Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth by Connor O. McCoy, Frederick A. Matsen IV

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Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming by Magdalena L Russell, Noah Simon, Philip Bradley, Frederick A Matsen IV

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Comparing T cell receptor repertoires using optimal transport. by Branden J Olson, Stefan A Schattgen, Paul G Thomas, Philip Bradley, Frederick A Matsen Iv

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Comparing T cell receptor repertoires using optimal transport by Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV

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PhyloSift: phylogenetic analysis of genomes and metagenomes by Aaron E. Darling, Guillaume Jospin, Eric Lowe, Frederick A. Matsen IV, Holly M. Bik, Jonathan A. Eisen

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Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV, Philip Bradley

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Deep generative models for T cell receptor protein sequences by Kristian Davidsen, Branden J Olson, William S DeWitt III, Jean Feng, Elias Harkins, Philip Bradley, Frederick A Matsen IV

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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 by Meghan E Garrett, Jared G Galloway, Caitlin Wolf, Jennifer K Logue, Nicholas Franko, Helen Y Chu, Frederick A Matsen IV, Julie M Overbaugh

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Reconstruction of a polyclonal ADCC antibody repertoire from an HIV-1 non-transmitting mother by Zak A. Yaffe, Shilei Ding, Kevin Sung, Vrasha Chohan, Lorie Marchitto, Laura Doepker, Duncan Ralph, Ruth Nduati, Frederick A. Matsen, IV, Andrés Finzi, Julie Overbaugh

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Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities by Magdalena L Russell, Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan, Noah Simon, Angel Balmaseda, Aubree Gordon, Paul G Thomas, Frederick A Matsen IV, Philip Bradley

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Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women. by Mark D Pankau, Daniel B Reeves, Elias Harkins, Keshet Ronen, Walter Jaoko, Kishor Mandaliya, Susan M Graham, R Scott McClelland, Frederick A Matsen Iv, Joshua T Schiffer, Julie Overbaugh, Dara A Lehman

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Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques. by Alexandra C Willcox, Kevin Sung, Meghan E Garrett, Jared G Galloway, Jesse H Erasmus, Jennifer K Logue, David W Hawman, Helen Y Chu, Kim J Hasenkrug, Deborah H Fuller, Frederick A Matsen Iv, Julie Overbaugh

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Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses. by Felicitas Ruiz, William B Foreman, Michelle Lilly, Viren A Baharani, Delphine M Depierreux, Vrasha Chohan, Ashley L Taylor, Jamie Guenthoer, Duncan Ralph, Frederick A Matsen Iv, Helen Y Chu, Paul D Bieniasz, Marceline Côté, Tyler N Starr, Julie Overbaugh

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Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies by Laura E Doepker, Sonja Danon, Elias Harkins, Duncan K Ralph, Zak Yaffe, Meghan E Garrett, Amrit Dhar, Cassia Wagner, Megan M Stumpf, Dana Arenz, James A Williams, Walter Jaoko, Kishor Mandaliya, Kelly K Lee, Frederick A Matsen IV, Julie M Overbaugh

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Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses. by Jay Lubow, Lisa M Levoir, Duncan K Ralph, Laura Belmont, Maya Contreras, Catiana H Cartwright-Acar, Caroline Kikawa, Shruthi Kannan, Edgar Davidson, Veronica Duran, David E Rebellon-Sanchez, Ana M Sanz, Fernando Rosso, Benjamin J Doranz, Shirit Einav, Frederick A Matsen Iv, Leslie Goo

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