David Fernández-Baca

ORCID

Publication Activity (10 Years)

Years Active: 1987-2023
Publications (10 Years): 18

Top Venues

CoRR

Algorithms Mol. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Algorithmica

Publications

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) (2023)
Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
Checking Phylogenetics Decisiveness in Theory and in Practice. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
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) (2022)
Ghazaleh Parvini, David Fernández-Baca
Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness. CoRR (2021)
David Fernández-Baca, Lei Liu
Testing the agreement of trees with internal labels. Algorithms Mol. Biol. 16 (1) (2021)
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) (2020)
Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
Checking Phylogenetic Decisiveness in Theory and in Practice. CoRR (2020)
David Fernández-Baca, Lei Liu
Testing the Agreement of Trees with Internal Labels. CoRR (2020)
Ghazaleh Parvini, Katherine Braught, David Fernández-Baca
Checking Phylogenetic Decisiveness in Theory and in Practice. ISBRA (2020)
David Fernández-Baca, Lei Liu
Testing the Agreement of Trees with Internal Labels. ISBRA (2020)
Balanand Jha, David Fernández-Baca, Akshay Deepak, Kumar Abhishek
EvoZip: Efficient Compression of Large Collections of Evolutionary Trees. CoRR (2019)
David Fernández-Baca, Lei Liu
Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study. Algorithms 12 (3) (2019)
David Fernández-Baca, Sudheer Vakati
On compatibility and incompatibility of collections of unrooted phylogenetic trees. Discret. Appl. Math. 245 (2018)
Yun Deng, David Fernández-Baca
Fast Compatibility Testing for Rooted Phylogenetic Trees. Algorithmica 80 (8) (2018)
Yun Deng, David Fernández-Baca
An efficient algorithm for testing the compatibility of phylogenies with nested taxa. Algorithms Mol. Biol. 12 (1) (2017)
Yun Deng, David Fernández-Baca
Fast Compatibility Testing for Phylogenies with Nested Taxa. WABI (2016)
Yun Deng, David Fernández-Baca
Fast Compatibility Testing for Phylogenies with Nested Taxa. CoRR (2016)
Yun Deng, David Fernández-Baca
Fast Compatibility Testing for Rooted Phylogenetic Trees. CPM (2016)
Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. CoRR (2015)
Ruchi Chaudhary, David Fernández-Baca, J. Gordon Burleigh
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. AlCoB (2015)
Sudheer Vakati, David Fernández-Baca
Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors. Electron. Notes Discret. Math. 50 (2015)
Yun Deng, David Fernández-Baca
Fast Compatibility Testing for Rooted Phylogenetic Trees. CoRR (2015)
Ruchi Chaudhary, David Fernández-Baca, John Gordon Burleigh
MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinform. 31 (3) (2015)
David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati
Fixed-Parameter Algorithms for Finding Agreement Supertrees. SIAM J. Comput. 44 (2) (2015)
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) (2014)
Sudheer Vakati, David Fernández-Baca
Characterizing compatibility and agreement of unrooted trees via cuts in graphs. Algorithms Mol. Biol. 9 (2014)
Akshay Deepak, David Fernández-Baca
Enumerating all maximal frequent subtrees in collections of phylogenetic trees. Algorithms Mol. Biol. 9 (2014)
David Fernández-Baca
Editorial. Algorithmica 70 (2) (2014)
Sudheer Vakati, David Fernández-Baca
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. CoRR (2013)
Sudheer Vakati, David Fernández-Baca
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs. WABI (2013)
Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
Extracting conflict-free information from multi-labeled trees. Algorithms Mol. Biol. 8 (2013)
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 (2013)
Brad Shutters, Sudheer Vakati, David Fernández-Baca
Incompatible quartets, triplets, and characters. Algorithms Mol. Biol. 8 (2013)
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)
Brad Shutters, David Fernández-Baca
A simple characterization of the minimal obstruction sets for three-state perfect phylogenies. Appl. Math. Lett. 25 (9) (2012)
Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
Extracting Conflict-Free Information from Multi-labeled Trees. WABI (2012)
Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance CoRR (2012)
Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
Extracting Conflict-free Information from Multi-labeled Trees CoRR (2012)
Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
Fast Local Search for Unrooted Robinson-Foulds Supertrees. IEEE ACM Trans. Comput. Biol. Bioinform. 9 (4) (2012)
David Fernández-Baca, Sylvain Guillemot, Brad Shutters, Sudheer Vakati
Fixed-Parameter Algorithms for Finding Agreement Supertrees. CPM (2012)
Akshay Deepak, Jianrong Dong, David Fernández-Baca
Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms. ISBRA (2012)
Sudheer Vakati, David Fernández-Baca
On Two Graph-Theoretic Characterizations of Tree Compatibility CoRR (2012)
Brad Shutters, Sudheer Vakati, David Fernández-Baca
Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. WABI (2012)
Brad Shutters, Sudheer Vakati, David Fernández-Baca
Improved Lower Bounds on the Compatibility of Multi-State Characters CoRR (2012)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and aggregating partially resolved trees. Theor. Comput. Sci. 412 (48) (2011)
Jianrong Dong, David Fernández-Baca
Constructing Large Conservative Supertrees. WABI (2011)
Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein
An ILP solution for the gene duplication problem. BMC Bioinform. 12 (S-1) (2011)
Sudheer Vakati, David Fernández-Baca
Graph triangulations and the compatibility of unrooted phylogenetic trees. Appl. Math. Lett. 24 (5) (2011)
Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
Fast Local Search for Unrooted Robinson-Foulds Supertrees. ISBRA (2011)
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) (2011)
Brad Shutters, David Fernández-Baca
A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies CoRR (2011)
Jianrong Dong, David Fernández-Baca, Fred R. McMorris
Constructing majority-rule supertrees. Algorithms Mol. Biol. 5 (2010)
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5 (2010)
Sudheer Vakati, David Fernández-Baca
Graph Triangulations and the Compatibility of Unrooted Phylogenetic Trees CoRR (2010)
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 (2010)
Jianrong Dong, David Fernández-Baca, Fred R. McMorris
Constructing Majority-Rule Supertrees. WABI (2009)
Mukul S. Bansal, David Fernández-Baca
Computing distances between partial rankings. Inf. Process. Lett. 109 (4) (2009)
Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB (2009)
David Fernández-Baca, Balaji Venkatachalam
Parametric analysis for ungapped Markov models of evolution. ACM Trans. Algorithms 5 (4) (2009)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and Aggregating Partially Resolved Trees CoRR (2009)
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
Comparing and Aggregating Partially Resolved Trees. LATIN (2008)
Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
Minimum-Flip Supertrees: Complexity and Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (2) (2006)
David Fernández-Baca, Balaji Venkatachalam
Parametric Analysis for Ungapped Markov Models of Evolution. CPM (2005)
David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
Parametric multiple sequence alignment and phylogeny construction. J. Discrete Algorithms 2 (2) (2004)
Duhong Chen, Oliver Eulenstein, David Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinform. 20 (16) (2004)
Fangting Sun, David Fernández-Baca, Wei Yu
Inverse parametric sequence alignment. J. Algorithms 53 (1) (2004)
David Fernández-Baca
Decomposable multi-parameter matroid optimization problems. Theor. Comput. Sci. 297 (1-3) (2003)
David Fernández-Baca, Jens Lagergren
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. SIAM J. Comput. 32 (5) (2003)
Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
Supertrees by Flipping. COCOON (2002)
David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
Bounds for parametric sequence comparison. Discret. Appl. Math. 118 (3) (2002)
Fangting Sun, David Fernández-Baca, Wei Yu
Inverse Parametric Sequence Alignment. COCOON (2002)
David Fernández-Baca
On Nonlinear Parametric Search. Algorithmica 30 (1) (2001)
Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
Flipping: A supertree construction method. Bioconsensus (2001)
David Fernández-Baca
Multi-parameter Minimum Spanning Trees. LATIN (2000)
David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
Parametric Multiple Sequence Alignment and Phylogeny Construction. CPM (2000)
David Fernández-Baca, Timo Seppäläinen, Giora Slutzki
Bounds for Parametric Sequence Comparison. SPIRE/CRIWG (1999)
David Fernández-Baca
Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry. LATIN (1998)
David Fernández-Baca, Jens Lagergren
On the Approximability of the Steiner Tree Problem in Phylogeny. Discret. Appl. Math. 88 (1-3) (1998)
David Fernández-Baca, Giora Slutzki
Optimal Parametric Search on Graphs of Bounded Tree-Width. J. Algorithms 22 (2) (1997)
David Fernández-Baca, Giora Slutzki
Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. Theor. Comput. Sci. 181 (1) (1997)
David Fernández-Baca, Jens Lagergren
A Polynomial-Time Algorithm for Near-Perfect Phylogeny. ICALP (1996)
David Fernández-Baca, Giora Slutzki, David Eppstein
Using Sparsification for Parametric Minimum Spanning Tree Problems. Nord. J. Comput. 3 (4) (1996)
Richa Agarwala, David Fernández-Baca
Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs. Int. J. Found. Comput. Sci. 7 (1) (1996)
David Fernández-Baca, Giora Slutzki, David Eppstein
Using Sparsification for Parametric Minimum Spanning Tree Problems. SWAT (1996)
Richa Agarwala, David Fernández-Baca
Weighted Multidimensional Search and Its Application to Convex Optimization. SIAM J. Comput. 25 (1) (1996)
David Fernández-Baca, Jens Lagergren
On the Approximability of the Steiner Tree Problem in Phylogeny. ISAAC (1996)
David Fernández-Baca, Giora Slutzki
Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. LATIN (1995)
Richa Agarwala, David Fernández-Baca, Giora Slutzki
Fast Algorithms for Inferring Evolutionary Trees. J. Comput. Biol. 2 (3) (1995)
Richa Agarwala, David Fernández-Baca
Weighted Search in the Plane. Inf. Process. Lett. 54 (2) (1995)
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) (1994)
David Fernández-Baca, Giora Slutzki
Parametric Problems on Graphs of Bounded Tree-Width. J. Algorithms 16 (3) (1994)
David Fernández-Baca, Giora Slutzki
Optimal Parametric Search on Graphs of Bounded Tree-Width. SWAT (1994)
Richa Agarwala, David Fernández-Baca
A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed FOCS (1993)
David Fernández-Baca, A. Medepalli
Parametric Module Allocation on Partial k-Trees. IEEE Trans. Computers 42 (6) (1993)
David Fernández-Baca, Giora Slutzki
Parametric Problems on Graphs of Bounded Tree-Width. SWAT (1992)
Richa Agarwala, David Fernández-Baca
Solving the Lagrangian Dual when the Number of Constraints is Fixed. FSTTCS (1992)
David Fernández-Baca, Mark A. Williams
On Matroids and Hierarchical Graphs. Inf. Process. Lett. 38 (3) (1991)
David Fernández-Baca, S. Srinivasan
Constructing the minimization diagram of a two-parameter problem. Oper. Res. Lett. 10 (2) (1991)
David Fernández-Baca
Space-Sweep Algorithms for Parametric Optimization (Extended Abstract). SWAT (1990)
David Fernández-Baca, Mark A. Williams
On Matroids and Hierarchical Graphs. SWAT (1990)

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Publication Activity (10 Years)

Top Topics

Top Venues

David Fernández-Baca