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ORCIDDavid Fernández-Baca
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2020 – today
- 2023
[j57]Ashish Ranjan
, Md. S. Fahad, David Fernández-Baca, Sudhakar Tripathi, Akshay Deepak:
MCWS-Transformers: Towards an Efficient Modeling of Protein Sequences via Multi Context-Window Based Scaled Self-Attention. IEEE ACM Trans. Comput. Biol. Bioinform. 20(2): 1188-1199 (2023)- 2022
- [j56]Ashish Ranjan, David Fernández-Baca, Sudhakar Tripathi, Akshay Deepak:
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation. IEEE ACM Trans. Comput. Biol. Bioinform. 19(5): 2685-2696 (2022) - [j55]Ghazaleh Parvini, Katherine Braught, David Fernández-Baca:
Checking Phylogenetics Decisiveness in Theory and in Practice. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3307-3316 (2022) - 2021
- [j54]David Fernández-Baca, Lei Liu:
Testing the agreement of trees with internal labels. Algorithms Mol. Biol. 16(1): 22 (2021) - [i15]Ghazaleh Parvini, David Fernández-Baca:
Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness. CoRR abs/2104.02103 (2021) - 2020
- [j53]Ashish Ranjan, Md. Shah Fahad, David Fernández-Baca, Akshay Deepak, Sudhakar Tripathi:
Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 17(5): 1648-1659 (2020) - [c35]David Fernández-Baca, Lei Liu:
Testing the Agreement of Trees with Internal Labels. ISBRA 2020: 127-139 - [c34]Ghazaleh Parvini, Katherine Braught, David Fernández-Baca:
Checking Phylogenetic Decisiveness in Theory and in Practice. ISBRA 2020: 189-202 - [i14]Ghazaleh Parvini, Katherine Braught, David Fernández-Baca:
Checking Phylogenetic Decisiveness in Theory and in Practice. CoRR abs/2002.09722 (2020) - [i13]David Fernández-Baca, Lei Liu:
Testing the Agreement of Trees with Internal Labels. CoRR abs/2002.09725 (2020)
2010 – 2019
- 2019
- [j52]David Fernández-Baca, Lei Liu:
Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study. Algorithms 12(3): 53 (2019) - [i12]Balanand Jha, David Fernández-Baca, Akshay Deepak, Kumar Abhishek:
EvoZip: Efficient Compression of Large Collections of Evolutionary Trees. CoRR abs/1910.07819 (2019) - 2018
- [j51]Yun Deng, David Fernández-Baca:
Fast Compatibility Testing for Rooted Phylogenetic Trees. Algorithmica 80(8): 2453-2477 (2018) - [j50]David Fernández-Baca, Sudheer Vakati:
On compatibility and incompatibility of collections of unrooted phylogenetic trees. Discret. Appl. Math. 245: 42-58 (2018) - [p1]David Fernández-Baca, Balaji Venkatachalam:
Sensitivity Analysis in Combinatorial Optimization. Handbook of Approximation Algorithms and Metaheuristics (1) 2018: 455-472 - 2017
- [j49]Yun Deng, David Fernández-Baca:
An efficient algorithm for testing the compatibility of phylogenies with nested taxa. Algorithms Mol. Biol. 12(1): 7:1-7:12 (2017) - 2016
- [c33]Yun Deng, David Fernández-Baca:
Fast Compatibility Testing for Rooted Phylogenetic Trees. CPM 2016: 12:1-12:12 - [c32]Yun Deng, David Fernández-Baca:
Fast Compatibility Testing for Phylogenies with Nested Taxa. WABI 2016: 90-101 - [i11]Yun Deng, David Fernández-Baca:
Fast Compatibility Testing for Phylogenies with Nested Taxa. CoRR abs/1605.02045 (2016) - 2015
- [j48]Ruchi Chaudhary, David Fernández-Baca, John Gordon Burleigh:
MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinform. 31(3): 432-433 (2015) - [j47]Sudheer Vakati, David Fernández-Baca:
Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors. Electron. Notes Discret. Math. 50: 337-342 (2015) - [j46]David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati:
Fixed-Parameter Algorithms for Finding Agreement Supertrees. SIAM J. Comput. 44(2): 384-410 (2015) - [c31]Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh:
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. AlCoB 2015: 97-108 - [i10]Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh:
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. CoRR abs/1503.03877 (2015) - [i9]Yun Deng, David Fernández-Baca:
Fast Compatibility Testing for Rooted Phylogenetic Trees. CoRR abs/1510.07758 (2015) - 2014
- [j45]David Fernández-Baca:
Editorial. Algorithmica 70(2): 149-151 (2014) - [j44]Sudheer Vakati, David Fernández-Baca:
Characterizing compatibility and agreement of unrooted trees via cuts in graphs. Algorithms Mol. Biol. 9: 13 (2014) - [j43]Akshay Deepak, David Fernández-Baca:
Enumerating all maximal frequent subtrees in collections of phylogenetic trees. Algorithms Mol. Biol. 9: 16 (2014) - [j42]Akshay Deepak, David Fernández-Baca, Srikanta Tirthapura, Michael J. Sanderson, Michelle M. McMahon:
EvoMiner: frequent subtree mining in phylogenetic databases. Knowl. Inf. Syst. 41(3): 559-590 (2014) - 2013
- [j41]Brad Shutters, Sudheer Vakati, David Fernández-Baca:
Incompatible quartets, triplets, and characters. Algorithms Mol. Biol. 8: 11 (2013) - [j40]Akshay Deepak, David Fernández-Baca, Michelle M. McMahon:
Extracting conflict-free information from multi-labeled trees. Algorithms Mol. Biol. 8: 18 (2013) - [j39]Ruchi Chaudhary, John Gordon Burleigh, David Fernández-Baca:
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms Mol. Biol. 8: 28 (2013) - [c30]Sudheer Vakati, David Fernández-Baca:
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. WABI 2013: 185-199 - [i8]Sudheer Vakati, David Fernández-Baca:
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. CoRR abs/1307.7828 (2013) - 2012
- [j38]Brad Shutters, David Fernández-Baca:
A simple characterization of the minimal obstruction sets for three-state perfect phylogenies. Appl. Math. Lett. 25(9): 1226-1229 (2012) - [j37]José Aguilar, John Atkinson, Yezid Donoso, David Fernández-Baca, Ernst L. Leiss, Gabriela Marín, Luciana Porcher Nedel, Oscar Pastor:
Preface to CLEI 2011 Special Issue. CLEI Electron. J. 15(2) (2012) - [j36]Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca:
Fast Local Search for Unrooted Robinson-Foulds Supertrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1004-1013 (2012) - [c29]David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati:
Fixed-Parameter Algorithms for Finding Agreement Supertrees. CPM 2012: 373-384 - [c28]Akshay Deepak, Jianrong Dong, David Fernández-Baca:
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms. ISBRA 2012: 87-98 - [c27]Akshay Deepak, David Fernández-Baca, Michelle M. McMahon:
Extracting Conflict-Free Information from Multi-labeled Trees. WABI 2012: 81-92 - [c26]Brad Shutters, Sudheer Vakati, David Fernández-Baca:
Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. WABI 2012: 190-200 - [e1]David Fernández-Baca:
LATIN 2012: Theoretical Informatics - 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings. Lecture Notes in Computer Science 7256, Springer 2012, ISBN 978-3-642-29343-6 [contents] - [i7]Brad Shutters, Sudheer Vakati, David Fernández-Baca:
Improved Lower Bounds on the Compatibility of Multi-State Characters. CoRR abs/1205.5779 (2012) - [i6]Akshay Deepak, David Fernández-Baca, Michelle M. McMahon:
Extracting Conflict-free Information from Multi-labeled Trees. CoRR abs/1205.6359 (2012) - [i5]Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca:
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance. CoRR abs/1210.2665 (2012) - [i4]Sudheer Vakati, David Fernández-Baca:
On Two Graph-Theoretic Characterizations of Tree Compatibility. CoRR abs/1210.3762 (2012) - 2011
- [j35]Sudheer Vakati, David Fernández-Baca:
Graph triangulations and the compatibility of unrooted phylogenetic trees. Appl. Math. Lett. 24(5): 719-723 (2011) - [j34]Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein:
An ILP solution for the gene duplication problem. BMC Bioinform. 12(S-1): S14 (2011) - [j33]Jianrong Dong, David Fernández-Baca, Fred R. McMorris, Robert C. Powers:
An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies. Discret. Appl. Math. 159(17): 2038-2044 (2011) - [j32]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and aggregating partially resolved trees. Theor. Comput. Sci. 412(48): 6634-6652 (2011) - [c25]Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca:
Fast Local Search for Unrooted Robinson-Foulds Supertrees. ISBRA 2011: 184-196 - [c24]Jianrong Dong, David Fernández-Baca:
Constructing Large Conservative Supertrees. WABI 2011: 61-72 - [i3]Brad Shutters, David Fernández-Baca:
A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies. CoRR abs/1106.0874 (2011) - 2010
- [j31]Jianrong Dong, David Fernández-Baca, Fred R. McMorris:
Constructing majority-rule supertrees. Algorithms Mol. Biol. 5: 2 (2010) - [j30]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca:
Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5: 18 (2010) - [j29]Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein:
iGTP: A software package for large-scale gene tree parsimony analysis. BMC Bioinform. 11: 574 (2010) - [i2]Sudheer Vakati, David Fernández-Baca:
Graph Triangulations and the Compatibility of Unrooted Phylogenetic Trees. CoRR abs/1004.4196 (2010)
2000 – 2009
- 2009
- [j28]Mukul S. Bansal, David Fernández-Baca:
Computing distances between partial rankings. Inf. Process. Lett. 109(4): 238-241 (2009) - [j27]David Fernández-Baca, Balaji Venkatachalam:
Parametric analysis for ungapped Markov models of evolution. ACM Trans. Algorithms 5(4): 44:1-44:20 (2009) - [c23]Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca:
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB 2009: 114-125 - [c22]Jianrong Dong, David Fernández-Baca, Fred R. McMorris:
Constructing Majority-Rule Supertrees. WABI 2009: 73-84 - [i1]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and Aggregating Partially Resolved Trees. CoRR abs/0906.5089 (2009) - 2008
- [c21]Mukul S. Bansal, Jianrong Dong, David Fernández-Baca:
Comparing and Aggregating Partially Resolved Trees. LATIN 2008: 72-83 - 2007
- [r1]Balaji Venkatachalam, David Fernández-Baca:
Sensitivity Analysis in Combinatorial Optimization. Handbook of Approximation Algorithms and Metaheuristics 2007 - 2006
- [j26]Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Minimum-Flip Supertrees: Complexity and Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 165-173 (2006) - 2005
- [c20]David Fernández-Baca, Balaji Venkatachalam:
Parametric Analysis for Ungapped Markov Models of Evolution. CPM 2005: 394-405 - 2004
- [j25]Duhong Chen, Oliver Eulenstein, David Fernández-Baca:
Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinform. 20(16): 2872-2873 (2004) - [j24]Fangting Sun, David Fernández-Baca, Wei Yu:
Inverse parametric sequence alignment. J. Algorithms 53(1): 36-54 (2004) - [j23]David Fernández-Baca, Timo Seppäläinen, Giora Slutzki:
Parametric multiple sequence alignment and phylogeny construction. J. Discrete Algorithms 2(2): 271-287 (2004) - 2003
- [j22]David Fernández-Baca, Jens Lagergren:
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. SIAM J. Comput. 32(5): 1115-1127 (2003) - [j21]David Fernández-Baca:
Decomposable multi-parameter matroid optimization problems. Theor. Comput. Sci. 297(1-3): 183-198 (2003) - 2002
- [j20]David Fernández-Baca, Timo Seppäläinen, Giora Slutzki:
Bounds for parametric sequence comparison. Discret. Appl. Math. 118(3): 181-198 (2002) - [c19]Fangting Sun, David Fernández-Baca, Wei Yu:
Inverse Parametric Sequence Alignment. COCOON 2002: 97-106 - [c18]Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Supertrees by Flipping. COCOON 2002: 391-400 - 2001
- [j19]David Fernández-Baca:
On Nonlinear Parametric Search. Algorithmica 30(1): 1-11 (2001) - [c17]Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Flipping: A supertree construction method. Bioconsensus 2001: 135-160 - 2000
- [c16]David Fernández-Baca, Timo Seppäläinen, Giora Slutzki:
Parametric Multiple Sequence Alignment and Phylogeny Construction. CPM 2000: 69-83 - [c15]David Fernández-Baca:
Multi-parameter Minimum Spanning Trees. LATIN 2000: 217-226
1990 – 1999
- 1999
- [c14]David Fernández-Baca, Timo Seppäläinen, Giora Slutzki:
Bounds for Parametric Sequence Comparison. SPIRE/CRIWG 1999: 55-62 - 1998
- [j18]David Fernández-Baca, Jens Lagergren:
On the Approximability of the Steiner Tree Problem in Phylogeny. Discret. Appl. Math. 88(1-3): 129-145 (1998) - [c13]David Fernández-Baca:
Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry. LATIN 1998: 33-41 - 1997
- [j17]David Fernández-Baca, Giora Slutzki:
Optimal Parametric Search on Graphs of Bounded Tree-Width. J. Algorithms 22(2): 212-240 (1997) - [j16]David Fernández-Baca, Giora Slutzki:
Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. Theor. Comput. Sci. 181(1): 57-74 (1997) - 1996
- [j15]Richa Agarwala, David Fernández-Baca:
Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs. Int. J. Found. Comput. Sci. 7(1): 11-22 (1996) - [j14]David Fernández-Baca, Giora Slutzki, David Eppstein:
Using Sparsification for Parametric Minimum Spanning Tree Problems. Nord. J. Comput. 3(4): 352-366 (1996) - [j13]Richa Agarwala, David Fernández-Baca:
Weighted Multidimensional Search and Its Application to Convex Optimization. SIAM J. Comput. 25(1): 83-99 (1996) - [c12]David Fernández-Baca, Jens Lagergren:
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. ICALP 1996: 670-680 - [c11]David Fernández-Baca, Jens Lagergren:
On the Approximability of the Steiner Tree Problem in Phylogeny. ISAAC 1996: 65-74 - [c10]David Fernández-Baca, Giora Slutzki, David Eppstein:
Using Sparsification for Parametric Minimum Spanning Tree Problems. SWAT 1996: 149-160 - 1995
- [j12]Richa Agarwala, David Fernández-Baca:
Weighted Search in the Plane. Inf. Process. Lett. 54(2): 97-100 (1995) - [j11]Richa Agarwala, David Fernández-Baca, Giora Slutzki:
Fast Algorithms for Inferring Evolutionary Trees. J. Comput. Biol. 2(3): 397-407 (1995) - [c9]David Fernández-Baca, Giora Slutzki:
Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. LATIN 1995: 257-271 - 1994
- [j10]David Fernández-Baca, Giora Slutzki:
Parametric Problems on Graphs of Bounded Tree-Width. J. Algorithms 16(3): 408-430 (1994) - [j9]Richa Agarwala, David Fernández-Baca:
A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. SIAM J. Comput. 23(6): 1216-1224 (1994) - [c8]David Fernández-Baca, Giora Slutzki:
Optimal Parametric Search on Graphs of Bounded Tree-Width. SWAT 1994: 155-166 - 1993
- [j8]David Fernández-Baca, A. Medepalli:
Parametric Module Allocation on Partial k-Trees. IEEE Trans. Computers 42(6): 738-742 (1993) - [c7]Richa Agarwala, David Fernández-Baca:
A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. FOCS 1993: 140-147 - 1992
- [c6]Richa Agarwala, David Fernández-Baca:
Solving the Lagrangian Dual when the Number of Constraints is Fixed. FSTTCS 1992: 164-175 - [c5]David Fernández-Baca, Giora Slutzki:
Parametric Problems on Graphs of Bounded Tree-Width. SWAT 1992: 304-316 - 1991
- [j7]David Fernández-Baca, Mark A. Williams:
On Matroids and Hierarchical Graphs. Inf. Process. Lett. 38(3): 117-121 (1991) - [j6]David Fernández-Baca, S. Srinivasan:
Constructing the minimization diagram of a two-parameter problem. Oper. Res. Lett. 10(2): 87-93 (1991) - 1990
- [c4]David Fernández-Baca:
Space-Sweep Algorithms for Parametric Optimization (Extended Abstract). SWAT 1990: 264-275 - [c3]David Fernández-Baca, Mark A. Williams:
On Matroids and Hierarchical Graphs. SWAT 1990: 320-331
1980 – 1989
- 1989
- [j5]David Fernández-Baca, Charles U. Martel:
On the Efficiency of Maximum-Flow Algorithms on Networks with Small Integer Capacities. Algorithmica 4(2): 173-189 (1989) - [j4]David Fernández-Baca, Giora Slutzki:
Solving Parametric Problems on Trees. J. Algorithms 10(3): 381-402 (1989) - [j3]David Fernández-Baca:
Allocating Modules to Processors in a Distributed System. IEEE Trans. Software Eng. 15(11): 1427-1436 (1989) - [c2]David Fernández-Baca, Mark A. Williams:
Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version). WADS 1989: 563-576 - 1988
- [j2]David Fernández-Baca:
Nonserial Dynamic Programming Formulations of Satisfiability. Inf. Process. Lett. 27(6): 323-326 (1988) - [c1]David Fernández-Baca, Giora Slutzki:
Solving Parametric Problems on Trees. STACS 1988: 52-60 - 1987
- [j1]Dan Gusfield, Charles U. Martel, David Fernández-Baca:
Fast Algorithms for Bipartite Network Flow. SIAM J. Comput. 16(2): 237-251 (1987)
Coauthor Index
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