Student Publications

Wang J, Telese F, Tan Y, Li W, Jin C, He X, Basnet H, Ma Q, Merkurjev D, Zhu X, Liu Z, Zhang J, Ohgi K, Taylor H, White RR, Tazearslan C, Suh Y, Macfarlan TS, Pfaff SL, Rosenfeld MG. "LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control." Nat Neurosci. 2015;18(9):1256-64. PubMed PMC DOI

Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC. "An alternative pluripotent state confers interspecies chimaeric competency." Nature. 2015;521(7552):316-21. PubMed PMC DOI

Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO. "Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data." Proc Natl Acad Sci U S A. 2015;112(34):10810-5. PubMed PMC DOI

Allison KA, Kaikkonen MU, Gaasterland T, Glass CK. "Vespucci: a system for building annotated databases of nascent transcripts." Nucleic Acids Res. 2014;42(4):2433-47. PubMed PMC DOI

Anandasabapathy N, Feder R, Mollah S, Tse SW, Longhi MP, Mehandru S, Matos I, Cheong C, Ruane D, Brane L, Teixeira A, Dobrin J, Mizenina O, Park CG, Meredith M, Clausen BE, Nussenzweig MC, Steinman RM. "Classical Flt3L-dependent dendritic cells control immunity to protein vaccine." J Exp Med. 2014;211(9):1875-91. PubMed PMC DOI

Appleton E, Tao J, Haddock T, Densmore D. "Interactive assembly algorithms for molecular cloning." Nat Methods. 2014;11(6):657-62. PubMed DOI

Bean GJ, Jaeger PA, Bahr S, Ideker T. "Development of ultra-high-density screening tools for microbial 'omics'." PLoS One. 2014;9(1):e85177. PubMed PMC DOI

Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. "Technical variations in low-input RNA-seq methodologies." Sci Rep. 2014;4:3678. PubMed PMC DOI

Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R. "The developmental potential of iPSCs is greatly influenced by reprogramming factor selection." Cell Stem Cell. 2014;15(3):295-309. PubMed PMC DOI

Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. "An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays." Mol Cell Proteomics. 2014;13(1):157-67. PubMed PMC DOI

Chan JK, Blansit K, Kiet T, Sherman A, Wong G, Earle C, Bourguignon LY. "The inhibition of miR-21 promotes apoptosis and chemosensitivity in ovarian cancer." Gynecol Oncol. 2014;132(3):739-44. PubMed DOI

Chan JK, Herzog TJ, Hu L, Monk BJ, Kiet T, Blansit K, Kapp DS, Yu X. "Bevacizumab in treatment of high-risk ovarian cancer--a cost-effectiveness analysis." Oncologist. 2014;19(5):523-7. PubMed PMC DOI

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