Student Publications

2021

Maurya MR, Gupta S, Li JY, Ajami NE, Chen ZB, Shyy JY, Chien S, Subramaniam S. "Longitudinal shear stress response in human endothelial cells to atheroprone and atheroprotective conditions." Proc Natl Acad Sci U S A. 2021;118(4). PubMed PMC DOI
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
Moshiri N. "ViralMSA: massively scalable reference-guided multiple sequence alignment of viral genomes." Bioinformatics. 2021;37(5):714-716. PubMed DOI
Moshiri N, Smith DM, Mirarab S. "HIV Care Prioritization Using Phylogenetic Branch Length." J Acquir Immune Defic Syndr. 2021;86(5):626-637. PubMed PMC DOI
Pang J, Nguyen N, Luebeck J, Ball L, Finegersh A, Ren S, Nakagawa T, Flagg M, Sadat S, Mischel PS, Xu G, Fisch K, Guo T, Cahill G, Panuganti B, Bafna V, Califano J. "Extrachromosomal DNA in HPV-Mediated Oropharyngeal Cancer Drives Diverse Oncogene Transcription." Clin Cancer Res. 2021;27(24):6772-6786. PubMed PMC DOI
Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. "Timing the SARS-CoV-2 index case in Hubei province." Science. 2021;372(6540):412-417. PubMed PMC DOI
Qin Y, Huttlin EL, Winsnes CF, Gosztyla ML, Wacheul L, Kelly MR, Blue SM, Zheng F, Chen M, Schaffer LV, Licon K, Bäckström A, Vaites LP, Lee JJ, Ouyang W, Liu SN, Zhang T, Silva E, Park J, Pitea A, Kreisberg JF, Gygi SP, Ma J, Harper JW, Yeo GW, Lafontaine DLJ, Lundberg E, Ideker T. "A multi-scale map of cell structure fusing protein images and interactions." Nature. 2021;600(7889):536-542. PubMed PMC DOI
Shu H, Zhou J, Lian Q, Li H, Zhao D, Zeng J, Ma J. "Modeling gene regulatory networks using neural network architectures." Nat Comput Sci. 2021;1(7):491-501. PubMed 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
Zhang Z, Zhou J, Tan P, Pang Y, Rivkin AC, Kirchgessner MA, Williams E, Lee CT, Liu H, Franklin AD, Miyazaki PA, Bartlett A, Aldridge AI, Vu M, Boggeman L, Fitzpatrick C, Nery JR, Castanon RG, Rashid M, Jacobs MW, Ito-Cole T, O'Connor C, Pinto-Duartec A, Dominguez B, Smith JB, Niu SY, Lee KF, Jin X, Mukamel EA, Behrens MM, Ecker JR, Callaway EM. "Epigenomic diversity of cortical projection neurons in the mouse brain." Nature. 2021;598(7879):167-173. 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
Castro A, Pyke RM, Zhang X, Thompson WK, Day CP, Alexandrov LB, Zanetti M, Carter H. "Strength of immune selection in tumors varies with sex and age." Nat Commun. 2020;11(1):4128. PubMed PMC DOI
Dosset M, Castro A, Carter H, Zanetti M. "Telomerase and CD4 T Cell Immunity in Cancer." Cancers (Basel). 2020;12(6). PubMed PMC DOI
Estaki M, Jiang L, Bokulich NA, McDonald D, González A, Kosciolek T, Martino C, Zhu Q, Birmingham A, Vázquez-Baeza Y, Dillon MR, Bolyen E, Caporaso JG, Knight R. "QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data." Curr Protoc Bioinformatics. 2020;70(1):e100. PubMed DOI
Fedarko MW, Martino C, Morton JT, González A, Rahman G, Marotz CA, Minich JJ, Allen EE, Knight R. "Visualizing 'omic feature rankings and log-ratios using Qurro." NAR Genom Bioinform. 2020;2(2):lqaa023. PubMed PMC DOI
Fouladi F, Bailey MJ, Patterson WB, Sioda M, Blakley IC, Fodor AA, Jones RB, Chen Z, Kim JS, Lurmann F, Martino C, Knight R, Gilliland FD, Alderete TL. "Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing." Environ Int. 2020;138:105604. PubMed PMC DOI
Goodman AM, Castro A, Pyke RM, Okamura R, Kato S, Riviere P, Frampton G, Sokol E, Zhang X, Ball ED, Carter H, Kurzrock R. "MHC-I genotype and tumor mutational burden predict response to immunotherapy." Genome Med. 2020;12(1):45. 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
Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. "Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers." Nat Genet. 2020;52(9):891-897. PubMed PMC DOI
Kim Y, Imani M, Moshiri N, Rosing T. "GenieHD: Efficient DNA Pattern Matching Accelerator Using Hyperdimensional Computing." DATE 2020. 2020. DOI
Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, Pai DA, Zhang C, Rajkumar U, Law JA, Mischel PS, Bafna V. "AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications." Nat Commun. 2020;11(1):4374. PubMed PMC DOI