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Computational techniques

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

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

published 01 Jun 2009

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

Athe M. N. Tsibris, Bette Korber, Ramy Arnaout, Carsten Russ, Chien-Chi Lo, Thomas Leitner, Brian Gaschen, James Theiler, Roger Paredes, Zhaohui Su, Michael D. Hughes, Roy M. Gulick, Wayne Greaves, Eoin Coakley, Charles Flexner, Chad Nusbaum, Daniel R. Kuritzkes

published 25 May 2009

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smyRNA: A Novel Ab Initio ncRNA Gene Finder

Raheleh Salari, Cagri Aksay, Emre Karakoc, Peter J. Unrau, Iman Hajirasouliha, S. Cenk Sahinalp

published 05 May 2009

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

Stacia K. Wyman, Rachael K. Parkin, Patrick S. Mitchell, Brian R. Fritz, Kathy O'Briant, Andrew K. Godwin, Nicole Urban, Charles W. Drescher, Beatrice S. Knudsen, Muneesh Tewari

published 23 Apr 2009

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An Anomalous Type IV Secretion System in Rickettsia Is Evolutionarily Conserved

Joseph J. Gillespie, Nicole C. Ammerman, Sheila M. Dreher-Lesnick, M. Sayeedur Rahman, Micah J. Worley, Joao C. Setubal, Bruno S. Sobral, Abdu F. Azad

published 12 Mar 2009

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

Armin Schmitt, Johannes Schuchhardt, Gudrun A. Brockmann

published 12 Mar 2009

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

Daniel Y. Little, Lu Chen

published 10 Mar 2009

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

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

published 05 Mar 2009

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

Sasha R. X. Dall, Jonathan Wright

published 25 Feb 2009

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

Stefan Lehnert, Peter Van Loo, Pushpike J. Thilakarathne, Peter Marynen, Geert Verbeke, Frans C. Schuit

published 11 Feb 2009

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

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

published 03 Feb 2009

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Ultraconserved Elements in the Olig2 Promoter

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

published 16 Dec 2008

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FastBLAST: Homology Relationships for Millions of Proteins

Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin

published 31 Oct 2008

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