Student Publications

Gross AM, Cohen EE. "Towards a personalized treatment of head and neck cancer." Am Soc Clin Oncol Educ Book. 2015:28-32. PubMed DOI

Gross AM, Ideker T. "Molecular networks in context." Nat Biotechnol. 2015;33(7):720-1. PubMed DOI

Gross AM, Kreisberg JF, Ideker T. "Analysis of Matched Tumor and Normal Profiles Reveals Common Transcriptional and Epigenetic Signals Shared across Cancer Types." PLoS One. 2015;10(11):e0142618. PubMed PMC DOI

He Y, Ecker JR. "Non-CG Methylation in the Human Genome." Annu Rev Genomics Hum Genet. 2015;16:55-77. PubMed PMC DOI

Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, Behrens TW. "The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression." Science. 2015;350(6259):455-9. PubMed PMC DOI

Lee SR, Pratt GA, Martinez FJ, Yeo GW, Lykke-Andersen J. "Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity." Mol Cell. 2015;59(3):413-25. PubMed PMC DOI

Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, Edsall L, Yang H, Chi NC, Zhang MQ, Ecker JR, Ren B. "Integrative analysis of haplotype-resolved epigenomes across human tissues." Nature. 2015;518(7539):350-354. PubMed PMC DOI

Li W, Hu Y, Oh S, Ma Q, Merkurjev D, Song X, Zhou X, Liu Z, Tanasa B, He X, Chen AY, Ohgi K, Zhang J, Liu W, Rosenfeld MG. "Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation." Mol Cell. 2015;59(2):188-202. PubMed PMC DOI

Ma H, Folmes CD, Wu J, Morey R, Mora-Castilla S, Ocampo A, Ma L, Poulton J, Wang X, Ahmed R, Kang E, Lee Y, Hayama T, Li Y, Van Dyken C, Gutierrez NM, Tippner-Hedges R, Koski A, Mitalipov N, Amato P, Wolf DP, Huang T, Terzic A, Laurent LC, Izpisua Belmonte JC, Mitalipov S. "Metabolic rescue in pluripotent cells from patients with mtDNA disease." Nature. 2015;524(7564):234-8. PubMed DOI

Ma Q, Telese F. "Genome-wide epigenetic analysis of MEF2A and MEF2C transcription factors in mouse cortical neurons." Commun Integr Biol. 2015;8(6):e1087624. PubMed PMC DOI

Mukund K, Subramaniam S. "Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis." BMC Res Notes. 2015;8:182. PubMed PMC DOI

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. "Gene-wide identification of episodic selection." Mol Biol Evol. 2015;32(5):1365-71. PubMed PMC DOI

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