Student Publications

Chan JK, Kiet TK, Blansit K, Ramasubbaiah R, Hilton JF, Kapp DS, Matei D. "MiR-378 as a biomarker for response to anti-angiogenic treatment in ovarian cancer." Gynecol Oncol. 2014;133(3):568-74. PubMed DOI

Chan JK, Kiet TK, Monk BJ, Young-Lin N, Blansit K, Kapp DS, Amanam I. "Applications for oncologic drugs: a descriptive analysis of the oncologic drugs advisory committee reviews." Oncologist. 2014;19(3):299-304. PubMed PMC DOI

Doan S, Lin KW, Conway M, Ohno-Machado L, Hsieh A, Feupe SF, Garland A, Ross MK, Jiang X, Farzaneh S, Walker R, Alipanah N, Zhang J, Xu H, Kim HE. "PhenDisco: phenotype discovery system for the database of genotypes and phenotypes." J Am Med Inform Assoc. 2014;21(1):31-6. PubMed PMC DOI

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. "NeXO Web: the NeXO ontology database and visualization platform." Nucleic Acids Res. 2014;42(Database issue):D1269-74. PubMed PMC DOI

Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K. "Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community." ISME J. 2014;8(4):757-67. PubMed PMC DOI

Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hofree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. "Multi-tiered genomic analysis of head and neck cancer ties TP53 mutation to 3p loss." Nat Genet. 2014;46(9):939-43. PubMed PMC DOI

Hauff SJ, Raju SC, Orosco RK, Gross AM, Diaz-Perez JA, Savariar E, Nashi N, Hasselman J, Whitney M, Myers JN, Lippman SM, Tsien RY, Ideker T, Nguyen QT. "Matrix-metalloproteinases in head and neck carcinoma-cancer genome atlas analysis and fluorescence imaging in mice." Otolaryngol Head Neck Surg. 2014;151(4):612-8. PubMed PMC DOI

Kim J, Levy E, Ferbrache A, Stepanowsky P, Farcas C, Wang S, Brunner S, Bath T, Wu Y, Ohno-Machado L. "MAGI: a Node.js web service for fast microRNA-Seq analysis in a GPU infrastructure." Bioinformatics. 2014;30(19):2826-7. PubMed PMC DOI

Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. "Inferring gene ontologies from pairwise similarity data." Bioinformatics. 2014;30(12):i34-42. PubMed PMC DOI

Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP. "Assessment of MS/MS search algorithms with parent-protein profiling." J Proteome Res. 2014;13(4):1823-32. PubMed PMC DOI

Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. "Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale." BMC Syst Biol. 2014;8:110. PubMed PMC DOI

Liu Z, Merkurjev D, Yang F, Li W, Oh S, Friedman MJ, Song X, Zhang F, Ma Q, Ohgi KA, Krones A, Rosenfeld MG. "Enhancer activation requires trans-recruitment of a mega transcription factor complex." Cell. 2014;159(2):358-73. PubMed PMC DOI

Ma H, Morey R, O'Neil RC, He Y, Daughtry B, Schultz MD, Hariharan M, Nery JR, Castanon R, Sabatini K, Thiagarajan RD, Tachibana M, Kang E, Tippner-Hedges R, Ahmed R, Gutierrez NM, Van Dyken C, Polat A, Sugawara A, Sparman M, Gokhale S, Amato P, Wolf DP, Ecker JR, Laurent LC, Mitalipov S. "Abnormalities in human pluripotent cells due to reprogramming mechanisms." Nature. 2014;511(7508):177-83. PubMed PMC DOI

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA. "NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly." BMC Bioinformatics. 2014;15:357. PubMed PMC DOI

Mollah SA, Dobrin JS, Feder RE, Tse SW, Matos IG, Cheong C, Steinman RM, Anandasabapathy N. "Flt3L dependence helps define an uncharacterized subset of murine cutaneous dendritic cells." J Invest Dermatol. 2014;134(5):1265-1275. PubMed PMC DOI

Morey R, Laurent LC. "Getting off the ground state: X chromosome inactivation knocks down barriers to differentiation." Cell Stem Cell. 2014;14(2):131-2. PubMed PMC DOI

Mukund K, Mathewson M, Minamoto V, Ward SR, Subramaniam S, Lieber RL. "Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin." Muscle Nerve. 2014;50(5):744-58. PubMed PMC DOI

Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A. "Systematic detection of internal symmetry in proteins using CE-Symm." J Mol Biol. 2014;426(11):2255-68. PubMed PMC DOI

Neumann S, Campbell GE, Szpankowski L, Goldstein LS, Encalada SE. "Characterizing the composition of molecular motors on moving axonal cargo using 'cargo mapping' analysis." J Vis Exp. 2014(92):e52029. PubMed PMC DOI

O Cuív P, Klaassens ES, Smith WJ, Mondot S, Durkin AS, Harkins DM, Foster L, McCorrison J, Torralba M, Nelson KE, Morrison M. "Draft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces." Genome Announc. 2014;2(1). PubMed PMC DOI

Ross MK, Wei W, Ohno-Machado L. "Big data and the electronic health record." Yearb Med Inform. 2014;9:97-104. PubMed PMC DOI

Sauls JT, Buescher JM. "Assimilating genome-scale metabolic reconstructions with modelBorgifier." Bioinformatics. 2014;30(7):1036-8. PubMed DOI

Skowronska-Krawczyk D, Ma Q, Schwartz M, Scully K, Li W, Liu Z, Taylor H, Tollkuhn J, Ohgi KA, Notani D, Kohwi Y, Kohwi-Shigematsu T, Rosenfeld MG. "Required enhancer-matrin-3 network interactions for a homeodomain transcription program." Nature. 2014;514(7521):257-61. PubMed PMC DOI

Stepanowsky P, Levy E, Kim J, Jiang X, Ohno-Machado L. "Prediction of MicroRNA Precursors Using Parsimonious Feature Sets." Cancer Inform. 2014;13(Suppl 1):95-102. PubMed PMC DOI

Thiagarajan RD, Morey R, Laurent LC. "The epigenome in pluripotency and differentiation." Epigenomics. 2014;6(1):121-37. PubMed DOI