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.