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Proteomics Section edited by Alexey I. Nesvizhskii

This section incorporates all aspects of proteomic analysis including but not limited to: methods and applications for the analysis of post-translational modifications, proteomic, mass spectroscopic, and chemoinformatic data.

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1.

Software   Open Access Highly Accessed

KNIME-CDK: Workflow-driven cheminformatics

Stephan Beisken, Thorsten Meinl, Bernd Wiswedel, Luis F de Figueiredo, Michael Berthold, Christoph Steinbeck BMC Bioinformatics 2013, 14:257 (22 August 2013)

Abstract | Full text | PDF | ePUB

2.

Methodology article   Open Access Highly Accessed

PKIS: computational identification of protein kinases for experimentally discovered protein phosphorylation sites

Liang Zou, Mang Wang, Yi Shen, Jie Liao, Ao Li, Minghui Wang BMC Bioinformatics 2013, 14:247 (13 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

3.

Methodology article   Open Access Highly Accessed

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

Varun Jaiswal, Sree Chanumolu, Ankit Gupta, Rajinder S Chauhan, Chittaranjan Rout BMC Bioinformatics 2013, 14:211 (1 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

4.

Methodology article   Open Access Highly Accessed

Comparison study on statistical features of predicted secondary structures for protein structural class prediction: From content to position

Qi Dai, Yan Li, Xiaoqing Liu, Yuhua Yao, Yunjie Cao, Pingan He BMC Bioinformatics 2013, 14:152 (4 May 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Software   Open Access

VaccImm: simulating peptide vaccination in cancer therapy

Joachim von Eichborn, Anna Woelke, Filippo Castiglione, Robert Preissner BMC Bioinformatics 2013, 14:127 (15 April 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Research article   Open Access

An efficient post-hoc integration method improving peak alignment of metabolomics data from GCxGC/TOF-MS

Jaesik Jeong, Xiang Zhang, Xue Shi, Seongho Kim, Changyu Shen BMC Bioinformatics 2013, 14:123 (10 April 2013)

Abstract | Full text | PDF | ePUB | PubMed

7.

Methodology article   Open Access Highly Accessed

An AUC-based permutation variable importance measure for random forests

Silke Janitza, Carolin Strobl, Anne-Laure Boulesteix BMC Bioinformatics 2013, 14:119 (5 April 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Methodology article   Open Access

Optimal precursor ion selection for LC-MALDI MS/MS

Alexandra Zerck, Eckhard Nordhoff, Hans Lehrach, Knut Reinert BMC Bioinformatics 2013, 14:56 (18 February 2013)

Abstract | Full text | PDF | ePUB | PubMed

9.

Software   Open Access Highly Accessed

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis

Brian L LaMarche, Kevin L Crowell, Navdeep Jaitly, Vladislav A Petyuk, Anuj R Shah, Ashoka D Polpitiya, John D Sandoval, Gary R Kiebel, Matthew E Monroe, Stephen J Callister, Thomas O Metz, Gordon A Anderson, Richard D Smith BMC Bioinformatics 2013, 14:49 (12 February 2013)

Abstract | Full text | PDF | PubMed

10.

Software   Open Access

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data

Karan Uppal, Quinlyn A Soltow, Frederick H Strobel, W Stephen Pittard, Kim M Gernert, Tianwei Yu, Dean P Jones BMC Bioinformatics 2013, 14:15 (16 January 2013)

Abstract | Full text | PDF | PubMed

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