Training Grant Publications

Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW. "Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes." Nat Methods. 2021;18(5):507-519. PubMed PMC DOI

Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. "A Systems View of the Heparan Sulfate Interactome." J Histochem Cytochem. 2021;69(2):105-119. PubMed PMC DOI

Horii M, Morey R, Bui T, Touma O, Nelson KK, Cho HY, Rishik H, Laurent LC, Parast MM. "Modeling preeclampsia using human induced pluripotent stem cells." Sci Rep. 2021;11(1):5877. PubMed PMC DOI

Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. "Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing." BMC Genomics. 2021;22(1):69. PubMed PMC DOI

Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. "Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition." Database (Oxford). 2021;2021. PubMed PMC DOI

Massarat AR, Sen A, Jaureguy J, Tyndale ST, Fu Y, Erikson G, McVicker G. "Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq." Nucleic Acids Res. 2021. PubMed DOI

Baxter SL, Klie AR, Radha Saseendrakumar B, Ye GY, Hogarth M. "Text Processing for Detection of Fungal Ocular Involvement in Critical Care Patients: Cross-Sectional Study." J Med Internet Res. 2020;22(8):e18855. PubMed PMC DOI

Baxter SL, Klie AR, Saseendrakumar BR, Ye GY, Hogarth M, Nemati S. "Predicting Mortality in Critical Care Patients with Fungemia Using Structured and Unstructured Data." Annu Int Conf IEEE Eng Med Biol Soc. 2020;2020:5459-5463. PubMed PMC DOI

Nachmanson D, Steward J, Yao H, Officer A, Jeong E, O'Keefe TJ, Hasteh F, Jepsen K, Hirst GL, Esserman LJ, Borowsky AD, Harismendy O. "Mutational profiling of micro-dissected pre-malignant lesions from archived specimens." BMC Med Genomics. 2020;13(1):173. PubMed PMC DOI

Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. "Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression." Proc Natl Acad Sci U S A. 2019;116(49):24881-24891. PubMed PMC DOI

Brigidi GS, Hayes MGB, Delos Santos NP, Hartzell AL, Texari L, Lin PA, Bartlett A, Ecker JR, Benner C, Heinz S, Bloodgood BL. "Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers." Cell. 2019;179(2):373-391.e27. PubMed PMC DOI

Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. "Exploring the landscape of focal amplifications in cancer using AmpliconArchitect." Nat Commun. 2019;10(1):392. PubMed PMC DOI

Sanders JG, Nurk S, Salido RA, Minich J, Xu ZZ, Zhu Q, Martino C, Fedarko M, Arthur TD, Chen F, Boland BS, Humphrey GC, Brennan C, Sanders K, Gaffney J, Jepsen K, Khosroheidari M, Green C, Liyanage M, Dang JW, Phelan VV, Quinn RA, Bankevich A, Chang JT, Rana TM, Conrad DJ, Sandborn WJ, Smarr L, Dorrestein PC, Pevzner PA, Knight R. "Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads." Genome Biol. 2019;20(1):226. PubMed PMC DOI

Zaramela LS, Martino C, Alisson-Silva F, Rees SD, Diaz SL, Chuzel L, Ganatra MB, Taron CH, Secrest P, Zuñiga C, Huang J, Siegel D, Chang G, Varki A, Zengler K. "Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates." Nat Microbiol. 2019. PubMed DOI

Zhang Y, Li T, Preissl S, Amaral ML, Grinstein JD, Farah EN, Destici E, Qiu Y, Hu R, Lee AY, Chee S, Ma K, Ye Z, Zhu Q, Huang H, Fang R, Yu L, Izpisua Belmonte JC, Wu J, Evans SM, Chi NC, Ren B. "Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells." Nat Genet. 2019;51(9):1380-1388. PubMed PMC DOI

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

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

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

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

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

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

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. "Virmid: accurate detection of somatic mutations with sample impurity inference." Genome Biol. 2013;14(8):R90. PubMed PMC DOI

Lo JH, von Maltzahn G, Douglass J, Park JH, Sailor MJ, Ruoslahti E, Bhatia SN. "Nanoparticle amplification via photothermal unveiling of cryptic collagen binding sites." J Mater Chem B. 2013;1(39):5235-5240. PubMed PMC DOI

Massanella M, Singhania A, Beliakova-Bethell N, Pier R, Lada SM, White CH, Pérez-Santiago J, Blanco J, Richman DD, Little SJ, Woelk CH. "Differential gene expression in HIV-infected individuals following ART." Antiviral Res. 2013;100(2):420-8. PubMed PMC DOI

Szpankowski L, Encalada SE, Goldstein LS. "Subpixel colocalization reveals amyloid precursor protein-dependent kinesin-1 and dynein association with axonal vesicles." Proc Natl Acad Sci U S A. 2012;109(22):8582-7. PubMed PMC DOI

Encalada SE, Szpankowski L, Xia CH, Goldstein LS. "Stable kinesin and dynein assemblies drive the axonal transport of mammalian prion protein vesicles." Cell. 2011;144(4):551-65. PubMed PMC DOI

Narayanan T, Gersten M, Subramaniam S, Grama A. "Modularity detection in protein-protein interaction networks." BMC Res Notes. 2011;4:569. PubMed PMC DOI

Payne SH, Loomis WF. "Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences." Eukaryot Cell. 2006;5(2):272-6. PubMed PMC DOI