Student Publications

Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA. "Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data." BMC Bioinformatics. 2017;18(1):207. PubMed PMC DOI

Guzman C, D'Orso I. "CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction." BMC Bioinformatics. 2017;18(1):363. PubMed PMC DOI

He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR. "Improved regulatory element prediction based on tissue-specific local epigenomic signatures." Proc Natl Acad Sci U S A. 2017;114(9):E1633-E1640. PubMed PMC DOI

Holtman IR, Skola D, Glass CK. "Transcriptional control of microglia phenotypes in health and disease." J Clin Invest. 2017;127(9):3220-3229. PubMed PMC DOI

Kim H, Bell E, Kim J, Sitapati A, Ramsdell J, Farcas C, Friedman D, Feupe SF, Ohno-Machado L. "iCONCUR: informed consent for clinical data and bio-sample use for research." J Am Med Inform Assoc. 2017;24(2):380-387. PubMed PMC DOI

Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. "Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy." Mol Cell. 2017;65(4):761-774.e5. PubMed PMC DOI

Lazzari E, Mondala PK, Santos ND, Miller AC, Pineda G, Jiang Q, Leu H, Ali SA, Ganesan AP, Wu CN, Costello C, Minden M, Chiaramonte R, Stewart AK, Crews LA, Jamieson CHM. "Alu-dependent RNA editing of GLI1 promotes malignant regeneration in multiple myeloma." Nat Commun. 2017;8(1):1922. PubMed PMC DOI

Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, Ecker JR. "Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex." Science. 2017;357(6351):600-604. PubMed PMC DOI

Ma H, O'Neil RC, Marti Gutierrez N, Hariharan M, Zhang ZZ, He Y, Cinnioglu C, Kayali R, Kang E, Lee Y, Hayama T, Koski A, Nery J, Castanon R, Tippner-Hedges R, Ahmed R, Van Dyken C, Li Y, Olson S, Battaglia D, Lee DM, Wu DH, Amato P, Wolf DP, Ecker JR, Mitalipov S. "Functional Human Oocytes Generated by Transfer of Polar Body Genomes." Cell Stem Cell. 2017;20(1):112-119. PubMed PMC DOI

Marty R, Kaabinejadian S, Rossell D, Slifker MJ, van de Haar J, Engin HB, de Prisco N, Ideker T, Hildebrand WH, Font-Burgada J, Carter H. "MHC-I Genotype Restricts the Oncogenic Mutational Landscape." Cell. 2017;171(6):1272-1283.e15. PubMed PMC DOI

Milner JJ, Toma C, Yu B, Zhang K, Omilusik K, Phan AT, Wang D, Getzler AJ, Nguyen T, Crotty S, Wang W, Pipkin ME, Goldrath AW. "Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours." Nature. 2017;552(7684):253-257. PubMed PMC DOI

Mitra I, Lavillaureix A, Yeh E, Traglia M, Tsang K, Bearden CE, Rauen KA, Weiss LA. "Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders." PLoS Genet. 2017;13(1):e1006516. PubMed PMC DOI

Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H, Feist AM, Palsson BO. "iML1515, a knowledgebase that computes Escherichia coli traits." Nat Biotechnol. 2017;35(10):904-908. PubMed PMC DOI

Nariai N, Greenwald WW, DeBoever C, Li H, Frazer KA. "Efficient Prioritization of Multiple Causal eQTL Variants via Sparse Polygenic Modeling." Genetics. 2017;207(4):1301-1312. PubMed PMC DOI

Opdam S, Richelle A, Kellman B, Li S, Zielinski DC, Lewis NE. "A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models." Cell Syst. 2017;4(3):318-329.e6. PubMed PMC DOI

Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. "iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types." Stem Cell Reports. 2017;8(4):1086-1100. PubMed PMC DOI

Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, Lewis NE, Chang AN, Kreisberg JF, Krogan N, Qi L, Ideker T, Mali P. "Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions." Nat Methods. 2017;14(6):573-576. PubMed PMC DOI

Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. "Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads." J Immunol. 2017;199(9):3369-3380. PubMed PMC DOI

Si F, Li D, Cox SE, Sauls JT, Azizi O, Sou C, Schwartz AB, Erickstad MJ, Jun Y, Li X, Jun S. "Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli." Curr Biol. 2017;27(9):1278-1287. PubMed PMC DOI

Tsagaratou A, González-Avalos E, Rautio S, Scott-Browne JP, Togher S, Pastor WA, Rothenberg EV, Chavez L, Lähdesmäki H, Rao A. "TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells." Nat Immunol. 2017;18(1):45-53. PubMed PMC DOI

Velez DO, Tsui B, Goshia T, Chute CL, Han A, Carter H, Fraley SI. "3D collagen architecture induces a conserved migratory and transcriptional response linked to vasculogenic mimicry." Nat Commun. 2017;8(1):1651. PubMed PMC DOI

Wang S, Jiang X, Singh S, Marmor R, Bonomi L, Fox D, Dow M, Ohno-Machado L. "Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States." Ann N Y Acad Sci. 2017;1387(1):73-83. PubMed PMC DOI

Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. "Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment." Genome Biol. 2017;18(1):57. PubMed PMC DOI

Wolf DP, Morey R, Kang E, Ma H, Hayama T, Laurent LC, Mitalipov S. "Concise Review: Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer: A Horse in the Race?." Stem Cells. 2017;35(1):26-34. PubMed DOI

Wright MS, McCorrison J, Gomez AM, Beck E, Harkins D, Shankar J, Mounaud S, Segubre-Mercado E, Mojica AMR, Bacay B, Nzenze SA, Kimaro SZM, Adrian P, Klugman KP, Lucero MG, Nelson KE, Madhi S, Sutton GG, Nierman WC, Losada L. "Strain Level Streptococcus Colonization Patterns during the First Year of Life." Front Microbiol. 2017;8:1661. PubMed PMC DOI