Note that searching for "Frederick Matsen" via search engines is complicated by Erick's father and his grandfather both being scientists and using the same name.

Deep mutational scanning of CYP2C19 reveals a substrate specificity-abundance tradeoff
Boyle, Sitko, Galloway, Haddox, Bianchi, Dixon, Thomson, Garge, Rettie, Rubin, Geck, Gillam, DeWitt, Matsen, and Fowler
bioRxiv, 2023.
Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs
Haddox, Galloway, Dadonaite, Bloom, IV, and DeWitt
bioRxiv, 2023.
Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
Dumm, Barker, Howard-Snyder, DeWitt III, and Matsen IV
J. Math. Biol., 2023.
phippery: a software suite for PhIP-Seq data analysis
Galloway, Sung, Minot, Garrett, Stoddard, Willcox, Yaffe, Yucha, Overbaugh, and Matsen
Bioinformatics, 2023.
Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses
Lubow, Levoir, Ralph, Belmont, Contreras, Cartwright-Acar, Kikawa, Kannan, Davidson, Duran, Rebellon-Sanchez, Sanz, Rosso, Doranz, Einav, Matsen IV, and Goo
PLoS Pathog., 2023.
Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers
Stoddard, Sung, Yaffe, Weight, Beaudoin-Bussi{\`e}res, Galloway, Gantt, Adhiambo, Begnel, Ojee, Slyker, Wamalwa, Kinuthia, Finzi, Matsen, Lehman, and Overbaugh
Nat. Commun., 2023.
Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming
Russell, Simon, Bradley, and Matsen
Elife, 2023.
Automatic Differentiation is no Panacea for Phylogenetic Gradient Computation
Fourment, Swanepoel, Galloway, Ji, Gangavarapu, Suchard, and Matsen
Genome Biol. Evol., 2023.
Reconstruction of a Polyclonal ADCC Antibody Repertoire from an HIV-1 Non-Transmitting Mother
Yaffe, Ding, Sung, Chohan, Marchitto, Doepker, Ralph, Nduati, Matsen, Finzi, and Overbaugh
iScience, 2023.
TreeFlow: probabilistic programming and automatic differentiation for phylogenetics
Swanepoel, Fourment, Ji, Nasif, Suchard, Matsen, and Drummond
arXiv, 2022.
A biophysical model of viral escape from polyclonal antibodies
Yu, Thornton, Hannon, DeWitt, Radford, Matsen, and Bloom
Virus Evol, 2022.
Comparing T cell receptor repertoires using optimal transport
Olson, Schattgen, Thomas, Bradley, and Matsen
PLoS Comput. Biol., 2022.
Inference of B cell clonal families using heavy/light chain pairing information
Ralph and Matsen
PLoS Comput. Biol., 2022.
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency
Matsen IV and Ralph
J. Comput. Biol., 2022.
Distinct Antibody Responses to Endemic Coronaviruses Pre- and Post-SARS-CoV-2 Infection in Kenyan Infants and Mothers
Stoddard, Sung, Ojee, Adhiambo, Begnel, Slyker, Gantt, Matsen, Kinuthia, Wamalwa, Overbaugh, and Lehman
Viruses, 2022.
Combining genotypes and T cell receptor distributions to infer genetic loci determining V(D)J recombination probabilities
Russell, Souquette, Levine, Schattgen, Allen, Kuan, Simon, Balmaseda, Gordon, Thomas, Matsen, and Bradley
Elife, 2022.
Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques
Willcox, Sung, Garrett, Galloway, Erasmus, Logue, Hawman, Chu, Hasenkrug, Fuller, Matsen, and Overbaugh
PLoS Pathog., 2022.
Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection
Garrett, Galloway, Wolf, Logue, Franko, Chu, Matsen, and Overbaugh
Elife, 2022.
How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
Magee, Karcher, Matsen, and Minin
arXiv, 2021.
Variational Bayesian Supertrees
Karcher, Zhang, and Matsen
arXiv, 2021.
SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma
Itell, Weight, Fish, Logue, Franko, Wolf, McCulloch, Galloway, Matsen, Chu, and Overbaugh
Microbiol Spectr, 2021.
Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection
Shipley, Mangala Prasad, Doepker, Dingens, Ralph, Harkins, Dhar, Arenz, Chohan, Weight, Mandaliya, Bloom, Matsen, Lee, and Overbaugh
Elife, 2021.
Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies
Doepker, Danon, Harkins, Ralph, Yaffe, Garrett, Dhar, Wagner, Stumpf, Arenz, Williams, Jaoko, Mandaliya, Lee, Matsen, and Overbaugh
Elife, 2021.
High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Garrett, Galloway, Chu, Itell, Stoddard, Wolf, Logue, McDonald, Weight, Matsen, and Overbaugh
Cell, 2021.
Epitope profiling reveals binding signatures of SARS-CoV-2 immune response in natural infection and cross-reactivity with endemic human CoVs
Stoddard, Galloway, Chu, Shipley, Sung, Itell, Wolf, Logue, Magedson, Garrett, Crawford, Laserson, Matsen, and Overbaugh
Cell Rep., 2021.
Estimation of cell lineage trees by maximum-likelihood phylogenetics
Feng, DeWitt, McKenna, Simon, Willis, and Matsen
Annals of Applied Statistics, 2021.
Dynamics of HIV DNA reservoir seeding in a cohort of superinfected Kenyan women
Pankau, Reeves, Harkins, Ronen, Jaoko, Mandaliya, Graham, McClelland, Matsen, Schiffer, Overbaugh, and Lehman
PLoS Pathog., 2020.
Using B cell receptor lineage structures to predict affinity
Ralph and Matsen
PLoS Comput. Biol., 2020.
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis
Dhar, Ralph, Minin, and Matsen IV
PLoS Comput. Biol., 2020.
OGRDB: a reference database of inferred immune receptor genes
Lees, Busse, Corcoran, Ohlin, Scheepers, Matsen, Yaari, Watson, {AIRR Community}, Collins, and Shepherd
Nucleic Acids Res., 2020.
Nonbifurcating Phylogenetic Tree Inference via the Adaptive LASSO
Zhang, Dinh, and Matsen
J. Am. Stat. Assoc., 2020.
Lack of Evidence for a Substantial Rate of Templated Mutagenesis in B Cell Diversification
Fukuyama, Olson, and Matsen
J. Immunol., 2020.
Diversity and function of maternal HIV-1-specific antibodies at the time of vertical transmission
Doepker, Simonich, Ralph, Shipley, Garrett, Gobillot, Vigdorovich, Sather, Nduati, Matsen, and Overbaugh
J. Virol., 2020.
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Whidden, Claywell, Fisher, Magee, Fourment, and Matsen
Syst. Biol., 2020.
19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology
Fourment, Magee, Whidden, Bilge, Matsen, and Minin
Syst. Biol., 2020.
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
Ho, Dinh, Matsen, and Suchard
J. Math. Biol., 2020.
Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage
Simonich, Doepker, Ralph, Williams, Dhar, Yaffe, Gentles, Small, Oliver, Vigdorovich, Mangala Prasad, Nduati, Sather, Lee, Matsen IV, and Overbaugh
Nat. Commun., 2019.
Joint maximum likelihood of phylogeny and ancestral states is not consistent
Shaw, Dinh, and Matsen IV
Mol. Biol. Evol., 2019.
Deep generative models for T cell receptor protein sequences
Davidsen, Olson, DeWitt, Feng, Harkins, Bradley, and Matsen
Elife, 2019.
Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data
Ralph and Matsen
PLoS Comput. Biol., 2019.
Survival analysis of DNA mutation motifs with penalized proportional hazards
Feng, Shaw, Minin, Simon, and Matsen
Ann. Appl. Stat., 2019.
Variational Bayesian Phylogenetic Inference
Zhang and Matsen
International Conference on Learning Representations ({ICLR}), 2019.
Generalizing Tree Probability Estimation via Bayesian Networks
Zhang and Matsen IV
Advances in Neural Information Processing Systems 31, Curran Associates, Inc., 2018.
Predicting B cell receptor substitution profiles using public repertoire data
Dhar, Davidsen, Matsen, and Minin
PLoS Comput. Biol., 2018.
Benchmarking Tree and Ancestral Sequence Inference for B Cell Receptor Sequences
Davidsen and Matsen
Front. Immunol., 2018.
Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity
DeWitt, Smith, Schoch, Hansen, Matsen, and Bradley
Elife, 2018.
The Bayesian optimist's guide to adaptive immune receptor repertoire analysis
Olson and Matsen IV
Immunol. Rev., 2018.
Consistency and convergence rate of phylogenetic inference via regularization
Dinh, Ho, Suchard, and Matsen IV
Ann. Stat., 2018.
Using genotype abundance to improve phylogenetic inference
DeWitt, Mesin, Victora, Minin, and Matsen IV
Mol. Biol. Evol., 2018.
Tanglegrams: A Reduction Tool for Mathematical Phylogenetics
Matsen IV, Billey, Kas, and Konvalinka
IEEE/ACM Trans. Comput. Biol. Bioinform., 2018.
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees
Whidden and Matsen IV
2018 Proceedings of the Fifteenth Workshop on Analytic Algorithmics and Combinatorics ({ANALCO}), Society for Industrial and Applied Mathematics, 2018.
A Surrogate Function for One-Dimensional Phylogenetic Likelihoods
Claywell, Dinh, Fourment, McCoy, and Matsen IV
Mol. Biol. Evol., 2018.
Effective online Bayesian phylogenetics via Sequential Monte Carlo with guided proposals
Fourment, Claywell, Dinh, McCoy, Matsen IV, and Darling
Syst. Biol., 2017.
Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo
Dinh, Darling, and Matsen IV
Syst. Biol., 2017.
Ricci--Ollivier curvature of the rooted phylogenetic subtree--prune--regraft graph
Whidden and Matsen IV
Theor. Comput. Sci., 2017.
Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data
Breden, Luning Prak, Peters, Rubelt, Schramm, Busse, Vander Heiden, Christley, Bukhari, Thorogood, Matsen IV, Wine, Laserson, Klatzmann, Douek, Lefranc, Collins, Bubela, Kleinstein, Watson, Cowell, Scott, and Kepler
Front. Immunol., 2017.
Comment on ``A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data''
Watson, Matsen IV, Jackson, Bashir, Smith, Glanville, Breden, Kleinstein, Collins, and Busse
The Journal of Immunology, 2017.
The combinatorics of discrete time-trees: theory and open problems
Gavryushkin, Whidden, and Matsen IV
J. Math. Biol., 2017.
Probabilistic Path Hamiltonian Monte Carlo
Dinh, Bilge, Zhang, and Matsen IV
International Conference on Machine Learning, PMLR, 2017.
The shape of the one-dimensional phylogenetic likelihood function
Dinh and Matsen IV
Ann. Appl. Probab., 2017.
On the enumeration of tanglegrams and tangled chains
Billey, Konvalinka, and Matsen IV
J. Combin. Theory Ser. A, 2017.
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance
Whidden and Matsen IV
arXiv, 2016.
Likelihood-Based Inference of B Cell Clonal Families
Ralph and Matsen IV
PLoS Comput. Biol., 2016.
Preexposure prophylaxis-selected drug resistance decays rapidly after drug cessation
Weis, Baeten, McCoy, Warth, Donnell, Thomas, Hendrix, Marzinke, Mugo, Matsen IV, Celum, Lehman, and {for Partners PrEP Study Team}
AIDS, 2016.
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Ralph and Matsen IV
PLOS Comput. Biol., 2016.
Calculating the Unrooted Subtree Prune-and-Regraft Distance
Whidden and Matsen IV
arXiv, 2015.
Quantifying evolutionary constraints on B-cell affinity maturation
McCoy, Bedford, Minin, Bradley, Robins, and Matsen IV
Philos. Trans. R. Soc. Lond. B Biol. Sci., 2015.
The evolution within us
Cobey, Wilson, and Matsen IV
Philos. Trans. R. Soc. Lond. B Biol. Sci., 2015.
Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett's Esophagus Cohort
Gall, Fero, McCoy, Claywell, Sanchez, Blount, Li, Vaughan, Matsen, Reid, and Salama
PLoS One, 2015.
Quantifying MCMC exploration of phylogenetic tree space
Whidden and Matsen IV
Systematic Biology, 2015.
Risk of Drug Resistance Among Persons Acquiring HIV Within a Randomized Clinical Trial of Single- or Dual-Agent Preexposure Prophylaxis
Lehman, Baeten, McCoy, Weis, Peterson, Mbara, Donnell, Thomas, Hendrix, Marzinke, Frenkel, Ndase, Mugo, Celum, Overbaugh, Matsen, and {The Partners PrEP study team}
J. Infect. Dis., 2015.
Phylogenetics and the human microbiome
Matsen IV
Syst. Biol. (invited review), 2015.
Computational Tools for Taxonomic Assignment
Hoffman and Matsen
Encyclopedia of Metagenomics, Springer New York, 2014.
PhyloSift: phylogenetic analysis of genomes and metagenomes
Darling, Jospin, Lowe, Matsen IV, Bik, and Eisen
PeerJ, 2014.
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Matsen IV, Small, Soliven, Engel, Feeroz, Wang, Craig, Hasan, Emerman, Linial, and Jones-Engel
PLoS Comput. Biol., 2014.
Simian Foamy Virus Infection of Rhesus Macaques in Bangladesh: Relationship of latent proviruses and transcriptionally active viruses
Soliven, Wang, Small, Feeroz, Lee, Craig, Hasan, Engel, Jones-Engel, Matsen, and Linial
Journal of virology, 2013.
Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection
Jones-Engel, Engel, Small, Soliven, Feeroz, Wang, Hasan, Oh, Alam, Craig, Jackson, IV, and Linial
Emerging Microbes and Infections, 2013.
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
McCoy and Matsen
PeerJ, 2013.
HIV-1 Superinfection Occurs Less Frequently than Initial Infection in a Cohort of High-Risk Kenyan Women
Ronen, McCoy, Matsen, Boyd, Emery, Odem-Davis, Jaoko, Mandaliya, McClelland, Richardson, and Overbaugh
PLOS Pathogens, 2013.
Gene loss and adaptation to hominoids underlie the ancient origin of HIV-1
Etienne, Hahn, Sharp, Matsen, and Emerman
Cell Host \& Microbe, 2013.
High-throughput sequencing of B-and T-lymphocyte antigen receptors in hematology
Warren, Matsen, and Chou
Blood, 2013.
Population Dynamics of Rhesus Macaques and Associated Foamy Virus in Bangladesh
Feeroz, Soliven, Small, Engel, Pacheco-Delgado, Yee, Wang, Hasan, Oh, Levine, Alam, Craig, Jackson, Lee, Barry, Lerche, Escalante, Matsen, Linial, and Jones-Engel
Emerging Microbes and Infections, 2013.
The mean and variance of phylogenetic diversity under rarefaction
Nipperess and Matsen
Methods in Ecology and Evolution, 2013.
Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
Salipante, Sengupta, Rosenthal, Costa, Spangler, Sims, Jacobs, Miller, Hoogestraat, Cookson, McCoy, Matsen, Shendure, Lee, Harkins, and Hoffman
PLOS ONE, 2013.
Minimizing the average distance to a closest leaf in a phylogenetic tree
Matsen, Gallagher, and McCoy
Systematic Biology, 2013.
nestly--- a framework for running software with nested parameter choices and aggregating results
Matsen, Gallagher, and McCoy
Bioinformatics, 2013.
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
Matsen and Evans
PLOS ONE, 2012.
Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family
Levine, McCoy, Vermaak, Lee, Hiatt, Matsen, and Malik
PLOS Genetics, 2012.
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria
Srinivasan, Hoffman, Morgan, Matsen, Fiedler, Hall, Ross, McCoy, Bumgarner, Marrazzo, and Fredricks
PLOS ONE, 2012.
Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment.
Lehman, Wamalwa, McCoy, Matsen, Langat, Chohan, Benki-Nugent, Custers-Allen, Bushman, John-Stewart, and Overbaugh
Journal of Acquired Immune Deficiency Syndromes, 2012.
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
Evans and Matsen
Journal of the Royal Statistical Society (B), 2012.
A format for phylogenetic placements
Matsen, Hoffman, Gallagher, and Stamatakis
PLOS ONE, 2012.
The ability of primate lentiviruses to degrade the monocyte restriction factor SAMHD1 preceded the birth of the viral accessory protein Vpx
Lim, Fregoso, McCoy, Matsen, Malik, and Emerman
Cell Host and Microbe, 2012.
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
Matsen and Gallagher
Algorithms for Molecular Biology, 2012.
Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials
Matsen and Evans
Algorithms for Molecular Biology, 2012.
Polyhedral geometry of phylogenetic rogue taxa
Cueto and Matsen
Bulletin of Mathematical Biology, 2011.
constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints
Journal of Computational Biology, 2010.
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Matsen, Kodner, and Armbrust
BMC Bioinformatics, 2010.
Fourier transform inequalities for phylogenetic trees
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2009.
A method for investigating relative timing information on phylogenetic trees
Ford, Matsen, and Stadler
Systematic Biology, 2009.
To what extent does genealogical ancestry imply genetic ancestry?
Matsen and Evans
Theoretical Population Biology, 2008.
Mixed-up trees: the structure of phylogenetic mixtures
Matsen, Mossel, and Steel
Bulletin of Mathematical Biology, 2008.
Optimization over a class of tree shape statistics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2007.
Phylogenetic mixtures on a single tree can mimic a tree of another topology
Matsen and Steel
Systematic Biology, 2007.
The Bayesian ``star paradox'' persists for long finite sequences
Steel and Matsen
Molecular Biology and Evolution, 2007.
Convergence to the island-model coalescent process in populations with restricted migration
Matsen and Wakeley
Genetics, 2006.
A geometric approach to tree shape statistics
Systematic Biology, 2006.
Win--stay, lose--shift in language learning from peers
Matsen and Nowak
Proceedings of the National Academy of Sciences of the United States of America, 2004.