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David Fernandez-Baca - Publications

Affiliations: 
Computer Science Iowa State University, Ames, IA, United States 
Area:
Computer Science, Bioinformatics Biology
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61 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
2022 Ranjan A, Fahad MS, Fernandez-Baca D, Tripathi S, Deepak A. MCWS-Transformers: Towards an Efficient Modeling of Protein Sequences via Multi Context-Window Based Scaled Self-Attention. Ieee/Acm Transactions On Computational Biology and Bioinformatics. PMID 35536815 DOI: 10.1109/TCBB.2022.3173789  0.523
2021 Fernández-Baca D, Liu L. Testing the agreement of trees with internal labels. Algorithms For Molecular Biology : Amb. 16: 22. PMID 34863219 DOI: 10.1186/s13015-021-00201-9  0.363
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  0.563
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  0.589
2019 Fernández-Baca D, Liu L. Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study Algorithms. 12: 53. DOI: 10.3390/a12030053  0.41
2018 Fernández-Baca D, Vakati SR. On compatibility and incompatibility of collections of unrooted phylogenetic trees Discrete Applied Mathematics. 245: 42-58. DOI: 10.1016/J.Dam.2017.05.002  0.346
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  0.448
2017 Deng Y, Fernández-Baca D. Fast Compatibility Testing for Rooted Phylogenetic Trees Algorithmica. 80: 2453-2477. DOI: 10.1007/S00453-017-0330-4  0.429
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  0.659
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  0.59
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  0.627
2015 Fernández-Baca D, Guillemot S, Shutters B, Vakati S. Fixed-Parameter Algorithms for Finding Agreement Supertrees Siam Journal On Computing. 44: 384-410. DOI: 10.1137/120897559  0.735
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  0.656
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  0.43
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  0.683
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  0.591
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  0.638
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  0.737
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  0.648
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  0.781
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  0.752
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  0.737
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  0.745
2011 Bansal MS, Dong J, Fernández-Baca D. Comparing and aggregating partially resolved trees Theoretical Computer Science. 412: 6634-6652. DOI: 10.1016/J.Tcs.2011.08.027  0.65
2011 Dong J, Fernández-Baca D, McMorris F, Powers RC. An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies Discrete Applied Mathematics. 159: 2038-2044. DOI: 10.1016/J.Dam.2011.07.002  0.581
2011 Vakati S, Fernández-Baca D. Graph triangulations and the compatibility of unrooted phylogenetic trees Applied Mathematics Letters. 24: 719-723. DOI: 10.1016/J.Aml.2010.12.015  0.402
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  0.604
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  0.633
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  0.438
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  0.615
2009 Dong J, Fernández-Baca D. Properties of majority-rule supertrees. Systematic Biology. 58: 360-7. PMID 20525590 DOI: 10.1093/Sysbio/Syp032  0.529
2009 Fernández-Baca D, Venkatachalam B. Parametric analysis for ungapped Markov models of evolution Acm Transactions On Algorithms. 5: 1-20. DOI: 10.1145/1597036.1597048  0.392
2009 Bansal MS, Fernández-Baca D. Computing distances between partial rankings Information Processing Letters. 109: 238-241. DOI: 10.1016/J.Ipl.2008.10.010  0.342
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  0.61
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  0.601
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  0.632
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  0.632
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  0.65
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  0.506
2004 Sun F, Fernández-Baca D, Yu W. Inverse parametric sequence alignment Journal of Algorithms. 53: 36-54. DOI: 10.1016/J.Jalgor.2004.04.008  0.388
2003 Fernández-Baca D, Lagergren J. A Polynomial-Time Algorithm for Near-Perfect Phylogeny Siam Journal On Computing. 32: 1115-1127. DOI: 10.1137/S0097539799350839  0.405
2003 Fernández-Baca D. Decomposable multi-parameter matroid optimization problems Theoretical Computer Science. 297: 183-198. DOI: 10.1016/S0304-3975(02)00638-2  0.388
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  0.334
2001 Fernández-Baca D. On Nonlinear Parametric Search Algorithmica. 30: 1-11. DOI: 10.1007/S00453-001-0001-2  0.382
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  0.353
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  0.321
1997 Fernández-Baca D, Slutzki G. Linear-time algorithms for parametric minimum spanning tree problems on planar graphs Theoretical Computer Science. 181: 57-74. DOI: 10.1016/S0304-3975(96)00262-9  0.323
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  0.408
1996 AGARWALA R, FERNÁNDEZ-BACA D. SIMPLE ALGORITHMS FOR PERFECT PHYLOGENY AND TRIANGULATING COLORED GRAPHS International Journal of Foundations of Computer Science. 7: 11-21. DOI: 10.1142/S0129054196000038  0.393
1996 Agarwala R, Fernández-Baca D. Weighted Multidimensional Search and Its Application to Convex Optimization Siam Journal On Computing. 25: 83-99. DOI: 10.1137/S0097539792241928  0.357
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  0.442
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  0.444
1995 Agarwala R, Fernández-Baca D. Weighted search in the plane Information Processing Letters. 54: 97-100. DOI: 10.1016/0020-0190(94)00236-R  0.31
1994 Agarwala R, Fernandez-Baca D. A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed Siam Journal On Computing. 23: 1216-1224. DOI: 10.1137/S0097539793244587  0.422
1993 Fernandez-Baca D, Medepalli A. Parametric module allocation on partial k-trees Ieee Transactions On Computers. 42: 738-742. DOI: 10.1109/12.277293  0.389
1992 Fernández-Baca D, Medepalli A. Allocating modules to processors in a distributed system with limited memory Computer Science. 335-347. DOI: 10.1007/978-1-4615-3422-8_29  0.335
1991 Fernández-Baca D, Williams MA. On matroids and hierarchial graphs Information Processing Letters. 38: 117-121. DOI: 10.1016/0020-0190(91)90232-7  0.388
1989 Fernandez-Baca D. Allocating modules to processors in a distributed system Ieee Transactions On Software Engineering. 15: 1427-1436. DOI: 10.1109/32.41334  0.387
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  0.352
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  0.594
1987 Gusfield D, Martel C, Fernandez-Baca D. Fast Algorithms for Bipartite Network Flow Siam Journal On Computing. 16: 237-251. DOI: 10.1137/0216020  0.577
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