F. A. Matsen

12.7k total citations · 4 hit papers
237 papers, 7.8k citations indexed

About

F. A. Matsen is a scholar working on Atomic and Molecular Physics, and Optics, Molecular Biology and Physical and Theoretical Chemistry. According to data from OpenAlex, F. A. Matsen has authored 237 papers receiving a total of 7.8k indexed citations (citations by other indexed papers that have themselves been cited), including 80 papers in Atomic and Molecular Physics, and Optics, 59 papers in Molecular Biology and 42 papers in Physical and Theoretical Chemistry. Recurrent topics in F. A. Matsen's work include Advanced Chemical Physics Studies (62 papers), Genomics and Phylogenetic Studies (33 papers) and Atomic and Molecular Physics (24 papers). F. A. Matsen is often cited by papers focused on Advanced Chemical Physics Studies (62 papers), Genomics and Phylogenetic Studies (33 papers) and Atomic and Molecular Physics (24 papers). F. A. Matsen collaborates with scholars based in United States, South Africa and Kenya. F. A. Matsen's co-authors include Robin B. Kodner, E. Virginia Armbrust, Connor O. McCoy, Duncan Ralph, Jeremiah N. Silverman, James C. Browne, Steven N. Evans, E. E. Ferguson, Aaron E. Darling and Noah G. Hoffman and has published in prestigious journals such as Nature, Cell and Proceedings of the National Academy of Sciences.

In The Last Decade

F. A. Matsen

228 papers receiving 7.5k citations

Hit Papers

Molecular Symmetry and Spectroscopy 1979 2026 1994 2010 1979 2010 2012 2014 250 500 750
What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

  1. Molecular Symmetry and Spectroscopy
    1979 798 citations F. A. Matsen et al. profile →
  2. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    2010 732 citations F. A. Matsen et al. profile →
  3. Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
    2012 516 citations F. A. Matsen, Connor O. McCoy et al. profile →
  4. PhyloSift: phylogenetic analysis of genomes and metagenomes
    2014 442 citations Aaron E. Darling, F. A. Matsen et al. profile →

Peers

F. A. Matsen
Stuart Carter United Kingdom
Roger E. Bumgarner United States
Tsutomu Watanabe Japan
T. Schneider Switzerland
David M. Ferguson United States
A. Rahman United States
Anthony Nicholls Australia
Shigenori Tanaka Japan
Robert J. Woods United States
Sándor Suhai Germany
Stuart Carter United Kingdom
F. A. Matsen
Citations per year, relative to F. A. Matsen F. A. Matsen (= 1×) peers Stuart Carter

Countries citing papers authored by F. A. Matsen

Since Specialization
Citations

This map shows the geographic impact of F. A. Matsen's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by F. A. Matsen with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites F. A. Matsen more than expected).

Fields of papers citing papers by F. A. Matsen

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by F. A. Matsen. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by F. A. Matsen. The network helps show where F. A. Matsen may publish in the future.

Co-authorship network of co-authors of F. A. Matsen

This figure shows the co-authorship network connecting the top 25 collaborators of F. A. Matsen. A scholar is included among the top collaborators of F. A. Matsen based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with F. A. Matsen. F. A. Matsen is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Haddox, Hugh K., Jared Galloway, Angie S. Hinrichs, et al.. (2025). 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. 53(11). 3 indexed citations
2.
Simon, Noah, et al.. (2025). Thrifty wide-context models of B cell receptor somatic hypermutation. eLife. 14. 3 indexed citations
3.
Matsen, F. A., Tyler N. Starr, Yun S. Song, et al.. (2025). A Sitewise Model of Natural Selection on Individual Antibodies via a Transformer–Encoder. Molecular Biology and Evolution. 42(8).
4.
Pae, Juhee, William S. DeWitt, Juliana Bortolatto, et al.. (2025). Transient silencing of hypermutation preserves B cell affinity during clonal bursting. Nature. 641(8062). 486–494. 7 indexed citations
5.
Suchard, Marc A., et al.. (2024). Phylogenetic Tree Instability After Taxon Addition: Empirical Frequency, Predictability, and Consequences For Online Inference. Systematic Biology. 74(1). 101–111. 1 indexed citations
6.
Gangavarapu, Karthik, Xiang Ji, Guy Baele, et al.. (2024). Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinformatics. 40(2). 5 indexed citations
7.
Magee, Andrew F., Andrew J. Holbrook, Jonathan E. Pekar, et al.. (2024). Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations. Systematic Biology. 73(3). 562–578. 5 indexed citations
8.
DeWitt, William S., et al.. (2023). Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph. Journal of Mathematical Biology. 87(5). 75–75. 4 indexed citations
9.
Galloway, Jared, Samuel S. Minot, Meghan Garrett, et al.. (2023). phippery: a software suite for PhIP-Seq data analysis. Bioinformatics. 39(10). 6 indexed citations
10.
Fourment, Mathieu, Jared Galloway, Xiang Ji, et al.. (2023). Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation. Genome Biology and Evolution. 15(6). 5 indexed citations
11.
Yu, Timothy C., William W. Hannon, William S. DeWitt, et al.. (2022). A biophysical model of viral escape from polyclonal antibodies. Virus Evolution. 8(2). veac110–veac110. 19 indexed citations
12.
Stoddard, Caitlin I., Jared Galloway, Helen Y. Chu, et al.. (2021). Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs. Cell Reports. 35(8). 109164–109164. 34 indexed citations
13.
Deforche, Koen, Pieter Libin, Alexei J. Drummond, et al.. (2019). SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination. Virus Evolution. 5(1). vez003–vez003. 18 indexed citations
14.
Lees, William, Christian E. Busse, Martin Corcoran, et al.. (2019). OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Research. 48(D1). D964–D970. 39 indexed citations
15.
Zhang, Cheng & F. A. Matsen. (2018). Generalizing Tree Probability Estimation via Bayesian Networks. Neural Information Processing Systems. 31. 1444–1453. 1 indexed citations
16.
Zhang, Cheng & F. A. Matsen. (2018). Variational Bayesian Phylogenetic Inference. International Conference on Learning Representations. 7 indexed citations
17.
Fourment, Mathieu, et al.. (2017). Effective Online Bayesian Phylogenetics via Sequential Monte Carlo with Guided Proposals. Systematic Biology. 67(3). 490–502. 22 indexed citations
18.
Gavryushkin, Alex, Chris Whidden, & F. A. Matsen. (2017). The combinatorics of discrete time-trees: theory and open problems. Journal of Mathematical Biology. 76(5). 1101–1121. 7 indexed citations
19.
Matsen, F. A., et al.. (2017). Probabilistic path Hamiltonian Monte Carlo. International Conference on Machine Learning. 1009–1018. 6 indexed citations
20.
Warren, Edus H., F. A. Matsen, & Jeffrey Chou. (2013). High-throughput sequencing of B- and T-lymphocyte antigen receptors in hematology. Blood. 122(1). 19–22. 19 indexed citations

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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