Frederick A. Matsen IV

According to our database, Frederick A. Matsen IV authored at least 34 papers between 2007 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of three.

2024

Many-core algorithms for high-dimensional gradients on phylogenetic trees.

Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard

Bioinform., February, 2024

A Variational Approach to Bayesian Phylogenetic Inference.

Cheng Zhang, Frederick A. Matsen IV

J. Mach. Learn. Res., 2024

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions.

Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang

CoRR, 2024

2023

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.

Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H. Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV

Algorithms Mol. Biol., December, 2023

<tt>phippery</tt>: a software suite for PhIP-Seq data analysis.

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

Bioinform., October, 2023

2022

Comparing T cell receptor repertoires using optimal transport.

Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV

PLoS Comput. Biol., December, 2022

Inference of B cell clonal families using heavy/light chain pairing information.

Duncan K. Ralph, Frederick A. Matsen IV

PLoS Comput. Biol., November, 2022

Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency.

Frederick A. Matsen IV, Peter L. Ralph

J. Comput. Biol., 2022

2020

Using B cell receptor lineage structures to predict affinity.

Duncan K. Ralph, Frederick A. Matsen IV

PLoS Comput. Biol., 2020

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

Amrit Dhar, Duncan K. Ralph, Vladimir N. Minin, Frederick A. Matsen IV

PLoS Comput. Biol., 2020

OGRDB: a reference database of inferred immune receptor genes.

William D. Lees, Christian E. Busse, Martin Corcoran, Mats Ohlin, Cathrine Scheepers, Frederick A. Matsen IV, Gur Yaari, Corey T. Watson, Andrew M. Collins, Adrian J. Shepherd

Nucleic Acids Res., 2020

2019

Calculating the Unrooted Subtree Prune-and-Regraft Distance.

Chris Whidden, Frederick A. Matsen IV

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data.

Duncan K. Ralph, Frederick A. Matsen IV

PLoS Comput. Biol., 2019

Variational Bayesian Phylogenetic Inference.

Cheng Zhang, Frederick A. Matsen IV

Proceedings of the 7th International Conference on Learning Representations, 2019

2018

Tanglegrams: A Reduction Tool for Mathematical Phylogenetics.

Frederick A. Matsen IV, Sara C. Billey, Arnold Kas, Matjaz Konvalinka

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Predicting B cell receptor substitution profiles using public repertoire data.

Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin

PLoS Comput. Biol., 2018

Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies.

Chris Whidden, Brian C. Claywell, Thayer Fisher, Andrew F. Magee, Mathieu Fourment, Frederick A. Matsen IV

CoRR, 2018

Generalizing Tree Probability Estimation via Bayesian Networks.

Cheng Zhang, Frederick A. Matsen IV

Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018

Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees.

Chris Whidden, Frederick A. Matsen IV

Proceedings of the Fifteenth Workshop on Analytic Algorithmics and Combinatorics, 2018

2017

Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph.

Chris Whidden, Frederick A. Matsen IV

Theor. Comput. Sci., 2017

On the enumeration of tanglegrams and tangled chains.

Sara C. Billey, Matjaz Konvalinka, Frederick A. Matsen IV

J. Comb. Theory A, 2017

Probabilistic Path Hamiltonian Monte Carlo.

Vu Dinh, Arman Bilge, Cheng Zhang, Frederick A. Matsen IV

Proceedings of the 34th International Conference on Machine Learning, 2017

2016

Likelihood-Based Inference of B Cell Clonal Families.

Duncan K. Ralph, Frederick A. Matsen IV

PLoS Comput. Biol., 2016

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

Duncan K. Ralph, Frederick A. Matsen IV

PLoS Comput. Biol., 2016

Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance.

Chris Whidden, Frederick A. Matsen IV

CoRR, 2016

2014

A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses.

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

PLoS Comput. Biol., 2014

2013

nestly - a framework for running software with nested parameter choices and aggregating results.

Connor McCoy, Aaron Gallagher, Noah G. Hoffman, Frederick A. Matsen IV

Bioinform., 2013

2012

Minimizing the average distance to a closest leaf in a phylogenetic tree

Frederick A. Matsen IV, Aaron Gallagher, Connor McCoy

CoRR, 2012

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots.

Frederick A. Matsen IV, Aaron Gallagher

Algorithms Mol. Biol., 2012

Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials.

Frederick A. Matsen IV, Steven N. Evans

Algorithms Mol. Biol., 2012

2010

constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints.

Frederick A. Matsen IV

J. Comput. Biol., 2010

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.

Frederick A. Matsen IV, Robin B. Kodner, E. Virginia Armbrust

BMC Bioinform., 2010

2009

Fourier Transform Inequalities for Phylogenetic Trees.

Frederick A. Matsen IV

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

2007

Optimization Over a Class of Tree Shape Statistics.

Frederick A. Matsen IV

IEEE ACM Trans. Comput. Biol. Bioinform., 2007