Frederick A. Matsen IV

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 25

Top Topics

Pruning Algorithms

Variational Bayesian

Sequence Analysis

Top Venues

PLoS Comput. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard
Many-core algorithms for high-dimensional gradients on phylogenetic trees. Bioinform. 40 (2) (2024)
Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H. Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm. Algorithms Mol. Biol. 18 (1) (2023)
Jared G. Galloway, Kevin Sung, Samuel Schwartz Minot, Meghan E. Garrett, Caitlin I Stoddard, Alexandra C. Willcox, Zak A. Yaffe, Ryan Yucha, Julie Overbaugh, Frederick A. Matsen IV
: a software suite for PhIP-Seq data analysis. Bioinform. 39 (10) (2023)
Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV
Comparing T cell receptor repertoires using optimal transport. PLoS Comput. Biol. 18 (12) (2022)
Cheng Zhang, Frederick A. Matsen IV
A Variational Approach to Bayesian Phylogenetic Inference. CoRR (2022)
Duncan K. Ralph, Frederick A. Matsen IV
Using B cell receptor lineage structures to predict affinity. PLoS Comput. Biol. 16 (11) (2020)
Amrit Dhar, Duncan K. Ralph, Vladimir N. Minin, Frederick A. Matsen IV
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis. PLoS Comput. Biol. 16 (8) (2020)
Chris Whidden, Frederick A. Matsen IV
Calculating the Unrooted Subtree Prune-and-Regraft Distance. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (3) (2019)
Cheng Zhang, Frederick A. Matsen IV
Variational Bayesian Phylogenetic Inference. ICLR (Poster) (2019)
Duncan K. Ralph, Frederick A. Matsen IV
Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. PLoS Comput. Biol. 15 (7) (2019)
Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin
Predicting B cell receptor substitution profiles using public repertoire data. PLoS Comput. Biol. 14 (10) (2018)
Chris Whidden, Frederick A. Matsen IV
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees. ANALCO (2018)
Frederick A. Matsen IV, Sara C. Billey, Arnold Kas, Matjaz Konvalinka
Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (1) (2018)
Cheng Zhang, Frederick A. Matsen IV
Generalizing Tree Probability Estimation via Bayesian Networks. NeurIPS (2018)
Chris Whidden, Brian C. Claywell, Thayer Fisher, Andrew F. Magee, Mathieu Fourment, Frederick A. Matsen IV
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies. CoRR (2018)
Sara C. Billey, Matjaz Konvalinka, Frederick A. Matsen IV
On the enumeration of tanglegrams and tangled chains. J. Comb. Theory, Ser. A 146 (2017)
Chris Whidden, Frederick A. Matsen IV
Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph. Theor. Comput. Sci. 699 (2017)
Vu Dinh, Arman Bilge, Cheng Zhang, Frederick A. Matsen IV
Probabilistic Path Hamiltonian Monte Carlo. ICML (2017)
Duncan K. Ralph, Frederick A. Matsen IV
Likelihood-Based Inference of B Cell Clonal Families. PLoS Comput. Biol. 12 (10) (2016)
Chris Whidden, Frederick A. Matsen IV
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees. CoRR (2016)
Chris Whidden, Frederick A. Matsen IV
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance. CoRR (2016)
Chris Whidden, Frederick A. Matsen IV
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph. ANALCO (2016)
Duncan K. Ralph, Frederick A. Matsen IV
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation. PLoS Comput. Biol. 12 (1) (2016)
Chris Whidden, Frederick A. Matsen IV
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph. CoRR (2015)
Chris Whidden, Frederick A. Matsen IV
Calculating the Unrooted Subtree Prune-and-Regraft Distance. CoRR (2015)
Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses. PLoS Comput. Biol. 10 (2) (2014)
Connor McCoy, Aaron Gallagher, Noah G. Hoffman, Frederick A. Matsen IV
nestly - a framework for running software with nested parameter choices and aggregating results. Bioinform. 29 (3) (2013)
Frederick A. Matsen IV, Aaron Gallagher
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. Algorithms Mol. Biol. 7 (2012)
Frederick A. Matsen IV, Steven N. Evans
Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials. Algorithms Mol. Biol. 7 (2012)
Frederick A. Matsen IV, Aaron Gallagher, Connor McCoy
Minimizing the average distance to a closest leaf in a phylogenetic tree CoRR (2012)
Frederick A. Matsen IV, Aaron Gallagher
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots CoRR (2011)
Frederick A. Matsen IV, Robin B. Kodner, E. Virginia Armbrust
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinform. 11 (2010)
Frederick A. Matsen IV
constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints. J. Comput. Biol. 17 (6) (2010)
Frederick A. Matsen IV
Fourier Transform Inequalities for Phylogenetic Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (1) (2009)
Frederick A. Matsen IV
Optimization Over a Class of Tree Shape Statistics. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (3) (2007)