Frederick A. Matsen

Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 68 papers. Top paper: “Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection”.

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

eLife(2022)10.7554/elife.73490

N/A

1.2DataRank · unranked

31 citations

Jared G Galloway, Caitlin Wolf, Jennifer K Logue, Nicholas Franko, Helen Y Chu +3 more

Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities

eLife(2022)10.7554/elife.73475

N/A

1.0DataRank · unranked

26 citations

Aisha Souquette, David M Levine, Stefan A Schattgen, E Kaitlynn Allen, Guillermina Kuan +7 more

High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

Cell(2021)10.1016/j.cell.2021.04.045

N/A

0.581DataRank · unranked

47 citations

Jared Galloway, Helen Y. Chu, Hannah L. Itell, Caitlin I. Stoddard, Caitlin R. Wolf +6 more

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

Cell Host & Microbe(2024)10.1016/j.chom.2024.06.015

N/A

0.557DataRank · unranked

40 citations

Rachel Eguia, Juhye Lee, Hugh K. Haddox, Jared Galloway, Nguyen Van Vinh Chau +14 more

Deep mutational scanning of CYP2C19 in human cells reveals a substrate specificity-abundance tradeoff

Genetics(2024)10.1093/genetics/iyae156

N/A

0.433DataRank · unranked

12 citations

Katherine A. Sitko, Jared Galloway, Hugh K. Haddox, Aisha Haley Bianchi, Ajeya Dixon +13 more

Diversity and Function of Maternal HIV-1-Specific Antibodies at the Time of Vertical Transmission

Journal of Virology(2020)10.1128/jvi.01594-19

N/A

0.406DataRank · unranked

14 citations

Cassandra A. Simonich, Duncan Ralph, Mackenzie M. Shipley, Meghan Garrett, Theodore A. Gobillot +6 more

Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations

Systematic Biology(2024)10.1093/sysbio/syae019

N/A

0.345DataRank · unranked

9 citations

Andrew J. Holbrook, Jonathan E. Pekar, Itzue W. Caviedes-Solis, Frederick A. Matsen, Guy Baele +5 more

A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder

Molecular Biology and Evolution(2025)10.1093/molbev/msaf186

N/A

0.312DataRank · unranked

7 citations

Kevin Sung, Mackenzie M. Johnson, Will Dumm, David Rich, Tyler N. Starr +5 more

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection

eLife(2021)10.7554/elife.68110

N/A

0.292DataRank · unranked

6 citations

Vidya Mangala Prasad, Laura Doepker, Adam S. Dingens, Duncan Ralph, Elias Harkins +10 more

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

eLife(2023)10.7554/elife.85145

N/A

0.269DataRank · unranked

5 citations

Noah Simon, Philip Bradley, Frederick A. Matsen, Magdalena L Russell

Thrifty wide-context models of B cell receptor somatic hypermutation

eLife(2025)10.7554/elife.105471.1

N/A

0.269DataRank · unranked

5 citations

Mackenzie M. Johnson, Will Dumm, Noah Simon, Hugh K. Haddox, Julia Fukuyama +2 more

Passively Acquired Constant Region 5–Specific Antibodies Associated With Improved Survival in Infants Who Acquire Human Immunodeficiency Virus

Open Forum Infectious Diseases(2023)10.1093/ofid/ofad316

N/A

0.241DataRank · unranked

4 citations

Kevin Sung, Rose Bosire, Carey Farquhar, Dorothy Mbori Ngacha, Barbara Lohman‐Payne +5 more

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.07.631013

N/A

0.241DataRank · unranked

4 citations

Georg Angehrn, Luca Sesta, Chris Jennings-Shaffer, Seth D Temple, Jared Galloway +5 more

Thrifty wide-context models of B cell receptor somatic hypermutation

eLife(2025)10.7554/elife.105471

N/A

0.232DataRank · unranked

3 citations

Mackenzie M. Johnson, Will Dumm, Noah Simon, Hugh K. Haddox, Julia Fukuyama +2 more

Thrifty wide-context models of B cell receptor somatic hypermutation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.11.26.625407

N/A

0.165DataRank · unranked

2 citations

Mackenzie M. Johnson, Will Dumm, Noah Simon, Hugh K. Haddox, Julia Fukuyama +2 more

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions

arXiv (Cornell University)(2024)10.48550/arxiv.2408.05058

N/A

0.104DataRank · unranked

1 citations

Frederick A. Matsen, Marc A. Suchard, Cheng Zhang, Tianyu Xie

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

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010723

N/A

0DataRank · unranked

33 citations

Frederick A. Matsen, Duncan Ralph

Comparing T cell receptor repertoires using optimal transport

PLoS Computational Biology(2022)10.1371/journal.pcbi.1010681

N/A

0DataRank · unranked

9 citations

Stefan Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen, Branden J Olson

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

PLoS Pathogens(2022)10.1371/journal.ppat.1010155

N/A

0DataRank · unranked

11 citations

Kevin Sung, Meghan Garrett, Jared Galloway, Jesse H. Erasmus, Jennifer K. Logue +7 more

Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers

Viruses(2022)10.3390/v14071517

N/A

0DataRank · unranked

10 citations

Kevin Sung, Ednah Ojee, Judith Adhiambo, Emily R. Begnel, Jennifer A. Slyker +7 more

A biophysical model of viral escape from polyclonal antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.17.508366

N/A

0DataRank · unranked

3 citations

Zorian Thornton, William W. Hannon, William S. DeWitt, Caelan E. Radford, Frederick A. Matsen +2 more

Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.08.519635

N/A

0DataRank · unranked

0 citations

Noah Simon, Philip Bradley, Frederick A. Matsen, Magdalena L Russell

phippery: a software suite for PhIP-Seq data analysis

Bioinformatics(2023)10.1093/bioinformatics/btad583

N/A

0DataRank · unranked

12 citations

Kevin Sung, Samuel S. Minot, Meghan Garrett, Caitlin I. Stoddard, Alexandra C. Willcox +5 more

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

PLoS Pathogens(2023)10.1371/journal.ppat.1011722

N/A

0DataRank · unranked

14 citations

Lisa M. Levoir, Duncan Ralph, Laura Belmont, Maya Contreras, Catiana H. Cartwright-Acar +12 more

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

Journal of Mathematical Biology(2023)10.1007/s00285-023-02006-3

N/A

0DataRank · unranked

10 citations

Mary Barker, William Howard-Snyder, William S. DeWitt, Frederick A. Matsen, Will Dumm

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

PLoS Pathogens(2023)10.1371/journal.ppat.1011861

N/A

0DataRank · unranked

3 citations

Carolyn S. Fish, Sara Drescher, Noah A.J. Cassidy, Pritha Chanana, Sarah Benki‐Nugent +11 more

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm

Algorithms for Molecular Biology(2023)10.1186/s13015-023-00235-1

N/A

0DataRank · unranked

8 citations

Hassan Nasif, Chris Jennings-Shaffer, David H Rich, Anna Kooperberg, Mathieu Fourment +4 more

Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation

Genome Biology and Evolution(2023)10.1093/gbe/evad099

N/A

0DataRank · unranked

7 citations

Christiaan Swanepoel, Jared Galloway, Xiang Ji, Karthik Gangavarapu, Marc A. Suchard +2 more

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers

Nature Communications(2023)10.1038/s41467-023-40554-w

N/A

0DataRank · unranked

2 citations

Kevin Sung, Zak A. Yaffe, Haidyn Weight, Guillaume Beaudoin-Bussières, Jared Galloway +12 more

Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.31.551037

N/A

0DataRank · unranked

25 citations

Jared Galloway, Bernadeta Dadonaite, Jesse D. Bloom, Frederick A. Matsen, William S. DeWitt +1 more

Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.12.571235

N/A

0DataRank · unranked

13 citations

Rachel Eguia, Juhye Lee, Hugh K. Haddox, Jared Galloway, Nguyễn Văn Vĩnh Châu +14 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.09.536175

N/A

0DataRank · unranked

4 citations

Lisa M. Levoir, Duncan Ralph, Laura Belmont, Maya Contreras, Catiana H. Cartwright-Acar +12 more

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.06.527330

N/A

0DataRank · unranked

0 citations

Kevin Sung, Zak A. Yaffe, Haidyn Weight, Guillaume Beaudoin-Bussières, Jared Galloway +12 more

Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex

Immunity(2024)10.1016/j.immuni.2024.06.013

N/A

0DataRank · unranked

26 citations

Katharine H. D. Crawford, Michael Murphy, Jared Galloway, Hugh K. Haddox, Frederick A. Matsen +4 more

Many-core algorithms for high-dimensional gradients on phylogenetic trees

Bioinformatics(2024)10.1093/bioinformatics/btae030

N/A

0DataRank · unranked

8 citations

Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen +2 more

Phylogenetic Tree Instability After Taxon Addition: Empirical Frequency, Predictability, and Consequences For Online Inference

Systematic Biology(2024)10.1093/sysbio/syae059

N/A

0DataRank · unranked

1 citations

Mary Barker, Marc A. Suchard, Frederick A. Matsen, Lena Collienne

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.02.05.579020

N/A

0DataRank · unranked

2 citations

Katharine H. D. Crawford, Michael Murphy, Jared Galloway, Hugh K. Haddox, Frederick A. Matsen +4 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.24.590836

N/A

0DataRank · unranked

1 citations

Will Foreman, Michael B. Lilly, Viren A. Baharani, Delphine Depierreux, Vrasha Chohan +10 more

Torchtree: flexible phylogenetic model development and inference using PyTorch

arXiv (Cornell University)(2024)10.48550/arxiv.2406.18044

N/A

0DataRank · unranked

0 citations

Matthew Macaulay, Christiaan Swanepoel, Xiang Ji, Marc A. Suchard, Frederick A. Matsen +1 more

Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.16.618753

N/A

0DataRank · unranked

0 citations

Assya Trofimov, Philip Bradley, Frederick A. Matsen, Magdalena L Russell

The mutation rate of SARS-CoV-2 is highly variable between sites and is influenced by sequence context, genomic region, and RNA structure

Nucleic Acids Research(2025)10.1093/nar/gkaf503

N/A

0DataRank · unranked

13 citations

Georg Angehrn, Luca Sesta, Chris Jennings-Shaffer, Seth D Temple, Jared Galloway +6 more

Leveraging DAGs to improve context-sensitive and abundance-aware tree estimation

Philosophical Transactions of the Royal Society B Biological Sciences(2025)10.1098/rstb.2023.0315

N/A

0DataRank · unranked

6 citations

Duncan Ralph, William S. DeWitt, A. B. Vora, Tatsuya Araki, Gabriel D. Victora +2 more

Learning antibody sequence constraints from allelic inclusion

Cell Systems(2025)10.1016/j.cels.2025.101368

N/A

0DataRank · unranked

1 citations

Chloe Hsu, Thomas Mazumder, Kevin Sung, William S. DeWitt, Jennifer Listgarten +4 more

Finding high posterior density phylogenies by systematically extending a directed acyclic graph

Algorithms for Molecular Biology(2025)10.1186/s13015-025-00273-x

N/A

0DataRank · unranked

2 citations

David H Rich, Matthew Macaulay, Michael D. Karcher, Tanvi Ganapathy, Shosuke Kiami +5 more

torchtree : Flexible Phylogenetic Model Development and Inference Using PyTorch

Systematic Biology(2025)10.1093/sysbio/syaf047

N/A

0DataRank · unranked

1 citations

Matthew Macaulay, Christiaan Swanepoel, Xiang Ji, Marc A. Suchard, Frederick A. Matsen +1 more

Nucleotide context models outperform protein language models for predicting antibody affinity maturation

PLoS Computational Biology(2025)10.1371/journal.pcbi.1013758

N/A

0DataRank · unranked

1 citations

Kevin Sung, Hugh K. Haddox, A. B. Vora, Tatsuya Araki, Gabriel D. Victora +4 more

Biological causes and impacts of rugged tree landscapes in phylodynamic inference

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.06.10.657742

N/A

0DataRank · unranked

4 citations

Marius Brusselmans, Luiz Mariano Carvalho, Marc A. Suchard, Guy Baele, Frederick A. Matsen +1 more

Clonal interference and changing selective pressures shape the escape of SARS-CoV-2 from hundreds of antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.22.634135

N/A

0DataRank · unranked

0 citations

Omar Abdel Aziz, Jared Galloway, Javen Kent, C. M. Cooper, Jesse D. Bloom +2 more

Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination

Nucleic Acids Research(2025)10.1093/nar/gkaf250

N/A

0DataRank · unranked

0 citations

Assya Trofimov, Philip Bradley, Frederick A. Matsen, Magdalena L Russell

Thrifty wide-context models of B cell receptor somatic hypermutation

eLife(2025)10.7554/elife.105471.2

N/A

0DataRank · unranked

0 citations

Mackenzie M. Johnson, Will Dumm, Noah Simon, Hugh K. Haddox, Julia Fukuyama +2 more

The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support Estimation

IEEE Transactions on Computational Biology and Bioinformatics(2025)10.1109/tcbbio.2025.3595782

N/A

0DataRank · unranked

0 citations

Will Dumm, Mary Barker, Ognian Milanov, Claris Winston, David H Rich +3 more

Unifying phylogenetic traversal and deep learning to guide tree exploration

bioRxiv (Cold Spring Harbor Laboratory)(2026)10.64898/2026.01.14.699358

N/A

0DataRank · unranked

0 citations

Harry Richman, David H. Rich, Mary Barker, Chris Jennings-Shaffer, Frederick A. Matsen +1 more

Thrifty wide-context models of B cell receptor somatic hypermutation

eLife(2025)10.7554/elife.105471.3

N/A

0DataRank · unranked

0 citations

Mackenzie M. Johnson, Will Dumm, Noah Simon, Hugh K. Haddox, Julia Fukuyama +2 more

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

PLoS Pathogens(2020)10.1371/journal.ppat.1008286

N/A

0DataRank · unranked

60 citations

Daniel B. Reeves, Elias Harkins, Keshet Ronen, Walter Jaoko, Kishor Mandaliya +7 more

Using B cell receptor lineage structures to predict affinity

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008391

N/A

0DataRank · unranked

19 citations

Frederick A. Matsen, Duncan Ralph

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis

PLoS Computational Biology(2020)10.1371/journal.pcbi.1008030

N/A

0DataRank · unranked

25 citations

Duncan Ralph, Vladimir N. Minin, Frederick A. Matsen, Amrit Dhar

Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification

The Journal of Immunology(2020)10.4049/jimmunol.2000092

N/A

0DataRank · unranked

1 citations

Branden J Olson, Frederick A. Matsen, Julia Fukuyama

High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.16.385278

N/A

0DataRank · unranked

17 citations

Jared Galloway, Helen Y. Chu, Hannah L. Itell, Caitlin I. Stoddard, Caitlin R. Wolf +5 more

Using B cell receptor lineage structures to predict affinity

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.04.24.060194

N/A

0DataRank · unranked

3 citations

Frederick A. Matsen, Duncan Ralph

Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs

Cell Reports(2021)10.1016/j.celrep.2021.109164

N/A

0DataRank · unranked

58 citations

Jared Galloway, Helen Y. Chu, Mackenzie M. Shipley, Kevin Sung, Hannah L. Itell +9 more

Estimation of cell lineage trees by maximum-likelihood phylogenetics

The Annals of Applied Statistics(2021)10.1214/20-aoas1400

N/A

0DataRank · unranked

41 citations

William S. DeWitt, Aaron McKenna, Noah Simon, Amy D. Willis, Frederick A. Matsen +1 more

SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma

Microbiology Spectrum(2021)10.1128/spectrum.01298-21

N/A

0DataRank · unranked

26 citations

Haidyn Weight, Carolyn S. Fish, Jennifer K. Logue, Nicholas Franko, Caitlin R. Wolf +6 more

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies

eLife(2021)10.7554/elife.63444

N/A

0DataRank · unranked

13 citations

Sonja Danon, Elias Harkins, Duncan Ralph, Zak A. Yaffe, Meghan Garrett +11 more

Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein after infection and/or vaccination

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.05.463210

N/A

0DataRank · unranked

2 citations

Jared Galloway, Caitlin R. Wolf, Jennifer K. Logue, Nicholas Franko, Helen Y. Chu +3 more

Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.01.470697

N/A

0DataRank · unranked

2 citations

Kevin Sung, Meghan Garrett, Jared Galloway, Megan A. O’Connor, Jesse H. Erasmus +8 more

SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma

medRxiv(2021)10.1101/2021.08.02.21261504

N/A

0DataRank · unranked

1 citations

Haidyn Weight, Carolyn S. Fish, Jennifer K. Logue, Nicholas Franko, Caitlin R. Wolf +6 more

Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.15.435484

N/A

0DataRank · unranked

0 citations

Vidya Mangala Prasad, Laura Doepker, Adam S. Dingens, Duncan Ralph, Elias Harkins +10 more

Enabling inference for context-dependent models of mutation by bounding the propagation of dependency

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.12.15.472813

N/A

0DataRank · unranked

0 citations

Peter L. Ralph, Frederick A. Matsen