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Computational techniques

Functional Equivalency Inferred from “Authoritative Sources” in Networks of Homologous Proteins

Shreedhar Natarajan, Eric Jakobsson

Gene Classification Based on Amino Acid Motifs and Residues: The DLX (distal-less) Test Case

Nuno A. Fonseca, Cristina P. Vieira, Jorge Vieira

Quantitative Deep Sequencing Reveals Dynamic HIV-1 Escape and Large Population Shifts during CCR5 Antagonist Therapy In Vivo

Athe M. N. Tsibris, Bette Korber, [ ... ], Daniel R. Kuritzkes

smyRNA: A Novel Ab Initio ncRNA Gene Finder

Raheleh Salari, Cagri Aksay, [ ... ], S. Cenk Sahinalp

Repertoire of microRNAs in Epithelial Ovarian Cancer as Determined by Next Generation Sequencing of Small RNA cDNA Libraries

Stacia K. Wyman, Rachael K. Parkin, [ ... ], Muneesh Tewari

An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved

Joseph J. Gillespie, Nicole C. Ammerman, [ ... ], Abdu F. Azad

The Action of Key Factors in Protein Evolution at High Temporal Resolution

Armin Schmitt, Johannes Schuchhardt, Gudrun A. Brockmann

Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution

Daniel Y. Little, Lu Chen

Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors

Sarosh N. Fatakia, Stefano Costanzi, Carson C. Chow

Rich Pickings Near Large Communal Roosts Favor ‘Gang’ Foraging by Juvenile Common Ravens, Corvus corax

Sasha R. X. Dall, Jonathan Wright

Evidence for Co-Evolution between Human MicroRNAs and Alu-Repeats

Stefan Lehnert, Peter Van Loo, [ ... ], Frans C. Schuit

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

Holly J. Atkinson, John H. Morris, Thomas E. Ferrin, Patricia C. Babbitt

Ultraconserved Elements in the Olig2 Promoter

Christina T. L. Chen, David I. Gottlieb, Barak A. Cohen

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