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ArticlesPeer ReviewedFull Text
Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women
Author / Creator:Pankau, Mark D. ; Reeves, Daniel B. ; Harkins, Elias ; Ronen, Keshet ; Jaoko, Walter ; Mandaliya, Kishor ; Graham, Susan M. ; McClelland, R. Scott ; Matsen IV, Frederick A. ; Schiffer, Joshua T. ; Overbaugh, Julie ; Lehman, Dara A.
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2020-02, Vol.16 (2), p.e1008286
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Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage
Author / Creator:Simonich, Cassandra A. ; Doepker, Laura ; Ralph, Duncan ; Williams, James A. ; Dhar, Amrit ; Yaffe, Zak ; Gentles, Lauren ; Small, Christopher T. ; Oliver, Brian ; Vigdorovich, Vladimir ; Mangala Prasad, Vidya ; Nduati, Ruth ; Sather, D. Noah ; Lee, Kelly K. ; Matsen IV, Frederick A. ; Overbaugh, Julie
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2019-05, Vol.10 (1), p.2190-12, Article 2190
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Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-Infection Estimation towards Enhanced Vaccine Efficacy Assessment
Author / Creator:Rossenkhan, Raabya ; Rolland, Morgane ; Labuschagne, Jan ; Ferreira, Roux-Cil ; Magaret, Craig ; Carpp, Lindsay ; Matsen IV, Frederick ; Huang, Yunda ; Rudnicki, Erika ; Zhang, Yuanyuan ; Ndabambi, Nonkululeko ; Logan, Murray ; Holzman, Ted ; Abrahams, Melissa-Rose ; Anthony, Colin ; Tovanabutra, Sodsai ; Warth, Christopher ; Botha, Gordon ; Matten, David ; Nitayaphan, Sorachai ; Kibuuka, Hannah ; Sawe, Fred ; Chopera, Denis ; Eller, Leigh ; Travers, Simon ; Robb, Merlin ; Williamson, Carolyn ; Gilbert, Peter ; Edlefsen, Paul
Publisher:Switzerland: MDPI AG
Journal title:Viruses, 2019-07, Vol.11 (7), p.607
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ArticlesPeer ReviewedFull Text
Comparing T cell receptor repertoires using optimal transport
Author / Creator:Olson, Branden J. ; Schattgen, Stefan A. ; Thomas, Paul G. ; Bradley, Philip ; Matsen IV, Frederick A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2022-12, Vol.18 (12), p.e1010681-e1010681
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Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses
Author / Creator:Ruiz, Felicitas ; Foreman, William B. ; Lilly, Michelle ; Baharani, Viren A. ; Depierreux, Delphine M. ; Chohan, Vrasha ; Taylor, Ashley L. ; Guenthoer, Jamie ; Ralph, Duncan ; Matsen IV, Frederick A. ; Chu, Helen Y. ; Bieniasz, Paul D. ; Côté, Marceline ; Starr, Tyler N. ; Overbaugh, Julie
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2024-10, Vol.20 (10), p.e1012650
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Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses
Author / Creator:Lubow, Jay ; Levoir, Lisa M. ; Ralph, Duncan K. ; Belmont, Laura ; Contreras, Maya ; Cartwright-Acar, Catiana H. ; Kikawa, Caroline ; Kannan, Shruthi ; Davidson, Edgar ; Duran, Veronica ; Rebellon-Sanchez, David E. ; Sanz, Ana M. ; Rosso, Fernando ; Doranz, Benjamin J. ; Einav, Shirit ; Matsen IV, Frederick A. ; Goo, Leslie
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2023-10, Vol.19 (10), p.e1011722
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Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques
Author / Creator:Willcox, Alexandra C. ; Sung, Kevin ; Garrett, Meghan E. ; Galloway, Jared G. ; Erasmus, Jesse H. ; Logue, Jennifer K. ; Hawman, David W. ; Chu, Helen Y. ; Hasenkrug, Kim J. ; Fuller, Deborah H. ; Matsen IV, Frederick A. ; Overbaugh, Julie
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2022-04, Vol.18 (4), p.e1010155
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ArticlesPeer ReviewedFull Text
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Author / Creator:Dumm, Will ; Barker, Mary ; Howard-Snyder, William ; DeWitt III, William S. ; Matsen IV, Frederick A.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Journal of mathematical biology, 2023-11, Vol.87 (5), p.75-75, Article 75
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ArticlesPeer ReviewedFull Text
PhyloSift: phylogenetic analysis of genomes and metagenomes
Author / Creator:Darling, Aaron E. ; Jospin, Guillaume ; Lowe, Eric ; Matsen, Frederick A. ; Bik, Holly M. ; Eisen, Jonathan A.
Publisher:United States: PeerJ. Ltd
Journal title:PeerJ (San Francisco, CA), 2014-01, Vol.2, p.e243-e243
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ArticlesPeer ReviewedFull Text
Inference of B cell clonal families using heavy/light chain pairing information
Author / Creator:Ralph, Duncan K. ; Matsen, Frederick A.
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2022-11, Vol.18 (11), p.e1010723-e1010723
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ArticlesPeer ReviewedFull Text
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
Author / Creator:McCoy, Connor O. ; Matsen, Frederick A.
Publisher:United States: PeerJ. Ltd
Journal title:PeerJ (San Francisco, CA), 2013-09, Vol.1, p.e157-e157
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ArticlesPeer ReviewedFull Text
Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison
Author / Creator:Matsen IV, Frederick A. ; Evans, Steven N.
Publisher:United States: Public Library of Science
Journal title:PloS one, 2013-03, Vol.8 (3), p.e56859-e56859
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ArticlesPeer ReviewedFull Text
Correction: Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison
Author / Creator:Matsen IV, Frederick A. ; Evans, Steven N.
Publisher:San Francisco: Public Library of Science
Journal title:PloS one, 2013-06, Vol.8 (6)
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ArticlesPeer ReviewedFull Text
Population dynamics of rhesus macaques and associated foamy virus in Bangladesh
Author / Creator:Feeroz, Mostafa M ; Soliven, Khanh ; Small, Christopher T ; Engel, Gregory A ; Andreina Pacheco, M ; Yee, JoAnn L ; Wang, Xiaoxing ; Kamrul Hasan, M ; Oh, Gunwha ; Levine, Kathryn L ; Rabiul Alam, SM ; Craig, Karen L ; Jackson, Dana L ; Lee, Eun-Gyung ; Barry, Peter A ; Lerche, Nicholas W ; Escalante, Ananias A ; Matsen IV, Frederick A ; Linial, Maxine L ; Jones-Engel, Lisa
Publisher:United States: Taylor & Francis Ltd
Journal title:Emerging microbes & infections, 2013-05, Vol.2 (1), p.1-14
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ArticlesPeer ReviewedFull Text
Comparing T cell receptor repertoires using optimal transport Comparing T cell receptor repertoires using optimal transport
Author / Creator:Branden J. Olson ; Stefan A. Schattgen ; Paul G. Thomas ; Philip Bradley ; Frederick A. Matsen IV
Publisher:Public Library of Science (PLoS)
Journal title:PLoS computational biology, 2022-12, Vol.18 (12)
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ArticlesPeer ReviewedFull Text
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity
Author / Creator:DeWitt, William S ; Smith, Anajane ; Schoch, Gary ; Hansen, John A ; Matsen, Frederick A ; Bradley, Philip
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2018-08, Vol.7
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ArticlesPeer ReviewedFull Text
Deep generative models for T cell receptor protein sequences
Author / Creator:Davidsen, Kristian ; Olson, Branden J ; DeWitt, William S ; Feng, Jean ; Harkins, Elias ; Bradley, Philip ; Matsen, Frederick A
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2019-09, Vol.8
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ArticlesPeer ReviewedFull Text
Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming
Author / Creator:Russell, Magdalena L ; Simon, Noah ; Bradley, Philip ; Matsen, Frederick A
Publisher:England: eLife Sciences Publications Ltd
Journal title:eLife, 2023-05, Vol.12
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ArticlesPeer ReviewedFull Text
Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection
Author / Creator:Garrett, Meghan E ; Galloway, Jared G ; Wolf, Caitlin ; Logue, Jennifer K ; Franko, Nicholas ; Chu, Helen Y ; Matsen, Frederick A ; Overbaugh, Julie M
Publisher:England: eLife Science Publications, Ltd
Journal title:eLife, 2022-01, Vol.11
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ArticlesPeer ReviewedFull Text
Using viral sequence diversity to estimate time of HIV infection in infants
Author / Creator:Russell, Magdalena L. ; Fish, Carolyn S. ; Drescher, Sara ; Cassidy, Noah A. J. ; Chanana, Pritha ; Benki-Nugent, Sarah ; Slyker, Jennifer ; Mbori-Ngacha, Dorothy ; Bosire, Rose ; Richardson, Barbra ; Wamalwa, Dalton ; Maleche-Obimbo, Elizabeth ; Overbaugh, Julie ; John-Stewart, Grace ; Matsen, Frederick A. ; Lehman, Dara A.
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2023-12, Vol.19 (12), p.e1011861
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Showing 1 to 20 of 39 results

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Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women

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Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage

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Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-Infection Estimation towards Enhanced Vaccine Efficacy Assessment

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Comparing T cell receptor repertoires using optimal transport

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Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses

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Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses

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Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques

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Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph

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PhyloSift: phylogenetic analysis of genomes and metagenomes

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Inference of B cell clonal families using heavy/light chain pairing information

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Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth

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Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

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Correction: Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison

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Population dynamics of rhesus macaques and associated foamy virus in Bangladesh

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Comparing T cell receptor repertoires using optimal transport Comparing T cell receptor repertoires using optimal transport

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Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity

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Deep generative models for T cell receptor protein sequences

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Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming

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Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection

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Using viral sequence diversity to estimate time of HIV infection in infants

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