Improved Phylogenetic Motif Detection Using Parsimony. - Usman Roshan; Dennis R. Livesay; David La (BIBE, 2005)

Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. - David La; Dennis R. Livesay (BMC Bioinform., 2005)

MINER: software for phylogenetic motif identification. - David La; Dennis R. Livesay (Nucleic Acids Res., 2005)

Improving progressive alignment for phylogeny reconstruction using parsimonious guide-trees. - Usman Roshan; Dennis R. Livesay; Satish Chikkagoudar (BIBE, 2006)

Probalign: multiple sequence alignment using partition function posterior probabilities. - Usman Roshan; Dennis R. Livesay (Bioinform., 2006)

Prediction of Enzyme Catalytic Sites from Sequence Using Neural Networks. - Swati Pande; Amar Raheja; Dennis R. Livesay (CIBCB, 2007)

How accurate and statistically robust are catalytic site predictions based on closeness centrality? - Eric Chea; Dennis R. Livesay (BMC Bioinform., 2007)

Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family. - Dennis R. Livesay; Patrick D. Kidd; Sepehr Eskandari; Usman Roshan (BMC Bioinform., 2007)

eProbalign: generation and manipulation of multiple sequence alignments using partition function posterior probabilities. - Satish Chikkagoudar; Usman Roshan; Dennis R. Livesay (Nucleic Acids Res., 2007)

Improving position-specific predictions of protein functional sites using phylogenetic motifs. - K. C. Dukka Bahadur; Dennis R. Livesay (Bioinform., 2008)

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. - Usman Roshan; Satish Chikkagoudar; Dennis R. Livesay (BMC Bioinform., 2008)

Conformational Entropy of an Ideal Cross-Linking Polymer Chain. - Oleg K. Vorov; Dennis R. Livesay; Donald J. Jacobs (Entropy, 2008)

PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences. - Satish Chikkagoudar; Dennis R. Livesay; Usman Roshan (Nucleic Acids Res., 2010)

Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble Game. - Luis C. González; Dennis R. Livesay; Donald J. Jacobs (BCB, 2011)

WaveMap: Interactively Discovering Features From Protein Flexibility Matrices Using Wavelet-based Visual Analytics. - Scott Barlowe; Yujie Liu 009; Jing Yang 001; Dennis R. Livesay; Donald J. Jacobs; James Mottonen; Deeptak Verma (Comput. Graph. Forum, 2011)

Topology Improves Phylogenetic Motif Functional Site Predictions. - K. C. Dukka Bahadur; Dennis R. Livesay (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged. - Deeptak Verma; Donald J. Jacobs; Dennis R. Livesay (PLoS Comput. Biol., 2012)

A visual analytics approach to exploring protein flexibility subspaces. - Scott Barlowe; Jing Yang 001; Donald J. Jacobs; Dennis R. Livesay; Jamal Alsakran; Ye Zhao 003; Deeptak Verma; James Mottonen (PacificVis, 2013)

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity. - Deeptak Verma; Donald J. Jacobs; Dennis R. Livesay (PLoS Comput. Biol., 2013)

A virtual pebble game to ensemble average graph rigidity. - Luis C. González; Hui Wang; Dennis R. Livesay; Donald J. Jacobs (Algorithms Mol. Biol., 2015)

Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments. - Tong Li; Malgorzata B. Tracka; Shahid Uddin; Jose Casas-Finet; Donald J. Jacobs; Dennis R. Livesay (PLoS Comput. Biol., 2015)