinton, Amanda DiDomizio, Marc A. Vittoria, Kristýna Kotýnková, Carlos J. Ticas, Sheena Patel, Yusuke Koga, Jasmine Vakhshoorzadeh, Nicole Hermance, Taruho S. Kuroda, Neha Parulekar, Alison M. Taylor, Amity L. Manning, Joshua D. Campbell, Neil J. Ganem. 2021. Whole-Genome Doubling Confers Unique Genetic Vulnerabilities on Tumour Cells. Nature. Jan 590,492–497 (2021). PMID: 33505027 View in PubMed

Hook H, Zhao RW, Bray D, Keenan JL, Siggers T. 2021. High-Throughput Analysis of the Cell and DNA Site-Specific Binding of Native NF-κB Dimers Using Nuclear Extract Protein-Binding Microarrays (NextPBMs). Methods Mol Biol. 2021;2366:43-66. doi: 10.1007/978-1-0716-1669-7_4. PMID: 34236632 View in PubMed

2020

Goldford JE, Hartman H, Marsland R, Segrè D., 2020, Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism, Nature ecology & evolution 3 (12), 1715-1724. 

Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, Pericak-Vance MA, Perola M, Psaty BM, Quenez O, Rajabli F, Redon R, Reitz C, Remes AM, Salomaa V, Sarnowski C, Schmidt H, Schmidt M, Schmidt R, Soininen H, Thornton TA, Tosto G, Tzourio C, van der Lee SJ, van Duijn CM, Valladares O, Vardarajan B, Wang LS, Wang W, Wijsman E, Wilson RK, Witten D, Worley KC, Zhang X; Alzheimer’s Disease Sequencing Project, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj AC, Fornage M, Farrer LA. 2020. Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry. 2020 Aug;25(8):1859-1875. doi: 10.1038/s41380-018-0112-7. PMID: 30108311 View in PubMed

Wang J, Belta C, Isaacson SA. 2020. How Retroactivity Affects the Behavior of Incoherent Feedforward Loops. iScience. 2020 Nov 7;23(12):101779. doi: 10.1016/j.isci.2020.101779. PMID: 33305173View in PubMed

Chandler KB, Alamoud KA, Stahl VL, Nguyen BC, Kartha VK, Bais MV, Nomoto K, Owa T, Monti S, Kukuruzinska MA, Costello CE. 2020. β-Catenin/CBP inhibition alters epidermal growth factor receptor fucosylation status in oral squamous cell carcinoma. Mol Omics. 2020 Jun 1;16(3):195-209. doi: 10.1039/d0mo00009d. Epub 2020 Mar 23.PMID: 32203567 View in PubMed

Torres-Arancivia CM, Chang D, Hackett WE, Zaia J, Connors LH. 2020. Glycosylation of Serum Clusterin in Wild-Type Transthyretin-Associated (ATTRwt) Amyloidosis: A Study of Disease-Associated Compositional Features Using Mass Spectrometry Analyses. Biochemistry. 2020 Nov 17;59(45):4367-4378. PMID: 33141553 View in PubMed

Hackett WE, Zaia J. 2020. Calculating glycoprotein similarities from mass spectrometric data. Mol Cell Proteomics. 2020 Sep 3: mcp.R120.002223. PMID: 32883803 View on PubMed

Lancour D, Dupuis J, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GC, Crovella M, Farrer LA, Kasif S. 2020. Analysis of brain region-specific co-expression networks reveals clustering of established and novel genes associated with Alzheimer disease. Alzheimers Res Ther. 2020 Sep 2;12(1):103. PMCID: 7469336.  View in PubMed

Koga Y, Song H, Chalmers ZR, Newberg J, Kim E, Carrot-Zhang J, Piou D, Polak P, Abdulkadir SA, Ziv E, Meyerson M, Frampton GM, Campbell JD, Huang FW. 2020. Genomic Profiling of Prostate Cancers from Men with African and European Ancestry. Clin Cancer Res. Sep 1;26(17):4651-4660. PMCID: 7597977  View in PubMed

Klein JA, Zaia J. 2020. A Perspective on the Confident Comparison of Glycoprotein Site-Specific Glycosylation in Sample Cohorts. Biochemistry. 2020 Sep 1;59(34):3089-3097. PMID: 31833756.  View in PubMed

Chang D, Hackett WE, Zhong L, Wan XF, Zaia J. 2020. Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty. Mol Cell Proteomics. 2020 Sep;19(9):1533-1545.  PMID: 3260117. View in PubMed

Raghunathan R, Hogan JD, Labadorf A, Myers RH, Zaia J. 2020. A glycomics and proteomics study of aging and Parkinson’s disease in human brain. Sci Rep. 2020 Jul 30;10(1):12804. PMID: 32733076.  View in PubMed 

Muraoka S, DeLeo AM, Sethi MK, Yukawa-Takamatsu K, Yang Z, Ko J, Hogan JD, Ruan Z, You Y, Wang Y, Medalla M, Ikezu S, Chen M, Xia W, Gorantla S, Gendelman HE, Issadore D, Zaia J, Ikezu T. 2020. Proteomic and biological profiling of extracellular vesicles from Alzheimer’s disease human brain tissues. Alzheimers Dement. 2020 Jun;16(6):896-907. PMID: 32301581. View in PubMed 

Karagiannis TT, Cleary JP Jr, Gok B, Henderson AJ, Martin NG, Yajima M, Nelson EC, Cheng CS. 2020. Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program. Nature Communications. May 26;11(1):2611. PMCID: PMC7250875. View in PubMed

Klein J, Zaia J. 2020. Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC-MS/MS. J Proteome Res. 2020 May 1;19(5):2113-2121. PMID: 32223173. View in PubMed

Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA. (2019) The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev Biol. 2020 Apr 15;460(2):139-154. PMID: 31816285. View in PubMed

Igwebuike C, Yaglom J, Huiting L, Feng H, Campbell JD, Wang Z, Havasi A, Pimentel D, Sherman MY, Borkan SC. 2020. Cross organelle stress response disruption promotes gentamicin-induced proteotoxicity. Cell Death Dis. 2020 Apr 3;11(4):217. PMCID: PMC7125232. View in PubMed 

Drizik E, Corbett S, Zheng Y, Vermeulen R, Dai Y, Hu W, Ren D, Duan H, Niu Y, Xu J, Fu W, Meliefste K, Zhou B, Zhang X, Yang J, Bassig B, Liu H, Ye M, Liu G, Jia X, Meng T, Bin P, Zhang J, Silverman D, Spira A, Rothman N, Lenburg ME, Lan Q. 2020. Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure. Environ Int. 2020 Apr;137:105506. PMID: 32044442. View in PubMed

Yang S, Corbett SE, Koga Y, Wang Z, Johnson WE, Yajima M, Campbell JD. 2020. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol. 2020 Mar 5;21(1):57. PMID: 32138770. View in PubMed

Zhong M, Lynch A, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, Allen KN, Whitty A. 2020. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Biochemistry. 2020 Feb 4;59(4):563-581. doi: 10.1021/acs.biochem.9b00943. PMID: 31851823. View in PubMed

Leong S, Zhao Y, Ribeiro-Rodrigues R, Jones-López EC, Acuña-Villaorduña C, Rodrigues PM, Palaci M, Alland D, Dietze R, Ellner JJ, Johnson WE, Salgame P.  2020. Cross-validation of existing signatures and derivation of a novel 29-gene transcriptomic signature predictive of progression to TB in a Brazilian cohort of household contacts of pulmonary TB. Tuberculosis (Edinb). 2020 Jan;120:101898. doi: 10.1016/j.tube.2020.101898. PMID: 32090859 View in PubMed

2019

Kartha VK, Sebastiani P, Kern JG, Zhang L, Varelas X, Monti S. CaDrA: A Computational Framework for Performing Candidate Driver Analyses Using Genomic Features. Front Genet. 2019 Feb 19;10:121. doi: 10.3389/fgene.2019.00121. eCollection 2019. PMID: 30838036 View in PubMed

Ma Y, Jun GR, Zhang X, Chung J, Naj AC, Chen Y, Bellenguez C, Hamilton-Nelson K, Martin ER, Kunkle BW, Bis JC, Debette S, DeStefano AL, Fornage M, Nicolas G, van Duijn C, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak-Vance MA, Seshadri S, Lambert JC, Schellenberg GD, Lunetta KL, Farrer LA; Analysis of Whole-Exome Sequencing Data for Alzheimer Disease Stratified by APOE Genotype. Alzheimer’s Disease Sequencing Project and Alzheimer’s Disease Exome Sequencing–France Project. JAMA Neurol. 2019 Sep 1;76(9):1099-1108. doi: 10.1001/jamaneurol.2019.1456. PMID: 31180460View in PubMed

LaBarre BA, Goncearenco A, Petrykowska HM, Jaratlerdsiri W, Bornman MSR, Hayes VM, Elnitski L. MethylToSNP: identifying SNPs in Illumina DNA methylation array data. Epigenetics Chromatin. 2019 Dec 20;12(1):79. doi: 10.1186/s13072-019-0321-6. PMID: 31861999 View in PubMed

Zhang X, Zhu C, Beecham G, Vardarajan BN, Ma Y, Lancour D, Farrell JJ, Chung J; Alzheimer’s Disease Sequencing Project, Mayeux R, Haines JL, Schellenberg GD, Pericak-Vance MA, Lunetta KL, Farrer LA.A rare missense variant of CASP7 is associated with familial late-onset Alzheimer’s disease. Alzheimers Dement. 2019 Mar;15(3):441-452. doi: 10.1016/j.jalz.2018.10.005. Epub 2019 Jan 3. PMID: 30503768 View in PubMed

Dai Y, Shaikho EM, Perez J, Wilson CA, Liu LY, White MR, Farrell JJ, Chui DHK, Sebastiani P, Steinberg MH. BCL2L1 is associated with γ-globin gene expression. Blood Adv. 2019 Oct 22;3(20):2995-3001. doi: 10.1182/bloodadvances.2019032243. PMID: 31648320 View in PubMed

Chung J, Jun GR, Dupuis J, Farrer LA. Eur J Hum Genet. Comparison of methods for multivariate gene-based association tests for complex diseases using common variants. 2019 May;27(5):811-823. doi: 10.1038/s41431-018-0327-8. Epub 2019 Jan 25. PMID: 30683923 View in PubMed

Li A, Lu X, Natoli T, Bittker J, Sipes NS, Subramanian A, Auerbach S, Sherr DH, Monti S. The Carcinogenome Project: In Vitro Gene Expression Profiling of Chemical Perturbations to Predict Long-Term Carcinogenicity. Environ Health Perspect. 2019 Apr;127(4):47002. doi: 10.1289/EHP3986. PMID: 30964323 View in PubMed

Li A, Chapuy B, Varelas X, Sebastiani P, Monti S. Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis. Sci Rep. 2019 Nov 15;9(1):16904. doi: 10.1038/s41598-019-52886-z. PMID: 31729402 View in PubMed

McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, Johnson WE, Yuan Y, Bild AH. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer. 2019 Sep 5;19(1):881. doi: 10.1186/s12885-019-6052-z. PMID: 31488082 View in PubMed

Libby ARG, Briers D, Haghighi I, Joy DA, Conklin BR, Belta C, McDevitt TC. (2019). Automated Design of Pluripotent Stem Cell Self-Organization. Cell Syst. 2019 Nov 27;9(5):483-495.e10. PMID: 31759947. View in PubMed

PubMedGene Expression Alterations in the Bronchial Epithelium of e-Cigarette Users.
Corbett SE, Nitzberg M, Moses E, Kleerup E, Wang T, Perdomo C, Perdomo C, Liu G, Xiao X, Liu H, Elashoff DA, Brooks DR, O’Connor GT, Dubinett SM, Spira A, Lenburg ME. Chest. 2019 Oct;156(4):764-773. doi: 10.1016/j.chest.2019.05.022. Epub 2019 Jun 22. PMID: 31233743 View in PubMed

Sebastiani P, Monti S, Morris M, Gurinovich A, Toshiko T, Andersen SL, Sweigart B, Ferrucci L, Jennings LL, Glass DJ, Perls TT. A serum protein signature of APOE genotypes in centenarians. Aging Cell. 2019 Aug 5:e13023. PMCID: PMC6826130.  View in PubMed

Naj AC, Lin H, Vardarajan BN, White S, Lancour D, Ma Y, Schmidt M, Sun F, Butkiewicz M, Bush WS, Kunkle BW, Malamon J, Amin N, Choi SH, Hamilton-Nelson KL, van der Lee SJ, Gupta N, Koboldt DC, Saad M, Wang B, Nato AQ Jr, Sohi HK, Kuzma A; Alzheimer’s Disease Sequencing Project (ADSP), Wang LS, Cupples LA, van Duijn C, Seshadri S, Schellenberg GD, Boerwinkle E, Bis JC, Dupuis J, Salerno WJ, Wijsman EM, Martin ER, DeStefano AL. (2019). Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer’s disease sequencing project. Genomics. 2019 Jul;111(4):808-818. PMID: 29857119 View in PubMed

Wang, J, Isaacson, S. A., and Belta, C. (2019). Modeling Genetic Circuit Behavior in Transiently Transfected Mammalian Cells. ACS Synthetic Biology, 2019, 8 (4), 697-707.View in PubMed

Federico AKaragiannis T, Karri K, Kishore D, Koga Y, Campbell JD, Monti S. Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines. Front Genet. 2019 Jun 28;10:614. PMID: 31316552. View in PubMed

Penvose A, Keenan JLBray D, Ramlall V, Siggers T. Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity.Nat Commun. 2019 Jun 7;10(1):2514. View in PubMed

Pacheco, AR, Segrè D. (2019). A multidimensional perspective on microbial interactions. FEMS, 2019 Jun 1;366(11). pii: fnz125. View in PubMed

Wang Z, Hu J, Johnson WE, Campbell JD. 2020. scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data.BMC Bioinformatics. 2019 May 2;20(1):222. PMCID: PMC6498700. View in PubMed 

Mohaghegh N, Bray D, Keenan J, Penvose A, Andrilenas KK, Ramlall V, Siggers T. NextPBM: a platform to study cell-specific transcription factor binding and cooperativity. Nucleic Acids Res. 2019 Apr 8;47(6):e31. doi: 10.1093/nar/gkz020. View in PubMed 

Klein J, Zaia J. (2019). Psims – A Declarative Writer for mzML and mzIdentML for Python. Mol Cell Proteomics 2019 Mar;18(3):571-575. PMCID: PMC6398200. View in PubMed

Zhang X, Zhu C, Beecham G, Vardarajan BN, Ma Y, Lancour D, Farrell JJ, Chung J; Alzheimer’s Disease Sequencing Project, Mayeux R, Haines JL, Schellenberg GD, Pericak-Vance MA, Lunetta KL, Farrer LA. (2019). A rare missense variant of CASP7 is associated with familial late-onset Alzheimer’s disease. Alzheimers Dement. 2019 Mar;15(3):441-452. View in PubMed

Marsland III R, Cui W, Goldford J, Sanchez A, Korolev K, Mehta P, 2019, Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities, PLoS Computational Biology 15 (2), e1006793. 

Pacheco AR, Moel M, Segrè D. (2019). Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun. 2019 Jan 9;10(1):103. doi: 10.1038/s41467-018-07946-9. View in PubMed 

Gurinovich A, Bae H, Farrell JJ, Andersen SL, Monti S, Puca A, Atzmon G, Barzilai N, Perls TT, Sebastiani P. opCluster: an algorithm to identify genetic variants with ethnicity-dependent effects.Bioinformatics. 2019 Jan 8. View in PubMed

Sebastiani P, Gurinovich A, Nygaard M, Sasaki T, Sweigart B, Bae H, Andersen S, Villa F, Atzmon G, Christensen K, Arai Y, Barzilai N, Puca A, Christiansen L, Hirose N, Perls TT. APOE Alleles and Extreme Human Longevity. J Gerontol A Biol Sci Med Sci. 2019 Jan 1;74(1):44-51. View in PubMed

2018

Zhang Y, Jenkins DF, Manimaran S, Johnson WE. Alternative empirical Bayes models for adjusting for batch effects in genomic studies. BMC Bioinformatics. 2018 Jul 13;19(1):262. doi: 10.1186/s12859-018-2263-6.PMID: 30001694 View in PubMed

Kim S, Li A, Monti S, Schlezinger JJ. Tributyltin induces a transcriptional response without a brite adipocyte signature in adipocyte models. Arch Toxicol. 2018 Sep;92(9):2859-2874. doi: 10.1007/s00204-018-2268-y. Epub 2018 Jul 19. PMID: 30027469 View in PubMed

Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA.Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679-690. doi: 10.1038/s41591-018-0016-8. Epub 2018 Apr 30.PMID: 29713087 View in PubMed

Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S. Exploring the structural origins of cryptic sites on proteins. Proc Natl Acad Sci U S A. 2018 Apr 10;115(15):E3416-E3425. doi: 10.1073/pnas.1711490115. Epub 2018 Mar 26. PMID: 2958126 View in PubMed

Cross RW, Speranza E, Borisevich V, Widen SG, Wood TG, Shim RS, Adams RD,Gerhardt DM, Bennett RS, Honko AN, Johnson JC, Hensley LE, Geisbert TW, ConnorJH. 2018. Comparative Transcriptomics in Ebola Makona-Infected Ferrets, Nonhuman Primates, and Humans. J Infect Dis. 2018 Nov 22;218(suppl_5):S486-S495 PMCID: PMC6249602. View in PubMed

Speranza E, Ruibal P, Port JR, Feng F, Burkhardt L, Grundhoff A, Günther S, Oestereich L, Hiscox JA, Connor JH, Muñoz-Fontela C. 2018. T-Cell Receptor Diversity and the Control of T-Cell Homeostasis Mark Ebola Virus Disease Survival in Humans. J Infect Dis. 2018 Nov 22;218(suppl 5):S508-S518. PMCID: PMC7191875 View in PubMed

DiMucci, D, Kon M, Segrè D. Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks. mSystems. 2018 Oct 30;3(5). pii: e00181-18. View in PubMed

Bae H, Gurinovich A, Malovini A, Atzmon G, Andersen SL, Villa F, Barzilai N, Puca A, Perls TT, Sebastiani P. J Gerontol A. Effects of FOXO3 Polymorphisms on Survival to Extreme Longevity in Four Centenarian Studies. Biol Sci Med Sci. 2018 Oct 8;73(11):1439-1447. View in PubMed

Maoz BM, Herland A, FitzGerald EA, Grevesse T, Vidoudez C, Pacheco AR, Sheehy SP, Park TE, Dauth S, Mannix R, Budnik N, Shores K, Cho A, Nawroth JC, Segrè D, Budnik B, Ingber DE, Parker KK. A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells. Nat Biotechnol. 2018 Oct;36(9):865-874. doi: 10.1038/nbt.4226. Epub 2018 Aug 20. View in PubMed

Cox JW, Patel D, Chung J, Zhu C, Lent S, Fisher V, Pitsillides A, Farrer L, Zhang X. (2018). An efficient analytic approach in genome-wide identification of methylation quantitative trait loci response to fenofibrate treatment.  BMC Proc. 2018 Sep 17;12(Suppl 9):44 View in PubMed

Carrasco Pro, S, Dafonte Imedio A, Santoso CS, Gan KA, Sewell JA, Martinez M, Sereda R, Mehta S, Fuxman Bass J.I. (2018). Global landscape of mouse and human cytokine transcriptional regulation. Nucleic Acids Research, 2018 Sep 3  View in PubMed

Raghunathan, R., Polinski, NK., Klein, JA., Hogan, J.D., Shao, C., Khatri, K., Leon, D., McComb, M.E., Manfredsson, F.P., Sortwell, C.E., Zaia, J. (2018). Glycomic and Proteomic Changes in Aging Brain Nigrostriatal Pathway. Molecular & Cellular Proteomics, 2018 Sep;17(9):1778-1787. View in PubMed

Logue MW, Lancour D, Farrell J, Simkina I, Fallin MD, Lunetta KL, Farrer LA. (2018). Targeted Sequencing of Alzheimer Disease Genes in African Americans Implicates Novel Risk Variants. Front Neurosci. 2018 Aug 27;12:592. View in PubMed

Bis JC, Jian X, Kunkle BW, Chen Y, Hamilton-Nelson KL, Bush WS, Salerno WJ, Lancour D, Ma Y, Renton AE, Marcora E, Farrell JJ, Zhao Y, Qu L, Ahmad S, Amin N, Amouyel P, Beecham GW, Below JE, Campion D, Cantwell L, Charbonnier C, Chung J, Crane PK, Cruchaga C, Cupples LA, Dartigues JF, Debette S, Deleuze JF, Fulton L, Gabriel SB, Genin E, Gibbs RA, Goate A, Grenier-Boley B, Gupta N, Haines JL, Havulinna AS, Helisalmi S, Hiltunen M, Howrigan DP, Ikram MA, Kaprio J, Konrad J, Kuzma A, Lander ES, Lathrop M, Lehtimäki T, Lin H, Mattila K, Mayeux R, Muzny DM, Nasser W, Neale B, Nho K, Nicolas G, Patel D, . . . Farrer LA. (2018). Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry. 2018 Aug 14. Erratum in: Mol Psychiatry. 2019 Oct 21 View in PubMed

Zhao Y, Johnson WE. 2021. Exploring Host-Microbe Interactions in Lung Cancer. Am J Respir Crit Care Med. 2018 Nov 1;198(9):1116-1118. doi: 10.1164/rccm.201807-1225ED.PMID: 30063838 View in PuMed

Goldford JE, Lu N, Bajić D, Estrela S, Tikhonov M, Sanchez-Gorostiaga A, Segrè D, Mehta P, Sanchez A.2018. Emergent simplicity in microbial community assembly. Science. 2018 Aug 3;361(6401):469-474. PMCID: PMC6405290. View in PubMed 

Zeng Y, Nie C, Min J, Chen H, Liu X, Ye R, Chen Z, Bai C, Xie E, Yin Z, Lv Y, Lu J, Li J, Ni T, Bolund L, Land KC, Yashin A, O’Rand AM, Sun L, Yang Z, Tao W, Gurinovich A, Franceschi C, Xie J, Gu J, Hou Y, Liu X, Xu X, Robine JM, Deelen J, Sebastiani P, Slagboom E, Perls T, Hauser E, Gottschalk W, Tan Q, Christensen K, Shi X, Lutz M, Tian XL, Yang H, Vaupel J. Sex Differences in Genetic Associations With Longevity. JAMA Netw Open. 2018 Aug;1(4). pii: e181670.  View in PubMed

Kartha VK, Alamoud KA, Sadykov K, Nguyen BC, Laroche F, Feng H, Lee J, Pai SI, Varelas X, Egloff AM, Snyder-Cappione JE, Belkina AC, Bais MV, Monti S, Kukuruzinska MA.2018. Functional and genomic analyses reveal therapeutic potential of targeting β-catenin/CBP activity in head and neck cancer. Genome Medicine, Jul 20;10(1):54. View in PubMed

Hogan, JD, Klein JA, Wu J, Chopra P, Boons GJ, Carvalho L, Lin C, Zaia J. (2018). Software for Peak Finding and Elemental Composition Assignment for Glycosaminoglycan Tandem Mass Spectra. Molecular & Cellular Proteomics, 2018 Jul;17(7):1448-1456. View in PubMed

Wu J, Wei J, Hogan JD, Chopra P, Joshi A, Lu W, Klein J, Boons GJ, Lin C, Zaia J., 2018, Negative Electron Transfer Dissociation Sequencing of 3-O-Sulfation-Containing Heparan Sulfate Oligosaccharides. J Am Soc Mass Spectrom. 2018 Jun;29(6):1262-1272. PMCID: PMC6004244 View in PubMed

Lancour D, Naj A, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Crovella M, Farrer LA, Kasif S. (2018). One for all and all for One: Improving replication of genetic studies through network diffusion. PLoS Genet. 2018 Apr 23;14(4):e1007306. View in PubMed

Goldford JE, D Segrè D., 2018, Modern views of ancient metabolic networks, Current Opinion in Systems Biology 8, 117-124. 

Speranza E, Bixler SL, Altamura LA, Arnold CE, Pratt WD, Taylor-Howell C, Burrows C, Aguilar W, Rossi F, Shamblin JD, Wollen SE, Zelko JM, Minogue T, Nagle E, Palacios G, Goff AJ, Connor JH. A conserved transcriptional response to intranasal Ebola virus exposure in nonhuman primates prior to onset of fever. Sci Transl Med. 2018 Mar 28;10(434). pii: eaaq1016. PMID: 29593102. View in PubMed

Leong S, Zhao, Y, Joseph NM, Hochberg NS, Sarkar S, Pleskunas J, Hom D, Lakshminarayanan S, Horsburgh CR Jr., Roy G, Ellner JJ, Johnson WE, Salgame P., 2018, Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India., Tuberculosis (Edinb). 2018 Mar;109:41-51. PMID: 29559120.  View in PubMed

Byrd AL, Belkaid Y, Segre JA. 2018. The Human Skin Microbiome. Nat Rev Microbiol. 2018 Mar;16(3):143-155. PMID: 29332945. View in PubMed

Chung, J, Zhang, X, Allen, M, Wang, X, Ma, Y, Beecham, G, Montine, TJ, Younkin, SG, Dickson, DW, Golde, TE, Price, N.D., Ertekin-Taner, N, Lunetta, KL, Mez, J; Alzheimer’s Disease Genetics Consortium, Mayeux, R, Haines, JL, Pericak-Vance, MA, Schellenberg, G, Jun, GR, Farrer, LA. (2018). Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer’s disease. Alzheimer’s Research & Therapy, 2018 Feb 20;10(1):22 View in PubMed

Yaglom JA, Wang Y, Li A, Li Z, Monti S, Alexandrov I, Lu X, Sherman MY. (2018). Cancer cell responses to Hsp70 inhibitor JG-98: Comparison with Hsp90 inhibitors and finding synergistic drug combinations., Sci Rep.; February 14 8(1):3010. PMCID: PMC5813176. View in PubMed

Linehan JL, Harrison OJ, Han SJ, Byrd AL, Vujkovic-Cvijin I, Villarino AV, Sen SK, Shaik J, Smelkinson M, Tamoutounour S, Collins N, Bouladoux N, Dzutsev A, Rosshart SP, Arbuckle JH9, Wang CR, Kristie TM, Rehermann B, Trinchieri G, Brenchley JM, O’Shea JJ, Belkaid Y. 2018. Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair. Cell. 2018 Feb 8;172(4):784-796.e18. View in PubMed

Gan, K.A., Carrasco Pro, S., Sewell, J.A., Bass, JIF. (2018). Identification of Single Nucleotide Non-coding Driver Mutations in Cancer. Frontiers in Genetics, 2018 Feb 2;9:16. doi: 10.3389/fgene.2018.00016. View in PubMed

2017

Sebastiani, P., Gurinovich, A., Bae, H., Andersen, S., Malovini, A., Atzmon, G., Villa, F., Kraja, A.T., Ben-Avraham, D., Barzilai, N., Puca, A., Perls, T.T. 2017. Four Genome-Wide Association Studies Identify New Extreme Longevity Variants. J Gerontol A Biol Sci Med Sci, 00(00), 1-12. View in PubMed

Sebastiani P, Gurinovich A, Bae H, Andersen SL, Perls TT. 2017. Assortative Mating by Ethnicity in Longevous Families. Front Genet. 2017 Nov 21;8:186. doi: 10.3389/fgene.2017.00186. eCollection 2017. View in PubMed

Speranza E, Altamura LA, Kulcsar K, Bixler SL, Rossi CA, Schoepp RJ, Nagle E, Aguilar W, Douglas CE, Delp KL, Minogue TD, Palacios G, Goff AJ, Connor JH. 2017. Comparison of Transcriptomic Platforms for Analysis of Whole Blood from Ebola-Infected Cynomolgus Macaques. Sci Rep. 2017 Nov 7;7(1):14756. doi:10.1038/s41598-017-15145-7. PubMed PMID: 29116224; PubMed Central PMCID: PMC5676990. View in PubMed

Lo J, Zhang D, Speranza E, Negron JA, Connor JH. 2017. HoTResDB: Host Transcriptional Response Database for Viral Hemorrhagic Fevers. Bioinformatics. 2017 Sep 22. doi: 10.1093/bioinformatics/btx599. [Epub ahead of print] PubMed PMID: 29028885; PubMed Central PMCID: PMC5860212. View in PubMed

Alsaqer SF, Tashkandi MM, Kartha VK, Yang YT, Alkheriji Y, Salama A, Varelas X, Kukuruzinska M, Monti S, Bais MV. Inhibition of LSD1 epigenetically attenuates oral cancer growth and metastasis. Oncotarget. 2017 Jul 27;8(43):73372-73386. doi: 10.18632/oncotarget.19637. eCollection 2017 Sep 26. PMID: 29088714 View in PubMed

Goldberg LR, Kirkpatrick SL, Yazdani N, Luttik KP, Lacki OA, Babbs RK, Jenkins DF, Johnson WE, Bryant CD. Casein kinase 1-epsilon deletion increases mu opioid receptor-dependent behaviors and binge eating1. Genes Brain Behav. 2017 Sep;16(7):725-738. doi: 10.1111/gbb.12397. Epub 2017 Jul 6. PMID: 28594147 View in PubMed

Speranza E, Connor JH. 2017. Host Transcriptional Response to Ebola Virus Infection. Vaccines (Basel). 2017 Sep 20;5(3). pii: E30. doi: 10.3390/vaccines5030030 Review. PubMed PMID: 28930167. View in PubMed

Goldford, J.E., Hartman, H., Smith, T.F., Segrè, D. (2017). Remnants of an Ancient Metabolism without Phosphate. Cell, 168(6): 1126-1134. View in PubMed

Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. 2017. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Rep. 2017 Sep. 12;20(11):2666-2677. doi: 10.1016/j.celrep.2017.08.066. View in PubMed

Pavel, A., Korolev, K. (2017). Genetic load makes cancer cells more sensitive to common drugs: evidence from Cancer Cell Line Encyclopedia. Scientific Reports, 7: 1938.

Rahman M, MacNeil SM, Jenkins DF, Shrestha G, Wyatt SR, McQuerry JA, Piccolo SR, Heiser LM, Gray JW, Johnson WE, Bild AH. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Med. 2017 Apr 26;9(1):40. doi: 10.1186/s13073-017-0429-x. PMID: 28446242 View in PubMed

Silterra, J., Gillette, M.A., Lanaspa, M., Pelle, K.G., Valim, C., Ahmad, R., Acacio, S., Almendinger, K.D., Tan, Y., Madrid, L., Alonso, P.L. Carr, S.A., Wiegand, R.C., Bassat, Q. Mesirov, J.P., Milner, D.A. Jr., Wirth, D.F. (2017). Transcriptional Categorization of the Etiology of Pneumonia Syndrome in Pediatric Patients in Malaria-Endemic Areas. J Infect Dis., 215(2): 312-320. View in PubMed

Mulas F, Li A, Sherr DH, Monti S. Network-based analysis of transcriptional profiles from chemical perturbations experiments. BMC Bioinformatics. 2017 Mar 23;18(Suppl 5):130. doi: 10.1186/s12859-017-1536-9. PMID: 28361664 View in PubMed

Park, S., Gianotti-Sommer, A., Molina-Estevez, F.J., Vanuytsel, K., Skvir, N., Leung, A., Rozelle, S.S., Shaikho, E.M., Weir, I., Jiang, Z., Luo, H.Y., Chui, D.H.K., Figueiredo, M.S., Alsultan, A., Al-Ali, A., Sebastiani, P., Steinberg, M.H., Mostoslavsky, G., Murphy, G.J. (2017). A Comprehensive, Ethnically Diverse Library of Sickle Cell Disease-Specific Induced Pluripotent Stem Cells. Stem Cell Reports. 8(4): 1076-1085. View in PubMed

Bohnuud, T., Luo, L., Wodak, S.J., Bonvin, A.M., Weng, Z., Vajda, S., Schueler-Furman, O., Kozakov D. (2017), A benchmark testing ground for integrating homology modeling and protein docking.Proteins. 85: 10–16. View in PubMed

Choi SH, Labadorf AT, Myers RH, Lunetta KL, Dupuis J, DeStefano AL. (2017) Evaluation of logistic regression models and effect of covariates for case-control study in RNA-Seq analysis. BMC Bioinformatics. 2017 Feb 6;18(1):91. View in PubMed

Moses, E., Wang, T., Corbett, S., Jackson, G.R., Drizik, E., Perdomo, C., Perdomo, C., Kleerup, E., Brooks, D., O’Connor, G., Dubinett, S., Hayden, P., Lenburg, M.E., Spira, A. (2017). Molecular Impact of Electronic Cigarette Aerosol Exposure in Human Bronchial Epithelium, Toxicology Sci, 155(1):248-257.

Shaikho EM, Farrell JJ, Alsultan A, Sebastiani P, Steinberg MH. Am J Hematol. Genetic determinants of HbF in Saudi Arabian and African Benin haplotype sickle cell anemia. 2017 Sep;92(9):E555-E557. doi: 10.1002/ajh.24822. Epub 2017 Jul 19. PMID: 28612458 View in PubMed

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH. Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3. PMID: 29093439 View in PubMed

Vajda, S., Yueh, C., Beglov, D., Bohnuud, T., Mottarella, S.E., Xia, B., Hall, D.R., Kozakov, D., 2017, New additions to the ClusPro server motivated by CAPRI, Proteins, 85(3):435-444.

Shaikho EM, Farrell JJ, Alsultan A, Qutub H, Al-Ali AK, Figueiredo MS, Chui DHK, Farrer LA, Murphy GJ, Mostoslavsky G, Sebastiani P, Steinberg MH. A phased SNP-based classification of sickle cell anemia HBB haplotypes. BMC Genomics. 2017 Aug 11;18(1):608. doi: 10.1186/s12864-017-4013-y. PMID: 28800727 View in PubMed

Jun GR, Chung J, Mez J, Barber R, Beecham GW, Bennett DA, Buxbaum JD, Byrd GS, Carrasquillo MM, Crane PK, Cruchaga C, De Jager P, Ertekin-Taner N, Evans D, Fallin MD, Foroud TM, Friedland RP, Goate AM, Graff-Radford NR, Hendrie H, Hall KS, Hamilton-Nelson KL, Inzelberg R, Kamboh MI, Kauwe JSK, Kukull WA, Kunkle BW, Kuwano R, Larson EB, Logue MW, Manly JJ, Martin ER, Montine TJ, Mukherjee S, Naj A, Reiman EM, Reitz C, Sherva R, St George-Hyslop PH, Thornton T, Younkin SG, Vardarajan BN, Wang LS, Wendlund JR, Winslow AR; Alzheimer’s Disease Genetics Consortium, Haines J, Mayeux R, Pericak-Vance MA, Schellenberg G, Lunetta KL, Farrer LA. Transethnic genome-wide scan identifies novel Alzheimer’s disease loci. Alzheimers Dement. 2017 Jul;13(7):727-738. doi: 10.1016/j.jalz.2016.12.012. Epub 2017 Feb 7. PMID: 28183528 View in PubMed

Khatri, K., Klein, J.A. and Zaia, J., 2017, Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation, Analytical and Bioanalytical Chemistry, 409(2):607-618. View in PubMed

Chung J, Wang X, Maruyama T, Ma Y, Zhang X, Mez J, Sherva R, Takeyama H; Alzheimer’s Disease Neuroimaging Initiative, Lunetta KL, Farrer LA, Jun GR. Genome-wide association study of Alzheimer’s disease endophenotypes at prediagnosis stages. Alzheimers Dement. 2018 May;14(5):623-633. doi: 10.1016/j.jalz.2017.11.006. Epub 2017 Dec 20. PMID: 29274321 View in PubMed

Jacobs, C., Lambourne, L., Xia, Y., Segrè, D., 2017, Upon Accounting for the Impact of Isoenzyme Loss, Gene Deletion Costs Anticorrelate with Their Evolutionary Rates, PLoS One, 12(1):e0170164. View in PubMed

Appleton, E., Madsen, C., Roehner, N., Densmore, D., (2017). Design Automation in Synthetic Biology, Cold Spring Harb Perspect Biol, pii: a023978. View in PubMed

Liu X, Speranza E, Muñoz-Fontela C, Haldenby S, Rickett NY, Garcia-Dorival I, Fang Y, Hall Y, Zekeng EG, Lüdtke A, Xia D, Kerber R, Krumkamp R, Duraffour S, Sissoko D, Kenny J, Rockliffe N, Williamson ED, Laws TR, N’Faly M, Matthews DA, Günther S, Cossins AR, Sprecher A, Connor JH, Carroll MW, Hiscox JA., 2017. “Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus.” Genome Biol. 2017 Jan 19;18(1). PMID: 28100256; PMCID: PMC5244546.                 View in PubMed

Sebastiani P, Bae H, Gurinovich A, Soerensen M, Puca A, Perls TT. 2017. Limitations and risks of meta-analyses of longevity studies. Mech Ageing Dev. 2017 Jul;165(Pt B):139-146. doi: 10.1016/j.mad.2017.01.008. Epub 2017 Jan 28. View in PubMed

2016

Pham, L.M., Carvalho, L., Schaus, S., Kolaczyk, E.D. (2016). Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach. J Am Stat Assoc., 111(513): 73-92. View in PubMed

Chapuy, B., Roemer, M.G., Stewart, C., Tan, Y., Abo, R.P., Zhang, L., Dunford, A.J., Meredith, D.M., Thorner, A.R., Jordanova, E.S., Liu, G., Feuerhake, F., Ducar, M.D., Illerhaus, G., Gusenleitner, D., Linden, E.A., Sun, H.H., Homer, H., Aono, M., Pinkus, G.S., Ligon, A.H., Ligon, K.L., Ferry, J.A., Freeman, G.J., van Hummelen, P., Golub, T.R., Getz, G., Rodig, S.J., de Jong, D., Monti, S., Shipp, M.A. (2016). Targetable genetic features of primary testicular and primary central nervous system lymphomas. Blood, 127(7): 869-881. View in PubMed

Chapuy, B., Cheng, H., Watahiki, A., Ducar, M.D., Tan, Y., Chen, L., Roemer, M.G., Ouyang, J., Christie, A.L., Zhang, L., Gusenleitner, D., Abo, R.P., Farinha, P., von Bonin, F., Thorner, A.R., Sun, H.H., Gascoyne. R.D., Pinkus, G.S., van Hummelen, P., Wulf, G.G., Aster, J.C., Weinstock, D.M., Monti, S., Rodig, S.J., Wang, Y., Shipp, M.A. (2016). Diffuse large B-cell lymphoma patient-derived xenograft models capture the molecular and biological heterogeneity of the disease. Blood, 127(18): 2203-2213. View in PubMed

Valim, C., Ahmad, R., Lanaspa, M., Tan, Y., Acacio, S., Gilette, M.A., Almendinger, K.D., Milner, D.A. Jr., Madrid, L., Pelle, K., Harezlak, J., Silterra, J., Alonso, P.L., Carr, S.A., Mesirov, J.P., Wirth, D.F., Wiegand, R.C., Bassat, Q. (2016). Responses to Bacteria, Virus, and Malaria Distinguish the Etiology of Pediatric Clinical Pneumonia. Am J Respir Crit Care Med., 193(4): 448-459. View in PubMed

Godec, J., Tan, Y., Liberzon, A., Tamayo, P., Bhattacharya, S., Butte, A.J., Mesirov, J.P., Haining, W.N. (2016). Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity, 44(1): 194-206. View in PubMed

Pavel, A.B., Vasile, C.I. (2016). Identifying cancer type specific oncogenes and tumor suppressors using limited size data. J Bioinform Comput Biol. 14(6): 1650031.  View in PubMed

Novikov, O., Wang, Z., Stanford, E. A., Parks, A. J., Ramirez-Cardenas, A., Landesman, E., , Laklouk, I., Sarita-Reyes, C., Gusenleitner, D., Li, A., Monti, S., Manteiga, S., Lee, K., Sherr, D.H. (2016). An Aryl Hydrocarbon Receptor-mediated Amplification Loop that Enforces Cell Migration in ER-/PR-/Her2- Human Breast Cancer Cells. Molecular Pharmacology. 90(5):674-688.

Kirkpatrick S.L., Goldberg, L.R., Yazdani, N., Babbs, R.K., Wu, J., Reed, E.R., Jenkins, D.F., Bolgioni, A.F., Landaverde, K.I., Luttik, K.P., Mitchell, K.S., Kumar, V., Johnson, W.E., Mulligan, M.K., Cottone, P., Bryant, C.D. (2016) Cytoplasmic FMR1-Interacting Protein 2 Is a Major Genetic Factor Underlying Binge Eating. Biol Psychiatry. pii: S0006-3223(16)32940-32947.

Zhang, W., Zhu, X., Fu, Y., Tsuji, J. and Weng, Z.,  (2016). The prediction of human splicing branchpoints by multi-label learning. In Bioinformatics and Biomedicine (BIBM), 2016 IEEE International Conference on (pp. 254-259). IEEE.

Wake C, Labadorf A, Dumitriu A, Hoss AG, Bregu J, Albrecht KH, DeStefano AL, Myers RH. (2016). Novel microRNA discovery using small RNA sequencing in post-mortem human brain. BMC Genomics. 2016 Oct 4;17(1):776. View in PubMed

Nagle MW, Latourelle JC, Labadorf A, Dumitriu A, Hadzi TC, Beach TG, Myers RH. (2016). The 4p16.3 Parkinson Disease Risk Locus Is Associated with GAK Expression and Genes Involved with the Synaptic Vesicle Membrane. PLoS One. 2016 Aug 10;11(8):e0160925. View in PubMed

Labadorf A, Hoss AG, Lagomarsino V, Latourelle JC, Hadzi TC, Bregu J, MacDonald ME, Gusella JF, Chen JF, Akbarian S, Weng Z, Myers RH. (2016). Correction: RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PLoS One. 2016 Jul 25;11(7):e0160295. View in PubMed

Hoss AG, Labadorf A, Beach TG, Latourelle JC, Myers RH. (2016). microRNA Profiles in Parkinson’s Disease Prefrontal Cortex. Front Aging Neurosci. 2016 Mar 1;8:36. View in PubMed

Dumitriu A, Golji J, Labadorf AT, Gao B, Beach TG, Myers RH, Longo KA, Latourelle JC. (2016) Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease. BMC Med Genomics. 2016 Jan 21;9:5. View in PubMed

Chen, B.H., Hivert, M.F., Peters, M.J., Pilling, L.C., Hogan, J.D., Pham, L.M., Harries, L.W., Fox, C.S., Bandinelli, S., Dehghan, A., Hernandez, D.G., Hofman, A., Hong, J., Joehanes, R., Johnson, A.D., Munson, P.J., Rybin, D.V., Singleton, A.B., Uitterlinden, A.G., Ying, S, MAGIC Investigators, Melzer, D., Levy, D., van Meurs, J.B., Ferrucci, L., Florez, J.C., Dupuis, J., Meigs, J.B., Kolaczyk, E.D. (2016). Peripheral Blood Transcriptomic Signatures of Fasting Glucose and Insulin Concentrations. Diabetes. 65(12): 3794-3804. View in PubMed

Caballero, I.S., Honko, A.N., Gire, S.K., Winnicki, S.M., Melé, M., Gerhardinger, C., Lin, A.E., Rinn, J.L., Sabeti, P.C., Hensley, L.E., Connor, J.H., 2016, In vivo Ebola virus infection leads to a strong innate response in circulating immune cells, BMC Genomics, 17:707. View in PubMed

Zhang, S., Wei, J.S., Li, S.Q., Badgett, T.C., Song, Y.K., Agarwal, S., Coarfa, C., Tolman, C., Hurd, L., Liao, H., He, J., Wen, X., Liu, Z., Thiele, C.J., Westermann, F., Asgharzadeh, S., Seeger, R.C., Maris, J.M., Guidry Auvil, J.M., Smith, M.A., Kolaczyk, E.D., Shohet, J., Khan, J., 2016, MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma, Cancer lett, 371(2):214-24. View in PubMed

Briers, D., Haghighi, I., White, D., Kemp, M.L., Belta, C., 2016, Pattern Synthesis in a 3D Agent Based Model of Stem Cell Differentiation, IEEE 55th Conference on Decision and Control.

Shaikho, E.M., Habara, A.H., Alsultan, A., Al-Rubaish, A.M., Al-Muhanna, F., Naserullah, Z., Alsuliman, A., Qutub, H.O., Patra, P.K., Sebastiani, P., Baltrusaitis, K., Farrell, J.J., Jiang, Z., Luo, H.Y., Chui, D.H., Al-Ali, A.K., Steinberg, M.H., 2016, Variants of ZBTB7A (LRF) and its β-globin gene cluster binding motifs in sickle cell anemia, Blood Cells Mol Dis, 59:49-51. View in PubMed

Quintin, M., Ma, N.J., Ahmed, S., Bhatia, S., Lewis, A., Isaacs, F.J., Densmore, D., 2016, Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE, ACS Synth Biol, 5(6):452-458. View in PubMed

Bohnuud, T., Luo, L., Wodak, S.J., Bonvin, A.M., Weng, Z., Vajda, S., Schueler-Furman, O., Kozakov, D., 2016, A benchmark testing ground for integrating homology modeling and protein docking, Proteins, 85(1):10-16. View in PubMed

Oh, J., Byrd, A.L., Park, M., NISC Comparative Sequencing Program, Kong, H.H., Segre, J.A., 2016, Temporal Stability of the Human Skin Microbiome, Cell, 165(4):854-866. View in PubMed

Kartha, V.K., Stawski, L., Han, R., Haines, P., Gallagher, G., Noonan, V., Kukuruzinska, M., Monti, S., Trojanowska, M., 2016, PDGFRβ Is a Novel Marker of Stromal Activation in Oral Squamous Cell Carcinoma, PLoS One, 11(4): e0154645. View in PubMed

Piacentino, M.L., Zuch, D.T., Fishman, J., Rose, S., Speranza, E., Li, C., Yu, J., Chung, O., Ramachandran, J., Ferrell, P., Patel, V., Reyna, A., Hameeduddin, H., Chaves, J., Hewitt, F.B., Bardot, E., Lee, D., Core, A.B., Hogan, J.D., Keenan, J.L., Luo, L., Coulombe-Huntington, J., Blute, T.A., Oleinik, E., Ibn-Salem, J., Poustka, A.J., Bradham, C.A., 2016, RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins, Development, 143(4):703-714. View in PubMed

Pavel, A.B., Sonkin, D., Reddy, A., 2016, Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity, BMC Syst Biol, 10:16. View in PubMed

Fleck, J.L., Pavel, A.B., Cassandras, C.G., 2016, Integrating mutation and gene expression cross-sectional data to infer cancer progression, BMC Syst Biol, 10:12. View in PubMed

Byrd, A.L., Segre J.A., 2016, Infectious disease. Adapting Koch’s postulates, Science, 351(6270): 224-226. View in PubMed

Jun, G., Ibrahim-Verbaas, C.A., Vronskaya, M., Lambert, J.C., Chung, J.,…Farrer, L.A., 2016, A novel Alzheimer disease locus located near the gene encoding tau protein, Mol Psychiatry, 21(1):108-117.

Tellez, C.S., Juri, D.E., Do, K., Picchi, M.A., Wang, T., Liu, G., Spira, A., Belinsky, S.A., 2016, miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis, Cancer res, 76(16):4741-4751.

Padhorny, D., Kazennov, A., Zerbe, B.S., Porter, K.A., Xia, B., Mottarella, S.E., Kholodov, Y., Ritchie, D.W., Vajda, S., Kozakov, D., 2016, Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds, Proc Natl Acad Sci USA, 113(30):E4286-4293.

Hu, H., Khatri, K., Klein, J., Leymarie, N., and Zaia, J., 2016, A review of methods for interpretation of glycopeptide tandem mass spectral data, Glycoconjugate journal, 33(3):285-296.

Khatri, K., Klein, J.A., White, M.R., Grant, O.C., Leymarie, N., and Woods, R.J., Hartshorn, K.L., and Zaia, J., 2016, Integrated omics and computational glycobiology reveal structural basis for influenza a virus glycan microheterogeneity and host interactions, Molecular & Cellular Proteomics, 15(6):1895-1912.

Zaia, J., Khatri, K., Klein, J., Shao, C., Sheng, Y., and Viner, R., 2016, Complete Molecular Weight Profiling of Low-Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High-Resolution Mass Spectrometry, Analytical Chemistry, 88(21):10654-10660.

2015

Christenson, S.A., Steiling, K., van den Berge, M., Hijazi, K., Hiemstra, P.S., Postma, D.S., Lenburg, M.E., Spira, A., Woodruff, P.G. (2015). Asthma-COPD overlap. Clinical relevance of genomic signatures of type 2 inflammation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med., 191(7): 758-766. View in PubMed

Wang, T.W., Vermeulen, R.C., Hu, W., Liu, G., Xiao, X., Alekseyev, Y., Xu, J., Reiss, B., Steiling, K., Downward, G.S., Silverman, D.T., Wei, F., Wu, G., Li, J., Lenburg, M.E., Rothman, N., Spira, A., Lan, Q. (2015). Gene-expression profiling of buccal epithelium among non-smoking women exposed to household air pollution from smoky coal. Carcinogenesis, 36(12): 1494-1501. View in PubMed

Campbell, J.D., Liu, G., Luo, L., Xiao, J., Gerrein, J., Juan-Gardela, B., Tedrow, J., Alekseyev, Y.O., Yang, I.V., Correll, M., Geraci, M., Quackenbush, J., Sciurba, F., Schwartz, D.A., Kaminski, N., Johnson, W.E., Monti, S., Spira, A., Beane, J., Lenburg, M.E. (2015). Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data. RNA, 21(2): 164-171.

Nogiec, C., Burkart, A., Dreyfuss, J.M., Lerin, C., Kasif, S., Patti, M.E. (2015). Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes. Mol Metab., 4(3):151-163.

Tan, Y., Tambouret, Y., Monti, S. (2015). SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq) Data. Biomed Res Int., 2015: 780519.

Tan, Y., Wu, F., Tamayo, P., Haining, W.N., Mesirov, J.P. (2015). Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res., 4:167.

Maxwell, E.K., Campbell, J.D., Spira, A., Baxevanis, A.D. (2015). SubmiRine: assessing variants in microRNA targets using clinical genomic data sets. Nucleic Acids Res., 43(8): 3886-3898.

Connor JH, Yen J, Caballero IS, Garamszegi S, Malhotra S, Lin K, Hensley L, Goff AJ. (2015) Transcriptional Profiling of the Immune Response to Marburg Virus Infection. Journal of Virology. 2015 Oct;89(19):9865-74.

Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. (2015) The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington’s Disease. PLoS One. 2015 Dec 4;10(12):e0144398. View in PubMed

Labadorf AT, Myers RH. (2015) Evidence of Extensive Alternative Splicing in Post Mortem Human Brain HTT Transcription by mRNA Sequencing. PLoS One. 2015 Oct 23;10(10):e0141298. View in PubMed

Lukose V, Luo L, Kozakov D, Vajda S, Allen KN, Imperiali B.Conservation and Covariance in Small Bacterial Phosphoglycosyltransferases Identify the Functional Catalytic Core. Biochemistry. 2015 Dec 22;54(50):7326-34. doi: 10.1021/acs.biochem.5b01086. Epub 2015 Dec 4. PMID: 26600273 View in PubMed

Melia, T., Hao, P., Yilmaz, F., Waxman, D.J., 2015, Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone, Mol Cell Biol, 36(1): 50-69. View in PubMed

Conforto TL, Steinhardt GF 4th, Waxman DJ. “Cross Talk Between GH-Regulated Transcription Factors HNF6 and CUX2 in Adult Mouse Liver.” Mol Endocrinol. 2015 Sep;29(9):1286-302. View in PubMed

Eleveld TF, Oldridge DA, Bernard V, Koster J, Daage LC, Diskin SJ, Schild L, Bentahar NB, Bellini A, Chicard M, Lapouble E, Combaret V, Legoix-Né P, Michon J, Pugh TJ, Hart LS, Rader J, Attiyeh EF, Wei JS, Zhang S, Naranjo A, Gastier-Foster JM, Hogarty MD, Asgharzadeh S, Smith MA, Guidry Auvil JM, Watkins TB, Zwijnenburg DA, Ebus ME, van Sluis P, Hakkert A, van Wezel E, van der Schoot CE, Westerhout EM, Schulte JH, Tytgat GA, Dolman ME, Janoueix-Lerosey I, Gerhard DS, Caron HN, Delattre O, Khan J, Versteeg R, Schleiermacher G, Molenaar JJ, Maris JM. “Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations.” Nat Genet. 2015 Aug;47(8):864-71. View in PubMed

Russell MR, Penikis A, Oldridge DA, Alvarez-Dominguez JR, McDaniel L, Diamond M, Padovan O, Raman P, Li Y, Wei JS, Zhang S, Gnanchandran J, Seeger R, Asgharzadeh S, Khan J, Diskin SJ, Maris JM, Cole KA. “CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus.” Cancer Res. 2015 Aug 1;75(15):3155-66. View in PubMed

Byrd AL, Segre JA. “Elucidating microbial codes to distinguish individuals.” Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6778-9. View in PubMed

Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE. “ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.” Bioinformatics. 2015 Jun 1;31(11):1745-53. View in PubMed

Hiemer SE, Zhang L, Kartha VK, Packer TS, Almershed M, Noonan V, Kukuruzinska M, Bais MV, Monti S, Varelas X. “A YAP/TAZ-Regulated Molecular Signature Is Associated with Oral Squamous Cell Carcinoma.” Mol Cancer Res. 2015 Jun;13(6):957-68. View in PubMed

Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. “Ligand deconstruction: Why some fragment binding positions are conserved and others are not.” Proc Natl Acad Sci U S A. 2015 May 19;112(20):E2585-94. View in PubMed

Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S. “The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins.” Nat Protoc. 2015 May;10(5):733-55. View in PubMed

Chubiz LM, Granger BR, Segre D, Harcombe WR. “Species interactions differ in their genetic robustness.” Front Microbiol. 2015 Apr 14;6:271. eCollection 2015. View in PubMed

Byrd AL, Segre JA. “Integrating host gene expression and the microbiome to explore disease pathogenesis.” Genome Biol. 2015 Apr 8;16:70. View in PubMed

Naik S, Bouladoux N, Linehan JL, Han SJ, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, Quinones M, Brenchley JM, Kong HH, Tussiwand R, Murphy KM, Merad M, Segre JA, Belkaid Y. “Commensal-dendritic-cell interaction specifies a unique protective skin immune signature.” Nature. 2015 Apr 2;520(7545):104-8. View in PubMed

Chen J, Hackett CS, Zhang S, Song YK, Bell RJ, Molinaro AM, Quigley DA, Balmain A, Song JS, Costello JF, Gustafson WC, Van Dyke T, Kwok PY, Khan J, Weiss WA. “The genetics of splicing in neuroblastoma.” Cancer Discov. 2015 Apr;5(4):380-95. View in PubMed

Jun G, Ibrahim-Verbaas CA, Vronskaya M, Lambert JC, Chung J, Naj AC, Kunkle BW, Wang LS, Bis JC, Bellenguez C, Harold D, Lunetta KL, Destefano AL, Grenier-Boley B, Sims R, Beecham GW, Smith AV, Chouraki V, Hamilton-Nelson KL, Ikram MA, Fievet N, Denning N, Martin ER, Schmidt H, Kamatani Y, Dunstan ML, Valladares O, Laza AR, Zelenika D, Ramirez A, Foroud TM, Choi SH, Boland A, Becker T, Kukull WA, van der Lee SJ, Pasquier F, Cruchaga C, Beekly D, Fitzpatrick AL, Hanon O, Gill M, Barber R, Gudnason V, Campion D, Love S, Bennett DA, Amin N, Berr C, Tsolaki M, Buxbaum JD, Lopez OL, Deramecourt V, Fox NC, Cantwell LB, Tárraga L, Dufouil C, Hardy J, Crane PK, Eiriksdottir G, Hannequin D, Clarke R, Evans D, Mosley TH Jr, Letenneur L, Brayne C, Maier W, De Jager P, Emilsson V, Dartigues JF, Hampel H, Kamboh MI, de Bruijn RF, Tzourio C, Pastor P, Larson EB, Rotter JI, O’Donovan MC, Montine TJ, Nalls MA, Mead S, Reiman EM, Jonsson PV, Holmes C, St George-Hyslop PH, Boada M, Passmore P, Wendland JR, Schmidt R, Morgan K, Winslow AR, Powell JF, Carasquillo M, Younkin SG, Jakobsdóttir J, Kauwe JS, Wilhelmsen KC, Rujescu D, Nöthen MM, Hofman A, Jones L; IGAP Consortium, Haines JL, Psaty BM, Van Broeckhoven C, Holmans P, Launer LJ, Mayeux R, Lathrop M, Goate AM, Escott-Price V, Seshadri S, Pericak-Vance MA, Amouyel P, Williams J, van Duijn CM, Schellenberg GD, Farrer LA. “A novel Alzheimer disease locus located near the gene encoding tau protein.” Mol Psychiatry. 2015 Mar 17. View in PubMed

Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. “miR-10b-5p expression in Huntington’s disease brain relates to age of onset and the extent of striatal involvement.” BMC Med Genomics. 2015 Mar 1;8:10. View in PubMed

Carey CD, Gusenleitner D, Chapuy B, Kovach AE, Kluk MJ, Sun HH, Crossland RE, Bacon CM, Rand V, Dal Cin P, Le LP, Neuberg D, Sohani AR, Shipp MA, Monti S, Rodig SJ. “Molecular classification of MYC-driven B-cell lymphomas by targeted gene expression profiling of fixed biopsy specimens.” J Mol Diagn. 2015 Jan;17(1):19-30. View in PubMed

2014

Christadore, L.M., Pham, L., Kolaczyk, E.D., Schaus, S.E. (2014). Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. BMC Syst Biol., 8:7.

Maxwell, E.K., Schnitzler, C.E., Havlak, P., Putnam, N.H., Nguyen, A.D., Moreland, R.T., Baxevanis, A.D. (2014). Evolutionary profiling reveals the heterogeneous origins of classes of human disease genes: implications for modeling disease genetics in animals. BMC Evol Biol., 14:212.

Gelfand, Y., Hernandez, Y., Loving, J., Benson, G. (2014). VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data. Nucleic Acids Res., 42(14):8884-8894.

Heiman, M., Heilbut, A., Francardo, V., Kulicke, R., Fenster, R.J., Kolaczyk, E.D., Mesirov, J.P., Surmeier, D.J., Cenci, M.A., Greengard, P. (2014). Molecular adaptations of striatal spiny projection neurons during levodopa-induced dyskinesia. Proc Natl Acad Sci U S A, 111(12):4578-4583.

Robasky, K., Lewis, N.E., Church, G.M. (2014). The role of replicates for error mitigation in next-generation sequencing. Nat Rev Genet., 15(1): 56-62.

Caballero IS, Yen JY, Hensley LE, Honko AN, Goff AJ, Connor JH. (2014) Lassa and Marburg viruses elicit distinct host transcriptional responses early after infection. BMC Genomics. 2014 Nov 6;15:960.

Tan, Y., Tamayo, P., Nakaya, H., Pulendran, B., Mesirov, J.P., Haining, W.N. (2014). Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol., 44(1): 285-295.

Khatri K, Staples GO, Leymarie N, Leon DR, Turiák L, Huang Y, Yip S, Hu H, Heckendorf CF, Zaia J. (2014) Confident Assignment of Site-Specific Glycosylation in Complex Glycoproteins in a Single Step. 2014 Sep 9. [Epub ahead of print] View on PubMed

Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. (2014) High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. PLoS One. 2014 Jun 23;9(6):e100325. View on PMC

Appleton E, Tao J, Wheatley FC, Desai DH, Lozanoski TM, Shah PD, Awtry JA, Jin SS, Haddock TL, Densmore DM. “Owl: electronic datasheet generator.” ACS Synth Biol. 2014 Dec 19;3(12):966-8.
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Van Tyne D, Tan Y, Daily JP, Kamiza S, Seydel K, Taylor T, Mesirov JP, Wirth DF, Milner DA Jr. “Plasmodium falciparum gene expression measured directly from tissue during human infection.” Genome Med. 2014 Nov 29;6(11):110.
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Loving J, Hernandez Y, Benson G. “BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm.” Bioinformatics. 2014 Nov 15;30(22):3166-73.
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Oh J, Byrd AL, Deming C, Conlan S; NISC Comparative Sequencing Program, Kong HH, Segre JA. “Biogeography and individuality shape function in the human skin metagenome.” Nature. 2014 Oct 2;514(7520):59-64. doi: 10.1038/nature13786. View in PubMed

Khatri K, Staples GO, Leymarie N, Leon DR, Turiák L, Huang Y, Yip S, Hu H, Heckendorf CF, Zaia J. “Confident Assignment of Site-Specific Glycosylation in Complex Glycoproteins in a Single Step.” J Proteome Res. 2014 Sep 9. [Epub ahead of print] View in PubMed

Hong C, Manimaran S, Shen Y, Perez-Rogers JF, Byrd AL, Castro-Nallar E, Crandall KA, Johnson WE. “PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples.” Microbiome. 2014 Sep 5;2:33. doi: 10.1186/2049-2618-2-33. eCollection 2014. View in PubMed

Byrd AL, Perez-Rogers JF, Manimaran S, Castro-Nallar E, Toma I, McCaffrey T, Siegel M, Benson G, Crandall KA, Johnson WE. “Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data.” BMC Bioinformatics. 2014 Aug 4;15:262. doi: 10.1186/1471-2105-15-262. View in PubMed

Oye KA, Esvelt K, Appleton E, Catteruccia F, Church G, Kuiken T, Lightfoot SB, McNamara J, Smidler A, Collins JP. “Biotechnology. Regulating gene drives.” Science. 2014 Aug 8;345(6197):626-8. doi: 10.1126/science.1254287. Epub 2014 Jul 17. View in PubMed

Garamszegi S, Yen JY, Honko AN, Geisbert JB, Rubins KH, Geisbert TW, Xia Y, Hensley LE, Connor JH. “Transcriptional Correlates of Disease Outcome in Anticoagulant-Treated Non-Human Primates Infected with Ebolavirus.” PLoS Negl Trop Dis. 2014 Jul 31;8(7):e3061. View in PubMed

Gusenleitner D, Auerbach SS, Melia T, Gómez HF, Sherr DH, Monti S. “Genomic models of short-term exposure accurately predict long-term chemical carcinogenicity and identify putative mechanisms of action.” PLoS One. 2014 Jul 24;9(7):e102579. doi: 10.1371/journal.pone.0102579. eCollection 2014. View in PubMed

Gomes AL, Abeel T, Peterson M, Azizi E, Lyubetskaya A, Carvalho L, Galagan J. “Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction.” Genome Res. 2014 Jul 14. pii: gr.161711.113. View in PubMed

Hu H, Huang Y, Mao Y, Yu X, Xu Y, Liu J, Zong C, Boons GJ, Lin C, Xia Y, Zaia J. “A Computational Framework for Heparan Sulfate Sequencing Using High-resolution Tandem Mass Spectra.” Mol Cell Proteomics. 2014 Sep;13(9):2490-502. doi: 10.1074/mcp.M114.039560. Epub 2014 Jun 12. View in PubMed

Harcombe, WR, Riehl WJ, Dukovski I, Granger BR, Betts A, Lang AH, Bonilla G, Kar A, Leiby N, Mehta P, Marx CJ, Segrè D. “Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics.” Cell Rep. 2014 May 22;7(4):1104-15. doi: 10.1016/j.celrep.2014.03.070. View in PubMed

Appleton E, Tao J, Haddock T, Densmore, D. ”Interactive assembly algorithms for molecular cloning.” Nature Methods. 2014 11, 657–662. Published online 2014 April 28. View in PubMed

Gindin Y, Valenzuela MS, Aladjem MI, Meltzer PS, Bilke S. “A chromatin structure-based model accurately predicts DNA replication timing in human cells.” Mol Syst Biol. 2014 10:722. Published online 2014 March 28. View in PubMed

Pandya C, Dunaway-Mariano D, Xia Y, Allen KN. “Structure-guided approach for detecting large domain inserts in protein sequences as illustrated using the haloacid dehalogenase superfamily.” Proteins. 2014. Published online 2014 February 27. View in PubMed

Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, Macdonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. “MicroRNAs Located in the Hox gene clusters are implicated in huntington’s disease pathogensis.” PLoS Genet. 2014 10(2):e1004188. Published online 2014 February 24. View in PubMed

Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J. “The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection.” PLoS Pathog. 2014 Feb 6;10(2):e1003904. doi: 10.1371/journal.ppat.1003904. eCollection 2014. View in PubMed

2013

Deng, T., Zhu, Z.I., Zhang, S., Leng, F., Cherukuri, S., Hansen, L., Mariño-Ramírez, L., Meshorer, E., Landsman, D., Bustin, M. (2013). HMGN1 modulates nucleosome occupancy and DNase I hypersensitivity at the CpG island promoters of embryonic stem cells. Mol Cell Biol., 33(16): 3377-3389.

McMurry, A.J., Fitch, B., Savova, G., Kohane, I.S., Reis, B.Y. (2013). Improved de-identification of physician notes through integrative modeling of both public and private medical text. BMC Med Inform Decis Mak., 13: 112.

McMurry, A.J., Murphy, S.N., MacFadden, D., Weber, G., Simons, W.W., Orechia, J., Bickel, J., Wattanasin, N., Gilbert, C., Trevvett, P., Churchill, S., Kohane, I.S. (2013). SHRINE: enabling nationally scalable multi-site disease studies. PLoS One, 8(3): e55811.

Sugathan, A., Waxman, D.J. (2013). Genome-wide analysis of chromatin states reveals distinct mechanisms of sex-dependent gene regulation in male and female mouse liver. Mol Cell Biol., 33(18): 3594-3610.

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Jun G, Vardarajan BN, Buros J, Yu CE, Hawk MV, Dombroski BA, Crane PK, Larson EB, Mayeux R, Haines JL, Lunetta KL, Pericak-Vance MA, Schellenberg GD, Farrer LA; Alzheimer’s Disease Genetics Consortium. “Comprehensive Search for Alzheimer Disease Susceptibility Loci in the APOE Region.” Arch Neurol. 2012 August 6:1-10. doi: 10.1001/archneurol.2012.2052. View in PubMed

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Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S. “Deep sequencing of the oral microbiome reveals signatures of periodontal disease.” PLoS One. 2012; 7(6): e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4. View on PubMed

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Alsultan A, Ngo DA, Farrell JJ, Akinsheye I, Solovieff N, Ghabbour HA, Al-Ali A, Alsuliman A, Al-Baghshi M, Albu-Ali W, Alabdulaali M, Baldwin CT, Farrer LA, Luo H, Melista E, Safaya S, Nwaru M Jr, Chui DH, Steinberg MH. “A functional promoter polymorphism of the δ-globin gene is a specific marker of the Arab-Indian haplotype.” Am J Hematol. 2012 August; 87(8): 824-6. doi: 10.1002/ajh.23239. Epub 2012 May 28. View on PubMed

Schu M, Sherva R, Farrer L, Green RC. “The Genetics of Alzheimer’s Disease.”  Alzheimer’s Disease – Modernizing Concept, Biological Diagnosis and Therapy. Advances in Biological Psychiatry, Vol. 28; Basel, Karger. April 23, 2012

Miles GD, Seiler M, Rodriguez L, Rajagopal G, Bhanot G. “Identifying microRNA/mRNA dysregulations in ovarian cancer.” BMC Res Notes. 2012 March 27; 5: 164. View in PubMed

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Shigemizu D, Hu Z, Hung JH, Huang CL, Wang Y, DeLisi C. “Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer.” PLoS Comput Biol. 2012 Feb; 8(2): e1002347. Epub 2012 Feb 0. View in PubMed

Yang HW, Kim TM, Song SS, Shrinath N, Park R, Kalamarides M, Park PJ, Black PM, Carroll RS, Johnson MD. “Alternative splicing of CHEK2 and codeletion with NF2 promote chromosomal instability in meningioma.” Neoplasia. 2012 Jan; 14(1): 20-8. View in PubMed

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Chiu, H.C., Segrè, D. (2008). Comparative determination of biomass composition in differentially active metabolic States. Genome Inform., 20: 171-182.

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Gower, A.C., Steiling, K., Brothers, J.F., Lenburg, M.E., Spira, A. (2011). Transcriptomic studies of the airway field of injury associated with smoking-related lung disease. Proc Am Thorac Soc., 8(2):173-179.

Luna, A., Sunshine, M.L., van Iersel, M.P., Aladjem, M.I., Kohn, K.W. (2011). PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics, 27(15): 2165-2166.

Luna, A., Karac, E.I., Sunshine, M., Chang, L., Nussinov, R., Aladjem, M.I., Kohn, K.W. (2011). A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics, 12:167.

Logue MW, Schu MVardarajan BN, Buros J, Green RC, Go RC, Griffith P, Obisesan TO, Shatz R, Borenstein A, Cupples LA, Lunetta KL, Fallin MD, Baldwin CT, Farrer LA; Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study Group. “A comprehensive genetic association study of Alzheimer disease in African Americans.” Arch Neurol. 2011 December; 68(12): 1569-79. View on PubMed

Yen JY, Garamszegi S, Geisbert JB, Rubins KH, Geisbert TW, Honko A, Xia Y, Connor JH, Hensley LE. “Therapeutics of Ebola hemorrhagic fever: whole-genome transcriptional analysis of successful disease mitigation.” J Infect Dis. 2011 204 Suppl 3:S1043-52. Published online 2011 November. View in PubMed

Cancer Genome Atlas Research Network, Bell D, Berchuck A, Birrer M, Chien J, Park R. “Integrated genomic analyses of ovarian carcinoma.” Nature. 2011 474(7353):609-15. Published online 2011 June 29. View in PubMed

Kim TM, Huang W, Park R, Park PJ, Johnson MD. “A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs.” Cancer Res.2011 71(9):3387-99. Published online 2011 May 1. View in PubMed

Bushell KN, Leeman SE, Gillespie E, Gower AC, Reed KL, Stucchi AF, Becker JM, Amar S . “LITAF mediation of increased TNF-α secretion from inflamed colonic lamina propria macrophages.” PLoS One. 2011; 6(9): e25849. Epub 2011 Sep 30. View on PubMed

Pankratz N, Dumitriu A, Hetrick KN, Sun M, Latourelle JC, Wilk JB, Halter C, Doheny KF, Gusella JF, Nichols WC, Myers RH, Foroud T, DeStefano A. “PSG–PROGENI and GenePD investigators, coordinators and molecular genetic laboratories, copy number variation in familial Parkinson disease.” PLoS ONE. 2011; 6(8): e20988. Epub 2011 Aug 2. View on PubMed

Pang K, Ryan JF, Baxevanis AD, and Martindale MQ. “Evolution of the TGF–β signaling pathway and its potential role in the ctenophore Mnemiopsis leidyi.” PLOS One. 2011; 2(1):3. Epub 2011 Sep 8. View on PubMed

Sherva R, Baldwin CT, Inzelberg R, Vardarajan B, Cupples LA, Lunetta K, Bowirrat A, Naj A, Pericak-Vance M, Friedland RP, Farrer LA. “Identification of novel candidate genes for Alzheimer’s disease by autozygosity mapping using genome wide SNP data.” J Alzheimers Dis. 2011; 23(2): 349-59. View on PubMed

Richard J. Roberts, Chang Y, Zhenjun Hu, John N. Rachlin, Anton B, Revonda M. Pokrzywa, Han-Pil Choi, Faller L, Jyotsna Guleria, Genevieve Housman, Klitgord N, Mazumdar V, Mark G. McGettrick, Lais Osmani, Rajeswari Swaminathan, Kevin R. Tao, Stan Letovsky, Dennis Vitkup, Daniel Segrè, Steven L. Salzberg, Charles Delisi, Martin Steffen and Simon Kasif. “COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.” Nucleic Acids Research. 2011 January; 39(Database issue): D11-4. Epub 2010 Nov 21. View on PubMed

Reitz C, Tokuhiro S, Clark LN, Conrad C, Vonsattel JP, Hazrati LN, Palotás A, Lantigua R, Medrano M, Z Jiménez-Velázquez I, Vardarajan B, Simkin I, Haines JL, Pericak-Vance MA, Farrer LA, Lee JH, Rogaeva E, George-Hyslop PS, Mayeux R. “SORCS1 alters amyloid precursor protein processing and variants may increase Alzheimer’s disease risk.” Ann Neurol. 2011 January; 69(1): 47-64. doi: 10.1002/ana.22308. View on PubMed

Hurle B, Marques-Bonet T, Antonacci F, Hughes I, Ryan JF. “NISC Comparative Sequencing Program, Eichler EE, Ornitz DM, and Green ED. Lineage-Specific Evolution of the Vertebrate Otopetrin Gene Family Revealed by Comparative Genomic Analyses.” BMC Evolutionary Biology. 2011 January 24; 11(1): 23. View on PubMed

Cuenco KT, Friedland R, Baldwin CT, Guo J, Vardarajan B, Lunetta KL, Cupples LA, Green RC, Decarli C, Farrer LA; for the MIRAGE Study Group. “Association of TTR polymorphisms with hippocampal atrophy in Alzheimer disease families.” Neurobiol Aging. 2011 February; 32(2): 249-56. Epub 2009 Mar 27. View on PubMed

Reitzel AM, Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ, and Tarrant AM. “Nuclear Receptors from the Ctenophore Mnemiopsis leidyi Lack a Zinc-Finger DNA-Binding Domain: Lineage- Specific Loss or Ancestral Condition in the Emergence of the Nuclear Receptor Superfamily?” BMC Evodevo. 2011 February 3; 2(1): 3. View on Pubmed

Ho JW, Bishop EP, Karchenko PV, Nègre N, White KP, Park PJ. “ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis.” BMC Genomics, 2011 February 28; 12: 134. View PubMed

Schneider S, Smith T, Hansen U. “SCOREM: statistical consolidation of redundant expression measures.” Nucleic Acids Res. 2012 March; 40(6): e46. Epub 2011 Dec 30. View on PubMed

Olsson M, Meadows JR, Truvé K, Rosengren Pielberg G, Puppo F, Mauceli E, Quilez J, Tonomura N, Zanna G, Docampo MJ, Bassols A, Avery AC, Karlsson EK, Thomas A, Kastner DL, Bongcam-Rudloff E, Webster MT, Sanchez A, Hedhammar A, Remmers EF, Andersson L, Ferrer L, Tintle L, Lindblad-Toh K. “A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.” PLoS Genet. 2011 March; 7(3): e1001332. Epub 2011 Mar 17. View on PubMed

Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI. “X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila.” Nature. 2011 March 3; 471: 115-118. View on PubMed

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ. “Comprehensive analysis of the chromatin landscape in Drosophila melanogaster”. Nature. 2011 March 24; 471: 480–485. Epub 2010 Dec 22. View on PubMed

Campbell J.D, Spira A, Lenburg ME. “Applying gene expression microarrays to pulmonary disease.” Respirology. 2011 April; 16(3): 407-418. View on PubMed

Dumitriu A, Pacheco CD, Wilk JB, Strathearn KE, Latourelle JC, Goldwurm S, Pezzoli G, Rochet JC, Lindquist S, Myers RH. “Cyclin-G-associated kinase modifies α-synuclein expression levels and toxicity in Parkinson’s disease: results from the GenePD Study.” Hum Mol Genet. 2011 April 15; 20(8): 1478-87. Epub 2011 Jan 21. View on PubMed

Gower AC, Steiling K, Brothers JF 2nd, Lenburg ME, Spira A. “Transcriptomic studies of the airway field of injury associated with smoking-related lung disease.” Proc Am Thorac Soc. 2011 May; 8(2): 173-9. View on PubMed

Naj AC, Jun G, . . . Vardarajan BN, . . . .Farrer LA, Schellenberg GD. “Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer’s disease.” Nat Genet. 2011 May; 43(5):4 36-41. doi: 10.1038/ng.801. Epub 2011 Apr 3. View on PubMed

Farrell JJ, Sherva RM, Chen ZY, Luo HY, Chu BF, Ha SY, Li CK, Lee AC, Li RC, Li CK, Yuen HL, So JC, Ma ES, Chan LC, Chan V, Sebastiani P, Farrer LA, Baldwin CT, Steinberg MH, Chui DH. “A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression.” Blood. 2011 May 5; 117(18): 4935-45. Epub 2011 Mar 8. View on PubMed

Beane J, Vick J, Schembri F, Anderlind C, Gower A, Campbell J, Luo L, Zhang XH, Xiao J, Alekseyev YO, Wang S, Levy S, Massion PP, Lenburg M, Spira A. “Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq.” Cancer Prev Res. 2011 June; 4(6): 803-17. View on PubMed

Hsin-Hung Chou, Hsuan-Chao Chiu, Nigel F. Delaney, Daniel Segrè, Christopher J. Marx. “Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation.” Science. 3 June 2011; 332(6034): 1190-1192. View on PubMed

E. A. Franzosa, Y. Xia. “Structural principles within the human-virus protein-protein interaction network.” Proceedings of the National Academy of Sciences. 2011 June 28; 108(26): 10538-43. Epub 2011 Jun 16. View on PubMed

Niels Klitgord and Daniel Segrè. “Ecosystems biology of microbial metabolism.” Current Opinions in Biotechnology. 2011 August; 22(4): 541-6. Epub 2011 May 16. View on PubMed

Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z. “A machine learning approach for the prediction of protein surface loop flexibility.” Proteins. 2011 August; 79(8): 2467-74. Epub 2011 Jun 1. View on PubMed

Pett W, Ryan JF, Pang K, NISC Comparative Sequencing Program, Martindale MQ, Mullikin J, Baxevanis AD, and Lavrov D. “Extreme Mitochondrial Genome Evolution in the Ctenophore Mnemiopsis leidyi.” Mitochondrial DNA. 2011 August; 22(4): 130-42. Epub 2011 Oct 10. View on PubMed

Gang Wei, Brian J. Abraham, Ryoji Yagi, Raja Jothi, Kairong Cui, Suveena Sharma, Leelavati Narlikar, Daniel L. Northrup, Qingsong Tang, William E. Paul, Jinfang Zhu, Keji Zhao “Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types.” Immunity. 2011 August 26; 35(2): 299-311. View on PubMed

Vreven T, Hwang H, Weng Z. “Integrating atom-based and residue-based scoring functions for protein-protein docking.” Protein Science. 2011 September; 20(9): 1576-86. Epub 2011 Aug 8. View on PubMed

Gower AC, Spira A, Lenburg ME. “Discovering biological connections between experimental conditions based on common patterns of differential gene expression.” BMC Bioinformatics. 2011 Sep 27; 12: 381. View on PubMed

Hua Huang, Yury Patskovsky, Rafael Toro, Jeremiah D. Farelli, Chetanya Pandya, Steven C. Almo, Karen N. Allen, and Debra Dunaway-Mariano “Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 Is an Inorganic Pyrophosphatase”. Biochemistry. 2011 October 18; 50(41): 8937-49. Epub 2011 Sep 21. View on PubMed

Traylor-Knowles N, Granger BR, Lubinski TJ, Parikh JR, Garamszegi S, Xia Y, Marto JA, Kaufman L, Finnerty JR. Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis.”BMC Genomics. 2011 November 29; 12: 585. View on PubMed

Dreyfuss JM, Jacobs C, Gindin Y, Benson G, Staples GO, Zaia J. “Targeted analysis of glycomics liquid chromatography/mass spectrometry data.” Anal Bioanal Chem. 2011 399(2):727-35. Published online 2011 January. View in PubMed

2010

Hansen, L., Mariño-Ramírez, L., Landsman, D. (2010). Many sequence-specific chromatin modifying protein-binding motifs show strong positional preferences for potential regulatory regions in the Saccharomyces cerevisiae genome. Nucleic Acids Res., 38(6): 1772-1779.

Riehl, W.J., Krapivsky, P.L., Redner, S., Segrè, D. (2010). Signatures of arithmetic simplicity in metabolic network architecture. PLoS Comput Biol., 6(4): e1000725.

Reznik, G.O., Vishwanath, P., Pynn, M.A., Sitnik, J.M., Todd, J.J., Wu, J., Jiang, Y., Keenan, B.G., Castle, A.B., Haskell, R.F., Smith, T.F., Somasundaran, P., Jarrell, K.A. (2010). Use of sustainable chemistry to produce an acyl amino acid surfactant. Appl Microbiol Biotechnol., 86(5): 1387-1397.

Shee, K., Strong, M., Guido, N.J., Lue, R.A., Church, G.M., Viel, A. (2010). Research, collaboration, and open science using web 2.0. J Microbiol Biol Educ., 11(2): 130-134.

Ling, G., Sugathan, A., Mazor, T., Fraenkel, E., Waxman, D.J. (2010). Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression. Mol Cell Biol., 30(23):5531-5544.

Wauthier, V., Sugathan, A., Meyer, R.D., Dombkowski, A.A., Waxman, D.J. (2010). Intrinsic sex differences in the early growth hormone responsiveness of sex-specific genes in mouse liver. Mol Endocrinol., 24(3): 667-678.

Anton, B.P., Russell, S.P., Vertrees, J., Kasif, S., Raleigh, E.A., Limbach, P.A., Roberts, R.J. (2010). Nucleic Acids Res., 38(18):6195-6205.

Linghu, B., DeLisi, C. (2010). Phenotypic connections in surprising places. Genome Biol., 11(4):116.

Chittenden, T.W., Pak, J., Rubio, R., Cheng, H., Holton, K., Prendergast, N., Glinskii, V., Cai, Y., Culhane, A., Bentink, S., Schwede, M., Mar, J.C., Howe, E.A., Aryee, M., Sultana, R., Lanahan, A.A., Taylor, J.M., Holmes, C., Hahn, W.C., Zhao, J.J., Iglehart, J.D., Quackenbush, J. (2010). Therapeutic implications of GIPC1 silencing in cancer. PLoS One, 5(12):e15581.

Antonescu, C., Antonescu, V., Sultana, R., Quackenbush, J. (2010). Using the DFCI gene index databases for biological discovery. Curr Protoc Bioinformatics, Chapter 1:Unit1.6.1-36.

Culhane, A.C., Schwarzl, T., Sultana, R., Picard, K.C., Picard, S.C., Lu, T.H., Franklin, K.R., French, S.J., Papenhausen, G., Correll, M., Quackenbush, J. (2010). GeneSigDB–a curated database of gene expression signatures. Nucleic Acids Res., 38(Database issue):D716-725.

Wilbe M, Jokinen P, Truvé K, Seppala EH, Karlsson EK, Biagi T, Hughes A, Bannasch D, Andersson G, Hansson-Hamlin H, Lohi H, Lindblad-Toh K. “Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex.” Nat Genet. 2010 March; 42(3): 250-4. Epub 2010 Jan 31. View on PubMed

Bushkin GG, Ratner DM, Cui J, Banerjee S, Duraisingh MT, Jennings CV, Dvorin JD, Gubbels MJ, Robertson SD, Steffen M, O’Keefe BR, Robbins PW, Samuelson J. “Suggestive evidence for Darwinian Selection against asparagine-linked glycans of Plasmodium falciparum and Toxoplasma gondii.” Eukaryot Cell. 2010 February; 9(2): 228-41. Epub 2009 Sep 25. View on PubMed

Bormann Chung CA, Boyd VL, McKernan KJ, Fu Y, Monighetti C, Peckham HE, Barker M. “Whole methylome analysis by ultra-deep sequencing using two-base encoding.” PLoS One. 2010 February 22; 5(2): e9320. View on PubMed

Nicodemus KK, Callicott JH, Higier RG, Luna A, Nixon DC, Lipska BK, Vakkalanka R, Giegling I, Rujescu D, Clair DS, Muglia P, Shugart YY, Weinberger DR. “Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging.” Hum Genet. 2010 April; 127(4):441-52. View on PubMed

Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. “Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network.” Cell Stem Cell. 2010 June 4; 6(6): 591-602. View on PubMed

Shen, B.W., Heiter, D.F., Chan, S.H., Wang, H., Xu, S.Y., Morgan, R.D., Wilson, G.G. and Stoddard, B.L. “Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.” Structure. 2010 June 9; 18(6): 734-43. View on PubMed

Stefan L. Ameres, Michael D. Horwich, Jui-Hung Hung, Jia Xu, Megha Ghildiyal, Zhiping Weng, Phillip D. Zamore. “Target RNA–Directed Trimming and Tailing of Small Silencing RNAs.” Science. 2010 June 18; 328(5985): 1534-1539. View on PubMed

Grabinska KA, Cui J, Chatterjee A, Guan Z, Raetz CR, Robbins PW, Samuelson J. “Molecular characterization of the cis-prenyltransferase of Giardia lamblia.” Glycobiology. 2010 July; 20(7): 824-32. Epub 2010 Mar 22. View on PubMed

Edwards JR, O’Donnell AH, Rollins RA, Peckham HE, Lee C, Milekic MH, Chanrion B, Fu Y, Su T, Hibshoosh H, Gingrich JA, Haghighi F, Nutter R, Bestor TH. “Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns.” Genome Res. 2010 July; 20(7): 972-80. Epub 2010 May 20. View on PubMed

Parikh JR, Klinger B, Xia Y, Marto JA, Blüthgen N. “Discovering causal signaling pathways through gene-expression patterns.” Nucleic Acids Res. 2010 July; 38(Web Server issue): W109-17. Epub 2010 May 21. View on PubMed

Cui J, Das S, Smith TF, Samuelson J. “Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes.” PLoS Negl Trop Dis. 2010 August 3; 4(8): e782. View on Pubmed

Ooi AT, Mah V, Nickerson DW, Gilbert JL, Ha VL, Hegab AE, Horvath S, Alavi M, Maresh EL, Chia D, Gower AC, Lenburg ME, Spira A, Solis LM, Wistuba II,Walser TC, Wallace WD, Dubinett SM, Goodglick L, Gomperts BN. “Presence of a putative tumor-initiating progenitor cell population predicts poor prognosis in smokers with non-small cell lung cancer.” Cancer Res. 2010 August 15; 70(16): 6639-48. View on Pubmed

Pierce BG, Haidar JN, Yu Y, and Weng Z. “Combinations of Affinity-Enhancing Mutations in a T Cell Receptor Reveal Highly Nonadditive Effects within and between Complementarity Determining Regions and Chains.” Biochemistry. 2010 August 24; 49(33): 7050-9. View on PubMed

Emek Demir . . . . Augustin Luna, et al.”The BioPAX community standard for pathway data sharing.” Nature Biotechnology. 2010 September; 28(9): 935-42. Epub 2010 Sep 9. View on PubMed

Mitra S, Cui J, Robbins PW, Samuelson J. “A deeply divergent phosphoglucomutase (PGM) of Giardia lamblia has both PGM and phosphomannomutase activities.” Glycobiology. 2010 October; 20(10): 1233-40. Epub 2010 May 27. View on PubMed

Ryan JF, Pang K. “NISC Comparative Sequencing Program, Mullikin JC, Martindale MQ, and Baxevanis AD. The Homeodomain Complement of the Ctenophore Mnemiopsis leidyi Suggests that Ctenophora and Porifera Diverged Prior to the ParaHoxozoa.” BMC Evodevo. 2010 October 4; 1(1): 9. View on PubMed

Carpentieri A, Ratner DM, Ghosh SK, Banerjee S, Bushkin GG, Cui J, Lubrano M, Steffen M, Costello CE, O’Keefe B, Robbins PW, Samuelson J. “The antiretroviral lectin cyanovirin-N targets well-known and novel targets on the surface of Entamoeba histolytica trophozoites.” Eukaryot Cell. 2010 November; 9(11): 1661-8. Epub 2010 Sep 17. View on PubMed

Dima Kozakov, David R. Hall, Dmitri Beglov, Ryan Brenke, Stephen R. Comeau, Yang Shen, Keyong Li, Jiefu Zheng, Pirooz Vakili, Ioannis Ch. Paschalidis, Sandor Vajda. “Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19.” Proteins: Structure, Function, and Bioinformatics. 2010 November 15; 78(15): 3065-3249. View on PubMed

Hwang H, Vreven T, Pierce B, Hung J, Weng Z. “Performance of ZDOCK and ZRANK in CAPRI round 13-19.” Proteins. 2010 November 15; 78(15): 3104-10. View on PubMed

2009

Hansen, L., Lee, E.A., Hestir, K., Williams, L.T., Farrelly, D. (2009). Controlling feature selection in random forests of decision trees using a genetic algorithm: classification of class I MHC peptides. Comb Chem High Throughput Screen., 12(5): 514-519.

Laz, E.V., Sugathan, A., Waxman, D.J. (2009). Dynamic in vivo binding of STAT5 to growth hormone-regulated genes in intact rat liver. Sex-specific binding at low- but not high-affinity STAT5 sites. Mol Endocrinol., 23(8): 1242-1254.

Lee, K.H., Saleh, L., Anton, B.P., Madinger, C.L., Benner, J.S., Iwig, D.F., Roberts, R.J., Krebs, C., Booker, S.J. (2009). Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry, 48(42):10162-10174.

Mariño-Ramírez L, Tharakaraman K, Bodenreider O, Spouge J, Landsman D. “Identification of cis-regulatory elements in gene co-expression networks using A-GLAM.” Methods Mol Biol. 2009; 541: 1-22. Review. View on PubMed

Steiling K, Kadar AY, Bergerate A, Flanigon J, Sridhar S, Shah V, Ahmad QR, Brody JS, Lenburg ME, Steffen M, Spira A. “Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers.” PLoS One. 2009; 4(4): e5043. Epub 2009 Apr 9. View on PubMed

Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C. “Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.” Genome Biol. 2009; 10(9): R91. Epub 2009 Sep 3. View on PubMed

Lun DS, Rockwell G, Guido NJ, Baym M, Kelner JA, Berger B, Galagan JE, Church GM. “Large-scale identification of genetic design strategies using local search.” Mol Syst Biol. 2009; 5: 296. Epub 2009 Aug 18. View on PubMed

Beane J, Spira A, Lenburg ME. “Clinical impact of high-throughput gene expression studies in lung cancer.” J Thorac Oncol. 2009 January; 4(1): 109-18. View on PubMed

Mazumdar V, Snitkin ES, Amar S, Segrè D. “Metabolic network model of a human oral pathogen.” J Bacteriol. 2009 January; 191(1): 74-90. Epub 2008 Oct 17. View on PubMed

Lorenz DR, Cantor CR, Collins JJ  “A network biology approach to aging in yeast.” Proc Natl Acad Sci U.S.A. 2009 January 27; 106(4): 1145-50. Epub 2009 Jan 21. View on PubMed

F.Schembri, S.Sridhar, C. Perdomo, A.M.Gustafson, X. Zhang, A. Ergun, J. Lu, Liu G, X. Zhang, J. Bowers, K. Sensinger, J. Collins, J. Brody, R. Getts, M. Lenburg, A. Spira. “MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium.” Proc Natl Acad Sci U S A. 2009 February 17; 106(7):2319-24. Epub 2009 Jan 23. View on PubMed

Fusaro VA, Mani DR, Mesirov JP, Carr SA. “Prediction of high-responding peptides for targeted protein assays by mass spectrometry.” Nat Biotechnol. 2009 February; 27(2): 190-8. Epub 2009 Jan 25. View on PubMed

Mak DY, Benson G. “All hits all the time: parameter-free calculation of spaced seed sensitivity.” Bioinformatics. 2009 February 1; 25(3): 302-8. Epub 2008 Dec 18. View on PubMed

Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David Hall, Melissa R. Landon, Carla Mattos and Sandor Vajda. “Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques.” Bioinformatics, 2009 March 1; 25(5): 621-7. Epub 2009 Jan 28. View on PubMed

Zhang X, Sebastiani P, Liu G, Schembri F, Dumas YM, Langer EM, Alekseyev Y, O’Connor GT, Brooks DR, Lenburg ME, Spira A. “Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium.” Physiol Genomics. 2010 March 3; 41(1): 1-8. Epub 2009 Dec 1. View on PubMed

Meng YA, Yu Y, Cupples LA, Farrer LA, Lunetta KL. “Performance of random forest when SNPs are in linkage disequilibrium.” BMC Bioinformatics. 2009 March 5; 10: 78. View on PubMed

Askenazi M, Parikh JR, Marto JA. “mzAPI: a new strategy for efficiently sharing mass spectrometry data.” Nat Methods. 2009 April; 6(4): 240-1. View on PubMed

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. “Local DNA topography correlates with functional noncoding regions of the human genome.” Science. 2009 April 17; 324(5925): 389-92. Epub 2009 Mar 12. View on PubMed

Chengjian Li, Vasily V. Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Hervé Seitz, Michael D. Horwich, Monika Syrzycka, Barry M. Honda, Ellen L.W. Kittler, Maria L. Zapp, Carla Klattenhoff, Nadine Schulz, William E. Theurkauf, Zhiping Weng, Phillip D. Zamore, “Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies.” Cell. 2009 May 1; 137(3): 509-21. Epub 2009 Apr 23. View on PubMed

Yu L, Coelho JE, Zhang X, Fu Y, Tillman A, Karaoz U, Fredholm BB, Weng Z, Chen JF. “Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling.” Physiol Genomics. 2009 May 13; 37(3): 199-210. Epub 2009 Mar 3. View on PubMed

Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C. “VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.” Nucleic Acids Res. 2009 July; 37(Web Server issue): W115-21. Epub 2009 May 21. View on PubMed

Butler G . . . Rheinbay, E. et al. “Evolution of pathogenicity and sexual reproduction in eight Candida genomes.” Nature. 2009 June 4; 459(7247): 657-62. View on PubMed

W. A. Beckstead, M. T. W. Ebbert, D. A. McClellan, and M. J. Rowe. “Evolutionary pressure on mitochondrial cytochrome b is consistent with a role for cytbI7T polymorphism affecting human aging and longevity during caloric restriction.” PLoS One. 2009 June 8; 4(6): e5836. View on PubMed

Brackney DE, Beane JE, Ebel GD. “RNAi targeting of West Nile virus in mosquito midguts promotes virus diversification.” PLoS Pathogens. 2009 July; 5(7): e1000502. Epub 2009 Jul 3. View on PubMed

Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A, Seitz H, Zamore PD, Weng Z, Theurkauf WE. “The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.” Cell. 2009 September 18; 138(6): 1137-49. Epub 2009 Sep 3. View on PubMed

Jeanne C Latourelle, Nathan Pankratz, Alexandra Dumitriu, Jemma B Wilk, Stefano Goldwurm, Gianni Pezzoli, Claudio B Mariani, Anita L DeStefano, Cheryl Halter, James F Gusella, William C Nichols, Richard H Myers, Tatiana Foroud, the PSG -PROGENI and GenePD Investigators, Coordinators and Molecular Genetic Laboratories. “Genome wide association study for onset age in Parkinson disease.” BMC Medical Genetics. 2009 September 22; 10: 98. View on PubMed

Parikh JR, Askenazi M, Ficarro SB, Cashorali T, Webber JT, Blank NC, Zhang Y, Marto JA. “multiplierz: an extensible API based desktop environment for proteomics data analysis.” BMC Bioinformatics. 2009 October 29; 10: 364. View on PubMed

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. “Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.” PLoS Genet. 2008 October; 4(10): e1000242. Epub 2008 Oct 31. View on PubMed

Hu, L, Temple F. Smith, and Gabriel Goldberger. “LFG: a candidate apoptosis regulatory gene family.” Apoptosis. 2009 November; 14: 1255-1265. View on PubMed

Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M. “A predictive phosphorylation signature of lung cancer.” PLoS One. 2009 November 25; 4(11): e7994. View on PubMed

Steiling K, Lenberg ME, Spira A. “Airway Gene Expression in Chronic Obstructive Pulmonary Disease.” Proc Am Thorac Soc. 2009 December; 6: 697-700. View on PubMed

Sebastiani P, Montano M, Puca A, Solovieff N, Kojima T, Wang MC, Melista E, Meltzer M, Fischer SE, Andersen S, Hartley SH, Sedgewick A, Arai Y, Bergman A, Barzilai N, Terry DF, Riva A, Anselmi CV, Malovini A, Kitamoto A, Sawabe M, Arai T, Gondo Y, Steinberg MH, Hirose N, Atzmon G, Ruvkun G, Baldwin CT, Perls TT. “RNA editing genes associated with extreme old age in humans and with lifespan in C. elegans.” PLoS One. 4(12):e8210. Erratum in: PLoS One. 2009 December 14; 4(12): e8210. View on PubMed

2008

Wiehe, K., Peterson, M.W., Pierce, B., Mintseris, J., Weng, Z. (2008). Protein-protein docking: overview and performance analysis. Methods Mol Bio, 413: 283-314.

Faith, J.J., Driscoll, M.E., Fusaro, V.A., Cosgrove, E.J., Hayete, B., Juhn, F.S., Schneider, S.J., Gardner, T.S. (2008). Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res, 36(Database issue): D866-870.

Faith, J.J., Driscoll, M.E., Fusaro, V.A., Cosgrove, E.J., Hayete, B., Juhn, F.S., Schneider, S.J., Gardner, T.S. (2008). Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic Acids Res., 36(Database issue): D866-870.

Fredrickson, J.K., Romine, M.F., Beliaev, A.S., Auchtung, J.M., Driscoll, M.E., Gardner, T.S., Nealson, K.H., Osterman, A.L., Pinchuk, G., Reed, J.L., Rodionov, D.A., Rodrigues, J.L., Saffarini, D.A., Serres, M.H., Spormann, A.M., Zhulin, I.B., Tiedje, J.M. (2008). Towards environmental systems biology of Shewanella. Nat Rev Microbiol., 6(8): 592-603.

Riehl, W.J., Segrè, D. (2008). Optimal metabolic regulation using a constraint-based model. Genome Inform., 20: 159-170.

Chiu, H.C., Segrè, D. (2008). Comparative determination of biomass composition in differentially active metabolic States. Genome Inform., 20: 171-182.

Zeskind, J.E., Lenburg, M.E., Spira, A. (2008). Translating the COPD transcriptome: insights into pathogenesis and tools for clinical management. Proc Am Thorac Soc., 5(8): 834-841.

Sridhar, S., Schembri, F., Zeskind, J., Shah, V., Gustafson, A.M., Steiling, K., Liu, G., Dumas, Y.M., Zhang, X., Brody, J.S., Lenburg, M.E., Spira, A. (2008). Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics, 9:259.

Anton, B.P., Saleh, L., Benner, J.S., Raleigh, E.A., Kasif, S., Roberts, R.J. (2008). RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A, 105(6):1826-1831.

Linghu, B., Snitkin, E.S., Holloway, D.T., Gustafson, A.M., Xia, Y., DeLisi, C. (2008). High-precision high-coverage functional inference from integrated data sources. BMC Bioinformatics, 9:119.

Chittenden, T.W., Howe, E.A., Culhane, A.C., Sultana, R., Taylor, J.M., Holmes, C., Quackenbush, J. (2008). Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. Genomics, 91(6):508-511.

Soohyun Lee, Simon Kasif, Zhiping Weng, Charles R Cantor. “Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation.” PLoS ONE. 2008; 3(12): e3906. Epub 2008 Dec 18. View on PubMed

Megha Ghildiyal, Hervé Seitz, Michael D. Horwich, Chengjian Li, Tingting Du, Soohyun Lee, Jia Xu, Ellen L.W. Kittler, Maria L. Zapp, Zhiping Weng, Phillip D. Zamore, “Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells.” Science. 2008 May 23; 320: pp1077-1081. Epub 2008 Apr 10. View on PubMed

J.E. Tobin, J.C. Latourelle, M.F. Lew, C. Klein, O. Suchowersky, H.A., Shill, L.I. Golbe, M.H. Mark, J.H. Growdon, G.F. Wooten, B.A. Racette, J.S. Perlmutter, R. Watts, M. Guttman, K.B. Baker, S. Goldwurm, G., Pezzoli, C. Singer, M.H. Saint-Hilaire, A.E. Hendricks, S. Williamson, M.W. Nagle, J.B. Wilk, T. Massood, J.M. Laramie, A.L. DeStefano, I., Litvan, G. Nicholson, A. Corbett, S. Isaacson, D.J. Burn, P.F., Chinnery, P.P. Pramstaller, S. Sherman, J. Al-hinti, E. Drasby, M., Nance, A.T. Moller, K. Ostergaard, R. Roxburgh, B. Snow, J.T. Slevin, F. Cambi, J.F. Gusella, R.H. Myers. “Haplotypes and gene expression implicate the MAPT region for Parkinson disease: The GenePD Study.” Neurology. 2008 July 1; 71(1): 28–34. Epub 2008 May 28. View on PubMed

Sedgewick AE, Timofeev N, Sebastiani P, So JC, Ma ES, Chan LC, Fucharoen G, Fucharoen S, Barbosa CG, Vardarajan BN, Farrer LA, Baldwin CT, Steinberg MH, Chui DH. “BCL11A is a major HbF quantitative trait locus in three different populations with beta-hemoglobinopathies.” Blood Cells Mol Dis. 2008 Nov-Dec; 41(3): 255-8. Epub 2008 Aug 8. View on PubMed

Jiang X, Nariai N, Steffen M, Kasif S, Kolaczyk ED. “Integration of relational and hierarchical network information for protein function prediction.” BMC Bioinformatics. 2008 August 22; 9(1): 350. View on PubMed

Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. “Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.” PLoS Genet. 2008 October; 4(10): e1000242. Epub 2008 Oct 31. View on PubMed

W. A. Beckstead, B. C. Bjork, D. R. Beier, and S. Sunyaev. “SNP2RFLP. A computational tool to facilitate genetic mapping using benchtop analysis of SNPs.” Mammalian Genome. 2008 Oct-Dec; 19(10-12): 687-690. View on Pubmed

Hwang H., Pierce B., Mintseris J., Janin J., Weng Z. “Protein-protein docking benchmark version 3.0.” Proteins. 2008 November 15; 73(3): 705-709. View on PubMed

Peisach, E., Wang, L., Burroughs, A.M., Aravind, L., Dunaway-Mariano, D., Allen, K.N., 2008, The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function, Proteins, 70(1):197-207.

2007

Reddy, T.E., Shakhnovich, B.E., Roberts, D.S., Russek, S.J., DeLisi, C. (2007). Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes. Nucleic Acids Res., 35(3): e20.

Mintseris, J., Pierce, B., Wiehe, K., Anderson, R., Chen, R., Weng, Z. (2007). Integrating statistical pair potentials into protein complex prediction. Proteins, 69(3), 511-520.

Wiehe, K., Pierce, B., Tong, W.W., Hwang, H., Mintseris, J., Weng, Z. (2007). The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins, 69(4): 719-725.

Guido, N.J., Lee, P., Wang, X., Elston, T.C., Collins, J.J. (2007). A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophys J., 93(11): L55-57.

Hu, L., Segrè, D., Smith, T.F. (2007). Evolutionary changes in gene regulation from a comparative analysis of multiple Drosophila species. Genome Inform., 18: 12-21.

Beane J, Sebastiani P, Liu G, Brody J, Lenburg M, Spira A. “Reversible and Permanent Effects of Tobacco Smoke Exposure on Airway Epithelial Gene Expression.” Genome Biology. 2007; 8(9): R201. View on PubMed

Spira A, Beane JE, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas YM, Calner P, Sebastiani P, Sridhar S, Beamis J, Lamb C, Anderson T, Gerry N, Keane J, Lenburg ME, Brody JS. “Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer.”  Nat Med. 2007 March; 13(3): 361-6. Epub 2007 Mar 4. View on PubMed

Bhutkar A, Gelbart WM, Smith TF. “Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study.” Genome Biology. 2007; 8(11): R236. View on PubMed

Bhutkar A, Russo SM, Smith TF, Gelbart WM. “Genome-scale analysis of positionally relocated genes.” Genome Research. 2007 December; 17(12): 1880-7. Epub 2007 Nov 7. View on PubMed

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Liu D, Brockman JM, Dass B, Hutchins LN, Singh P, McCarrey J, MacDonald C, Graber JH. “Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis.” Nucleic Acids Research. 2007; 35(1): 234-246. Epub 2006 Dec 8. View on PubMed

Clodfelter KH, Miles GD, Wauthier V, Holloway MG, Zhang X, Hodor P, Ray WJ, Waxman DJ. “Role of STAT5a in regulation of sex-specific gene expression in female but not male mouse liver revealed by microarray analysis.” Physiol Genomics. 2007 September 19; 31(1): 63-74. Epub 2007 May 29. View on PubMed

Banerjee S, Vishwanath P, Cui J, Kelleher DJ, Gilmore R, Robbins PW, Samuelson J. “Evolution of quality control of protein- folding in the ER lumen.” Proc. Natl. Acad. Sci. USA. 2007 July 10; 104(28): 11676. Epub 2007 Jul 2. View on PubMed

Das S, Van Dellen K, Bulik D, Magnelli P, Cui J, Head J, Robbins PW, Samuelson J. “The cyst wall of Entamoeba invadens contains chitosan (deacetylated chitin).” Mol. Biochem. Parasitol. 2006 July; 48: 86-92. Epub 2006 Mar 31. View on PubMed

Samuelson J, Magnelli P, Banerjee S, Cui J, Kelleher D, Gilmore R, Loftus B, Robbins P. “The diversity of protist and fungal dolichol-linked precursors to Asn-linked glycans (Alg) likely results from secondary loss of sets of Alg enzymes.” Proc. Natl. Acad. Sci. USA. 2005 February 1; 102:1548-1553. Epub 2005 Jan 21. View on PubMed

Tobin JE, Cui J, Wilk JB, Latourelle JC, Laramie JM, McKee AC, Guttman M, Karamohamed S, Destefano AL, Myers RH. “Sepiapterin reductase expression is increased in Parkinson’s disease brain tissue.” Brain Res. 2007 March 30; 1139: 42-7. View on PubMed

Eichler, GS, Reimers, M, Kane, D, Weinstein, JN, “The LeFE algorithm, embracing the complexity of gene expression in the interpretation of microarray data.” Genome Biology. 2007; 8(9):R185. View on PubMed

Petricoin EF 3rd, Espina V, Araujo RP, Midura B, Yeung C, Wan X, Eichler GS, Johann DJ Jr, Qualman S, Tsokos M, Krishnan K, Helman LJ, Liotta LA. “Phosphoprotein pathway mapping: Akt/mammalian target of rapamycin activation is negatively associated with childhood rhabdomyosarcoma survival.” Cancer Res. April 2007 April 1; 67(7): 3431-40. View on PubMed

Sheehan KM, Gulmann C, Eichler GS, Weinstein JN, Barrett HL, Kay EW, Conroy RM, Liotta LA, Petricoin EF., “Signal pathway profiling of epithelial and stromal compartments of colonic carcinoma reveals epithelial-mesenchymal transition.” Oncogene. 2008 January 10; 27(3):323-31. Epub 2007 Jul 9. View on PubMed

Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, et al. “Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles.” PLoS Biol. 2007 January; 5(1): e8. View on PubMed

Greenbaum JA, Parker SCJ, Tullius, TD. “Detection of DNA structural motifs in functional genomic elements.” Genome Research. 2007 June; 17(6): 940-946. View on PubMed

Greenbaum JA, Pang B, Tullius, TD. “Construction of a genome-scale structural map at single-nucleotide resolution.” Genome Research 17, 947-953. View on PubMed

ENCODE Consortium, [authors include Tullius TD, Greenbaum JA, and Parker SCJ.] “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.” Nature. 2007 June 14; 447(7146): 799-816. View in PubMed

T. D. Tullius & J. A. Greenbaum. 2005. “Mapping nucleic acid structure by hydroxyl radical cleavage.” Curr. Opinion Chem. Biol. 2007 April; 9(2): 127–134. View on PubMed

Dwyer D, Kohanski M, Hayete B, Collins JJ.  “Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli.” Mol Syst. Biol. 2007; 3: 91. Epub 2007 Mar 13. View on PubMed

Hayete B, Gardner TS, Collins JJ. “Size Matters: network inference tackles the genome scale.” Mol Syst Biol. 2007; 3: 77. Epub Feb 13. View on PubMed

L. Hu, D. Segre, T. F. Smith. “Evolutionary Changes in Gene Regulation from a Comparative Analysis of Multiple Drosophila Species.” Genome Inform. 2007; 18: 12-22. View on PubMed

Salmon Hillbertz NH, Isaksson M, Karlsson EK et al. “Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in Ridgeback dogs.” Nat Genet. 2007 November; 39(11): 1318-20. Epub 2007 Sep 30. View on PubMed

Thomas R,…, Karlsson EK et al. “A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog.” J Hered. 2007; 98(5): 474-84. Epub 2007 Aug 16. View on PubMed

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Landon MR, Lancia DR Jr, Yu J, Thiel SC, Vajda S. “Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins.” J Med Chem. 2007 March 22; 50(6): 1231-40. Epub 2007 Feb 17. View on PubMed

Laramie JM, Chung TP, Brownstein B, Stormo GD, Cobb JP. “Transcriptional Profiles of Human Epithelial Cells in Response to Heat: Computational Evidence for Novel Heat Shock Proteins.” Shock. 2008 May; 29(5): 623-30. View on PubMed

Laramie JM, Wilk JB, DeStefano AL, Myers RH. “HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies.” Bioinformatics. 2007 August 15; 23(16): 2190-2. Epub 2007 Jun 22. View on PubMed

Cupples LA, Arruda HT, Benjamin EJ, D’Agostino RB Sr, Demissie S, DeStefano AL, Dupuis J, Falls KM, Fox CS, Gottlieb DJ, Govindaraju DR, Guo CY, Heard-Costa NL, Hwang SJ, Kathiresan S, Kiel DP, Laramie JM, Larson MG, Levy D, Liu CY, Lunetta KL, Mailman MD, Manning AK, Meigs JB, Murabito JM, Newton-Cheh C, O’Connor GT, O’Donnell CJ, Pandey M, Seshadri S, Vasan RS, Wang ZY, Wilk JB, Wolf PA, Yang Q, Atwood LD. “The Framingham Heart Study 100K SNP genome-wide association study” resource: overview of 17 phenotype working group reports.” BMC Med Genet. 2007; 8 Suppl 1: S1. View on PubMed

Wilk JB, Walter RE, Laramie JM, Gottlieb DJ, O’Connor GT. “Framingham Heart Study genome-wide association: results for pulmonary function measures.” BMC Med Genet. 2007 September 19; 8 Suppl 1:S8. View on PubMed

Mak D, Benson G. “All Hits All The Time: Parameter Free Calculation of Seed Sensitivity.” APBC. 2009 Feb 1;25(3):302-8. Epub 2008 Dec 18. View on PubMed

Zhenjun Hu, Joe Mellor, Jie Wu, Minoru Kanehisa, Joshua M Stuart & Charles DeLisi, et al., “Towards zoomable multidimensional maps of the cell.” Nat Biotechnol. 2007 May;25(5):547-54. View on PubMed

Zhenjun Hu1, David M. Ng, Takuji Yamada, Chunnuan Chen, Shuichi Kawashima, Joe Mellor, Bolan Linghu, Minoru Kanehisa, Joshua M. Stuart and Charles DeLisi.”VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.” Nucl. Acids Res. 2007 Jul; 35: W625-32. Epub 2007 Jun 22. View on PubMed

Nariai N, Kolaczyk ED, Kasif S. “Probabilistic protein function prediction from heterogeneous genome-wide data.” PLoS ONE. Mar 28;2:e337. View on PubMed

Nariai N, Kasif S. “Context specific protein function prediction.” Genome Inform. 2007; 18:173-82. View on PubMed

Pierce B, Weng Z. “ZRANK: Reranking Protein Docking Predictions with an Optimized Energy Function.” Proteins. 2007 Jun; 1:67(4):1078-86. View on PubMed

Pierce B, Phillips AT, Weng Z.  “Structure Prediction of Protein Complexes.” In Xu Y, Xu D & Liang J. (Eds.), Computational Methods for Protein Structure Prediction and Modeling Volume 2: Structure Prediction. pp. 109-134. New York: Springer.

Timothy Reddy, Boris Shakhnovich, Daniel S Roberts, Shelley J Russek and Charles DeLisi. “Computational Binding Site Detection Using Positional Clustering Enables Identification of Novel Cis-Regulatory Sites in Mammalian GABAA Receptor Subunit Genes.” Nucl Acids Res. Feb 2007; 35: e20. View on PubMed

Timothy Reddy, Charles DeLisi, Boris Shakhnovich, “Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites.” PLoS Comput Biol. 2007 May; 3(5): e90. View on PubMed

Ryan JF, Mazza ME, Pang K, Matus DQ, Baxevanis AD, Martindale MQ, Finnerty JR. “Pre-Bilaterian Origins of the Hox Cluster and the Hox Code: Evidence from the Sea Anemone, Nematostella vectensis.” PLoS ONE. 2007 Jan 24;2:e153. View on PubMed

Sullivan JC, Ryan JF, Mullikin JC, Finnerty JR. “Conserved and novel Wnt clusters in the basal eumetazoan Nematostella vectensis.” Dev Genes Evol. 2007 Mar;217(3):235-9. View on PubMed

Cheng, A.C.; Coleman, R.G.; Smyth, K.T.; Cao, Q.; Soulard, P.; Caffrey, D.R.; Salzberg, A.C.; Huang, E.S. “Structure-based maximal affinity model predicts small-molecule druggability.”  Nature Biotechnology. 2007 Jan; 25(1):71-75. View on PubMed

O’Lone R*, Knorr K*, Jaffe IZ, Schaffer ME, Martini PGV, Karas RH, Bienkowska J, Mendelsohn ME, Hansen U. “Estrogen receptors alpha and beta mediate distinct pathways of vascular gene expression, including genes involved in mitochondrial electron transport and generation of reactive oxygen species.” Mol Endocrinol. 2007 Jun; 21:1281-1296. View on PubMed

Tullai, J.W., Chen, J., Schaffer, M.E., Kamenetsky, E., Kasif, S. and Cooper, G.M. “GSK-3b mediates repression of CREB target genes in quiescent cells.” J. Biol. Chem. 282:9482-9491.

Tullai, J.W., Schaffer, M.E., Mullenbrock, S., Sholder, G., Kasif, S. and Cooper, G.M. “Immediate-early and delayed primary response genes are distinct in function and genomic architecture.” J Biol Chem. 2007 Aug 17;282:23981-23995. View on PubMed

Sebastiani, Paola, Zhao Z, Abad-Grau M, Riva A, Hartley S, Sedgewick A, Doria A, Montano M, Melista E, Terry D, Perls T, Steinberg M, Clinton B. “A Hierarchical and Modular Approach to the Discovery of Robust Associations in Genome-Wide Association Studies from Pooled DNA Samples.” BMC Genetic. 2008 Jan 14; 9:6.doi:10.1186/1471-2156-9-6. View on PubMed

Zhang X, Liu G, Lenburg M, Spira A. “Comparison of smoking-induced gene expression on Affymetrix exon and 3’ based expression arrays.” Genome Informatics. 2007; 18:247-57. View on PubMed

2006

Nahum, L.A., Reynolds, M.T., Wang, Z.O., Faith, J.J., Jonna, R., Jiang, Z.J., Meyer, T.J., Pollock, D.D. (2006). EGenBio: a data management system for evolutionary genomics and biodiversity. BMC Bioinformatics, 7 Suppl 2:S7.

Murali, T.M., Wu, C.J., Kasif, S. (2006). The art of gene function prediction. Nat Biotechnol, 24(12): 1474-1475.

Li, J.L., Hayden, M.R., Warby, S.C., Durr, A., Morrison, P.J., Nance, M., Ross, C.A., Margolis, R.L., Rosenblatt, A., Squitieri, F., Frati, L., Gómez-Tortosa, E., García, C.A., Suchowersky, O., Klimek, M.L., Trent, R.J., McCusker, E., Novelletto, A., Frontali, M., Paulsen, J.S., Jones, R., Ashizawa, T., Lazzarini, A., Wheeler, V.C., Prakash, R., Xu, G., Djoussé, L., Mysore, J.S., Gillis, T., Hakky, M., Cupples, L.A., Saint-Hilaire, M.H., Cha, J.H., Hersch, S.M., Penney, J.B., Harrison, M.B., Perlman, S.L., Zanko, A., Abramson, R.K., Lechich, A.J., Duckett, A., Marder, K., Conneally, P.M., Gusella, J.F., MacDonald, M.E., Myers, R.H. (2006). Genome-wide significance for a modifier of age at neurological onset in Huntington’s disease at 6q23-24: the HD MAPS study. BMC Med Genet., 7:71.

Wang, K., Vishwanath, P., Eichler, G.S., Al-Sebaei, M.O., Edgar, C.M., Einhorn, T.A., Smith, T.F., Gerstenfeld, L.C. (2006). Analysis of fracture healing by large-scale transcriptional profile identified temporal relationships between metalloproteinase and ADAMTS mRNA expression. Matrix Biol., 25(5): 271-281.

Guido, N.J., Wang, X., Adalsteinsson, D., McMillen, D., Hasty, J., Cantor, C.R., Elston, T.C., Collins, J.J. (2006). A bottom-up approach to gene regulation. Nature, 439(70780: 856-860.

Malek, R.L., Wang, H.Y., Kwitek, A.E., Greene, A.S., Bhagabati, N., Borchardt, G., Cahill, L., Currier, T., Frank, B., Fu, X., Hasinoff, M., Howe, E., Letwin, N., Luu, T.V., Saeed, A., Sajadi, H., Salzberg, S.L., Sultana, R., Thiagarajan, M., Tsai, J., Veratti, K., White, J., Quackenbush, J., Jacob, H.J., Lee, N.H. (2006). Physiogenomic resources for rat models of heart, lung and blood disorders. Nat Genet., 38(2):234-239.

Beane, J., A. Kadar, A. Spira. “Diagnostic and prognostic impact of high-throughput genomic and proteomic technologies.” Henry’s Clinical Diagnosis and Management by Laboratory Methods. 21st edition. Saunders/Elsevier, Philadelphia. 2006.

Blower, P.E., K.P. Cross, G.S. Eichler, et al. “Comparison of methods for sequential screening of large compound sets.” Comb Chem High Throughput Screen. 2006 Feb; 9(2):115-22. View on PubMed

Burroughs AM, Allen KN, Dunaway-Mariano D, Aravind L. “Evolutionary Genomics of the HAD Superfamily: Understanding the Structural Adaptations and Catalytic Diversity in a Superfamily of Phosphoesterases and Allied Enzymes.”  J. Molecular Biology. 2006 Sep 1;361(5):1003-34. View on PubMed

Chung TP, Laramie JM, Meyer DJ, Downey T, Tam LH, Ding H, Buchman TG, Karl I, Stormo GD, Hotchkiss RS, Cobb JP. “Molecular diagnostics in sepsis: from bedside to bench.” J Am Coll Surg. 2006 Nov;203(5):585-598. View on PubMed

Clodfelter KH, Waxman DJ, Vajda S. “Computational solvent mapping reveals the importance of local conformational changes for broad substrate specificity in mammalian cytochromes P450.” Biochemistry, 2006 Aug 8;45(31):9393-407. View on PubMed

Clodfelter KH, Holloway MG, Hodor P, Park SH, Ray WJ, Waxman DJ. “Sex-Dependent Liver Gene Expression Is Extensive and Largely Dependent upon Signal Tranducer and Activator of Transcription 5b (STAT5b): STAT5b-Dependent Activation of Male Genes and Repression of Female genes Revealed by Microarray Analysis.” Mol Endocrinol. 2006 Jun; 20, 1333–1351. View on PubMed

Coleman R.G.; Salzberg, A.C.; Cheng A.C. (2006) “Structure-based identification of binding sites using a free energy model.”  J. Chem. Inf. Model. 2006 Nov-Dec; 46(6):2631-2637. View on PubMed

Demidov, V.V., N.V. Dokholyan, C. Witte-Hoffman, P. Chalasani, et al. “Fast complementation of split fluorescent protein triggered by DNA hybridization.” PNAS. 2006 Feb 14; 103(7):2052-2056. View on PubMed

Driscoll ME, Gardner TS. “Identification and control of gene networks in living organisms via supervised and unsupervised learning.” Journal of Process Control. 2006; 16:303-311.

Evsikov, A.V., Graber, J.H., Brockman, J.M., Singh, P., et al. “Cracking the egg: development dynamics and molecular transitions from the fully grown oocyte to embryo.” Genes and Development. 2006 Oct 1; 20(19).

Gustafson AM, Snitkin ES, Parker SC, et. al. “Towards the identification of essential genes using targeted genome sequencing and comparative analysis.” BMC Genomics. 2006 Oct 19; 7:265. View on PubMed

Iyer LM, Burroughs AM, Aravind L. “The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism.” Bioinformatics. 2006 Feb 1; 22(3):257-63. View on PubMed

Iyer LM, Burroughs AM, Aravind L. “The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.” Genome Biology.  2006;7(7):R60. View on PubMed

Jothi, R. Cherukuri, PF., Tasneem, A., Przytycka, TM. “Co-evolutionary analysis of domains in interacting proteins reveals insights inot domain-domain interactions mediating protein-protein interactions.” J Mol Biol. 2006 Sep 29; 362(4): 861-75.

Kozakov D, Brenke R, Comeau SR, Vajda S. (2006) “PIPER: An FFT-based protein docking program with pairwise potentials” Proteins. 2006 Nov 1;65(2):392-406. View on PubMed

Kim NK, Tharakaraman K, Spouge JL. “Adding sequence context to a Markov background model improves the identification of regulatory elements.” Bioinformatics. 2006 Dec 1;22(23):2870-5. Epub Oct 26. View on PubMed

Landon, M.R., D.R. Lancia, Jr., K.H. Clodfelter, S. Vajda. “Clustering of domains of functionally related enzymes in the interaction database PRECISE by the generation of primary sequence patterns.” J Mol Graph Model. 2006 May; 24(6):426-33. View on PubMed

Landon MR, Schaus SE. “JEDA: Joint entropy diversity analysis. An information-theoretic method for choosing diverse and representative subsets from combinatorial libraries.” Mol Divers. 2006 Aug;10(3):333-9. Epub 2006 Sep 21. View on PubMed

Laramie, J.M., et al. “Evidence for a gene influencing heart rate on chromosome 5p13-14 in a meta-analysis of genome-wide scans from the NHLBI Family Blood Pressure Program.” BMC Med Genet. 2006 Mar 1; 7:17. View on Pubmed

Lee, Soohyun & Simon Kasif. “The complete genome sequence of a dog: a perspective.” BioEssays. 2006 Jun; 28(6):569-573. View on PubMed

Mak, D., Gelfand, Y., Benson, G. “Indel seeds for homology search.” Bioinformatics. 2006 Jul 15; 22(14):e341-9. View on PubMed

McDunn, J.E., T.P. Chung, J.M. Laramie, et al. “Physiologic genomics.” Surgery. 2006 Feb; 139(2):133-9. View on PubMed

Meng Y., et.al. ″Association of the Angiotensin-converting Enzyme Gene with Alzheimer Disease in an Israeli-Arab Community.” Am J Hum Genet. 2006 May;78(5):871-7. Epub Mar 16. View on PubMed

Nusbaum, C., et al…S. Parker. “DNA Sequence and Analysis of Human Chromosome 8.”  Nature. 2006 Jan 19; 439:331-335. View on PubMed

Ryan, J.F., et al. “The cnidarian-bilaterian ancestor possesed at least 56 homeoboxes. Evidence from the starlet sea anemone, Nematostella vectensis.” Genome Biology. 2006; 7(7):R64. View on PubMed

Snitkin ES, Gustafson AM, Mellor J, Wu J, et. al. “Comparative assessment of performance and genome dependence among phylogenetic profiling methods.” BMC Bioinformatics. 2006 Sep 27; 7:420. View on Pubmed

Sullivan J.C., J.F. Ryan, et al. “StellaBase: The Nematostella vectensis Genomics Database.” Nucleic Acids Research. 2006 Jan 1;34(Database issue):D495-9. View on PubMed

Tharakaraman, K., Marino-Ramirez, L., Sheetlin, S.L., Landsman, D., Spouge, J.L. “Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements.” BMC Bioinformatics.” 2006 Sep 8;7:408. View on PubMed

Wu, J., Z. Hu, C. DeLisi. “Gene annotation and network inference by phylogenetic profiling.” BMC Bioinformatics. 2006 Feb 17; 7:80. View on PubMed

2005

Reddy, T.E., DeLisi, C., Shakhnovich, B.E. (2005). Assessing transcription factor motif drift from noisy decoy sequences. Genome Inform., 16(1): 59-67.

Wu, C.J., Kasif, S. (2005). GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res, 33(Web Server issue): W596-599.

Leyfer, D., Weng, Z. (2005). Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics, 12 Suppl 2: ii197-203.

Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J.J., Ladd-Acosta, C., Mesirov, J., Golub, T.R., Jacks, T. (2005). An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis.  Nat Genet., 37(1):48-55.

Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A,  102(43):15545-15550.

Bernstein, B. E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas, E.J., 3rd, Gingeras, T.R., Schreiber, S.L., Lander, E.S. (2005). “Genomic maps and comparative analysis of histone modifications in human and mouse.” Cell 120(2): 169-81. [Abstract]

Bhutkar, A. (2005). “Synthetic biology: Navigating the challenges ahead.” J. Biolaw & Business 8(2). [Abstract]

Brockman, J. M., Singh, P., Liu, D., Quinlan, S., Salisbury, J., Graber, J.H. (2005). “Pacdb: Polya cleavage site and 3′-utr database.” Bioinformatics 21(18): 3691-3. [Abstract]

Burroughs, A.M. (2005). “The medical examination in United States immigration applications: the potential use of genetic testing leads to heightened privacy concerns.” J. Biolaw & Business 8(2):22-32. [Abstract]

Comeau, S. R. and C. J. Camacho (2005). “Predicting oligomeric assemblies: N-mers a primer.” J Struct Biol 150(3): 233-44. [Abstract]

Comeau, S. R., S. Vajda, et al. (2005). “Performance of the first protein docking server cluspro in capri rounds 3-5.” Proteins 60(2): 239-44. [Abstract]

Dilley, W.G., S. Kalyanaraman, S. Verma, J.P. Cobb, J.M. Laramie, T.C. Lairmore. (2005). “Global gene expression in neuroendocrine tumors from patients with the MENI syndrome.” Mol Cancer 4(1):9. [Abstract]

Favaretto, P., A. Bhutkar, et al. (2005). “Constraining ribosomal rna conformational space.” Nucleic Acids Res 33(16): 5106-11. [Abstract]

Gardner, T. S., Faith, J.J. (2005). “Reverse-engineering transcription control networks.” Physics of Life Reviews 2:65-88.

Hu, Z., J. Mellor, et al. (2005). “Visant: Data-integrating visual framework for biological networks and modules.” Nucleic Acids Res 33(Web Server issue): W352-7. [Abstract]

Kozakov, D., K. H. Clodfelter, S. Vajda, C.J. Camacho (2005). “Optimal clustering for detecting near-native conformations in protein docking.” Biophys J 89(2): 867-75. [Abstract]

Lake, A.C., Y. Sun, J.L. Li, et. al. (2005). “Expressions, regulation, and triglyceride hydrolase activity of Adiponutrin family members.” J. Lipid Res 46(11):2477-87. [Abstract]

Landon, M.R. (2005). “Ethics and policy perspectives on personalized medicine in the post-genomic era.” J Biolaw Bus 8(3):28-36. [Abstract]

Lee, S., I. Kohane, S. Kasif (2005). “Genes involved in complex adaptive processes tend to have highly conserved upstream regions.” BMC Genomics 6:168. [Abstract]

Lindblad-Toh, K., C.M. Wade, T.S. Mikkelsen, E.K. Karlsson et al. (2005). “Genome sequence, comparative analysis and haplotype structure of the domestic dog.” Nature 438(7069):803-19. [Abstract]

Ma, Q., Y. Yu, Y. Meng, et al. (2005).  ″Genome-wide linkage analysis for alcohol dependence: a comparison between single-nucleotide polymorphism and microsatellite marker assays.” BMC Genetics, 6(Suppl 1):S8. [Abstract]

Marchler-Bauer, A., J.B. Anderson, P.F. Cherukuri, et al. (2005). “Cdd: A conserved domain database for protein classification.” Nucleic Acids Res 1(33): D192-6. [Abstract]

Meng, Y., Q. Ma, Y. Yu , et.al (2005). ″Multifactor-dimensionality reduction versus family-based association tests in detecting susceptibility loci in discordant sib-pair studies.” BMC Genetics, 6(Suppl 1):S146. [Abstract]

Mintseris, J. and Z. Weng (2005). “Structure, function, and evolution of transient and obligate protein-protein interactions.” Proc Natl Acad Sci U.S.A. 102(31): 10930-5. [Abstract]

Mintseris, J., K. Wiehe, et al. (2005). “Protein-protein docking benchmark 2.0: An update.” Proteins 60(2): 214-6. [Abstract]

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Sato, C., A. Morgan, A.E. Lang, S. Salehi-Rad, T. Kawarai, Y. Meng, et al. (2005).  “Analysis of the glucocerebrosidase gene in Parkinson’s disease.” Mov. Disord. Mar;20(3):367-70. [Abstract]

Seong, I.S., E. Ivanova, J.M. Lee, Y.S. Choo, E. Fossale, M. Anderson, J.F. Gusella, J.M. Laramie, et al. (2005). “HD CAG repeat implicates a dominant property of huntingtin in mitochondrial energy metabolism.” Hum Mol Genet 14(19):2871-80. [Abstract]

Shah, V., S. Sridhar, J. Beane, J.S. Brody, A. Spira. (2005). “Siege: Smoking induced epithelial gene expression database.” Nucleic Acids Res 33(Database issue): D573-9. [Abstract]

Shakhnovich, B. E. (2005). “Improving the precision of the structure-function relationship by considering phylogenetic context.” PLoS Comput Biol 1(1): e9. [Abstract]

Shakhnovich, B. E., E. Deeds, et al. (2005). “Protein structure and evolutionary history determine sequence space topology.” Genome Res 15(3): 385-92. [Abstract]

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Sheu, S. H., D. R. Lancia, Jr., K.H. Clodfelter, M.R. Landon, S. Vajda (2005). “Precise: A database of predicted and consensus interaction sites in enzymes.” Nucleic Acids Res 33(Database issue): D206-11. [Abstract]

Tharakaraman, K., L. Marino-Ramirez, S. Sheetlin, D. Landsman, J. L. Spouge “Alignments anchored on genomic landmarks can aid in the identification of regulatory elements”(2005) Bioinformatics 21 Suppl 1: i440-i448. [Abstract] (AWARD FOR BEST PAPER AT ISMB 2005 CONFERENCE)

Thomas, R., A. Scott, C.F. Langford, S.P. Fosmire, C.M. Jubala, T.D. Lorentzen, C. Hitte, E.K. Karlsson, et al. (2005).  “M. Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors.” Genome Res 15(12):1831-7. [Abstract]

Vinson, J. P., Jaffe, D.B., O’Neill, K., Karlsson, E.K., Stange-Thomann, N., Anderson, S., Mesirov, J.P., Satoh, N,. Satou, Y., Nusbaum, C., Birren, B., Galagan, J.E., Lander, E.S. (2005). “Assembly of polymorphic genomes: Algorithms and application to ciona savignyi.” Genome Res 15(8): 1127-35. [Abstract]

Wade, C.M. and E.K. Karlsson, et al. “The Dog Genome: Sequence, Evolution and Haplotype Structure.” In The Dog and Its Genome (ed. EA Ostrander, U Giger, K Lindblad-Toh). 2005 Dec 8;438(7069):803-19. View on PubMed

Wiehe, K., B. Pierce, et al. (2005). “Zdock and rdock performance in capri rounds 3, 4, and 5.” Proteins 60(2): 207-13. [Abstract]

Wu, C. J. and S. Kasif (2005). “Gems: A web server for biclustering analysis of expression data.” Nucleic Acids Res 33(Web Server issue): W596-9. [Abstract]

Wu, J., J.C. Mellor, C. DeLisi. “Deciphering protein network organization using phylogenetic profile groups.” Genome Inform Ser Workshop Genome Inform. 2005; 16(1):142-9. View on PubMed

Young, D.W., J. Pratap, A. Javed, B. Weiner, et al. “SWI/SNF chromatin remodeling complex is obligatory for BMP2-induced, RUNx2-dependent skeletal gene expression that controls osteoblast differentiation.” J Cell Biochem 94(4):720-30. [Abstract]

Yu, L., P. M. Haverty, et al. (2005). “Genetic and pharmacological inactivation of adenosine a2a receptor reveals an egr-2-mediated transcriptional regulatory network in the mouse striatum.” Physiol Genomics 23(1): 89-102. [Abstract]

Yu, Y., Y. Meng, Q. Ma, et al (2005).  ″Whole-genome variance components linkage analysis using single-nucleotide polymorphisms versus microsatellites on quantitative traits of derived phenotypes from factor analysis of electroencephalogram waves.” BMC Genetics, 6(Suppl 1):S15. [Abstract]

Yu, Y., et al. (2005). “Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia.” J Lipid Research 46(10):2202-13. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2005). “Characterization of two new aminopeptidases in escherichia coli.” J Bacteriol 187(11): 3671-7. [Abstract]

Zheng, Y., B.P. Anton, R.J. Roberts, S. Kasif (2005). “Phylogenetic detection of conserved gene clusters in microbial genomes.” BMC Bioinformatics 6:243. [Abstract]

Zhu, J. and Z. Weng (2005). “Fast: A novel protein structure alignment algorithm.” Proteins 58(3): 618-27. [Abstract]

2004

Wu, C.J., Fu, Y., Murali, T.M., Kasif, S. (2004). Gene expression module discovery using gibbs sampling. Genome Inform, 15(1): 239-248.

Vishwanath, P., Favaretto, P., Hartman, H., Mohr, S.C., Smith, T.F. (2004). Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Mol Phylogenet Evol., 33(3): 615-625.

Yang, Z., Shipman, L., Zhang, M., Anton, B.P., Roberts, R.J., Cheng, X. (2004). Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J Mol Biol., 340(4):695-706.

Beane, J. (2004). “A look behind the scenes: bioterrorism, smallpox, and public health policy. Journal of Biolaw and Business 7:40-53. [Abstract]

Comeau, S. R., D. W. Gatchell, et al. (2004). “Cluspro: A fully automated algorithm for protein-protein docking.” Nucleic Acids Res 32(Web Server issue): W96-9. [Abstract]

Comeau, S. R., D. W. Gatchell, et al. (2004). “Cluspro: An automated docking and discrimination method for the prediction of protein complexes.” Bioinformatics 20(1): 45-50. [Abstract]

Dasu, M.R., J.P. Cobb, J.M. Laramie, et al. (2004). “Gene expression profiles of livers from thermally injured rats.” Gene 327(1):51-60. [Abstract]

Ding, C. and C. R. Cantor (2004). “Quantitative analysis of nucleic acids–the last few years of progress.” J Biochem Mol Biol 37(1): 1-10. [Abstract]

Ding, C., R. W. Chiu, et al. (2004). “MS analysis of single-nucleotide differences in circulating nucleic acids: Application to noninvasive prenatal diagnosis.” Proc Natl Acad Sci U.S.A. 101(29): 10762-7. [Abstract]

Ding, C., E. Maier, et al. (2004). “Simultaneous quantitative and allele-specific expression analysis with real competitive pcr.” BMC Genet 5(1): 8. [Abstract]

Feezor, R., Baker, HV, Mindrinos, M, Hayden, D, Tannahill, CL, Brownstein, BH, Fay, A,  MacMillan, SK, Laramie, JM, Xiao, W, Moldawer, LL, Cobb, JP, Miller-Graziano, CL, Maier, RV, Schoenfeld, D, Davis, RW, Tompkins, RG (2004). “Whole blood and leukocyte rna isolation for gene expression analyses.” Physiological Genomics 19(3):247-54. [Abstract]

Frith, M. C., Y. Fu, et al. (2004). “Detection of functional DNA motifs via statistical over-representation.” Nucleic Acids Res 32(4): 1372-81. [Abstract]

Frith, M. C., A. S. Halees, et al. (2004). “Site2genome: Locating short DNA sequences in whole genomes.” Bioinformatics 20(9): 1468-9. [Abstract]

Frith, M. C., U. Hansen, et al. (2004). “Finding functional sequence elements by multiple local alignment.” Nucleic Acids Res 32(1): 189-200. [Abstract]

Fu, Y., M. C. Frith, et al. (2004). “Motifviz: An analysis and visualization tool for motif discovery.” Nucleic Acids Res 32(Web Server issue): W420-3. [Abstract]

Halees, A. S. and Z. Weng (2004). “PromoSer: Improvements to the algorithm, visualization and accessibility.” Nucleic Acids Res 32(Web Server issue): W191-4. [Abstract]

Haverty, P. M., M. C. Frith, et al. (2004). “Carrie web service: Automated transcriptional regulatory network inference and interactive analysis.” Nucleic Acids Res 32(Web Server issue): W213-6. [Abstract]

Haverty, P. M., U. Hansen, et al. (2004). “Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.” Nucleic Acids Res 32(1): 179-88. [Abstract]

Haverty, P. M. and Z. Weng (2004). “Cisml: An xml-based format for sequence motif detection software.” Bioinformatics 20(11): 1815-7. [Abstract]

Hoffman, A., Awad, T., Spira, A., Palma, J., Webster, T., Wright, G., Buckley, J., Davis, R., Hubbell, E., Jones, W., Tibshirani, R., Tompkins, R., Triche, T., Xiao, W., West, M., Warrington, J. (2004). “Expression profiling – best practices for data generation and interpretation in clinical trials.” Nature Reviews Genetics 5: 229-37. [Abstract]

Hu, Z., Y. Fu, et al. (2004). “Seqvista: A new module of integrated computational tools for studying transcriptional regulation.” Nucleic Acids Res 32(Web Server issue): W235-41. [Abstract]

Hu, Z., J. Mellor, et al. (2004). “Visant: An online visualization and analysis tool for biological interaction data.” BMC Bioinformatics 5: 17. [Abstract]

Karaoz, U., T. M. Murali, et al. (2004). “Whole-genome annotation by using evidence integration in functional-linkage networks.” Proc Natl Acad Sci U.S.A. 101(9): 2888-93. [Abstract]

Leyfer, D., A. Bond, et al. (2004). “Cis-element clustering correlates with dose-dependent pro- and antisignaling effects of il18.” Genes Immun 5(5): 354-62. [Abstract]

Liu, J., Farmer, S.R. (2004). “Regulating the balance between peroxisome proliferator-activated receptor ? And ?-catenin signaling during adipogenesis.” J. Biol. Chem. 279: 45020-27.

Logan, B., Karaoz, U., Moreno, P., Weng, Z., Kasif, S. (2004). “Protein seer: A web server for protein homology detection.” EMBS 2004 (26th Annual International Conference, IEEE Engineering in Medicine and Biology Society).

Mellor, J. C., J. Wu, et al. (2004). “Constructing networks with correlation maximization methods.” Genome Inform Ser Workshop Genome Inform 15(1): 149-59. [Abstract]

Mintseris, J. and Z. Weng (2004). “Optimizing protein representations with information theory.” Genome Inform Ser Workshop Genome Inform 15(1): 160-9. [Abstract]

Prasad, J. C., S. Vajda, and Camacho, C.J. (2004). “Consensus alignment server for reliable comparative modeling with distant templates.” Nucleic Acids Res 32(Web Server issue): W50-4. [Abstract]

Rajamani, D., S. Thiel, et al. (2004). “Anchor residues in protein-protein interactions.” Proc Natl Acad Sci U.S.A. 101(31): 11287-92. [Abstract]

Shakhnovich, B. E., J. M. Harvey, et al. (2004). “Elisa: A unified, multidimensional view of the protein domain universe.” Genome Inform Ser Workshop Genome Inform 15(1): 213-20. [Abstract]

Shakhnovich, B. E. and J. Max Harvey (2004). “Quantifying structure-function uncertainty: A graph theoretical exploration into the origins and limitations of protein annotation.” J Mol Biol 337(4): 933-49. [Abstract]

Shakhnovich, B. E., T. E. Reddy, et al. (2004). “Comparisons of predicted genetic modules: Identification of co-expressed genes through module gene flow.” Genome Inform Ser Workshop Genome Inform 15(1): 221-8. [Abstract]

Spira, A., J. Beane, F. Schembri, G. Liu, X. Yang, C. Ding, S. Gilman, C. Cantor, J.S. Brody (2004). “Noninvasive method for obtaining rna from buccal mucosa epithelial cells for gene expression profiling.” Biotechniques 36(3): 484-87.[Abstract]

Spira, A., J. Beane, V. Pinto-Plata, A. Kadar, G. Liu, V. Shah, B. Celli, J.S. Brody (2004). “Gene expression profiling of human lung tissue from smokers with severe emphysema.” Am J Respir Cell Mol Biol. Dec;31(6):601-10. Epub 2004 Sep 16. [Abstract]

Spira, A., J. Beane, V. Shah, G. Liu, F. Schembri, X. Yang, J. Palma, J.S. Brody (2004). “Effects of cigarette smoke on the human airway epithelial cell transcriptome.” PNAS USA 101(27): 10143-8. [Abstract]

Spira, A., F. Schembri, J. Beane, V. Shah, G. Liu, J.S. Brody (2004). “Impact of cigarette smoke on the normal airway transcriptome.” Chest 125(5 Suppl):115S. [Abstract]

Tullai, J. W., Schaffer, M.E., Mullenbrock, S., Kasif, S., Cooper, G.M (2004). “Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and mek/erk signaling pathways.” J. Biol. Chem. 279(19): 20167-77. [Abstract]

Wizorek, J.J., C.M. Coopersmith, J.M. Laramie, et al. (2004). “Sequence makes a difference: paradoxical effects of stress in vivo.” Shock 22(3):229-33. [Abstract]

Wu, C. J., Y. Fu, et al. (2004). “Gene expression module discovery using gibbs sampling.” Genome Inform Ser Workshop Genome Inform 15(1): 239-48. [Abstract]

Yanai, I. (2004). “The integrated world of functional genomics.” Genome Biol 4(301). [Abstract]

Yu, L., M. C. Frith, et al. (2004). “Characterization of genomic organization of the adenosine a2a receptor gene by molecular and bioinformatics analyses.” Brain Res 1000(1-2): 156-73. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2004). “Identification of genes with fast-evolving regions in microbial genomes.” Nucleic Acids Res 32(21): 6347-57. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2004). “Segmentally variable genes: A new perspective on adaptation.” PLoS Biol 2(4): E81. [Abstract]

2003

Mootha, V.K., Lindgren, C.M., Eriksson, K.F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., Houstis, N., Daly, M.J., Patterson, N., Mesirov, J.P., Golub, T.R., Tamayo, P., Spiegelman, B., Lander, E.S., Hirschhorn, J.N., Altshuler, D., Groop, L.C. (2003). PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet., 34(3):267-273.

Bhanot, G., Lousoun, y., Zhu, J., DeLisi, C. (2003). “The importance of thermodynamic equilibrium for high throughput gene expression arrays.” Biophysical J 84(1):124-35. [Abstract]

Blake, W. J., K. A. M, et al. (2003). “Noise in eukaryotic gene expression.” Nature 242(6932): 633-7. [Abstract]

Chen, R., L. Li, et al. (2003). “Zdock: An initial-stage protein-docking algorithm.” Proteins 52(1): 80-7. [Abstract]

Chen, R., J. Mintseris, et al. (2003). “A protein-protein docking benchmark.” Proteins 52(1): 88-91.

Chen, R., W. Tong, et al. (2003). “Zdock predictions for the capri challenge.” Proteins 52(1): 68-73. [Abstract]

Chen, R. and Z. Weng (2003). “A novel shape complementarity scoring function for protein-protein docking.” Proteins 51(3): 397-408.

Ding, C. and C. R. Cantor (2003). “Direct molecular haplotyping of long-range genomic DNA with m1-pcr.” Proc Natl Acad Sci U S A 100(13): 7449-53. [Abstract]

Ding, C. and C. R. Cantor (2003). “A high-throughput gene expression analysis technique using competitive pcr and matrix-assisted laser desorption ionization time-of-flight ms.” Proc Natl Acad Sci U S A 100(6): 3059-64. [Abstract]

Frith, M. C., M. C. Li, et al. (2003). “Cluster-buster: Finding dense clusters of motifs in DNA sequences.” Nucleic Acids Res 31(13): 3666-8. [Abstract]

Gardner, T. S., D. di Bernardo, D. Lorenz, et al. (2003). “Inferring genetic networks and identifying compound mode of action via expression profiling.” Science 301(5629): 102-5. [Abstract]

Halees, A. S., D. Leyfer, et al. (2003). “Promoser: A large-scale mammalian promoter and transcription start site identification service.” Nucleic Acids Res 31(13): 3554-9. [Abstract]

Hu, Z., M. Frith, et al. (2003). “Seqvista: A graphical tool for sequence feature visualization and comparison.” BMC Bioinformatics 4: 1. [Abstract]

Isaacs, F. J., J. Hasty, et al. (2003). “Prediction and measurement of an autoregulatory genetic module.” Proc Natl Acad Sci U S A 100(13): 7714-9. [Abstract]

Kaern, M., W. J. Blake, et al. (2003). “The engineering of gene regulatory networks.” Annu Rev Biomed Eng 5: 179-206.

Kortvelyesi, T., Dennis, S., Silberstein, M., Brown III, L., and Vajda, S. (2003). “Algorithms for computational solvent mapping of proteins.” Proteins 15;51(3):340-51. [Abstract]

Kortvelyesi, T., Silberstein, M., Dennis, S., and Vajda, S (2003). “Improved mapping of protein binding sites.” J Comput Aided Mol Des 17(2-4): 173-86. [Abstract]

Letovsky, S. and S. Kasif (2003). “Predicting protein function from protein/protein interaction data: A probabilistic approach.” Bioinformatics 19 Suppl 1: i197-204. [Abstract]

Li, J.L., et. al (2003). “A genome scan for modifiers of age at onset in Huntington disease: The HD MAPS study.” Am J Hum Genet 73(3):682-7.

Li, L., R. Chen, et al. (2003). “Rdock: Refinement of rigid-body protein docking predictions.” Proteins 53(3): 693-707. [Abstract]

Lorenz, D. R. (2003). “Behavioral genetics: Scientific and social acceptance.” J Biolaw Bus 6(2): 30-9. [Abstract]

Mintseris, J. and Z. Weng (2003). “Atomic contact vectors in protein-protein recognition.” Proteins 53(3): 629-39. [Abstract]

Murphy, J., D. W. Gatchell, J.C. Prasad, S. Vajda (2003). “Combination of scoring functions improves discrimination in protein-protein docking.” Proteins 53(4): 840-54. [Abstract]

Pervouchine, D. D., J. H. Graber, et al. (2003). “On the normalization of rna equilibrium free energy to the length of the sequence.” Nucleic Acids Res 31(9): e49.

Powell, C. A., Spira, A., Derti, A., DeLisi, C., Borczuk, A., Busch, S., Sahasrabudhe, S., Chen, Y., Sugarbaker, D., Bueno, R., Richards, W.G., Brody, J.S. (2003). “Gene expression in lung adenocarcinomas of smokers and non smokers.” Am J Respiratory Cell and  Mol Biol. Aug;29(2):157-62. [Abstract]

Prasad, J. C., Comeau, S.R., Vajda, S. and Camacho, C.J (2003). “Consensus alignment for reliable framework prediction in homology modeling.” Bioinformatics, Sep 1;19(13):1682-91. [Abstract]

Ryan, J. F., Finnerty, J.R. (2003). “Cnidbase: The cnidarian evolutionary genomics database.” Nucleic Acids Research 31(1): 159-63. [Abstract]

Sebastiani, P., Y. H. Yu, et al. (2003). “Bayesian machine learning and its potential applications to the genomic study of oral oncology.” Adv Dent Res 17: 104-8. [Abstract]

Shakhnovich, B. E. (2003). “Patent protection as a paradigm against bio-terrorism.” J BioLaw & Business 6(1): 39-50.

Shakhnovich, B. E., N. V. Dokholyan, et al. (2003). “Functional fingerprints of folds: Evidence for correlated structure-function evolution.” J Mol Biol 326(1): 1-9. [Abstract]

Shakhnovich, B. E., J. M. Harvey, et al. (2003). “Elisa: Structure-function inferences based on statistically significant and evolutionarily inspired observations.” BMC Bioinformatics 4: 34. [Abstract]

Silberstein, M., S. Dennis, et al. (2003). “Identification of substrate binding sites in enzymes by computational solvent mapping.” J Mol Biol 332(5): 1095-113. [Abstract]

Spira, A. (2003). “To tell or not to tell: Genetic testing and the physician’s duty to disclose results to relatives.” J BioLaw & Business, Special Bio-Ethics Supplement: 3-9.

Spira, A., J.D. Carroll, G. Liu, Z. Aziz, V. Shah, H. Kornfeld, J. Keane (2003). “Apoptosis genes in human alveolar macrophages infected with virulent or attenuated Mycobacterium tuberculosis: a pivotal role for tumor necrosis factor.” Am J Respir Cell Mol Biol 29(5):545-51. [Abstract]

Su, Y., T. M. Murali, V. Pavlovic, M. Shaffer, S. Kasif (2003). “RankGene: Identification of diagnostic genes based on expression data.” Bioinformatics 19(12): 1578-9. [Abstract]

Venkatesan, K., H. R. McManus, et al. (2003). “Functional conservation between members of an ancient duplicated transcription factor family, lsf/grainyhead.” Nucleic Acids Res 31(15): 4304-16. [Abstract]

Wu, J., S. Kasif, et al. (2003). “Identification of functional links between genes using phylogenetic profiles.” Bioinformatics 19(12): 1524-30. [Abstract]

Zhang, L., V. Pavlovic, et al. (2003). “Human-mouse gene identification by comparative evidence integration and evolutionary analysis.” Genome Res 13(6A): 1190-202.

2002

Betley, J. N., Frith, M.C., Graber, J.H., Choo, S., Deshler, J.O. (2002). “A ubiquitous and conserved signal for RNA localization in chordates.” Current Biology 12(20): 1756. [Abstract]

Blake, W. (2002). “Ethical and legal issues in the use of criminal DNA databases and possible implications for gene-based rehabilitation.” J BioLaw & Business, Special Informatics Supplement: 42-8.

Chen, R. and Z. Weng (2002). “Docking unbound proteins using shape complementarity, desolvation, and electrostatics.” Proteins 47(3): 281-94.

Chung, T.P., J.M. Laramie, M. Province, J.P. Cobb. (2002). “Functional genomics of critical illness and injury.” Crit Care Med 30(1 Supp):S51-S57.

Clodfelter, K. (2002). “Clinical trials in the face of adversity.” J Biolaw Bus 5(3): 34-8.

Cobb, J.P., J.M. Laramie, et al. (2002). “Sepsis gene expression profiling: murine splenic compared with hepatic responses determined by using complementary DNA microarrays. Crit Care Med 30(12):2711-21.

Frith, M. C., Graber, J.H., Weng, Z., Spouge, J.L. (2002). “Gapless local alignment of multiple sequences.” Genome Informatics 13: 436-7.

Frith, M. C., J. L. Spouge, et al. (2002). “Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences.” Nucleic Acids Res 30(14): 3214-24. [Abstract]

Harrison, R. and C. DeLisi (2002). “Condition specific transcription factor binding site characterization in saccharomyces cerevisiae.” Bioinformatics 18(10): 1289-96.

Haverty, P. M., Z. Weng, et al. (2002). “Hugeindex: A database with visualization tools for high-density oligonucleotide array data from normal human tissues.” Nucleic Acids Res 30(1): 214-7. [Abstract]

Kasif, S., Z. Weng, Derti, A., et al. (2002). “A computational framework for optimal masking in the synthesis of oligonucleotide microarrays.” Nucleic Acids Res 30(20): e106. [Abstract]

Mellor, J. C., Yanai, I., Clodfelter, K.H., Mintseris, J., and DeLisi, C. (2002). “Predictome: A database of putative functional links between proteins.” Nucleic Acids Res 30(1): 306-9. [Abstract]

Silberstein, M. (2002). “Financial conflicts of interest in biomedical research: A survey of national and institutional policies.” J BioLaw & Business, Special Bio-Ethics Supplement: 10-21.

Walker, M., V. Pavlovic, et al. (2002). “A comparative genomic method for computational identification of prokaryotic translation initiation sites.” Nucleic Acids Res 30(14): 3181-91. [Abstract]

Yanai, I. and C. DeLisi (2002). “The society of genes: Networks of functional links between genes from comparative genomics.” Genome Biol 3(11): research0064. [Abstract]

Yanai, I., J. C. Mellor, et al. (2002). “Identifying functional links between genes using conserved chromosomal proximity.” Trends Genet 18(4): 176-9. [Abstract]

Yanai, I., Y. I. Wolf, et al. (2002). “Evolution of gene fusions: Horizontal transfer versus independent events.” Genome Biol 3(5): research0024. [Abstract]

Zheng, Y., R. J. Roberts, et al. (2002). “Genomic functional annotation using co-evolution profiles of gene clusters.” Genome Biol 3(11): research0060. [Abstract]

Zheng, Y., J. D. Szustakowski, et al. (2002). “Computational identification of operons in microbial genomes.” Genome Res 12(8): 1221-30. [Abstract]

2001

Aach, J., Bulyk, M.L., Church, G.M., Comander, J., Derti, A., Shendure, J. (2001). “Computational comparison of two draft sequences of the human genome.” Nature 409(6822): 856-859. [Abstract]

Frith, M. (2001). “Implications of biology for free will, moral responsibility, and criminal law: What if science can explain actions?” J. Biolaw & Business 4(3).

Frith, M. C., U. Hansen, et al. (2001). “Detection of cis-element clusters in higher eukaryotic DNA.” Bioinformatics 17(10): 878-89. [Abstract]

Glusman, G., Yanai, I., Rubin, I. (2001). “The complete human olfactory subgenome.” Genome Res May;11(5):685-702. [Abstract]

Hasty, J., Isaacs, F., Dolnik, M. (2001). “Designer gene networks: Towards fundamental cellular control.” Chaos 17: 878-89.

Hasty, J., D. McMillen, Isaacs, F., et al. (2001). “Computational studies of gene regulatory networks: In numero molecular biology.” Nat Rev Genet 2(4): 268-79. [Abstract]

Hsiao, L., Yoshida, T., Hong, R., Jensen, R., Dangond, F. Misra, J., Haverty, P., Weng, Z.,Mutter, G., Milford, E. L., Crum, C., Bueno, R., Pratt, R. E., Mahadevappa, M.,  Warrington,J. A., Stephanopoulos, G., Stephanopoulos, G. and Gullans, S. (2001). “A compendium of gene expression in normal human tissues reveals tissue-selective genes and distinct expression patterns of housekeeping genes.” Physiological Genomics 7: 97-104. Abstract

Yanai, I. (2001). “New patents: The law of DNA worship.” J. Biolaw & Business 4(2).

Yanai, I., A. Derti, et al. (2001). “Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes.” Proc Natl Acad Sci U S A 98(14): 7940-5. [Abstract]

2000

Yanai, I., Camacho, C., and DeLisi, C. (2000). “Predictions of gene family distributions in microbial genomes:  Evolution by gene duplication and modification.” Physical Review of Letters 2641. [Abstract]