default search action
Frederick A. Matsen IV
Person information
- affiliation: Fred Hutchinson Cancer Research Center, USA
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
2020 – today
- 2024
- [j26]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) - [j25]Cheng Zhang, Frederick A. Matsen IV:
A Variational Approach to Bayesian Phylogenetic Inference. J. Mach. Learn. Res. 25: 145:1-145:56 (2024) - [i9]Tianyu Xie, Frederick A. Matsen IV, Marc A. Suchard, Cheng Zhang:
Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions. CoRR abs/2408.05058 (2024) - 2023
- [j24]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): 10 (2023) - [j23]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:
phippery: a software suite for PhIP-Seq data analysis. Bioinform. 39(10) (2023) - 2022
- [j22]Frederick A. Matsen IV, Peter L. Ralph:
Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency. J. Comput. Biol. 29(8): 802-824 (2022) - [j21]Duncan K. Ralph, Frederick A. Matsen IV:
Inference of B cell clonal families using heavy/light chain pairing information. PLoS Comput. Biol. 18(11): 1010723 (2022) - [j20]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): 1010681 (2022) - [i8]Cheng Zhang, Frederick A. Matsen IV:
A Variational Approach to Bayesian Phylogenetic Inference. CoRR abs/2204.07747 (2022) - 2020
- [j19]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:
OGRDB: a reference database of inferred immune receptor genes. Nucleic Acids Res. 48(Database-Issue): D964-D970 (2020) - [j18]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) - [j17]Duncan K. Ralph, Frederick A. Matsen IV:
Using B cell receptor lineage structures to predict affinity. PLoS Comput. Biol. 16(11) (2020)
2010 – 2019
- 2019
- [j16]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) - [j15]Chris Whidden, Frederick A. Matsen IV:
Calculating the Unrooted Subtree Prune-and-Regraft Distance. IEEE ACM Trans. Comput. Biol. Bioinform. 16(3): 898-911 (2019) - [c5]Cheng Zhang, Frederick A. Matsen IV:
Variational Bayesian Phylogenetic Inference. ICLR (Poster) 2019 - 2018
- [j14]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) - [j13]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): 343-349 (2018) - [c4]Chris Whidden, Frederick A. Matsen IV:
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees. ANALCO 2018: 77-91 - [c3]Cheng Zhang, Frederick A. Matsen IV:
Generalizing Tree Probability Estimation via Bayesian Networks. NeurIPS 2018: 1451-1460 - [i7]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 abs/1811.11007 (2018) - 2017
- [j12]Sara C. Billey, Matjaz Konvalinka, Frederick A. Matsen IV:
On the enumeration of tanglegrams and tangled chains. J. Comb. Theory A 146: 239-263 (2017) - [j11]Chris Whidden, Frederick A. Matsen IV:
Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph. Theor. Comput. Sci. 699: 1-20 (2017) - [c2]Vu Dinh, Arman Bilge, Cheng Zhang, Frederick A. Matsen IV:
Probabilistic Path Hamiltonian Monte Carlo. ICML 2017: 1009-1018 - 2016
- [j10]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) - [j9]Duncan K. Ralph, Frederick A. Matsen IV:
Likelihood-Based Inference of B Cell Clonal Families. PLoS Comput. Biol. 12(10) (2016) - [c1]Chris Whidden, Frederick A. Matsen IV:
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph. ANALCO 2016: 106-120 - [i6]Chris Whidden, Frederick A. Matsen IV:
Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees. CoRR abs/1606.08893 (2016) - [i5]Chris Whidden, Frederick A. Matsen IV:
Chain Reduction Preserves the Unrooted Subtree Prune-and-Regraft Distance. CoRR abs/1611.02351 (2016) - 2015
- [i4]Chris Whidden, Frederick A. Matsen IV:
Ricci-Ollivier Curvature of the Rooted Phylogenetic Subtree-Prune-Regraft Graph. CoRR abs/1504.00304 (2015) - [i3]Chris Whidden, Frederick A. Matsen IV:
Calculating the Unrooted Subtree Prune-and-Regraft Distance. CoRR abs/1511.07529 (2015) - 2014
- [j8]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) - 2013
- [j7]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): 387-388 (2013) - 2012
- [j6]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: 8 (2012) - [j5]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: 14 (2012) - [i2]Frederick A. Matsen IV, Aaron Gallagher, Connor McCoy:
Minimizing the average distance to a closest leaf in a phylogenetic tree. CoRR abs/1205.6867 (2012) - 2011
- [i1]Frederick A. Matsen IV, Aaron Gallagher:
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. CoRR abs/1109.5423 (2011) - 2010
- [j4]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: 538 (2010) - [j3]Frederick A. Matsen IV:
constNJ: An Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints. J. Comput. Biol. 17(6): 799-818 (2010)
2000 – 2009
- 2009
- [j2]Frederick A. Matsen IV:
Fourier Transform Inequalities for Phylogenetic Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 6(1): 89-95 (2009) - 2007
- [j1]Frederick A. Matsen IV:
Optimization Over a Class of Tree Shape Statistics. IEEE ACM Trans. Comput. Biol. Bioinform. 4(3): 506-512 (2007)
Coauthor Index
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from , , and to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from .
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-10-07 22:11 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint