Training Grant Publications

2021

Mitra I, Huang B, Mousavi N, Ma N, Lamkin M, Yanicky R, Shleizer-Burko S, Lohmueller KE, Gymrek M. "Patterns of de novo tandem repeat mutations and their role in autism." Nature. 2021;589(7841):246-250. PubMed PMC DOI
Morey R, Farah O, Kallol S, Requena DF, Meads M, Moretto-Zita M, Soncin F, Laurent LC, Parast MM. "Transcriptomic Drivers of Differentiation, Maturation, and Polyploidy in Human Extravillous Trophoblast." Front Cell Dev Biol. 2021;9:702046. PubMed PMC DOI
Vo DT, Fuller MR, Tindle C, Anandachar MS, Das S, Sahoo D, Ghosh P. "SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia." IScience. 2021;24(10):103121. PubMed PMC DOI

2020

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
Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, Garvin TH, Pham QT, Harrington AN, Mannion BJ, Lee EA, Fukuda-Yuzawa Y, He Y, Preissl S, Chee S, Han JY, Williams BA, Trout D, Amrhein H, Yang H, Cherry JM, Wang W, Gaulton K, Ecker JR, Shen Y, Dickel DE, Visel A, Pennacchio LA, Ren B. "An atlas of dynamic chromatin landscapes in mouse fetal development." Nature. 2020;583(7818):744-751. PubMed PMC DOI
Hyun JC, Kavvas ES, Monk JM, Palsson BO. "Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens." PLoS Comput Biol. 2020;16(3):e1007608. PubMed PMC DOI
Jakubosky D, D'Antonio M, Bonder MJ, Smail C, Donovan MKR, Young Greenwald WW, Matsui H, i2QTL Consortium, D'Antonio-Chronowska A, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA. "Properties of structural variants and short tandem repeats associated with gene expression and complex traits." Nat Commun. 2020;11(1):2927. 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
Xie X, Shah S, Holtz A, Rose J, Basisty N, Schilling B. "Simultaneous Affinity Enrichment of Two Post-Translational Modifications for Quantification and Site Localization." J Vis Exp. 2020(156). PubMed PMC DOI

2019

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
D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. "Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease." Elife. 2019;8. 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
Sauls JT, Cox SE, Do Q, Castillo V, Ghulam-Jelani Z, Jun S. "Control of Bacillus subtilis Replication Initiation during Physiological Transitions and Perturbations." MBio. 2019;10(6). 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

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