Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis

Refinements to Label Free Proteome Quantitation: How to Deal with Peptides Shared by Multiple Proteins

(2010) Ying Zhang et al.   ANALYTICAL CHEMISTRY

PepC: proteomics software for identifying differentially expressed proteins based on spectral counting

(2010) N. L. Heinecke et al.   BIOINFORMATICS

Role of spectral counting in quantitative proteomics

(2010) Deborah H Lundgren et al.   Expert Review of Proteomics

In-Depth Proteomic Analyses of Direct Expressed Prostatic Secretions

(2010) Richard R. Drake et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Shotgun Proteomics Using Spectral Count Data and Quasi-Likelihood Modeling

(2010) Ming Li et al.   JOURNAL OF PROTEOME RESEARCH

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

(2010) Hyungwon Choi et al.   Molecular Systems Biology

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

(2010) Hyungwon Choi et al.   NATURE METHODS

Protein and gene model inference based on statistical modeling in k-partite graphs

(2010) S. Gerster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ReSASC: A resampling-based algorithm to determine differential protein expression from spectral count data

(2010) Kristina M. Little et al.   PROTEOMICS

Scaffold: A bioinformatic tool for validating MS/MS-based proteomic studies

(2010) Brian C. Searle   PROTEOMICS

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

A Global Protein Kinase and Phosphatase Interaction Network in Yeast

(2010) A. Breitkreutz et al.   SCIENCE

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics

(2009) Thang V. Pham et al.   BIOINFORMATICS

Estimating accuracy of RNA-Seq and microarrays with proteomics

(2009) Xing Fu et al.   BMC GENOMICS

Mass Spectrometry-Based Label-Free Quantitative Proteomics

(2009) Wenhong Zhu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics

(2009) Yong Fuga Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Network-assisted protein identification and data interpretation in shotgun proteomics

(2009) Jing Li et al.   Molecular Systems Biology

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PatternLab for proteomics: a tool for differential shotgun proteomics

(2008) Paulo C Carvalho et al.   BMC BIOINFORMATICS

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

(2008) Hyungwon Choi et al.   MOLECULAR & CELLULAR PROTEOMICS

Sorting Signals, N-Terminal Modifications and Abundance of the Chloroplast Proteome

(2008) Boris Zybailov et al.   PLoS One