Student Publications


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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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


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

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

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

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

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

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

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

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