Publications

Jia BB, Jussila A, Kern C, Zhu Q, Ren B. "A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH." Nat Biotechnol. 2023. PubMed DOI

Armstrong G, Martino C, Morris J, Khaleghi B, Kang J, DeReus J, Zhu Q, Roush D, McDonald D, Gonazlez A, Shaffer JP, Carpenter C, Estaki M, Wandro S, Eilert S, Akel A, Eno J, Curewitz K, Swafford AD, Moshiri N, Rosing T, Knight R. "Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases." MSystems. 2022:e0137821. PubMed DOI

Armstrong G, Rahmn G, Martino C, McDonald D, Gonzalez A, Mishne G, Knight R. "Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data." Front Bioinform. 2022;2:821861. DOI

Bergstrom EN, Luebeck J, Petljak M, Khandekar A, Barnes M, Zhang T, Steele CD, Pillay N, Landi MT, Bafna V, Mischel PS, Harris RS, Alexandrov LB. "Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA." Nature. 2022;602(7897):510-517. 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

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

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 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

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

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

Dehkordi SR, Luebeck J, Bafna V. "FaNDOM: Fast nested distance-based seeding of optical maps." Patterns. 2021;2:100248. DOI

Ding B, Liu Y, Liu Z, Zheng L, Xu P, Chen Z, Wu P, Zhao Y, Pan Q, Guo Y, Wei W, Wang W. "Noncoding loci without epigenomic signals can be essential for maintaining global chromatin organization and cell viability." Sci Adv. 2021;7(45):eabi6020. PubMed PMC DOI

Gómez Toledo A, Sorrentino JT, Sandoval DR, Malmström J, Lewis NE, Esko JD. "A Systems View of the Heparan Sulfate Interactome." J Histochem Cytochem. 2021;69(2):105-119. PubMed PMC DOI

Guccione C, Yadlapati R, Shah S, Knight R, Curtius K. "Challenges in Determining the Role of Microbiome Evolution in Barrett's Esophagus and Progression to Esophageal Adenocarcinoma." Microorganisms. 2021;9(10). PubMed PMC DOI

Hasenstab KA, Yuan N, Retson T, Conrad DJ, Kligerman S, Lynch DA, Hsiao A. "Automated CT Staging of Chronic Obstructive Pulmonary Disease Severity for Predicting Disease Progression and Mortality with a Deep Learning Convolutional Neural Network." Radiol Cardiothorac Imaging. 2021;3(2):e200477. PubMed PMC DOI

Horii M, Morey R, Bui T, Touma O, Nelson KK, Cho HY, Rishik H, Laurent LC, Parast MM. "Modeling preeclampsia using human induced pluripotent stem cells." Sci Rep. 2021;11(1):5877. PubMed PMC DOI

Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong IT, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. "ecDNA hubs drive cooperative intermolecular oncogene expression." Nature. 2021;600(7890):731-736. PubMed DOI

Kellman BP, Baghdassarian HM, Pramparo T, Shamie I, Gazestani V, Begzati A, Li S, Nalabolu S, Murray S, Lopez L, Pierce K, Courchesne E, Lewis NE. "Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing." BMC Genomics. 2021;22(1):69. PubMed PMC DOI

Klie A, Tsui BY, Mollah S, Skola D, Dow M, Hsu CN, Carter H. "Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition." Database (Oxford). 2021;2021. PubMed PMC DOI

Massarat AR, Sen A, Jaureguy J, Tyndale ST, Fu Y, Erikson G, McVicker G. "Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq." Nucleic Acids Res. 2021. PubMed DOI