Training Grant Publications | Bioinformatics and Systems Biology

2018

Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. "ProteoStorm: An Ultrafast Metaproteomics Database Search Framework." Cell Syst. 2018;7(4):463-467.e6. PubMed PMC DOI
Bui N, Huang JK, Bojorquez-Gomez A, Licon K, Sanchez KS, Tang SN, Beckett AN, Wang T, Zhang W, Shen JP, Kreisberg JF, Ideker T. "Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation." Mol Cancer Ther. 2018;17(7):1585-1594. 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
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
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
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
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

2017

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
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
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
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

2016

Cremer J, Segota I, Yang CY, Arnoldini M, Sauls JT, Zhang Z, Gutierrez E, Groisman A, Hwa T. "Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel." Proc Natl Acad Sci U S A. 2016;113(41):11414-11419. PubMed PMC DOI
Sauls JT, Li D, Jun S. "Adder and a coarse-grained approach to cell size homeostasis in bacteria." Curr Opin Cell Biol. 2016;38:38-44. PubMed PMC DOI
Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, Kollenstart L, van Attikum H, Aza-Blanc P, Sobol RW, Ideker T. "A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy." Mol Cell. 2016;63(3):514-25. PubMed PMC DOI
Yu MK, Kramer M, Dutkowski J, Srivas R, Licon K, Kreisberg J, Ng CT, Krogan N, Sharan R, Ideker T. "Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems." Cell Syst. 2016;2(2):77-88. PubMed PMC DOI

2015

Bliven SE, Bourne PE, Prlić A. "Detection of circular permutations within protein structures using CE-CP." Bioinformatics. 2015;31(8):1316-8. PubMed PMC DOI
Choueiri MB, Shen JP, Gross AM, Huang JK, Ideker T, Fanta P. "ERCC1 and TS Expression as Prognostic and Predictive Biomarkers in Metastatic Colon Cancer." PLoS One. 2015;10(6):e0126898. PubMed PMC DOI
Taheri-Araghi S, Brown SD, Sauls JT, McIntosh DB, Jun S. "Single-Cell Physiology." Annu Rev Biophys. 2015;44:123-42. PubMed PMC DOI

2014

Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. "NeXO Web: the NeXO ontology database and visualization platform." Nucleic Acids Res. 2014;42(Database issue):D1269-74. PubMed PMC DOI
Liu JK, O'Brien EJ, Lerman JA, Zengler K, Palsson BO, Feist AM. "Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale." BMC Syst Biol. 2014;8:110. PubMed PMC DOI
Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A. "Systematic detection of internal symmetry in proteins using CE-Symm." J Mol Biol. 2014;426(11):2255-68. PubMed PMC DOI
Neumann S, Campbell GE, Szpankowski L, Goldstein LS, Encalada SE. "Characterizing the composition of molecular motors on moving axonal cargo using 'cargo mapping' analysis." J Vis Exp. 2014(92):e52029. PubMed PMC DOI

2013

Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol Cell. 2013;51(3):310-25. PubMed PMC DOI