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Biological databases

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

Alison R. Erickson, Brandi L. Cantarel, Regina Lamendella, Youssef Darzi, Emmanuel F. Mongodin, Chongle Pan, Manesh Shah, Jonas Halfvarson, Curt Tysk, Bernard Henrissat, Jeroen Raes, Nathan C. Verberkmoes, Claire M. Fraser, Robert L. Hettich, Janet K. Jansson

published 28 Nov 2012

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Identification of Nucleotide-Binding Sites in Protein Structures: A Novel Approach Based on Nucleotide Modularity

Luca Parca, Pier Federico Gherardini, Mauro Truglio, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello

published 27 Nov 2012

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Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

Amit Kumar Yadav, Dhirendra Kumar, Debasis Dash

published 26 Nov 2012

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Prediction of Protein-Destabilizing Polymorphisms by Manual Curation with Protein Structure

Craig Alan Gough, Keiichi Homma, Yumi Yamaguchi-Kabata, Makoto K. Shimada, Ranajit Chakraborty, Yasuyuki Fujii, Hisakazu Iwama, Shinsei Minoshima, Shigetaka Sakamoto, Yoshiharu Sato, Yoshiyuki Suzuki, Masahito Tada-Umezaki, Ken Nishikawa, Tadashi Imanishi, Takashi Gojobori

published 26 Nov 2012

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De-MetaST-BLAST: A Tool for the Validation of Degenerate Primer Sets and Data Mining of Publicly Available Metagenomes

Christopher A. Gulvik, T. Chad Effler, Steven W. Wilhelm, Alison Buchan

published 26 Nov 2012

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OTU Analysis Using Metagenomic Shotgun Sequencing Data

Xiaolin Hao, Ting Chen

published 26 Nov 2012

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CyanoPhyChe: A Database for Physico-Chemical Properties, Structure and Biochemical Pathway Information of Cyanobacterial Proteins

P. V. Parvati Sai Arun, Ranjith Kumar Bakku, Mranu Subhashini, Pankaj Singh, N. Prakash Prabhu, Iwane Suzuki, Jogadhenu S. S. Prakash

published 21 Nov 2012

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Exploring Pandora's Box: Potential and Pitfalls of Low Coverage Genome Surveys for Evolutionary Biology

Florian Leese, Philipp Brand, Andrey Rozenberg, Christoph Mayer, Shobhit Agrawal, Johannes Dambach, Lars Dietz, Jana S. Doemel, William P. Goodall-Copstake, Christoph Held, Jennifer A. Jackson, Kathrin P. Lampert, Katrin Linse, Jan N. Macher, Jennifer Nolzen, Michael J. Raupach, Nicole T. Rivera, Christoph D. Schubart, Sebastian Striewski, Ralph Tollrian, Chester J. Sands

published 21 Nov 2012

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BCL::Score—Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

Nils Woetzel, Mert Karakaş, Rene Staritzbichler, Ralf Müller, Brian E. Weiner, Jens Meiler

published 16 Nov 2012

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BCL::Fold - De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements

Mert Karakaş, Nils Woetzel, Rene Staritzbichler, Nathan Alexander, Brian E. Weiner, Jens Meiler

published 16 Nov 2012

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Expression of Small RNA in Aphis gossypii and Its Potential Role in the Resistance Interaction with Melon

Sampurna Sattar, Charles Addo-Quaye, Yan Song, James A. Anstead, Ramanjulu Sunkar, Gary A. Thompson

published 16 Nov 2012

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Identification and Re-Evaluation of Freshwater Catfishes through DNA Barcoding

Maloyjo J. Bhattacharjee, Boni A. Laskar, Bishal Dhar, Sankar K. Ghosh

published 15 Nov 2012

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An Integrative Computational Framework Based on a Two-Step Random Forest Algorithm Improves Prediction of Zinc-Binding Sites in Proteins

Cheng Zheng, Mingjun Wang, Kazuhiro Takemoto, Tatsuya Akutsu, Ziding Zhang, Jiangning Song

published 14 Nov 2012

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