Frederick A. Matsen IV

45 papers A* 3Journal 39Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
Conditionally Site-Independent Neural Evolution of Antibody Sequences.
CoRR
Stephen Zhewen Lu, Aakarsh Vermani, Kohei Sanno, Jiarui Lu, Frederick A. Matsen IV, Milind Jagota, Yun S. Song
2025 J jnl
Finding high posterior density phylogenies by systematically extending a directed acyclic graph.
Algorithms Mol. Biol.
Chris Jennings-Shaffer, David H. Rich, Matthew Macaulay, Michael D. Karcher, Tanvi Ganapathy, Shosuke Kiami, Anna Kooperberg, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
2025 J jnl
Nucleotide context models outperform protein language models for predicting antibody affinity maturation.
PLoS Comput. Biol.
Mackenzie M. Johnson, Kevin Sung, Hugh K. Haddox, Ashni A. Vora, Tatsuya Araki, Gabriel D. Victora, Yun S. Song, Julia Fukuyama, Frederick A. Matsen IV
2025 A* conf
PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders.
ICLR
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A. Matsen IV, Cheng Zhang
2025 J jnl
PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders.
CoRR
Tianyu Xie, Harry Richman, Jiansi Gao, Frederick A. Matsen IV, Cheng Zhang
2025 J jnl
The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support Estimation.
IEEE Trans. Comput. Biol. Bioinform.
William Howard-Snyder, Will Dumm, Mary Barker, Ognian Milanov, Claris Winston, David H. Rich, Marc A. Suchard, Frederick A. Matsen IV
2024 J jnl
A Variational Approach to Bayesian Phylogenetic Inference.
J. Mach. Learn. Res.
Cheng Zhang, Frederick A. Matsen IV
2024 J jnl
Many-core algorithms for high-dimensional gradients on phylogenetic trees.
Bioinform.
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey, Frederick A. Matsen IV, Marc A. Suchard
2024 J jnl
Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions.
CoRR
Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang
2023 J jnl
A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.
Algorithms Mol. Biol.
Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H. Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A. Suchard, Frederick A. Matsen IV
2022 J jnl
A Variational Approach to Bayesian Phylogenetic Inference.
CoRR
Cheng Zhang, Frederick A. Matsen IV
2022 J jnl
Comparing T cell receptor repertoires using optimal transport.
PLoS Comput. Biol.
Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen IV
2022 J jnl
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency.
J. Comput. Biol.
Frederick A. Matsen IV, Peter L. Ralph
2022 J jnl
Inference of B cell clonal families using heavy/light chain pairing information.
PLoS Comput. Biol.
Duncan K. Ralph, Frederick A. Matsen IV
2020 J jnl
A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.
PLoS Comput. Biol.
Amrit Dhar, Duncan K. Ralph, Vladimir N. Minin, Frederick A. Matsen IV
2020 J jnl
OGRDB: a reference database of inferred immune receptor genes.
Nucleic Acids Res.
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
2020 J jnl
Using B cell receptor lineage structures to predict affinity.
PLoS Comput. Biol.
Duncan K. Ralph, Frederick A. Matsen IV
2019 J jnl
Calculating the Unrooted Subtree Prune-and-Regraft Distance.
IEEE ACM Trans. Comput. Biol. Bioinform.
Chris Whidden, Frederick A. Matsen IV
2019 J jnl
Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data.
PLoS Comput. Biol.
Duncan K. Ralph, Frederick A. Matsen IV
2019 — conf
Variational Bayesian Phylogenetic Inference.
ICLR (Poster)
Cheng Zhang, Frederick A. Matsen IV
2018 — conf
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees.
ANALCO
Chris Whidden, Frederick A. Matsen IV
2018 A* conf
Generalizing Tree Probability Estimation via Bayesian Networks.
NeurIPS
Cheng Zhang, Frederick A. Matsen IV
2018 J jnl
Predicting B cell receptor substitution profiles using public repertoire data.
PLoS Comput. Biol.
Amrit Dhar, Kristian Davidsen, Frederick A. Matsen IV, Vladimir N. Minin
2018 J jnl
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies.
CoRR
Chris Whidden, Brian C. Claywell, Thayer Fisher, Andrew F. Magee, Mathieu Fourment, Frederick A. Matsen IV
2018 J jnl
Tanglegrams: A Reduction Tool for Mathematical Phylogenetics.
IEEE ACM Trans. Comput. Biol. Bioinform.
Frederick A. Matsen IV, Sara C. Billey, Arnold Kas, Matjaz Konvalinka
2017 J jnl
On the enumeration of tanglegrams and tangled chains.
J. Comb. Theory A
Sara C. Billey, Matjaz Konvalinka, Frederick A. Matsen IV
2017 A* conf
Probabilistic Path Hamiltonian Monte Carlo.
ICML
Vu Dinh, Arman Bilge, Cheng Zhang, Frederick A. Matsen IV
2017 J jnl
Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph.
Theor. Comput. Sci.
Chris Whidden, Frederick A. Matsen IV
2016 J jnl
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance.
CoRR
Chris Whidden, Frederick A. Matsen IV
2016 J jnl
Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.
PLoS Comput. Biol.
Duncan K. Ralph, Frederick A. Matsen IV
2016 J jnl
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees.
CoRR
Chris Whidden, Frederick A. Matsen IV
2016 J jnl
Likelihood-Based Inference of B Cell Clonal Families.
PLoS Comput. Biol.
Duncan K. Ralph, Frederick A. Matsen IV
2016 — conf
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph.
ANALCO
Chris Whidden, Frederick A. Matsen IV
2015 J jnl
Calculating the Unrooted Subtree Prune-and-Regraft Distance.
CoRR
Chris Whidden, Frederick A. Matsen IV
2015 J jnl
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph.
CoRR
Chris Whidden, Frederick A. Matsen IV
2014 J jnl
A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses.
PLoS Comput. Biol.
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
2013 J jnl
nestly - a framework for running software with nested parameter choices and aggregating results.
Bioinform.
Connor McCoy, Aaron Gallagher, Noah G. Hoffman, Frederick A. Matsen IV
2012 J jnl
Minimizing the average distance to a closest leaf in a phylogenetic tree
CoRR
Frederick A. Matsen IV, Aaron Gallagher, Connor McCoy
2012 J jnl
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots.
Algorithms Mol. Biol.
Frederick A. Matsen IV, Aaron Gallagher
2012 J jnl
Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials.
Algorithms Mol. Biol.
Frederick A. Matsen IV, Steven N. Evans
2011 J jnl
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots
CoRR
Frederick A. Matsen IV, Aaron Gallagher
2010 J jnl
constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints.
J. Comput. Biol.
Frederick A. Matsen IV
2010 J jnl
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.
BMC Bioinform.
Frederick A. Matsen IV, Robin B. Kodner, E. Virginia Armbrust
2009 J jnl
Fourier Transform Inequalities for Phylogenetic Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
Frederick A. Matsen IV
2007 J jnl
Optimization Over a Class of Tree Shape Statistics.
IEEE ACM Trans. Comput. Biol. Bioinform.
Frederick A. Matsen IV