Student Publications

2022

Hyun JC, Monk JM, Palsson BO. "Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity." BMC Genomics. 2022;23(1):7. PubMed PMC DOI
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. "FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA." NAR Genom Bioinform. 2022;4(2):lqac032. PubMed PMC DOI
Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. "Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3." Elife. 2022;11. PubMed PMC DOI
Liu Y, Ding B, Zheng L, Xu P, Liu Z, Chen Z, Wu P, Zhao Y, Pan Q, Guo Y, Wang W, Wei W. "Regulatory elements can be essential for maintaining broad chromatin organization and cell viability." Nucleic Acids Res. 2022. PubMed DOI
Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR. "Single nucleus multi-omics identifies human cortical cell regulatory genome diversity." Cell Genom. 2022;2(3). PubMed PMC DOI
Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. "The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ." NPJ Breast Cancer. 2022;8(1):6. PubMed PMC DOI
Nachmanson D, Pagadala M, Steward J, Cheung C, Bruce LK, Lee NQ, O'Keefe TJ, Lin GY, Hasteh F, Morris GP, Carter H, Harismendy O. "Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes." J Transl Med. 2022;20(1):623. PubMed PMC DOI
Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli AE. "Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms." Nucleic Acids Res. 2022;50(8):4685-4702. PubMed PMC DOI
Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO. "The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2." Science. 2022:eabp8337. PubMed DOI
Shu H, Ding F, Zhou J, Xue Y, Zhao D, Zeng J, Ma J. "Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data." Brief Bioinform. 2022;23(5). PubMed DOI
Soncin F, Morey R, Bui T, Requena DF, Cheung VC, Kallol S, Kittle R, Jackson MG, Farah O, Chousal J, Meads M, Pizzo D, Horii M, Fisch KM, Parast MM. "Derivation of functional trophoblast stem cells from primed human pluripotent stem cells." Stem Cell Reports. 2022;17(6):1303-1317. PubMed PMC DOI
Song K, Minami JK, Huang A, Dehkordi SR, Lomeli SH, Luebeck J, Goodman MH, Moriceau G, Krijgsman O, Dharanipragada P, Ridgley T, Crosson WP, Salazar J, Pazol E, Karin G, Jayaraman R, Balanis NG, Alhani S, Sheu K, Ten Hoeve J, Palermo A, Motika SE, Senaratne TN, Paraiso KH, Hergenrother PJ, Rao PN, Multani AS, Peeper DS, Bafna V, Lo RS, Graeber TG. "Plasticity of Extrachromosomal and Intrachromosomal BRAF Amplifications in Overcoming Targeted Therapy Dosage Challenges." Cancer Discov. 2022;12(4):1046-1069. PubMed PMC DOI
Sorrentino JT, Golden GJ, Morris C, Painter CD, Nizet V, Campos AR, Smith JW, Karlsson C, Malmström J, Lewis NE, Esko JD, Gómez Toledo A. "Vascular Proteome Responses Precede Organ Dysfunction in a Murine Model of Staphylococcus aureus Bacteremia." MSystems. 2022;7(4):e0039522. PubMed PMC DOI
Worobey M, Levy JI, Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG. "The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic." Science. 2022:abp8715. PubMed DOI
Zhang Y, Amaral ML, Zhu C, Grieco SF, Hou X, Lin L, Buchanan J, Tong L, Preissl S, Xu X, Ren B. "Single-cell epigenome analysis reveals age-associated decay of heterochromatin domains in excitatory neurons in the mouse brain." Cell Res. 2022;32(11):1008-1021. PubMed PMC DOI

2021

Almaraz K, Jang T, Lewis M, Ngo T, Song M, Moshiri N. "SEPIA: simulation-based evaluation of prioritization algorithms." BMC Med Inform Decis Mak. 2021;21(1):177. PubMed PMC DOI
Armingol E, Officer A, Harismendy O, Lewis NE. "Deciphering cell-cell interactions and communication from gene expression." Nat Rev Genet. 2021;22(2):71-88. PubMed PMC DOI
Armstrong G, Cantrell K, Huang S, McDonald D, Haiminen N, Carrieri AP, Zhu Q, Gonzalez A, McGrath I, Beck KL, Hakim D, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Jain M, Inouye M, Swafford AD, Kim HC, Parida L, Vázquez-Baeza Y, Knight R. "Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes." Genome Res. 2021;31(11):2131-2137. PubMed PMC DOI
Armstrong G, Martino C, Rahman G, Gonzalez A, Vázquez-Baeza Y, Mishne G, Knight R. "Uniform Manifold Approximation and Projection (UMAP) Reveals Composite Patterns and Resolves Visualization Artifacts in Microbiome Data." MSystems. 2021;6(5):e0069121. PubMed PMC DOI
BRAIN Initiative Cell Census Network (BICCN). "A multimodal cell census and atlas of the mammalian primary motor cortex." Nature. 2021;598(7879):86-102. PubMed PMC DOI
Brannan KW, Chaim IA, Marina RJ, Yee BA, Kofman ER, Lorenz DA, Jagannatha P, Dong KD, Madrigal AA, Underwood JG, Yeo GW. "Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes." Nat Methods. 2021;18(5):507-519. PubMed PMC DOI
Castro A, Ozturk K, Zanetti M, Carter H. "In silico analysis suggests less effective MHC-II presentation of SARS-CoV-2 RBM peptides: Implication for neutralizing antibody responses." PLoS One. 2021;16(2):e0246731. PubMed PMC DOI
Castro A, Zanetti M, Carter H. "Neoantigen Controversies." Annu Rev Biomed Data Sci. 2021;4. DOI
Chiang AWT, Baghdassarian HM, Kellman BP, Bao B, Sorrentino JT, Liang C, Kuo CC, Masson HO, Lewis NE. "Systems glycobiology for discovering drug targets, biomarkers, and rational designs for glyco-immunotherapy." J Biomed Sci. 2021;28(1):50. PubMed PMC DOI
Dehkordi SR, Luebeck J, Bafna V. "FaNDOM: Fast nested distance-based seeding of optical maps." Patterns. 2021;2:100248. PubMed PMC DOI