Optimization Over a Class of Tree Shape Statistics. - Frederick A. Matsen IV (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

Fourier Transform Inequalities for Phylogenetic Trees. - Frederick A. Matsen IV (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

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)

constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints. - Frederick A. Matsen IV (J. Comput. Biol., 2010)

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)

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)

Minimizing the average distance to a closest leaf in a phylogenetic tree - Frederick A. Matsen IV; Aaron Gallagher; Connor McCoy (CoRR, 2012)

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)

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)

Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance. - Chris Whidden; Frederick A. Matsen IV (CoRR, 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)

Likelihood-Based Inference of B Cell Clonal Families. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2016)

Probabilistic Path Hamiltonian Monte Carlo. - Vu Dinh; Arman Bilge; Cheng Zhang; Frederick A. Matsen IV (ICML, 2017)

On the enumeration of tanglegrams and tangled chains. - Sara C. Billey; Matjaz Konvalinka; Frederick A. Matsen IV (J. Comb. Theory A, 2017)

Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph. - Chris Whidden; Frederick A. Matsen IV (Theor. Comput. Sci., 2017)

Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees. - Chris Whidden; Frederick A. Matsen IV (ANALCO, 2018)

Generalizing Tree Probability Estimation via Bayesian Networks. - Cheng Zhang; Frederick A. Matsen IV (NeurIPS, 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)

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)

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)

Variational Bayesian Phylogenetic Inference. - Cheng Zhang; Frederick A. Matsen IV (ICLR (Poster), 2019)

Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2019)

Calculating the Unrooted Subtree Prune-and-Regraft Distance. - Chris Whidden; Frederick A. Matsen IV (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

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)

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)

Using B cell receptor lineage structures to predict affinity. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 2020)

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)

Inference of B cell clonal families using heavy/light chain pairing information. - Duncan K. Ralph; Frederick A. Matsen IV (PLoS Comput. Biol., 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., 2022)

phippery: 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., 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., 2023)

Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions. - Tianyu Xie 001; Frederick A. Matsen IV; Marc A. Suchard; Cheng Zhang (CoRR, 2024)

A Variational Approach to Bayesian Phylogenetic Inference. - Cheng Zhang; Frederick A. Matsen IV (J. Mach. Learn. Res., 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., 2024)

PhyloVAE: Unsupervised Learning of Phylogenetic Trees via Variational Autoencoders. - Tianyu Xie 001; Harry Richman; Jiansi Gao; Frederick A. Matsen IV; Cheng Zhang (ICLR, 2025)

Finding high posterior density phylogenies by systematically extending a directed acyclic graph. - 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 (Algorithms Mol. Biol., 2025)