Publications

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Students, please keep the Graduate Program Coordinator appraised of your new publications and any inaccuracies or omissions on this list. Most articles are indexed in PubMed; please provide the PubMed ID numbers (PMID) for your articles if available, to expedite the maintenance of this list. Please remember to acknowledge your grants in your papers, including the training grant if you were a recipient; see here for sample wording.

2022

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
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
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
Golden GJ, Toledo AG, Marki A, Sorrentino JT, Morris C, Riley RJ, Spliid C, Chen Q, Cornax I, Lewis NE, Varki N, Le D, Malmström J, Karlsson C, Ley K, Nizet V, Esko JD. "Endothelial Heparan Sulfate Mediates Hepatic Neutrophil Trafficking and Injury during Staphylococcus aureus Sepsis." MBio. 2021;12(5):e0118121. 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
Her HL, Lin PT, Wu YW. "PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains." BMC Bioinformatics. 2021;22(1):548. 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 PMC 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
Kuo CC, Chiang AWT, Baghdassarian HM, Lewis NE. "Dysregulation of the secretory pathway connects Alzheimer's disease genetics to aggregate formation." Cell Syst. 2021;12(9):873-884.e4. PubMed PMC DOI

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