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Database and informatics methods

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads

Harish Nagarajan, Jessica E. Butler, Anna Klimes, Yu Qiu, Karsten Zengler, Joy Ward, Nelson D. Young, Barbara A. Methé, Bernhard Ø. Palsson, Derek R. Lovley, Christian L. Barrett

published 08 Jun 2010

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Nucleic Acid Template and the Risk of a PCR-Induced HIV-1 Drug Resistance Mutation

Vici Varghese, Elijah Wang, Farbod Babrzadeh, Michael H. Bachmann, Rajin Shahriar, Tommy Liu, Svetlana Jean M. Mappala, Baback Gharizadeh, W. Jeffrey Fessel, David Katzenstein, Seble Kassaye, Robert W. Shafer

published 07 Jun 2010

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“Topological Significance” Analysis of Gene Expression and Proteomic Profiles from Prostate Cancer Cells Reveals Key Mechanisms of Androgen Response

Adaikkalam Vellaichamy, Zoltán Dezső, Lellean JeBailey, Arul M. Chinnaiyan, Arun Sreekumar, Alexey I. Nesvizhskii, Gilbert S. Omenn, Andrej Bugrim

published 03 Jun 2010

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Oligonucleotide Sequence Motifs as Nucleosome Positioning Signals

Clayton K. Collings, Alfonso G. Fernandez, Chad G. Pitschka, Troy B. Hawkins, John N. Anderson

published 03 Jun 2010

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VitAL: Viterbi Algorithm for de novo Peptide Design

E. Besray Unal, Attila Gursoy, Burak Erman

published 02 Jun 2010

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W-Curve Alignments for HIV-1 Genomic Comparisons

Douglas J. Cork, Steven Lembark, Sodsai Tovanabutra, Merlin L. Robb, Jerome H. Kim

published 01 Jun 2010

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Validation of Coevolving Residue Algorithms via Pipeline Sensitivity Analysis: ELSC and OMES and ZNMI, Oh My!

Christopher A. Brown, Kevin S. Brown

published 01 Jun 2010

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Genome-Wide Identification of Calcium-Response Factor (CaRF) Binding Sites Predicts a Role in Regulation of Neuronal Signaling Pathways

Andreas R. Pfenning, Tae-Kyung Kim, James M. Spotts, Martin Hemberg, Dan Su, Anne E. West

published 27 May 2010

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A Framework for Classification of Prokaryotic Protein Kinases

Nidhi Tyagi, Krishanpal Anamika, Narayanaswamy Srinivasan

published 26 May 2010

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Identification of Novel Pathogenicity Loci in Clostridium perfringens Strains That Cause Avian Necrotic Enteritis

Dion Lepp, Bryan Roxas, Valeria R. Parreira, Pradeep R. Marri, Everett L. Rosey, Joshua Gong, J. Glenn Songer, Gayatri Vedantam, John F. Prescott

published 24 May 2010

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A Data Integration Approach to Mapping OCT4 Gene Regulatory Networks Operative in Embryonic Stem Cells and Embryonal Carcinoma Cells

Marc Jung, Hedi Peterson, Lukas Chavez, Pascal Kahlem, Hans Lehrach, Jaak Vilo, James Adjaye

published 21 May 2010

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What Leads Indians to Participate in Clinical Trials? A Meta-Analysis of Qualitative Studies

Jatin Y. Shah, Amruta Phadtare, Dimple Rajgor, Meenakshi Vaghasia, Shreyasee Pradhan, Hilary Zelko, Ricardo Pietrobon

published 20 May 2010

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Allelic Gene Structure Variations in Anopheles gambiae Mosquitoes

Jun Li, Jose M. C. Ribeiro, Guiyun Yan

published 19 May 2010

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