Student Publications

2014

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

Logue MW, Schu M, Vardarajan BN, Farrell J, Lunetta KL, Jun G, Baldwin CT, Deangelis MM, Farrer LA. “A search for age-related macular degeneration risk variants in Alzheimer disease genes and pathways.” Neurobiol Aging 2014 35(6):1510.e7-1510.e18. Published online 2013 December 19.  View in PubMed

Hu H, Dittwald P, Zaia J, Valkenborg D “Comment on “Computation of isotopic peak center-mass distribution by fourier transform.” Anal Chem 2013 85(24):12189-92. Published online 2013 December 17. View in PubMed

Gomes Al, Galagan JE, Segrè D.“Resource competition may lead to effective treatment of antibiotic resistant infections.” PLoS One. 2013 8(12):E80775. Published online 2013 December 13. View in PubMed

Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. “How good is automated protein docking?” Proteins. 2013 81(12):2159-66. Published online 2013 December. View in PubMed

Lavi A, Ngan CH, Movshovitz-Attias D, Bohnuud T, Yueh C, Beglov D, Schueler-Furman O, Kozakov D. “Detection of peptide-binding sites on protein surfaces: the first step toward the modeling and targeting of peptide-mediated interactions.” Proteins. 2013 81(12):2096-105. Published online 2013 December. View in PubMed

Perdomo C, Campbell JD, Gerrein J, Tellez CS, Garrison CB, Walser TC, Drizik E, Si H, Gower AC, Vick J, Anderlind C, Jackson GR, Mankus C, Schembri F, O’Hara C, Gomperts BN, Dubinett SM, Hayden P, Belinsky SA, Lenburg ME, Spira A. “MicroRNA 4423 is a primate-specific regulator of airway epithelial cell differentiation and lung carcinogenesis.” Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):18946-51. doi: 10.1073/pnas.1220319110. View in PubMed

Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. “Consequences of domain insertion on sequence-structure divergence in a superfold.” Proc Natl Acad Sci U S A. 2013 110(36):E3381-7. Published online 2013 September 3. View in PubMed

Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, et al. “The COMBREX Project: Design, Methodology, and Initial Results.” PLoS Biol 2013 Aug;11(8): e1001638. doi:10.1371/journal.pbio.1001638. View in PubMed

Richard G, Trivedi N, Belta C, Amar S. “Partial restoration of macrophage alteration from diet-induced obesity in response to Porphyromonas gingivalis infection.” PLoS One. 2013 8(7):e70320. Published online 2013 July 29. View in PubMed

Brothers JF, Hijazi K, Mascaux C, El-Zein RA, Spitz MR, Spira A. “Bridging the clinical gaps: genetic, epigenetic and transcriptomic biomarkers for the early detection of lung cancer in the post-National Lung Screening Trial era.” BMC Medicine 2013 11:168. Published online 2013 July 19. View in PubMed

Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. “Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.” PLoS Comput Biol. 2013;9(7):e1003126. doi: 10.1371/journal.pcbi.1003126. Epub 2013 Jul 18. View in PubMed

Abaan OD, Polley EC, Davis SR, Zhu YJ, Bilke S, Walker RL, Pineda M, Gindin Y, Jiang Y, Reinhold WC, Holbeck SL, Simon RM, Doroshow JH, Pommier Y, Meltzer PS. “The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.” Cancer Res. 2013 73(14):4372-82. Published online 2013 July 15. View in PubMed

Galagan J, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, Gomes A, Rustad T, Dolganov G, Glotova I, Abeel T, Mahwinney C, Kennedy AD, Allard R, Brabant W, Krueger A, Jaini S, Honda B, Yu W-H, Hickey MJ, Zucker J, Garay C, Weiner B, Sisk P, Stolte C, Winkler JK, Van de Peer Y, Iazzetti P, Camacho D, Dreyfuss J, et al. “The Mycobacterium tuberculosis regulatory network and hypoxia.” Nature 2013 doi:10.1038/nature12337 Published online 03 July 2013.  View in PubMed

Galagan J, Lyubetskaya A, Gomes A. “ChIP-Seq and the complexity of bacterial transcriptional regulation.” Curr Top Microbiol Immunol. 2013;363:43-68. doi: 10.1007/82_2012_257. View in PubMed

Zhenjun Hu, Yi-Chien Chang, Yan Wang, Chia-Ling Huang, Yang Liu, Feng Tian, Brian Granger, Charles DeLisi. “VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.” Nucleic Acids Res. 2013 July; 41(Web Server issue): W225–W231. Published online 2013 May 28. doi: 10.1093/nar/gkt401 PMCID: PMC3692070. View in PubMed

Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. “An aberrant transcription factor network essential for wnt signaling and stem cell maintenance in glioblastoma.” Cell Rep. 2013 May 30;3(5):1567-79. doi: 10.1016/j.celrep.2013.04.021. View in PubMed

Fritsche LG1, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP Jr, et al; AMD Gene Consortium. “Seven new loci associated with age-related macular degeneration.” Nature Genet. 2013 45(4):433-9, 439e1-2. Published online 2013 May 3. View in PubMed

Steiling K, van den Berge M, Hijazi K, Florido R, Campbell J, Liu G, Xiao J, Zhang X, Duclos G, Drizik E, Si H, Perdomo C, Dumont C, Coxson HO, Alekseyev YO, Sin D, Pare P, Hogg JC, McWilliams A, Hiemstra PS, Sterk PJ, Timens W, Chang JT, Sebastiani P, O’Connor GT, Bild AH, Postma DS, Lam S, Spira A, Lenburg ME. “A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment.” Am J Respir Crit Care Med. 2013 187(9):933-42. Published online 2013 May 1. View in PubMed

Malhotra S, Yen JY, Honko AN, Garamszegi S, Caballero IS, Johnson JC, Mucker EM, Trefry JC, Hensley LE, Connor JH. “Transcriptional profiling of the circulating immune response to lassa virus in an aerosol model of exposure.” PLoS Negl Trop Dis. 2013 Apr 25;7(4):e2171. doi: 10.1371. View in PubMed

Kim TM, Xi R, Luquette LJ, Park RW, Johnson MD, Park PJ. “Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes.” Genome Res. 2013 Feb;23(2):217-27. doi: 10.1101/gr.140301.112. View on PubMed

Rockwell G, Guido NJ, Church GM. “Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective.” PLoS Comput Biol. 2013 9(1). 2013 January 17. View in PubMed

Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. “Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.” Nucleic Acids Res. 2013 41(Database issue):D171-6. Published online 2013 January. View in PubMed

2012

Franzosa EAGaramszegi S, Xia Y. “Toward a three-dimensional view of protein networks between species.” Front Microbiol. 21 December 2012 3:428. doi: 10.3389/fmicb.2012.00428

Maxwell, E.K., Ryan, J.F., Schnitzler, C.E., Browne, W.E., and Baxevanis, A.D. “MicroRNAs and Essential Components of the microRNA Processing Machinery are Not Encoded in the Genome of the Ctenophore Mnemiopsis leidyi.” BMC Genomics, 13:714. 2012. View in PubMed

Piccolo SR, Sun Y, Campbell JD, Lenburg ME, Bild AH, Johnson WE. “A single-sample microarray normalization method to facilitate personalized-medicine workflows.” Genomics. 2012 December; 100(6): 337-44. doi: 10.1016/j.ygeno.2012.08.003. View on PubMed

Bilke S, Gindin Y. “Analyzing the association of SCNA boundaries with replication timing.” Nat Biotechnol. 2012 30(11):1043-5. Published online 2012 November 30. View in PubMed

Whitcomb DC, Larusch J, . . . Vardarajan BN, Vinters HV, Vonsattel JP, Wang LS, Weintraub S, Welsh-Bohmer KA, Williamson J, Woltjer RL, Wright CB, Younkin SG, Yu CE, Yu L, Alkaade S, Amann ST, Anderson MA, Baillie J, Banks PA, Conwell D, Coté GA, Cotton PB, Disario J, Farrer LA, et.al. “Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis.” Nat Genet. 2012 Nov 11;44(12):1349-54. doi: 10.1038/ng.2466. View on PubMed

Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL. “Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.” Biol Direct. 2012 October 30; 7(1): 37. View on PubMed

Chiu HC, Marx CJ, Segrè D. “Epistasis from functional dependence of fitness on underlying traits.” Proc Biol Sci. 2012 October 22; 279(1745): 4156-64. View on PubMed

Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D. “Application of asymmetric statistical potentials to antibody-protein docking.” Bioinformatics 2012 28(20):2608-14. Published online 2012 October 15. View in PubMed

Latourelle JC, Dumitriu A, Hadzi TC, Beach TG, Myers RH. “Evaluation of Parkinson Disease Risk Variants as Expression-QTLs.” PLoS One. 2012; 7(10): e46199. Epub 2012 Oct 5. View on PubMed

Friedland RP, Shah JJ, Farrer LA, Vardarajan B, Rebolledo-Mendez JD, Mok K, Hardy J. “Behavioral variant frontotemporal lobar degeneration with amyotrophic lateral sclerosis with a chromosome 9p21 hexanucleotide repeat.” Front Neurol. 04 October 2012 | doi: 10.3389/fneur.2012.00136. View on PubMed

Ahn S, Huang CL, Ozkumur E, Zhang X, Chinnala J, Yalcin A, Bandyopadhyay S, Russek S, Unlü MS, DeLisi C, Irani RJ. “TATA binding proteins can recognize nontraditional DNA sequences.” Biophys J. 2012 Oct 3;103(7):1510-7. doi: 10.1016/j.bpj.2012.08.030. PubMed PMID: 23062343 View on PubMed

Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE “H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.” Genome Biol. 2012 October 3; 13(10): R85. View on PubMed

Franzosa EA, Xia Y. “Independent effects of protein core size and expression on residue-level structure-evolution relationships.” PLoS One. 2012 October 3; 7(10): e46602. doi: 10.1371/journal.pone.0046602. Epub 2012 Oct 2. View on PubMed

Byrne D, Dumitriu A, Segrè D. “Comparative multi-goal tradeoffs in systems engineering of microbial metabolism.” BMC Syst Biol. 2012 September 26; 6: 127. doi: 10.1186/1752-0509-6-127. View on PubMed

Maxwell E, Tan Y, Tan Y, Hu H, Benson G, et al. “GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data.” PLoS ONE 2012 September 26:7(9): e45474. doi:10.1371/journal.pone.0045474. View on PLOS ONE

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. “Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.” Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112. View in PubMed

Parikh JR, Xia Y, Marto JA. “Multi-Edge Gene Set Networks Reveal Novel Insights into Global Relationships between Biological Themes” PLoS One. 2012; 7(9): e45211. Epub 2012 Sept 13. View on PubMed

Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. “Gene set enrichment analysis: performance evaluation and usage guidelines.” Brief Bioinform. 2012 May; 13(3): 281-91. Epub 2011 Sept 7. View on PubMed

Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D. “Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde.” Nucleic Acid Res. 2012 40(16):7644-52. Published online 2012 September. View in PubMed

Vardarajan BN, Bruesegem SY, Harbour ME, St George-Hyslop P, Seaman MN, Farrer LA. “Identification of Alzheimer disease-associated variants in genes that regulate retromer function.” Neurobiol Aging. 2012 September; 33(9): 2231.e15-2231.e30. View on PubMed

Campbell JD, McDonough JE, Zeskind JE, Hackett TL, Pechkovsky DV, Brandsma CA, Suzuki M, Gosselink JV, Liu G, Alekseyev YO, Xiao J, Zhang X, Hayashi S, Cooper JD, Timens W, Postma DS, Knight DA, Lenburg ME, Hogg JC, Spira A. “A gene expression signature of emphysema-related lung destruction and its reversal by the tripeptide GHK.” Genome Med. 2012 August 31; 4(8): 67. View on PubMed

Parker SC, Gartner J, Cardenas-Navia I, Wei X, Ozel Abaan H, Ajay SS, Hansen NF, Song L, Bhanot UK, Killian JK, Gindin Y, Walker RL, Meltzer PS, Mullikin JC, Furey TS, Crawford GE, Rosenberg SA, Samuels Y, Margulies EH. “Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.” PLoS Genet. 2012 8(8):e1002871. Published online 2012 August 9. View in PubMed

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

Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF “How accurate can genetic predictions be?” BMC Genomics. 2012 Jul 24;13:340. doi: 10.1186/1471-2164-13-340. View in PubMed

Beal J, Weiss R, Densmore D, Adler A, Appleton E, Babb J, Bhatia S, Davidsohn N, Haddock T, Loyall J, Schantz R, Vasilev V, Yaman F. “An end-to-end workflow for engineering of biological networks from high-level specifications.” ACS Synth Biol. 2012 Aug 17;1(8):317-31. doi: 10.1021/sb300030d. Epub 2012 Jul 17. View in PubMed

Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. “A public resource facilitating clinical use of genomes.” Proc Natl Acad Sci U S A. 2012 July 24; 109(30): 11920-7. doi: 10.1073/pnas.1201904109. Epub 2012 Jul 13. View on PubMed

Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. “Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.” Nature. 2012 July 11; 487(7406): 190-5. doi: 10.1038/nature11236. View on PubMed

Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S. “FTMAP: extended protein mapping with user-selected probe molecules.” Nucleic Acid Res. 2012 40(Web Server issue):W271-5. Published online 2012 July. View in PubMed

Dumitriu A, Latourelle JC, Hadzi TC, Pankratz N, Garza D, Miller JP, Vance JM, Foroud T, Beach TG, Myers RH. “Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation.” PLoS Genet. 2012 June; 8(6): e1002794. Epub 2012 June 28. View on PubMed

Melville SA, Buros J, Parrado AR, Vardarajan B, Logue MW, Shen L, Risacher SL, Kim S, Jun G, DeCarli C, Lunetta KL, Baldwin CT, Saykin AJ, Farrer LA; Alzheimer’s Disease Neuroimaging Initiative. “Multiple loci influencing hippocampal degeneration identified by genome scan.” Ann Neurol. 2012 July; 72(1): 65-75. doi: 10.1002/ana.23644. Epub 2012 Jun 28. View on PubMed

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

Miletti-González KE, Murphy K, Kumaran MN, Ravindranath AK, Wernyj RP, Kaur S, Miles GD, Lim E, Chan R, Chekmareva M, Heller DS, Foran D, Chen W, Reiss M, Bandera EV, Scotto K, Rodríguez-Rodríguez L. “Identification of function for CD44 intracytoplasmic domain (CD44-ICD): modulation of matrix metalloproteinase 9 (MMP-9) transcription via novel promoter response element.” J Biol Chem. 2012 June 1; 287(23): 18995-9007. View on PubMed

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

Beg QK, Zampieri M, Klitgord NCollins SB, Altafini C, Serres MH, Segrè D. “Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.” Nucleic Acids Res. 2012 August; 40(15): 7132-49. doi: 10.1093/nar/gks467. Epub 2012 May 25. View in PubMed

Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, Delisi C, Ziemek D. “Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.” BMC Bioinformatics. 2012 March 23; 13:46. View in PubMed

Rheinbay E, Louis DN, Bernstein BE, Suvà ML. “A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma.” Cancer Cell. 2012 March 20; 21(3): 329-31. View in PubMed

Dumitriu A, Moser C, Hadzi TC, Williamson SL, Pacheco CD, Hendricks AE, Latourelle JC, Wilk JB, Destefano AL, Myers RH. “Postmortem Interval Influences α-Synuclein Expression in Parkinson Disease Brain.” Parkinsons Dis. 2012; 2012: 614212. Epub 2012 March 13. View in PubMed

Richard G, Belta C, Julius AA, Amar S. “Controlling the outcome of the Toll-like receptor signaling pathways.” PLoS One. 2012 7(2):e31341. Published online 2012 February 20. View in PubMed

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

Cardoza JD, Parikh JR, Ficarro SB, Marto JA. “Mass spectrometry-based proteomics: qualitative identification to activity-based protein profiling.” Wiley Interdiscip Rev Syst Biol Med. 2012 March-April; 4(2): 141-62. Epub 2012 Jan 9. View in PubMed

Tagne JB, Gupta S, Gower AC, Shen SS, Varma S, Lakshminarayanan M, Cao Y, Spira A, Volkert TL, Ramirez MI. “Genome-wide analyses of Nkx2-1 binding to transcriptional target genes uncover novel regulatory patterns conserved in lung development and tumors.” PLoS One. 2012; 7(1): e29907. Epub 2012 Jan 5. View in PubMed

Franzosa EA, Xia Y. “Structural models for host-pathogen protein-protein interactions: assessing coverage and bias.” Pac Symp Biocomput. 2012; 287-98. View in PubMed

Jacobs C, Segrè D. “Organization principles in genetic interaction networks. “Advances in Experimental Medicine and Biology. 2012; 751:53-78. View in PubMed

Collins SB, Reznik E, Segrè D. “Temporal Expression-based Analysis of Metabolism.” PLoS Comput Biol 8(11): e1002781. doi:10.1371/journal.pcbi.1002781. View in PubMed

2011

Logue MW, Schu M, Vardarajan 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, Yi-Chien Chang, Zhenjun Hu, John N. Rachlin, Brian P. Anton, Revonda M. Pokrzywa, Han-Pil Choi, Lina L. Faller, Jyotsna Guleria, Genevieve Housman, Niels Klitgord, Varun Mazumdar, 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

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

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

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

2007

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

Drosophila 12 Genomes Consortium (… Bhutkar, A. ..). “Evolution of genes and genomes on the Drosophila phylogeny.” Nature. 2007 November 8; 450(7167): 203-18. View on PubMed

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

Van den Berg L,…, Karlsson EK et al. “Evaluation of the Serotonergic Genes htr1A, htr1B, htr2A, and slc6A4 in Aggressive Behavior of Golden Retriever Dogs.” Behav Genet. 2008 January; 38(1): 55-66.  Epub 2007 Dec 7. View on PubMed

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

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

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]

Pierce, B., W. Tong, et al. (2005). “M-zdock: A grid-based approach for cn symmetric multimer docking.” Bioinformatics 21(8): 1472-8. [Abstract]

Rachlin, J., C. Ding, et al. (2005). “Computational tradeoffs in multiplex pcr assay design for snp genotyping.” BMC Genomics 6: 102. [Abstract]

Rachlin, J., C. Ding, et al. (2005). “Muplex: Multi-objective multiplex pcr assay design.” Nucleic Acids Res 33(Web Server issue): W544-7. [Abstract]

Raina, S. Z., Faith, J.J., Seligmann, H., Disotell, T., Stewart, C-B., Pollock, D.D. (2005). “Evolution of base substitution gradients in primate mitochondrial genomes.” Genome Research 15(5): 665-73. [Abstract]

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]

Sheu, S. H., T. Kaya, et al. (2005). “Exploring the binding site structure of the ppar gamma ligand-binding domain by computational solvent mapping.” Biochemistry 44(4): 1193-209. [Abstract]

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

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

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]

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.”  2014 Sep 9. [Epub ahead of print]