Student Publications

Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO. "ssbio: a Python framework for structural systems biology." Bioinformatics. 2018;34(12):2155-2157. PubMed PMC DOI

Moshiri N, Izhikevich L. "Design and Analysis of Data Structures." Amazon KDP. 2018. ISBN

Moshiri N, Mirarab S. "A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition." Syst Biol. 2018;67(3):475-489. PubMed PMC DOI

Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. "ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer." Nucleic Acids Res. 2018;46(7):3309-3325. PubMed PMC DOI

Plouffe SW, Lin KC, Moore JL 3rd, Tan FE, Ma S, Ye Z, Qiu Y, Ren B, Guan KL. "The Hippo pathway effector proteins YAP and TAZ have both distinct and overlapping functions in the cell." J Biol Chem. 2018;293(28):11230-11240. PubMed PMC DOI

Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B. "Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation." Nat Neurosci. 2018;21(3):432-439. PubMed PMC DOI

Wang J, Saijo K, Skola D, Jin C, Ma Q, Merkurjev D, Glass CK, Rosenfeld MG. "Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock." Proc Natl Acad Sci U S A. 2018;115(2):E244-E252. PubMed PMC DOI

Wei W, Ji Z, He Y, Zhang K, Ha Y, Li Q, Ohno-Machado L. "Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge." Database (Oxford). 2018;2018. PubMed PMC DOI

Yan J, Chen SA, Local A, Liu T, Qiu Y, Dorighi KM, Preissl S, Rivera CM, Wang C, Ye Z, Ge K, Hu M, Wysocka J, Ren B. "Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers." Cell Res. 2018;28(3):387. PubMed PMC DOI

Yang L, Yurkovich JT, King ZA, Palsson BO. "Modeling the multi-scale mechanisms of macromolecular resource allocation." Curr Opin Microbiol. 2018;45:8-15. PubMed PMC DOI

Yurkovich JT, Bordbar A, Sigurjónsson ÓE, Palsson BO. "Systems biology as an emerging paradigm in transfusion medicine." BMC Syst Biol. 2018;12(1):31. PubMed PMC DOI

Yurkovich JT, Palsson BO. "Quantitative -omic data empowers bottom-up systems biology." Curr Opin Biotechnol. 2018;51:130-136. PubMed DOI

Zhao D, Badur MG, Luebeck J, Magaña JH, Birmingham A, Sasik R, Ahn CS, Ideker T, Metallo CM, Mali P. "Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis." Mol Cell. 2018;69(4):699-708.e7. PubMed PMC DOI

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