David Fernandez-Baca - Publications

Affiliations: 
Computer Science Iowa State University, Ames, IA, United States 
Area:
Computer Science, Bioinformatics Biology

38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Ranjan A, Fernandez-Baca D, Tripathi S, Deepak A. An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 34185646 DOI: 10.1109/TCBB.2021.3093060  1
2019 Ranjan A, Fahad MS, Fernandez-Baca D, Deepak A, Tripathi S. Deep Robust Framework for Protein Function Prediction using Variable-Length Protein Sequences. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 30998479 DOI: 10.1109/Tcbb.2019.2911609  1
2017 Deng Y, Fernández-Baca D. An efficient algorithm for testing the compatibility of phylogenies with nested taxa. Algorithms For Molecular Biology : Amb. 12: 7. PMID 28331536 DOI: 10.1186/S13015-017-0099-7  0.32
2015 McMahon MM, Deepak A, Fernández-Baca D, Boss D, Sanderson MJ. STBase: one million species trees for comparative biology. Plos One. 10: e0117987. PMID 25679219 DOI: 10.1371/Journal.Pone.0117987  1
2015 Chaudhary R, Boussau B, Burleigh JG, Fernández-Baca D. Assessing approaches for inferring species trees from multi-copy genes. Systematic Biology. 64: 325-39. PMID 25540456 DOI: 10.1093/Sysbio/Syu128  1
2015 Chaudhary R, Fernández-Baca D, Burleigh JG. MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinformatics (Oxford, England). 31: 432-3. PMID 25273112 DOI: 10.1093/Bioinformatics/Btu648  1
2015 Chaudhary R, Fernández-Baca D, Burleigh JG. Constructing and employing tree alignment graphs for phylogenetic synthesis Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9199: 97-108. DOI: 10.1007/978-3-319-21233-3_8  1
2014 Deepak A, Fernández-Baca D. Enumerating all maximal frequent subtrees in collections of phylogenetic trees. Algorithms For Molecular Biology : Amb. 9: 16. PMID 25061474 DOI: 10.1186/1748-7188-9-16  1
2014 Vakati S, Fernández-Baca D. Characterizing compatibility and agreement of unrooted trees via cuts in graphs. Algorithms For Molecular Biology : Amb. 9: 13. PMID 24742332 DOI: 10.1186/1748-7188-9-13  0.8
2014 Deepak A, Fernández-Baca D, Tirthapura S, Sanderson MJ, McMahon MM. EvoMiner: frequent subtree mining in phylogenetic databases Knowledge and Information Systems. 41: 559-590. DOI: 10.1007/S10115-013-0676-0  1
2013 Chaudhary R, Burleigh JG, Fernández-Baca D. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms For Molecular Biology : Amb. 8: 28. PMID 24180377 DOI: 10.1186/1748-7188-8-28  1
2013 Deepak A, Fernández-Baca D, McMahon MM. Extracting conflict-free information from multi-labeled trees. Algorithms For Molecular Biology : Amb. 8: 18. PMID 23837994 DOI: 10.1186/1748-7188-8-18  1
2013 Shutters B, Vakati S, Fernández-Baca D. Incompatible quartets, triplets, and characters. Algorithms For Molecular Biology : Amb. 8: 11. PMID 23547777 DOI: 10.1186/1748-7188-8-11  1
2012 Chaudhary R, Burleigh JG, Fernández-Baca D. Fast local search for unrooted Robinson-Foulds supertrees. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 1004-13. PMID 22431553 DOI: 10.1109/Tcbb.2012.47  1
2012 Fernández-Baca D, Guillemot S, Shutters B, Vakati S. Fixed-parameter algorithms for finding agreement supertrees Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7354: 373-384. DOI: 10.1137/120897559  1
2012 Shutters B, Fernández-Baca D. A simple characterization of the minimal obstruction sets for three-state perfect phylogenies Applied Mathematics Letters. 25: 1226-1229. DOI: 10.1016/J.Aml.2012.02.060  1
2012 Shutters B, Vakati S, Fernández-Baca D. Improved lower bounds on the compatibility of quartets, triplets, and multi-state characters Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7534: 190-200. DOI: 10.1007/978-3-642-33122-0_15  1
2012 Deepak A, Dong J, Fernández-Baca D. Identifying rogue taxa through reduced consensus: NP-hardness and exact algorithms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7292: 87-98. DOI: 10.1007/978-3-642-30191-9_9  1
2011 Chang WC, Burleigh GJ, Fernández-Baca DF, Eulenstein O. An ILP solution for the gene duplication problem. Bmc Bioinformatics. 12: S14. PMID 21342543 DOI: 10.1186/1471-2105-12-S1-S14  0.76
2010 Chaudhary R, Bansal MS, Wehe A, Fernández-Baca D, Eulenstein O. iGTP: a software package for large-scale gene tree parsimony analysis. Bmc Bioinformatics. 11: 574. PMID 21092314 DOI: 10.1186/1471-2105-11-574  0.6
2010 Dong J, Fernández-Baca D, McMorris FR, Powers RC. Majority-rule (+) consensus trees. Mathematical Biosciences. 228: 10-5. PMID 20708021 DOI: 10.1016/J.Mbs.2010.08.002  1
2010 Bansal MS, Burleigh JG, Eulenstein O, Fernández-Baca D. Robinson-Foulds supertrees. Algorithms For Molecular Biology : Amb. 5: 18. PMID 20181274 DOI: 10.1186/1748-7188-5-18  1
2010 Dong J, Fernández-Baca D, McMorris FR. Constructing majority-rule supertrees. Algorithms For Molecular Biology : Amb. 5: 2. PMID 20047658 DOI: 10.1186/1748-7188-5-2  1
2009 Dong J, Fernández-Baca D. Properties of majority-rule supertrees. Systematic Biology. 58: 360-7. PMID 20525590 DOI: 10.1093/Sysbio/Syp032  1
2008 Chen D, Burleigh JG, Bansal MS, Fernández-Baca D. PhyloFinder: an intelligent search engine for phylogenetic tree databases. Bmc Evolutionary Biology. 8: 90. PMID 18366717 DOI: 10.1186/1471-2148-8-90  1
2007 Chen D, Burleigh GJ, Fernández-Baca D. Spectral partitioning of phylogenetic data sets based on compatibility. Systematic Biology. 56: 623-32. PMID 17654366 DOI: 10.1080/10635150701499571  0.76
2006 Chen D, Eulenstein O, Fernández-Baca D, Burleigh JG. Improved heuristics for minimum-flip supertree construction. Evolutionary Bioinformatics Online. 2: 347-56. PMID 19455229 DOI: 10.4137/Ebo.S0  0.76
2006 Chen D, Eulenstein O, Fernández-Baca D, Sanderson M. Minimum-flip supertrees: Complexity and algorithms Ieee/Acm Transactions On Computational Biology and Bioinformatics. 3: 165-173. PMID 17048402 DOI: 10.1109/Tcbb.2006.26  1
2004 Eulenstein O, Chen D, Burleigh JG, Fernández-Baca D, Sanderson MJ. Performance of flip supertree construction with a heuristic algorithm. Systematic Biology. 53: 299-308. PMID 15205054 DOI: 10.1080/10635150490423719  1
2004 Chen D, Eulenstein O, Fernández-Baca D. Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinformatics (Oxford, England). 20: 2872-3. PMID 15145807 DOI: 10.1093/Bioinformatics/Bth313  0.76
2002 Fernández-Baca D, Seppäläinen T, Slutzki G. Bounds for parametric sequence comparison Discrete Applied Mathematics. 118: 181-198. DOI: 10.1016/S0166-218X(01)00206-2  1
2000 Fernández-Baca D, Seppäläinen T, Slutzki G. Parametric multiple sequence alignment and phylogeny construction Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1848: 69-83. DOI: 10.1016/S1570-8667(03)00078-9  1
1998 Chen SF, Oliver JH, Fernandez-Baca D. A fast algorithm for planning collision-free paths with rotations Journal of Mechanical Design, Transactions of the Asme. 120: 52-57. DOI: 10.1115/1.2826676  1
1997 Fernández-Baca D, Slutzki G. Optimal Parametric Search on Graphs of Bounded Tree-Width Journal of Algorithms. 22: 212-240. DOI: 10.1006/Jagm.1996.0816  1
1995 Agarwala R, Fernández-Baca D, Slutzki G. Fast algorithms for inferring evolutionary trees. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 2: 397-407. PMID 8521270 DOI: 10.1089/Cmb.1995.2.397  1
1995 Fernández-Baca D, Slutzki G. Linear-time algorithms for parametric minimum spanning tree problems on planar graphs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 911: 257-271. DOI: 10.1016/S0304-3975(96)00262-9  1
1989 Fernández-Baca D, Slutzki G. Solving parametric problems on trees Journal of Algorithms. 10: 381-402. DOI: 10.1016/0196-6774(89)90035-7  1
1989 Fernández-Baca D, Martel CU. On the efficiency of maximum-flow algorithms on networks with small integer capacities Algorithmica. 4: 173-189. DOI: 10.1007/Bf01553885  1
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