David Fernández-Baca

David Fernández-Baca

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David Fernández-Baca

David Fernández-Baca

Publications by authors named "David Fernández-Baca"

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23Publications

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: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family.

Front Plant Sci 2019 11;10:345. Epub 2019 Apr 11.

Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, IA, United States.

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https://www.frontiersin.org/article/10.3389/fpls.2019.00345/
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http://dx.doi.org/10.3389/fpls.2019.00345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499179PMC
April 2019

An efficient algorithm for testing the compatibility of phylogenies with nested taxa.

Algorithms Mol Biol 2017 16;12. Epub 2017 Mar 16.

Department of Computer Science, Iowa State University, Atanasoff Hall, Ames, IA USA.

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http://dx.doi.org/10.1186/s13015-017-0099-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5356459PMC
March 2017

STBase: one million species trees for comparative biology.

PLoS One 2015 13;10(2):e0117987. Epub 2015 Feb 13.

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117987PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332655PMC
November 2015

Assessing approaches for inferring species trees from multi-copy genes.

Syst Biol 2015 Mar 23;64(2):325-39. Epub 2014 Dec 23.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; and Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne F-69622, France.

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http://dx.doi.org/10.1093/sysbio/syu128DOI Listing
March 2015

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

Bioinformatics 2015 Feb 1;31(3):432-3. Epub 2014 Oct 1.

Department of Biology, University of Florida, Gainesville, FL 32611 and Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu648DOI Listing
February 2015

Characterizing compatibility and agreement of unrooted trees via cuts in graphs.

Algorithms Mol Biol 2014 17;9:13. Epub 2014 Apr 17.

Department of Computer Science, Iowa State University, Ames, Iowa, USA.

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http://dx.doi.org/10.1186/1748-7188-9-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4013835PMC
August 2014

Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

Algorithms Mol Biol 2014 18;9:16. Epub 2014 Jun 18.

Department of Computer Science, Iowa State University, Ames, Iowa, USA.

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http://dx.doi.org/10.1186/1748-7188-9-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4085724PMC
July 2014

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.

Algorithms Mol Biol 2013 Nov 1;8(1):28. Epub 2013 Nov 1.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1748-7188-8-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874668PMC
November 2013

Extracting conflict-free information from multi-labeled trees.

Algorithms Mol Biol 2013 Jul 9;8(1):18. Epub 2013 Jul 9.

Department of Computer Science, Iowa State University, Ames, Iowa, USA.

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http://dx.doi.org/10.1186/1748-7188-8-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716922PMC
July 2013

Incompatible quartets, triplets, and characters.

Algorithms Mol Biol 2013 Apr 1;8(1):11. Epub 2013 Apr 1.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1748-7188-8-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694002PMC
April 2013

Fast local search for unrooted Robinson-Foulds supertrees.

IEEE/ACM Trans Comput Biol Bioinform 2012 Jul-Aug;9(4):1004-13

Department of Computer Science, Iowa State University, Atanasoff Hall, Ames, IA 50011-1041, USA.

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http://dx.doi.org/10.1109/TCBB.2012.47DOI Listing
October 2012

An ILP solution for the gene duplication problem.

BMC Bioinformatics 2011 Feb 15;12 Suppl 1:S14. Epub 2011 Feb 15.

Department of Computer Science, Iowa State University, Ames 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S1-S14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044268PMC
February 2011

Majority-rule (+) consensus trees.

Math Biosci 2010 Nov 11;228(1):10-5. Epub 2010 Aug 11.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00255564100012
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http://dx.doi.org/10.1016/j.mbs.2010.08.002DOI Listing
November 2010

iGTP: a software package for large-scale gene tree parsimony analysis.

BMC Bioinformatics 2010 Nov 23;11:574. Epub 2010 Nov 23.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2105-11-574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002902PMC
November 2010

Robinson-Foulds supertrees.

Algorithms Mol Biol 2010 Feb 24;5:18. Epub 2010 Feb 24.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1748-7188-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846952PMC
February 2010

Constructing majority-rule supertrees.

Algorithms Mol Biol 2010 Jan 4;5. Epub 2010 Jan 4.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1748-7188-5-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826330PMC
January 2010

Properties of majority-rule supertrees.

Syst Biol 2009 Jun 3;58(3):360-7. Epub 2009 Jul 3.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1093/sysbio/syp032DOI Listing
June 2009

PhyloFinder: an intelligent search engine for phylogenetic tree databases.

BMC Evol Biol 2008 Mar 21;8:90. Epub 2008 Mar 21.

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1186/1471-2148-8-90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2362120PMC
March 2008

Spectral partitioning of phylogenetic data sets based on compatibility.

Syst Biol 2007 Aug;56(4):623-32

Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

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http://dx.doi.org/10.1080/10635150701499571DOI Listing
August 2007

Improved heuristics for minimum-flip supertree construction.

Evol Bioinform Online 2007 Feb 28;2:347-56. Epub 2007 Feb 28.

Department of Computer Science, Iowa State University, Ames, IA 50011, U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674677PMC
February 2007

Minimum-flip supertrees: complexity and algorithms.

IEEE/ACM Trans Comput Biol Bioinform 2006 Apr-Jun;3(2):165-73

Department of Computer Science, Iowa State University, Ames, IA 50011-1040, USA.

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http://dx.doi.org/10.1109/TCBB.2006.26DOI Listing
November 2006