David Fernández-Baca

110 papers A* 2A 1B 11C 6Misc 2Journal 72Unranked 14

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	MCWS-Transformers: Towards an Efficient Modeling of Protein Sequences via Multi Context-Window Based Scaled Self-Attention. IEEE ACM Trans. Comput. Biol. Bioinform. Ashish Ranjan, Md. S. Fahad, David Fernández-Baca, Sudhakar Tripathi, Akshay Deepak
2022	J	`jnl`	An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation. IEEE ACM Trans. Comput. Biol. Bioinform. Ashish Ranjan, David Fernández-Baca, Sudhakar Tripathi, Akshay Deepak
2022	J	`jnl`	Checking Phylogenetics Decisiveness in Theory and in Practice. IEEE ACM Trans. Comput. Biol. Bioinform. Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
2021	J	`jnl`	Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness. CoRR Ghazaleh Parvini, David Fernández-Baca
2021	J	`jnl`	Testing the agreement of trees with internal labels. Algorithms Mol. Biol. David Fernández-Baca, Lei Liu
2020	—	`conf`	Checking Phylogenetic Decisiveness in Theory and in Practice. ISBRA Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
2020	J	`jnl`	Checking Phylogenetic Decisiveness in Theory and in Practice. CoRR Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
2020	J	`jnl`	Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. Ashish Ranjan, Md. Shah Fahad, David Fernández-Baca, Akshay Deepak, Sudhakar Tripathi
2020	—	`conf`	Testing the Agreement of Trees with Internal Labels. ISBRA David Fernández-Baca, Lei Liu
2020	J	`jnl`	Testing the Agreement of Trees with Internal Labels. CoRR David Fernández-Baca, Lei Liu
2019	J	`jnl`	EvoZip: Efficient Compression of Large Collections of Evolutionary Trees. CoRR Balanand Jha, David Fernández-Baca, Akshay Deepak, Kumar Abhishek
2019	J	`jnl`	Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study. Algorithms David Fernández-Baca, Lei Liu
2018	J	`jnl`	Fast Compatibility Testing for Rooted Phylogenetic Trees. Algorithmica Yun Deng, David Fernández-Baca
2018	J	`jnl`	On compatibility and incompatibility of collections of unrooted phylogenetic trees. Discret. Appl. Math. David Fernández-Baca, Sudheer Vakati
2018	—	`ch.`	Sensitivity Analysis in Combinatorial Optimization. Handbook of Approximation Algorithms and Metaheuristics (1) David Fernández-Baca, Balaji Venkatachalam
2017	J	`jnl`	An efficient algorithm for testing the compatibility of phylogenies with nested taxa. Algorithms Mol. Biol. Yun Deng, David Fernández-Baca
2016	C	`conf`	Fast Compatibility Testing for Phylogenies with Nested Taxa. WABI Yun Deng, David Fernández-Baca
2016	J	`jnl`	Fast Compatibility Testing for Phylogenies with Nested Taxa. CoRR Yun Deng, David Fernández-Baca
2016	B	`conf`	Fast Compatibility Testing for Rooted Phylogenetic Trees. CPM Yun Deng, David Fernández-Baca
2015	J	`jnl`	Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors. Electron. Notes Discret. Math. Sudheer Vakati, David Fernández-Baca
2015	—	`conf`	Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. AlCoB Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh
2015	J	`jnl`	Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. CoRR Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh
2015	J	`jnl`	Fast Compatibility Testing for Rooted Phylogenetic Trees. CoRR Yun Deng, David Fernández-Baca
2015	J	`jnl`	Fixed-Parameter Algorithms for Finding Agreement Supertrees. SIAM J. Comput. David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati
2015	J	`jnl`	MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinform. Ruchi Chaudhary, David Fernández-Baca, John Gordon Burleigh
2014	J	`jnl`	Characterizing compatibility and agreement of unrooted trees via cuts in graphs. Algorithms Mol. Biol. Sudheer Vakati, David Fernández-Baca
2014	J	`jnl`	Editorial. Algorithmica David Fernández-Baca
2014	J	`jnl`	Enumerating all maximal frequent subtrees in collections of phylogenetic trees. Algorithms Mol. Biol. Akshay Deepak, David Fernández-Baca
2014	J	`jnl`	EvoMiner: frequent subtree mining in phylogenetic databases. Knowl. Inf. Syst. Akshay Deepak, David Fernández-Baca, Srikanta Tirthapura, Michael J. Sanderson, Michelle M. McMahon
2013	C	`conf`	Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. WABI Sudheer Vakati, David Fernández-Baca
2013	J	`jnl`	Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. CoRR Sudheer Vakati, David Fernández-Baca
2013	J	`jnl`	Extracting conflict-free information from multi-labeled trees. Algorithms Mol. Biol. Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
2013	J	`jnl`	Incompatible quartets, triplets, and characters. Algorithms Mol. Biol. Brad Shutters, Sudheer Vakati, David Fernández-Baca
2013	J	`jnl`	Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms Mol. Biol. Ruchi Chaudhary, John Gordon Burleigh, David Fernández-Baca
2012	J	`jnl`	A simple characterization of the minimal obstruction sets for three-state perfect phylogenies. Appl. Math. Lett. Brad Shutters, David Fernández-Baca
2012	C	`conf`	Extracting Conflict-Free Information from Multi-labeled Trees. WABI Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
2012	J	`jnl`	Extracting Conflict-free Information from Multi-labeled Trees CoRR Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
2012	J	`jnl`	Fast Local Search for Unrooted Robinson-Foulds Supertrees. IEEE ACM Trans. Comput. Biol. Bioinform. Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
2012	B	`conf`	Fixed-Parameter Algorithms for Finding Agreement Supertrees. CPM David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati
2012	—	`conf`	Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms. ISBRA Akshay Deepak, Jianrong Dong, David Fernández-Baca
2012	J	`jnl`	Improved Lower Bounds on the Compatibility of Multi-State Characters CoRR Brad Shutters, Sudheer Vakati, David Fernández-Baca
2012	C	`conf`	Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. WABI Brad Shutters, Sudheer Vakati, David Fernández-Baca
2012	J	`jnl`	Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance CoRR Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
2012	B	`ed.`	LATIN 2012: Theoretical Informatics - 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings LATIN David Fernández-Baca
2012	J	`jnl`	On Two Graph-Theoretic Characterizations of Tree Compatibility CoRR Sudheer Vakati, David Fernández-Baca
2012	J	`jnl`	Preface to CLEI 2011 Special Issue. CLEI Electron. J. José Aguilar, John Atkinson, Yezid Donoso, David Fernández-Baca, Ernst L. Leiss, Gabriela Marín, Luciana Porcher Nedel, Oscar Pastor
2011	J	`jnl`	A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies CoRR Brad Shutters, David Fernández-Baca
2011	J	`jnl`	An ILP solution for the gene duplication problem. BMC Bioinform. Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein
2011	J	`jnl`	An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies. Discret. Appl. Math. Jianrong Dong, David Fernández-Baca, Fred R. McMorris, Robert C. Powers
2011	J	`jnl`	Comparing and aggregating partially resolved trees. Theor. Comput. Sci. Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2011	C	`conf`	Constructing Large Conservative Supertrees. WABI Jianrong Dong, David Fernández-Baca
2011	—	`conf`	Fast Local Search for Unrooted Robinson-Foulds Supertrees. ISBRA Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
2011	J	`jnl`	Graph triangulations and the compatibility of unrooted phylogenetic trees. Appl. Math. Lett. Sudheer Vakati, David Fernández-Baca
2010	J	`jnl`	Constructing majority-rule supertrees. Algorithms Mol. Biol. Jianrong Dong, David Fernández-Baca, Fred R. McMorris
2010	J	`jnl`	Graph Triangulations and the Compatibility of Unrooted Phylogenetic Trees CoRR Sudheer Vakati, David Fernández-Baca
2010	J	`jnl`	Robinson-Foulds Supertrees. Algorithms Mol. Biol. Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
2010	J	`jnl`	iGTP: A software package for large-scale gene tree parsimony analysis. BMC Bioinform. Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein
2009	J	`jnl`	Comparing and Aggregating Partially Resolved Trees CoRR Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2009	J	`jnl`	Computing distances between partial rankings. Inf. Process. Lett. Mukul S. Bansal, David Fernández-Baca
2009	C	`conf`	Constructing Majority-Rule Supertrees. WABI Jianrong Dong, David Fernández-Baca, Fred R. McMorris
2009	—	`conf`	Generalized Binary Tanglegrams: Algorithms and Applications. BICoB Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
2009	J	`jnl`	Parametric analysis for ungapped Markov models of evolution. ACM Trans. Algorithms David Fernández-Baca, Balaji Venkatachalam
2008	B	`conf`	Comparing and Aggregating Partially Resolved Trees. LATIN Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
2007	—	`ch.`	Sensitivity Analysis in Combinatorial Optimization. Handbook of Approximation Algorithms and Metaheuristics Balaji Venkatachalam, David Fernández-Baca
2006	J	`jnl`	Minimum-Flip Supertrees: Complexity and Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
2005	B	`conf`	Parametric Analysis for Ungapped Markov Models of Evolution. CPM David Fernández-Baca, Balaji Venkatachalam
2004	J	`jnl`	Inverse parametric sequence alignment. J. Algorithms Fangting Sun, David Fernández-Baca, Wei Yu
2004	J	`jnl`	Parametric multiple sequence alignment and phylogeny construction. J. Discrete Algorithms David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
2004	J	`jnl`	Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinform. Duhong Chen, Oliver Eulenstein, David Fernández-Baca
2003	J	`jnl`	A Polynomial-Time Algorithm for Near-Perfect Phylogeny. SIAM J. Comput. David Fernández-Baca, Jens Lagergren
2003	J	`jnl`	Decomposable multi-parameter matroid optimization problems. Theor. Comput. Sci. David Fernández-Baca
2002	J	`jnl`	Bounds for parametric sequence comparison. Discret. Appl. Math. David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
2002	Misc	`conf`	Inverse Parametric Sequence Alignment. COCOON Fangting Sun, David Fernández-Baca, Wei Yu
2002	Misc	`conf`	Supertrees by Flipping. COCOON Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
2001	—	`conf`	Flipping: A supertree construction method. Bioconsensus Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
2001	J	`jnl`	On Nonlinear Parametric Search. Algorithmica David Fernández-Baca
2000	B	`conf`	Multi-parameter Minimum Spanning Trees. LATIN David Fernández-Baca
2000	B	`conf`	Parametric Multiple Sequence Alignment and Phylogeny Construction. CPM David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
1999	—	`conf`	Bounds for Parametric Sequence Comparison. SPIRE/CRIWG David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
1998	B	`conf`	Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry. LATIN David Fernández-Baca
1998	J	`jnl`	On the Approximability of the Steiner Tree Problem in Phylogeny. Discret. Appl. Math. David Fernández-Baca, Jens Lagergren
1997	J	`jnl`	Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. Theor. Comput. Sci. David Fernández-Baca, Giora Slutzki
1997	J	`jnl`	Optimal Parametric Search on Graphs of Bounded Tree-Width. J. Algorithms David Fernández-Baca, Giora Slutzki
1996	A*	`conf`	A Polynomial-Time Algorithm for Near-Perfect Phylogeny. ICALP David Fernández-Baca, Jens Lagergren
1996	B	`conf`	On the Approximability of the Steiner Tree Problem in Phylogeny. ISAAC David Fernández-Baca, Jens Lagergren
1996	J	`jnl`	Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs. Int. J. Found. Comput. Sci. Richa Agarwala, David Fernández-Baca
1996	—	`conf`	Using Sparsification for Parametric Minimum Spanning Tree Problems. SWAT David Fernández-Baca, Giora Slutzki, David Eppstein
1996	J	`jnl`	Using Sparsification for Parametric Minimum Spanning Tree Problems. Nord. J. Comput. David Fernández-Baca, Giora Slutzki, David Eppstein
1996	J	`jnl`	Weighted Multidimensional Search and Its Application to Convex Optimization. SIAM J. Comput. Richa Agarwala, David Fernández-Baca
1995	J	`jnl`	Fast Algorithms for Inferring Evolutionary Trees. J. Comput. Biol. Richa Agarwala, David Fernández-Baca, Giora Slutzki
1995	B	`conf`	Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. LATIN David Fernández-Baca, Giora Slutzki
1995	J	`jnl`	Weighted Search in the Plane. Inf. Process. Lett. Richa Agarwala, David Fernández-Baca
1994	J	`jnl`	A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. SIAM J. Comput. Richa Agarwala, David Fernández-Baca
1994	—	`conf`	Optimal Parametric Search on Graphs of Bounded Tree-Width. SWAT David Fernández-Baca, Giora Slutzki
1994	J	`jnl`	Parametric Problems on Graphs of Bounded Tree-Width. J. Algorithms David Fernández-Baca, Giora Slutzki
1993	A*	`conf`	A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed FOCS Richa Agarwala, David Fernández-Baca
1993	J	`jnl`	Parametric Module Allocation on Partial k-Trees. IEEE Trans. Computers David Fernández-Baca, A. Medepalli
1992	—	`conf`	Parametric Problems on Graphs of Bounded Tree-Width. SWAT David Fernández-Baca, Giora Slutzki
1992	—	`conf`	Solving the Lagrangian Dual when the Number of Constraints is Fixed. FSTTCS Richa Agarwala, David Fernández-Baca
1991	J	`jnl`	Constructing the minimization diagram of a two-parameter problem. Oper. Res. Lett. David Fernández-Baca, S. Srinivasan
1991	J	`jnl`	On Matroids and Hierarchical Graphs. Inf. Process. Lett. David Fernández-Baca, Mark A. Williams
1990	—	`conf`	On Matroids and Hierarchical Graphs. SWAT David Fernández-Baca, Mark A. Williams
1990	—	`conf`	Space-Sweep Algorithms for Parametric Optimization (Extended Abstract). SWAT David Fernández-Baca
1989	J	`jnl`	Allocating Modules to Processors in a Distributed System. IEEE Trans. Software Eng. David Fernández-Baca
1989	B	`conf`	Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version). WADS David Fernández-Baca, Mark A. Williams
1989	J	`jnl`	On the Efficiency of Maximum-Flow Algorithms on Networks with Small Integer Capacities. Algorithmica David Fernández-Baca, Charles U. Martel
1989	J	`jnl`	Solving Parametric Problems on Trees. J. Algorithms David Fernández-Baca, Giora Slutzki
1988	J	`jnl`	Nonserial Dynamic Programming Formulations of Satisfiability. Inf. Process. Lett. David Fernández-Baca
1988	A	`conf`	Solving Parametric Problems on Trees. STACS David Fernández-Baca, Giora Slutzki
1987	J	`jnl`	Fast Algorithms for Bipartite Network Flow. SIAM J. Comput. Dan Gusfield, Charles U. Martel, David Fernández-Baca