Student Publications

O'Brien EJ, Monk JM, Palsson BO. "Using Genome-scale Models to Predict Biological Capabilities." Cell. 2015;161(5):971-987. PubMed PMC DOI

O'Brien EJ, Palsson BO. "Computing the functional proteome: recent progress and future prospects for genome-scale models." Curr Opin Biotechnol. 2015;34:125-34. PubMed PMC DOI

Raju SC, Hauff SJ, Lemieux AJ, Orosco RK, Gross AM, Nguyen LT, Savariar E, Moss W, Whitney M, Cohen EE, Lippman SM, Tsien RY, Ideker T, Advani SJ, Nguyen QT. "Combined TP53 mutation/3p loss correlates with decreased radiosensitivity and increased matrix-metalloproteinase activity in head and neck carcinoma." Oral Oncol. 2015;51(5):470-5. PubMed PMC DOI

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR. "Human body epigenome maps reveal noncanonical DNA methylation variation." Nature. 2015;523(7559):212-6. PubMed PMC DOI

Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, Sobol RW, Ideker T. "Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition." Oncotarget. 2015;6(34):35755-69. PubMed PMC DOI

Simons E, Blansit K, Tsuei T, Brooks R, Ueda S, Kapp DS, Chan JK. "Foreign- vs US-born Asians and the association of type I uterine cancer." Am J Obstet Gynecol. 2015;212(1):43.e1-6. PubMed DOI

Singh G, Pratt G, Yeo GW, Moore MJ. "The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion." Annu Rev Biochem. 2015;84:325-54. PubMed PMC DOI

Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. "Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development." Genome Biol. 2015;16:126. PubMed PMC DOI

Taheri-Araghi S, Bradde S, Sauls JT, Hill NS, Levin PA, Paulsson J, Vergassola M, Jun S. "Cell-size control and homeostasis in bacteria." Curr Biol. 2015;25(3):385-391. PubMed PMC DOI

Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42. PubMed PMC DOI

Telese F, Ma Q, Perez PM, Notani D, Oh S, Li W, Comoletti D, Ohgi KA, Taylor H, Rosenfeld MG. "LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation." Neuron. 2015;86(3):696-710. PubMed PMC DOI

Usach I, Blansit K, Chen LM, Ueda S, Brooks R, Kapp DS, Chan JK. "Survival differences in women with serous tubal, ovarian, peritoneal, and uterine carcinomas." Am J Obstet Gynecol. 2015;212(2):188.e1-6. PubMed DOI

Wang A, Yue F, Li Y, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M. "Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates." Cell Stem Cell. 2015;16(4):386-99. PubMed PMC DOI

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