Student Publications

Martino C, Morton JT, Marotz CA, Thompson LR, Tripathi A, Knight R, Zengler K. "A Novel Sparse Compositional Technique Reveals Microbial Perturbations." MSystems. 2019;4(1). PubMed PMC DOI

Moshiri N, Ragonnet-Cronin M, Wertheim JO, Mirarab S. "FAVITES: simultaneous simulation of transmission networks, phylogenetic trees and sequences." Bioinformatics. 2019;35(11):1852-1861. PubMed DOI

Ngo V, Chen Z, Zhang K, Whitaker JW, Wang M, Wang W. "Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse." Proc Natl Acad Sci U S A. 2019;116(9):3668-3677. PubMed PMC DOI

Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F, Corbett KD. "Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase." Nat Struct Mol Biol. 2019;26(3):164-174. PubMed PMC DOI

Phaneuf PV, Gosting D, Palsson BO, Feist AM. "ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation." Nucleic Acids Res. 2019;47(D1):D1164-D1171. PubMed PMC DOI

Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, Bafna V. "EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA." IScience. 2019;21:428-435. PubMed PMC DOI

Rule A, Birmingham A, Zuniga C, Altintas I, Huang SC, Knight R, Moshiri N, Nguyen MH, Rosenthal SB, Pérez F, Rose PW. "Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks." PLoS Comput Biol. 2019;15(7):e1007007. 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

Si F, Le Treut G, Sauls JT, Vadia S, Levin PA, Jun S. "Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria." Curr Biol. 2019;29(11):1760-1770.e7. PubMed PMC DOI

Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. "Circular ecDNA promotes accessible chromatin and high oncogene expression." Nature. 2019;575(7784):699-703. PubMed PMC DOI

Yokoi A, Villar-Prados A, Oliphint PA, Zhang J, Song X, De Hoff P, Morey R, Liu J, Roszik J, Clise-Dwyer K, Burks JK, O'Halloran TJ, Laurent LC, Sood AK. "Mechanisms of nuclear content loading to exosomes." Sci Adv. 2019;5(11):eaax8849. 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 K, Wang M, Zhao Y, Wang W. "Taiji: System-level identification of key transcription factors reveals transcriptional waves in mouse embryonic development." Sci Adv. 2019;5(3):eaav3262. PubMed PMC 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

Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR. "Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation." Proc Natl Acad Sci U S A. 2019;116(28):14011-14018. PubMed PMC DOI

Ai R, Laragione T, Hammaker D, Boyle DL, Wildberg A, Maeshima K, Palescandolo E, Krishna V, Pocalyko D, Whitaker JW, Bai Y, Nagpal S, Bachman KE, Ainsworth RI, Wang M, Ding B, Gulko PS, Wang W, Firestein GS. "Comprehensive epigenetic landscape of rheumatoid arthritis fibroblast-like synoviocytes." Nat Commun. 2018;9(1):1921. PubMed PMC DOI

Al-Bassam MM, Kim JN, Zaramela LS, Kellman BP, Zuniga C, Wozniak JM, Gonzalez DJ, Zengler K. "Optimization of carbon and energy utilization through differential translational efficiency." Nat Commun. 2018;9(1):4474. PubMed PMC DOI

Autran CA, Kellman BP, Kim JH, Asztalos E, Blood AB, Spence ECH, Patel AL, Hou J, Lewis NE, Bode L. "Human milk oligosaccharide composition predicts risk of necrotising enterocolitis in preterm infants." Gut. 2018;67(6):1064-1070. PubMed DOI

Bauman N, Akella S, Hann E, Morey R, Schwartz AS, Brown R, Richardson TH. "Next-Generation Sequencing of Haematococcus lacustris Reveals an Extremely Large 1.35-Megabase Chloroplast Genome." Genome Announc. 2018;6(12). 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

Bluemel S, Wang L, Martino C, Lee S, Wang Y, Williams B, Horvath A, Stadlbauer V, Zengler K, Schnabl B. "The Role of Intestinal C-type Regenerating Islet Derived-3 Lectins for Nonalcoholic Steatohepatitis." Hepatol Commun. 2018;2(4):393-406. PubMed PMC DOI

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO. "Recon3D enables a three-dimensional view of gene variation in human metabolism." Nat Biotechnol. 2018;36(3):272-281. 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

Her HL, Wu YW. "A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains." Bioinformatics. 2018;34(13):i89-i95. PubMed PMC DOI