Student Publications

Her HL, Wu YW. "A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains." Bioinformatics. 2018;34(13):i89-i95. PubMed PMC DOI

Huang JK, Carlin DE, Yu MK, Zhang W, Kreisberg JF, Tamayo P, Ideker T. "Systematic Evaluation of Molecular Networks for Discovery of Disease Genes." Cell Syst. 2018;6(4):484-495.e5. PubMed PMC DOI

Huang JK, Jia T, Carlin DE, Ideker T. "pyNBS: a Python implementation for network-based stratification of tumor mutations." Bioinformatics. 2018;34(16):2859-2861. PubMed PMC DOI

Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM. "Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions." BMC Syst Biol. 2018;12(1):25. PubMed PMC DOI

Kuo CC, Chiang AW, Shamie I, Samoudi M, Gutierrez JM, Lewis NE. "The emerging role of systems biology for engineering protein production in CHO cells." Curr Opin Biotechnol. 2018;51:64-69. PubMed PMC DOI

Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. "Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function." Cell. 2018;173(7):1796-1809.e17. PubMed PMC DOI

Lu J, Cao X, Zhong S. "A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome." PLoS Comput Biol. 2018;14(12):e1006673. PubMed PMC DOI

Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, Mash DC, Behrens MM, Ecker JR. "Robust single-cell DNA methylome profiling with snmC-seq2." Nat Commun. 2018;9(1):3824. PubMed PMC DOI

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. "Using deep learning to model the hierarchical structure and function of a cell." Nat Methods. 2018;15(4):290-298. PubMed PMC DOI

Marty R, de Prisco N, Carter H, Font-Burgada J. "MHC-I genotype drives early immune selection of oncogenic mutations." Mol Cell Oncol. 2018;5(2):e1409863. PubMed PMC DOI

Meng Z, Qiu Y, Lin KC, Kumar A, Placone JK, Fang C, Wang KC, Lu S, Pan M, Hong AW, Moroishi T, Luo M, Plouffe SW, Diao Y, Ye Z, Park HW, Wang X, Yu FX, Chien S, Wang CY, Ren B, Engler AJ, Guan KL. "RAP2 mediates mechanoresponses of the Hippo pathway." Nature. 2018;560(7720):655-660. PubMed PMC DOI

Miao Y, Ajami NE, Huang TS, Lin FM, Lou CH, Wang YT, Li S, Kang J, Munkacsi H, Maurya MR, Gupta S, Chien S, Subramaniam S, Chen Z. "Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function." Nat Commun. 2018;9(1):292. PubMed PMC DOI

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