Student Publications

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

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

Moshiri N. "TreeSwift: A massively scalable Python tree package." SoftwareX. 2020;11:100436. 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

Rocca CJ, Rainaldi JN, Sharma J, Shi Y, Haquang JH, Luebeck J, Mali P, Cherqui S. "CRISPR-Cas9 Gene Editing of Hematopoietic Stem Cells from Patients with Friedreich's Ataxia." Mol Ther Methods Clin Dev. 2020;17:1026-1036. PubMed PMC DOI

Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, Litwin N, Humphrey G, Martino C, Miller-Montgomery S, Dorrestein PC, Veiga P, Song SJ, McDonald D, Derrien M, Knight R. "Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome." MSystems. 2020;5(2). PubMed 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

Balaban M, Moshiri N, Mai U, Jia X, Mirarab S. "TreeCluster: Clustering biological sequences using phylogenetic trees." PLoS One. 2019;14(8):e0221068. 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