Fast Algorithms for Bipartite Network Flow. - Dan Gusfield; Charles U. Martel; David Fernández-Baca (SIAM J. Comput., 1987)

Nonserial Dynamic Programming Formulations of Satisfiability. - David Fernández-Baca (Inf. Process. Lett., 1988)

Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version). - David Fernández-Baca; Mark A. Williams (WADS, 1989)

On the Efficiency of Maximum-Flow Algorithms on Networks with Small Integer Capacities. - David Fernández-Baca; Charles U. Martel (Algorithmica, 1989)

Solving Parametric Problems on Trees. - David Fernández-Baca; Giora Slutzki (J. Algorithms, 1989)

Allocating Modules to Processors in a Distributed System. - David Fernández-Baca (IEEE Trans. Software Eng., 1989)

Space-Sweep Algorithms for Parametric Optimization (Extended Abstract). - David Fernández-Baca (SWAT, 1990)

On Matroids and Hierarchical Graphs. - David Fernández-Baca; Mark A. Williams (Inf. Process. Lett., 1991)

Constructing the minimization diagram of a two-parameter problem. - David Fernández-Baca; S. Srinivasan (Oper. Res. Lett., 1991)

Solving the Lagrangian Dual when the Number of Constraints is Fixed. - Richa Agarwala; David Fernández-Baca (FSTTCS, 1992)

Parametric Module Allocation on Partial k-Trees. - David Fernández-Baca; A. Medepalli (IEEE Trans. Computers, 1993)

Parametric Problems on Graphs of Bounded Tree-Width. - David Fernández-Baca; Giora Slutzki (J. Algorithms, 1994)

A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed. - Richa Agarwala; David Fernández-Baca (SIAM J. Comput., 1994)

Weighted Search in the Plane. - Richa Agarwala; David Fernández-Baca (Inf. Process. Lett., 1995)

Fast Algorithms for Inferring Evolutionary Trees. - Richa Agarwala; David Fernández-Baca; Giora Slutzki (J. Comput. Biol., 1995)

Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs. - Richa Agarwala; David Fernández-Baca (Int. J. Found. Comput. Sci., 1996)

Using Sparsification for Parametric Minimum Spanning Tree Problems. - David Fernández-Baca; Giora Slutzki; David Eppstein (Nord. J. Comput., 1996)

Weighted Multidimensional Search and Its Application to Convex Optimization. - Richa Agarwala; David Fernández-Baca (SIAM J. Comput., 1996)

Optimal Parametric Search on Graphs of Bounded Tree-Width. - David Fernández-Baca; Giora Slutzki (J. Algorithms, 1997)

Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs. - David Fernández-Baca; Giora Slutzki (Theor. Comput. Sci., 1997)

Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry. - David Fernández-Baca (LATIN, 1998)

On the Approximability of the Steiner Tree Problem in Phylogeny. - David Fernández-Baca; Jens Lagergren (Discret. Appl. Math., 1998)

Multi-parameter Minimum Spanning Trees. - David Fernández-Baca (LATIN, 2000)

Flipping: A supertree construction method. - Duhong Chen; Lixia Diao; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (Bioconsensus, 2001)

On Nonlinear Parametric Search. - David Fernández-Baca (Algorithmica, 2001)

Supertrees by Flipping. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (COCOON, 2002)

Bounds for parametric sequence comparison. - David Fernández-Baca; Timo Seppäläinen; Giora Slutzki (Discret. Appl. Math., 2002)

A Polynomial-Time Algorithm for Near-Perfect Phylogeny. - David Fernández-Baca; Jens Lagergren (SIAM J. Comput., 2003)

Decomposable multi-parameter matroid optimization problems. - David Fernández-Baca (Theor. Comput. Sci., 2003)

Rainbow: a toolbox for phylogenetic supertree construction and analysis. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca (Bioinform., 2004)

Inverse parametric sequence alignment. - Fangting Sun; David Fernández-Baca; Wei Yu 003 (J. Algorithms, 2004)

Parametric multiple sequence alignment and phylogeny construction. - David Fernández-Baca; Timo Seppäläinen; Giora Slutzki (J. Discrete Algorithms, 2004)

Minimum-Flip Supertrees: Complexity and Algorithms. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Sensitivity Analysis in Combinatorial Optimization. - Balaji Venkatachalam; David Fernández-Baca (Handbook of Approximation Algorithms and Metaheuristics, 2007)

Generalized Binary Tanglegrams: Algorithms and Applications. - Mukul S. Bansal; Wen-Chieh Chang 002; Oliver Eulenstein; David Fernández-Baca (BICoB, 2009)

Computing distances between partial rankings. - Mukul S. Bansal; David Fernández-Baca (Inf. Process. Lett., 2009)

Parametric analysis for ungapped Markov models of evolution. - David Fernández-Baca; Balaji Venkatachalam (ACM Trans. Algorithms, 2009)

Robinson-Foulds Supertrees. - Mukul S. Bansal; J. Gordon Burleigh; Oliver Eulenstein; David Fernández-Baca (Algorithms Mol. Biol., 2010)

Constructing majority-rule supertrees. - Jianrong Dong; David Fernández-Baca; Fred R. McMorris (Algorithms Mol. Biol., 2010)

iGTP: A software package for large-scale gene tree parsimony analysis. - Ruchi Chaudhary; Mukul S. Bansal; André Wehe; David Fernández-Baca; Oliver Eulenstein (BMC Bioinform., 2010)

Constructing Large Conservative Supertrees. - Jianrong Dong; David Fernández-Baca (WABI, 2011)

Graph triangulations and the compatibility of unrooted phylogenetic trees. - Sudheer Vakati; David Fernández-Baca (Appl. Math. Lett., 2011)

An ILP solution for the gene duplication problem. - Wen-Chieh Chang 002; J. Gordon Burleigh; David Fernández-Baca; Oliver Eulenstein (BMC Bioinform., 2011)

An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies. - Jianrong Dong; David Fernández-Baca; Fred R. McMorris; Robert C. Powers (Discret. Appl. Math., 2011)

Comparing and aggregating partially resolved trees. - Mukul S. Bansal; Jianrong Dong; David Fernández-Baca (Theor. Comput. Sci., 2011)

Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms. - Akshay Deepak; Jianrong Dong; David Fernández-Baca (ISBRA, 2012)

Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters. - Brad Shutters; Sudheer Vakati; David Fernández-Baca (WABI, 2012)

A simple characterization of the minimal obstruction sets for three-state perfect phylogenies. - Brad Shutters; David Fernández-Baca (Appl. Math. Lett., 2012)

Preface to CLEI 2011 Special Issue. - José Aguilar 001; John Atkinson 001; Yezid Donoso; David Fernández-Baca; Ernst L. Leiss; Gabriela Marín; Luciana Porcher Nedel; Oscar Pastor 001 (CLEI Electron. J., 2012)

Improved Lower Bounds on the Compatibility of Multi-State Characters - Brad Shutters; Sudheer Vakati; David Fernández-Baca (CoRR, 2012)

On Two Graph-Theoretic Characterizations of Tree Compatibility - Sudheer Vakati; David Fernández-Baca (CoRR, 2012)

Fast Local Search for Unrooted Robinson-Foulds Supertrees. - Ruchi Chaudhary; J. Gordon Burleigh; David Fernández-Baca (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. - Ruchi Chaudhary; John Gordon Burleigh; David Fernández-Baca (Algorithms Mol. Biol., 2013)

Extracting conflict-free information from multi-labeled trees. - Akshay Deepak; David Fernández-Baca; Michelle M. McMahon (Algorithms Mol. Biol., 2013)

Incompatible quartets, triplets, and characters. - Brad Shutters; Sudheer Vakati; David Fernández-Baca (Algorithms Mol. Biol., 2013)

Editorial. - David Fernández-Baca (Algorithmica, 2014)

Enumerating all maximal frequent subtrees in collections of phylogenetic trees. - Akshay Deepak; David Fernández-Baca (Algorithms Mol. Biol., 2014)

Characterizing compatibility and agreement of unrooted trees via cuts in graphs. - Sudheer Vakati; David Fernández-Baca (Algorithms Mol. Biol., 2014)

EvoMiner: frequent subtree mining in phylogenetic databases. - Akshay Deepak; David Fernández-Baca; Srikanta Tirthapura; Michael J. Sanderson; Michelle M. McMahon (Knowl. Inf. Syst., 2014)

Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis. - Ruchi Chaudhary; David Fernández-Baca; J. Gordon Burleigh (AlCoB, 2015)

MulRF: a software package for phylogenetic analysis using multi-copy gene trees. - Ruchi Chaudhary; David Fernández-Baca; John Gordon Burleigh (Bioinform., 2015)

Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors. - Sudheer Vakati; David Fernández-Baca (Electron. Notes Discret. Math., 2015)

Fixed-Parameter Algorithms for Finding Agreement Supertrees. - David Fernández-Baca; Sylvain Guillemot; Brad Shutters; Sudheer Vakati (SIAM J. Comput., 2015)

Fast Compatibility Testing for Phylogenies with Nested Taxa. - Yun Deng 003; David Fernández-Baca (WABI, 2016)

An efficient algorithm for testing the compatibility of phylogenies with nested taxa. - Yun Deng 003; David Fernández-Baca (Algorithms Mol. Biol., 2017)

Sensitivity Analysis in Combinatorial Optimization. - David Fernández-Baca; Balaji Venkatachalam (Handbook of Approximation Algorithms and Metaheuristics (1), 2018)

Fast Compatibility Testing for Rooted Phylogenetic Trees. - Yun Deng 003; David Fernández-Baca (Algorithmica, 2018)

On compatibility and incompatibility of collections of unrooted phylogenetic trees. - David Fernández-Baca; Sudheer Vakati (Discret. Appl. Math., 2018)

Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study. - David Fernández-Baca; Lei Liu 055 (Algorithms, 2019)

EvoZip: Efficient Compression of Large Collections of Evolutionary Trees. - Balanand Jha; David Fernández-Baca; Akshay Deepak; Kumar Abhishek 004 (CoRR, 2019)

Checking Phylogenetic Decisiveness in Theory and in Practice. - Ghazaleh Parvini; Katherine Braught; David Fernández-Baca (ISBRA, 2020)

Testing the Agreement of Trees with Internal Labels. - David Fernández-Baca; Lei Liu (CoRR, 2020)

Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences. - Ashish Ranjan 003; Md. Shah Fahad; David Fernández-Baca; Akshay Deepak; Sudhakar Tripathi (IEEE ACM Trans. Comput. Biol. Bioinform., 2020)

Testing the agreement of trees with internal labels. - David Fernández-Baca; Lei Liu 055 (Algorithms Mol. Biol., 2021)

Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness. - Ghazaleh Parvini; David Fernández-Baca (CoRR, 2021)

Checking Phylogenetics Decisiveness in Theory and in Practice. - Ghazaleh Parvini; Katherine Braught; David Fernández-Baca (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation. - Ashish Ranjan 003; David Fernández-Baca; Sudhakar Tripathi; Akshay Deepak (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

MCWS-Transformers: Towards an Efficient Modeling of Protein Sequences via Multi Context-Window Based Scaled Self-Attention. - Ashish Ranjan 003; Md. S. Fahad; David Fernández-Baca; Sudhakar Tripathi; Akshay Deepak (IEEE ACM Trans. Comput. Biol. Bioinform., 2023)