Student Publications | Bioinformatics and Systems Biology

Aevermann B, McCorrison J, Venepally P, Hodge R, Bakken T, Miller J, Novotny M, Tran DN, Diezfuertes F, Christiansen L, Zhang F, Steemers F, Lasken RS, Lein ED, Schork N, Scheuermann RH. "PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX." Pac Symp Biocomput. 2017;22:564-575. PubMed PMC DOI

Ajami NE, Gupta S, Maurya MR, Nguyen P, Li JY, Shyy JY, Chen Z, Chien S, Subramaniam S. "Systems biology analysis of longitudinal functional response of endothelial cells to shear stress." Proc Natl Acad Sci U S A. 2017;114(41):10990-10995. PubMed PMC DOI

Amir H, Touboul T, Sabatini K, Chhabra D, Garitaonandia I, Loring JF, Morey R, Laurent LC. "Spontaneous Single-Copy Loss of TP53 in Human Embryonic Stem Cells Markedly Increases Cell Proliferation and Survival." Stem Cells. 2017;35(4):872-885. PubMed DOI

Bakken T, Cowell L, Aevermann BD, Novotny M, Hodge R, Miller JA, Lee A, Chang I, McCorrison J, Pulendran B, Qian Y, Schork NJ, Lasken RS, Lein ES, Scheuermann RH. "Cell type discovery and representation in the era of high-content single cell phenotyping." BMC Bioinformatics. 2017;18(Suppl 17):559. PubMed PMC DOI

Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson ÓE, Palsson BO. "Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics." Sci Rep. 2017;7:46249. PubMed PMC DOI

Carrat GR, Hu M, Nguyen-Tu MS, Chabosseau P, Gaulton KJ, van de Bunt M, Siddiq A, Falchi M, Thurner M, Canouil M, Pattou F, Leclerc I, Pullen TJ, Cane MC, Prabhala P, Greenwald W, Schulte A, Marchetti P, Ibberson M, MacDonald PE, Manning Fox JE, Gloyn AL, Froguel P, Solimena M, McCarthy MI, Rutter GA. "Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice." Am J Hum Genet. 2017;100(2):238-256. PubMed PMC DOI

Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. "Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer." Cancer Discov. 2017;7(4):410-423. PubMed PMC DOI

Chen K, Gao Y, Mih N, O'Brien EJ, Yang L, Palsson BO. "Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation." Proc Natl Acad Sci U S A. 2017;114(43):11548-11553. PubMed PMC DOI

D'Antonio M, Woodruff G, Nathanson JL, D'Antonio-Chronowska A, Arias A, Matsui H, Williams R, Herrera C, Reyna SM, Yeo GW, Goldstein LSB, Panopoulos AD, Frazer KA. "High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells." Stem Cell Reports. 2017;8(4):1101-1111. PubMed PMC DOI

DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA. "Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells." Cell Stem Cell. 2017;20(4):533-546.e7. PubMed PMC DOI

Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B. "A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells." Nat Methods. 2017;14(6):629-635. PubMed PMC DOI

Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO. "Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities." Proc Natl Acad Sci U S A. 2017;114(38):10286-10291. PubMed PMC DOI

Gao X, Lee HY, Li W, Platt RJ, Barrasa MI, Ma Q, Elmes RR, Rosenfeld MG, Lodish HF. "Thyroid hormone receptor beta and NCOA4 regulate terminal erythrocyte differentiation." Proc Natl Acad Sci U S A. 2017;114(38):10107-10112. PubMed PMC DOI

Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, Jaeger BN, O'Connor C, Fitzpatrick C, Pasillas MP, Pena M, Adair A, Gonda DD, Levy ML, Ransohoff RM, Gage FH, Glass CK. "An environment-dependent transcriptional network specifies human microglia identity." Science. 2017;356(6344). PubMed PMC DOI

Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W. "Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies." BMC Genomics. 2017;18(1):296. PubMed PMC DOI

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