Student Publications

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

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