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.

Probabilistic Path Hamiltonian Monte Carlo
Dinh, Vu, Bilge, Arman, Zhang, Cheng, and Matsen, IV, Frederick A
arXiv, 2017.
On the enumeration of tanglegrams and tangled chains
Billey, Sara C, Konvalinka, Matja{\v z}, and Matsen, IV, Frederick A
J. Combin. Theory Ser. A, 2017.
The combinatorics of discrete time-trees: theory and open problems
Gavryushkin, Alex, Whidden, Chris, and Matsen, Frederick
bioRxiv, 2016.
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance
Whidden, Chris and Matsen, IV, Frederick A
arXiv, 2016.
Online Bayesian phylogenetic inference: theoretical foundations via Sequential Monte Carlo
Dinh, Vu, Darling, Aaron E, and Matsen, IV, Frederick A
arXiv; submitted to Systematic Biology, 2016.
Consistency and convergence rate of phylogenetic inference via regularization
Dinh, Vu, Ho, Lam Si Tung, Suchard, Marc A, and Matsen IV, Frederick A
arXiv; accepted to Annals of Statistics, 2016.
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees
Whidden, Chris and Matsen IV, Frederick A
arXiv, 2016.
Likelihood-Based Inference of B Cell Clonal Families
Ralph, Duncan K and Matsen, IV, Frederick A
PLoS Comput. Biol., 2016.
Tanglegrams: a Reduction Tool for Mathematical Phylogenetics
Matsen, F, Billey, S, Kas, A, and Konvalinka, M
IEEE/ACM Trans. Comput. Biol. Bioinform., 2016.
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph
Whidden, Chris and Matsen IV, Frederick A
2016 Proceedings of the Thirteenth Workshop on Analytic Algorithmics and Combinatorics ({ANALCO}), SIAM, 2016.
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Ralph, Duncan K and Matsen IV, Frederick A
PLOS Comput. Biol., 2016.
Calculating the Unrooted Subtree Prune-and-Regraft Distance
Whidden, Chris and Matsen IV, Frederick A
arXiv, 2015.
The shape of the one-dimensional phylogenetic likelihood function
Dinh, Vu and Matsen IV, Frederick A
Under revision, Annals of Applied Probability, 2015.
Quantifying evolutionary constraints on B-cell affinity maturation
McCoy, Connor O, Bedford, Trevor, Minin, Vladimir N, Bradley, Philip, Robins, Harlan, and Matsen IV, Frederick A
Philos. Trans. R. Soc. Lond. B Biol. Sci., 2015.
The evolution within us
Cobey, Sarah, Wilson, Patrick, and Matsen IV, Frederick A
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, Alevtina, Fero, Jutta, McCoy, Connor, Claywell, Brian C, Sanchez, Carissa A, Blount, Patricia L, Li, Xiaohong, Vaughan, Thomas L, Matsen, Frederick A, Reid, Brian J, and Salama, Nina R
PLoS One, 2015.
Quantifying MCMC exploration of phylogenetic tree space
Whidden, Chris and Matsen IV, Frederick A
Systematic Biology, 2015.
Risk of Drug Resistance Among Persons Acquiring HIV Within a Randomized Clinical Trial of Single- or Dual-Agent Preexposure Prophylaxis
Lehman, Dara A, Baeten, Jared M, McCoy, Connor O, Weis, Julie F, Peterson, Dylan, Mbara, Gerald, Donnell, Deborah, Thomas, Katherine K, Hendrix, Craig W, Marzinke, Mark A, Frenkel, Lisa, Ndase, Patrick, Mugo, Nelly R, Celum, Connie, Overbaugh, Julie, Matsen, Frederick A, and {The Partners PrEP study team}
J. Infect. Dis., 2015.
Phylogenetics and the human microbiome
Matsen IV, Frederick A
Syst. Biol. (invited review), 2015.
Computational Tools for Taxonomic Assignment
Hoffman, Noah G and Matsen, Frederick A
Encyclopedia of Metagenomics, Springer New York, 2014.
PhyloSift: phylogenetic analysis of genomes and metagenomes
Darling, Aaron E, Jospin, Guillaume, Lowe, Eric, Matsen IV, Frederick A, Bik, Holly M, and Eisen, Jonathan A
PeerJ, 2014.
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Matsen IV, Frederick A, Small, Christopher T, Soliven, Khanh, Engel, Gregory A, Feeroz, Mostafa M, Wang, Xiaoxing, Craig, Karen L, Hasan, M Kamrul, Emerman, Michael, Linial, Maxine L, and Jones-Engel, Lisa
PLoS Comput. Biol., 2014.
Simian Foamy Virus Infection of Rhesus Macaques in Bangladesh: Relationship of latent proviruses and transcriptionally active viruses
Soliven, Khanh, Wang, Xiaoxing, Small, Christopher T, Feeroz, Mostafa M, Lee, Eun-Gyung, Craig, Karen L, Hasan, Kamrul, Engel, Gregory A, Jones-Engel, Lisa, Matsen, Frederick A, and Linial, Maxine L.
Journal of virology, 2013.
Zoonotic simian foamy virus in Bangladesh reflects diverse patterns of transmission and co-infection
Jones-Engel, L., Engel, G., Small, C., Soliven, K., Feeroz, M., Wang, X., Hasan, M., Oh, G., Alam, S. M. R., Craig, K., Jackson, D., IV, F. Matsen, and Linial, M. L.
Emerging Microbes and Infections, 2013.
Abundance-weighted phylogenetic diversity measures distinguish microbial community states and are robust to sampling depth
McCoy, C.O. and Matsen, F.A.
PeerJ, 2013.
HIV-1 Superinfection Occurs Less Frequently than Initial Infection in a Cohort of High-Risk Kenyan Women
Ronen, K., McCoy, C. O., Matsen, F. A., Boyd, D. F., Emery, S., Odem-Davis, K., Jaoko, W., Mandaliya, K., McClelland, R. S., Richardson, B. A., and Overbaugh, J.
PLOS Pathogens, 2013.
Gene loss and adaptation to hominoids underlie the ancient origin of HIV-1
Etienne, L., Hahn, B.H., Sharp, P.M., Matsen, F.A., and Emerman, M.
Cell Host \& Microbe, 2013.
High-throughput sequencing of B-and T-lymphocyte antigen receptors in hematology
Warren, E. H., Matsen, F.A., and Chou, J.
Blood, 2013.
Population Dynamics of Rhesus Macaques and Associated Foamy Virus in Bangladesh
Feeroz, M.M., Soliven, K., Small, C.T., Engel, G.A., Pacheco-Delgado, M.A., Yee, J.L., Wang, X., Hasan, M. Kamrul, Oh, G., Levine, K.L., Alam, S.M.R., Craig, K. L., Jackson, D.L., Lee, E., Barry, P.A., Lerche, N.W., Escalante, A.A., Matsen, F.A., Linial, M.L., and Jones-Engel, L.
Emerging Microbes and Infections, 2013.
The mean and variance of phylogenetic diversity under rarefaction
Nipperess, D.A. and Matsen, F.A.
Methods in Ecology and Evolution, 2013.
Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections
Salipante, S. J., Sengupta, D. J., Rosenthal, C., Costa, G., Spangler, J., Sims, E. H., Jacobs, M. A., Miller, S. I., Hoogestraat, D. R., Cookson, B. T., McCoy, C. O., Matsen, F. A., Shendure, J., Lee, C. C., Harkins, T. T., and Hoffman, N. G.
PLOS ONE, 2013.
Minimizing the average distance to a closest leaf in a phylogenetic tree
Matsen, F.A., Gallagher, A., and McCoy, C.
Systematic Biology, 2013.
nestly--- a framework for running software with nested parameter choices and aggregating results
Matsen, F.A., Gallagher, A., and McCoy, C.
Bioinformatics, 2013.
Edge principal components and squash clustering: using the special structure of phylogenetic placement data for sample comparison
Matsen, F.A. and Evans, S.N.
PLOS ONE, 2012.
Phylogenomic Analysis Reveals Dynamic Evolutionary History of the Drosophila Heterochromatin Protein 1 (HP1) Gene Family
Levine, M.T., McCoy, C., Vermaak, D., Lee, Y.C.G., Hiatt, M.A., Matsen, F.A., and Malik, H.S.
PLOS Genetics, 2012.
Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria
Srinivasan, S., Hoffman, N.G., Morgan, M.T., Matsen, F.A., Fiedler, T.L., Hall, R.W., Ross, F.J., McCoy, C.O., Bumgarner, R., Marrazzo, J.M., and Fredricks, D.N.
PLOS ONE, 2012.
Low-frequency nevirapine resistance at multiple sites may predict treatment failure in infants on nevirapine-based treatment.
Lehman, D.A., Wamalwa, D.C., McCoy, C.O., Matsen, F.A., Langat, A., Chohan, B.H., Benki-Nugent, S., Custers-Allen, R., Bushman, F.D., John-Stewart, G.C., and Overbaugh, J.
Journal of Acquired Immune Deficiency Syndromes, 2012.
The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
Evans, S. N. and Matsen, F. A.
Journal of the Royal Statistical Society (B), 2012.
A format for phylogenetic placements
Matsen, F.A., Hoffman, N.G., Gallagher, A., and Stamatakis, A.
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, E.S., Fregoso, O.I., McCoy, C.O., Matsen, F.A., Malik, H.S., and Emerman, M.
Cell Host and Microbe, 2012.
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
Matsen, F. A. and Gallagher, A.
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, F.A. and Evans, S.N.
Algorithms for Molecular Biology, 2012.
Polyhedral geometry of phylogenetic rogue taxa
Cueto, M.A. and Matsen, F.A.
Bulletin of Mathematical Biology, 2011.
constNJ: an algorithm to reconstruct sets of phylogenetic trees satisfying pairwise topological constraints
Matsen, F.A.
Journal of Computational Biology, 2010.
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
Matsen, F.A., Kodner, R., and Armbrust, E.V.
BMC Bioinformatics, 2010.
Fourier transform inequalities for phylogenetic trees
Matsen, F.A.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2009.
A method for investigating relative timing information on phylogenetic trees
Ford, D., Matsen, F.A., and Stadler, T.
Systematic Biology, 2009.
To what extent does genealogical ancestry imply genetic ancestry?
Matsen, F.A. and Evans, S.N.
Theoretical Population Biology, 2008.
Mixed-up trees: the structure of phylogenetic mixtures
Matsen, F.A., Mossel, E., and Steel, M.
Bulletin of Mathematical Biology, 2008.
Optimization over a class of tree shape statistics
Matsen, F.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2007.
Phylogenetic mixtures on a single tree can mimic a tree of another topology
Matsen, F.A. and Steel, M.
Systematic Biology, 2007.
The Bayesian ``star paradox'' persists for long finite sequences
Steel, M. and Matsen, F.A.
Molecular Biology and Evolution, 2007.
Convergence to the island-model coalescent process in populations with restricted migration
Matsen, F.A. and Wakeley, J.
Genetics, 2006.
A geometric approach to tree shape statistics
Matsen, F.A.
Systematic Biology, 2006.
Win--stay, lose--shift in language learning from peers
Matsen, F.A. and Nowak, M.A.
Proceedings of the National Academy of Sciences of the United States of America, 2004.