Student Publications

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

Fan S, Tang J, Li N, Zhao Y, Ai R, Zhang K, Wang M, Du W, Wang W. "Integrative analysis with expanded DNA methylation data reveals common key regulators and pathways in cancers." NPJ Genom Med. 2019;4:2. PubMed PMC DOI

Gazestani VH, Pramparo T, Nalabolu S, Kellman BP, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. "A perturbed gene network containing PI3K-AKT, RAS-ERK and WNT-β-catenin pathways in leukocytes is linked to ASD genetics and symptom severity." Nat Neurosci. 2019;22(10):1624-1634. PubMed PMC DOI

Greenwald WW, Chiou J, Yan J, Qiu Y, Dai N, Wang A, Nariai N, Aylward A, Han JY, Kadakia N, Regue L, Okino ML, Drees F, Kramer D, Vinckier N, Minichiello L, Gorkin D, Avruch J, Frazer KA, Sander M, Ren B, Gaulton KJ. "Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk." Nat Commun. 2019;10(1):2078. PubMed PMC DOI

Jiang Q, Isquith J, Zipeto MA, Diep RH, Pham J, Delos Santos N, Reynoso E, Chau J, Leu H, Lazzari E, Melese E, Ma W, Fang R, Minden M, Morris S, Ren B, Pineda G, Holm F, Jamieson C. "Hyper-Editing of Cell-Cycle Regulatory and Tumor Suppressor RNA Promotes Malignant Progenitor Propagation." Cancer Cell. 2019;35(1):81-94.e7. PubMed PMC DOI

Jin Song S, Woodhams DC, Martino C, Allaband C, Mu A, Javorschi-Miller-Montgomery S, Suchodolski JS, Knight R. "Engineering the microbiome for animal health and conservation." Exp Biol Med (Maywood). 2019;244(6):494-504. PubMed PMC DOI

Joshi S, Singh AR, Liu KX, Pham TV, Zulcic M, Skola D, Chun HB, Glass CK, Morales GA, Garlich JR, Durden DL. "SF2523: Dual PI3K/BRD4 Inhibitor Blocks Tumor Immunosuppression and Promotes Adaptive Immune Responses in Cancer." Mol Cancer Ther. 2019;18(6):1036-1044. PubMed DOI

Juric I, Yu M, Abnousi A, Raviram R, Fang R, Zhao Y, Zhang Y, Qiu Y, Yang Y, Li Y, Ren B, Hu M. "MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments." PLoS Comput Biol. 2019;15(4):e1006982. PubMed PMC DOI

Kolmogorov M, Yuan J, Lin Y, Pevzner PA. "Assembly of long, error-prone reads using repeat graphs." Nat Biotechnol. 2019;37(5):540-546. PubMed DOI

Landig CS, Hazel A, Kellman BP, Fong JJ, Schwarz F, Agarwal S, Varki N, Massari P, Lewis NE, Ram S, Varki A. "Evolution of the exclusively human pathogen Neisseria gonorrhoeae: Human-specific engagement of immunoregulatory Siglecs." Evol Appl. 2019;12(2):337-349. PubMed PMC DOI

Lee DS, Luo C, Zhou J, Chandran S, Rivkin A, Bartlett A, Nery JR, Fitzpatrick C, O'Connor C, Dixon JR, Ecker JR. "Simultaneous profiling of 3D genome structure and DNA methylation in single human cells." Nat Methods. 2019;16(10):999-1006. PubMed PMC DOI

Lu J, Cao X, Zhong S. "EpiAlignment: alignment with both DNA sequence and epigenomic data." Nucleic Acids Res. 2019;47(W1):W11-W19. PubMed PMC DOI

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