Frederick A Matsen (Frederick A Matsen Iv)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 43

Top Topics

Induced Pluripotent Stem Cells

Top Venues

bioRxiv : the preprint server for biology

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Caleb R Carr, Katharine H D Crawford, Michael Murphy, Jared G Galloway, Hugh K Haddox, Frederick A Matsen, Kristian G Andersen, Neil P King, Jesse D Bloom
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. bioRxiv : the preprint server for biology (2024)
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A Matsen, Marc A Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics (Oxford, England) 40 (2) (2024)
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A Matsen, Marc A Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics (Oxford, England) 40 (2) (2024)
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A Matsen, Marc A Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics (Oxford, England) 40 (2) (2024)
Caleb R Carr, Katharine H D Crawford, Michael Murphy, Jared G Galloway, Hugh K Haddox, Frederick A Matsen, Kristian G Andersen, Neil P King, Jesse D Bloom
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. bioRxiv : the preprint server for biology (2024)
Caleb R Carr, Katharine H D Crawford, Michael Murphy, Jared G Galloway, Hugh K Haddox, Frederick A Matsen, Kristian G Andersen, Neil P King, Jesse D Bloom
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. bioRxiv : the preprint server for biology (2024)
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A Matsen, Marc A Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics (Oxford, England) 40 (2) (2024)
Caleb R Carr, Katharine H D Crawford, Michael Murphy, Jared G Galloway, Hugh K Haddox, Frederick A Matsen, Kristian G Andersen, Neil P King, Jesse D Bloom
Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex. bioRxiv : the preprint server for biology (2024)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Magdalena L Russell, Carolyn S Fish, Sara Drescher, Noah A J Cassidy, Pritha Chanana, Sarah Benki-Nugent, Jennifer Slyker, Dorothy Mbori-Ngacha, Rose Bosire, Barbra Richardson, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Julie Overbaugh, Grace John-Stewart, Frederick A Matsen, Caitlin I Stoddard
Using viral sequence diversity to estimate time of HIV infection in infants. PLoS pathogens 19 (12) (2023)
Hugh K Haddox, Jared G Galloway, Bernadeta Dadonaite, Jesse D Bloom, Frederick A Matsen, William S DeWitt
Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs. bioRxiv : the preprint server for biology (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Magdalena L Russell, Carolyn S Fish, Sara Drescher, Noah A J Cassidy, Pritha Chanana, Sarah Benki-Nugent, Jennifer Slyker, Dorothy Mbori-Ngacha, Rose Bosire, Barbra Richardson, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Julie Overbaugh, Grace John-Stewart, Frederick A Matsen, Caitlin I Stoddard
Using viral sequence diversity to estimate time of HIV infection in infants. PLoS pathogens 19 (12) (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Magdalena L Russell, Carolyn S Fish, Sara Drescher, Noah A J Cassidy, Pritha Chanana, Sarah Benki-Nugent, Jennifer Slyker, Dorothy Mbori-Ngacha, Rose Bosire, Barbra Richardson, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Julie Overbaugh, Grace John-Stewart, Frederick A Matsen, Caitlin I Stoddard
Using viral sequence diversity to estimate time of HIV infection in infants. PLoS pathogens 19 (12) (2023)
Magdalena L Russell, Carolyn S Fish, Sara Drescher, Noah A J Cassidy, Pritha Chanana, Sarah Benki-Nugent, Jennifer Slyker, Dorothy Mbori-Ngacha, Rose Bosire, Barbra Richardson, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Julie Overbaugh, Grace John-Stewart, Frederick A Matsen, Caitlin I Stoddard
Using viral sequence diversity to estimate time of HIV infection in infants. PLoS pathogens 19 (12) (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Caitlin I Stoddard, Kevin Sung, Zak A Yaffe, Haidyn Weight, Guillaume Beaudoin-Bussières, Jared G Galloway, Soren Gantt, Judith Adhiambo, Emily R Begnel, Ednah Ojee, Jennifer Slyker, Dalton Wamalwa, John Kinuthia, Andrés Finzi, Frederick A Matsen, Dara A Lehman, Julie M Overbaugh
Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers. Nature communications 14 (1) (2023)
Frances C Welsh, Rachel T Eguia, Juhye M Lee, Hugh K Haddox, Jared Galloway, Nguyen Van Vinh Chau, Andrea N Loes, John Huddleston, Timothy C Yu, Mai Quynh Le, Nguyen T D Nhat, Nguyen Thi Le Thanh, Alexander L Greninger, Helen Y Chu, Janet A Englund, Trevor Felix Bedford, Frederick A Matsen, Maciej F Boni, Jesse D Bloom
Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv : the preprint server for biology (2023)
Will Dumm, Mary Barker, William Howard-Snyder, William S DeWitt, Frederick A Matsen
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph. Journal of mathematical biology 87 (5) (2023)
Magdalena L Russell, Carolyn S Fish, Sara Drescher, Noah A J Cassidy, Pritha Chanana, Sarah Benki-Nugent, Jennifer Slyker, Dorothy Mbori-Ngacha, Rose Bosire, Barbra Richardson, Dalton Wamalwa, Elizabeth Maleche-Obimbo, Julie Overbaugh, Grace John-Stewart, Frederick A Matsen, Caitlin I Stoddard
Using viral sequence diversity to estimate time of HIV infection in infants. PLoS pathogens 19 (12) (2023)
Magdalena L Russell, Noah Simon, Philip G Bradley, Frederick A Matsen
Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming. eLife 12 (2023)
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, Philip G Bradley
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities. eLife 11 (2022)
Duncan K Ralph, Frederick A Matsen
Inference of B cell clonal families using heavy/light chain pairing information. PLoS computational biology 18 (11) (2022)
Caitlin I Stoddard, Kevin Sung, Ednah Ojee, Judith Adhiambo, Emily R Begnel, Jennifer Slyker, Soren Gantt, Frederick A Matsen, John Kinuthia, Dalton Wamalwa, Julie Overbaugh, Dara A Lehman
Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers. Viruses 14 (7) (2022)
Branden J Olson, Stefan A Schattgen, Paul Glyndwr Thomas, Philip Bradley, Frederick A Matsen
Comparing T cell receptor repertoires using optimal transport. PLoS computational biology 18 (12) (2022)
Meghan E Garrett, Jared G Galloway, Caitlin Wolf, Jennifer K Logue, Nicholas M Franko, Helen Y Chu, Frederick A Matsen, Julie M Overbaugh
Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection. eLife 11 (2022)
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, Julie M Overbaugh
Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies. eLife 10 (2021)
Mark D Pankau, Daniel B Reeves, Elias Harkins, Keshet Ronen, Walter Jaoko, Kishor Mandaliya, Susan M Graham, R Scott McClelland, Frederick A Matsen, Joshua T Schiffer, Julie Overbaugh, Caitlin I Stoddard
Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women. PLoS pathogens 16 (2) (2020)
Duncan K Ralph, Frederick A Matsen
Using B cell receptor lineage structures to predict affinity. PLoS computational biology 16 (11) (2020)
Amrit Dhar, Duncan K Ralph, Volodymyr M Minin, Frederick A Matsen
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis. PLoS computational biology 16 (8) (2020)
Julia Fukuyama, Branden J Olson, Frederick A Matsen
Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification. Journal of immunology (Baltimore, Md. : 1950) 205 (4) (2020)
Cassandra A Simonich, Laura E Doepker, Duncan Ralph, James A Williams, Amrit Dhar, Zak Yaffe, Lauren Gentles, Christopher T Small, Brian Oliver, Vladimir Vigdorovich, Vidya Mangala Prasad, Ruth Nduati, D Noah Sather, Kelly K Lee, Frederick A Matsen, Julie Overbaugh
Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage. Nature communications 10 (1) (2019)
Kristian Davidsen, Branden J Olson, William S DeWitt, Jean Feng, Elias Harkins, Philip G Bradley, Frederick A Matsen
Deep generative models for T cell receptor protein sequences. eLife 8 (2019)
Amrit Dhar, Kristian Davidsen, Frederick A Matsen, Volodymyr M Minin
Predicting B cell receptor substitution profiles using public repertoire data. PLoS computational biology 14 (10) (2018)
Corey T Watson, Frederick A Matsen, Katherine J L Jackson, Ali Bashir, Melissa Laird Smith, Jacob Glanville, Felix Breden, Steven H Kleinstein, Andrew M Collins, Christian E Busse
Comment on "A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data". Journal of immunology (Baltimore, Md. : 1950) 198 (9) (2018)
William S DeWitt, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen, Philip G Bradley
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity. eLife 7 (2018)
Alex Gavryushkin, Chris Whidden, Frederick A Matsen
The combinatorics of discrete time-trees: theory and open problems. Journal of mathematical biology 76 (5) (2017)
Sarah Cobey, Patrick Wilson, Frederick A Matsen
The evolution within us. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 370 (1676) (2016)
Duncan K Ralph, Frederick A Matsen
Likelihood-Based Inference of B Cell Clonal Families. PLoS computational biology 12 (10) (2016)
Connor O McCoy, Trevor Felix Bedford, Vladimir N Minin, Philip G Bradley, Harlan S Robins, Frederick A Matsen
Quantifying evolutionary constraints on B-cell affinity maturation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 370 (1676) (2016)