44 citations · 52 across the 14 of their papers we have counts for
14 papers
Testing the Agreement of Trees with Internal Labels
David Fernández-Baca, Lei Liu
The input to the agreement problem is a collection of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question…
EvoZip: Efficient Compression of Large Collections of Evolutionary Trees
Balanand Jha, David Fernández-Baca, Akshay Deepak +1
Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a…
Deep Robust Framework for Protein Function Prediction using Variable-Length Protein Sequences
Ashish Ranjan, Md Shah Fahad, David Fernandez-Baca +2
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a part…
Fast Compatibility Testing for Phylogenies with Nested Taxa
Yun Deng, David Fernández-Baca
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labele…
Fast Compatibility Testing for Rooted Phylogenetic Trees
Yun Deng, David Fernández-Baca
We consider the following basic problem in phylogenetic tree construction. Let be a collection of rooted phylogenetic trees over various subset…
Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis
Ruchi Chaudhary, David Fernandez-Baca, J. Gordon Burleigh
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially ac…
Characterizing Compatibility and Agreement of Unrooted Trees via Cuts in Graphs
Sudheer Vakati, David Fernández-Baca
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We c…
On Two Graph-Theoretic Characterizations of Tree Compatibility
Sudheer Vakati, David Fernández-Baca
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have…
Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance
Ruchi Chaudhary, J. Gordon Burleigh, David Fernández-Baca
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees…
Extracting Conflict-free Information from Multi-labeled Trees
Akshay Deepak, David Fernández-Baca, Michelle M. McMahon
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relat…
Improved Lower Bounds on the Compatibility of Multi-State Characters
Brad Shutters, Sudheer Vakati, David Fernández-Baca
We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function such that, for any se…
A Simple Characterization of the Minimal Obstruction Sets for Three-State Perfect Phylogenies
Brad Shutters, David Fernández-Baca
Lam, Gusfield, and Sridhar (2009) showed that a set of three-state characters has a perfect phylogeny if and only if every subset of three characters has a perfect phylogeny. They…
Graph Triangulations and the Compatibility of Unrooted Phylogenetic Trees
Sudheer Vakati, David Fernández-Baca
We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has…
Comparing and Aggregating Partially Resolved Trees
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies…