Student Publications

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

Castro A, Ozturk K, Pyke RM, Xian S, Zanetti M, Carter H. "Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes." BMC Med Genomics. 2019;12(Suppl 6):107. PubMed PMC DOI

Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. "Multi-platform discovery of haplotype-resolved structural variation in human genomes." Nat Commun. 2019;10(1):1784. PubMed PMC DOI

Chiang AWT, Li S, Kellman BP, Chattopadhyay G, Zhang Y, Kuo CC, Gutierrez JM, Ghazi F, Schmeisser H, Ménard P, Bjørn SP, Voldborg BG, Rosenberg AS, Puig M, Lewis NE. "Combating viral contaminants in CHO cells by engineering innate immunity." Sci Rep. 2019;9(1):8827. PubMed PMC DOI

Connor R, Brister R, Buchmann JP, Deboutte W, Edwards R, Martí-Carreras J, Tisza M, Zalunin V, Andrade-Martínez J, Cantu A, D'Amour M, Efremov A, Fleischmann L, Forero-Junco L, Garmaeva S, Giluso M, Glickman C, Henderson M, Kellman B, Kristensen D, Leubsdorf C, Levi K, Levi S, Pakala S, Peddu V, Ponsero A, Ribeiro E, Roy F, Rutter L, Saha S, Shakya M, Shean R, Miller M, Tully B, Turkington C, Youens-Clark K, Vanmechelen B, Busby B. "NCBI's Virus Discovery Hackathon: Engaging Research Communities to Identify Cloud Infrastructure Requirements." Genes (Basel). 2019;10(9). PubMed 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

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