Student Publications

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

Xiao S, Lu J, Sridhar B, Cao X, Yu P, Zhao T, Chen CC, McDee D, Sloofman L, Wang Y, Rivas-Astroza M, Telugu BPVL, Levasseur D, Zhang K, Liang H, Zhao JC, Tanaka TS, Stormo G, Zhong S. "SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination." Cell Rep. 2017;18(13):3117-3128. PubMed PMC DOI

Yang F, Ma Q, Liu Z, Li W, Tan Y, Jin C, Ma W, Hu Y, Shen J, Ohgi KA, Telese F, Liu W, Rosenfeld MG. "Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program." Mol Cell. 2017;66(3):321-331.e6. PubMed PMC DOI

Yu B, Zhang K, Milner JJ, Toma C, Chen R, Scott-Browne JP, Pereira RM, Crotty S, Chang JT, Pipkin ME, Wang W, Goldrath AW. "Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation." Nat Immunol. 2017;18(5):573-582. PubMed PMC DOI

Yurkovich JT, Yang L, Palsson BO. "Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells." PLoS Comput Biol. 2017;13(3):e1005424. PubMed PMC DOI

Yurkovich JT, Yang L, Palsson BO. "Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells." Proc. IEEE Conference on Control Technology and Applications. 2017. DOI

Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA. "A Padawan Programmer's Guide to Developing Software Libraries." Cell Syst. 2017;5(5):431-437. PubMed DOI

Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson ÓE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S, Palsson S, Gudmundsson S, Palsson BO. "Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks." J Biol Chem. 2017;292(48):19556-19564. PubMed PMC DOI

Zare F, Dow M, Monteleone N, Hosny A, Nabavi S. "An evaluation of copy number variation detection tools for cancer using whole exome sequencing data." BMC Bioinformatics. 2017;18(1):286. PubMed PMC DOI

Baker CW, Miller CR, Thaweethai T, Yuan J, Baker MH, Joyce P, Weinreich DM. "Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174." G3 (Bethesda). 2016;6(4):939-55. PubMed PMC DOI

Brandler WM, Antaki D, Gujral M, Noor A, Rosanio G, Chapman TR, Barrera DJ, Lin GN, Malhotra D, Watts AC, Wong LC, Estabillo JA, Gadomski TE, Hong O, Fajardo KV, Bhandari A, Owen R, Baughn M, Yuan J, Solomon T, Moyzis AG, Maile MS, Sanders SJ, Reiner GE, Vaux KK, Strom CM, Zhang K, Muotri AR, Akshoomoff N, Leal SM, Pierce K, Courchesne E, Iakoucheva LM, Corsello C, Sebat J. "Frequency and Complexity of De Novo Structural Mutation in Autism." Am J Hum Genet. 2016;98(4):667-79. PubMed PMC DOI