Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets

PDV: an integrative proteomics data viewer

(2018) Kai Li et al.   BIOINFORMATICS

The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics

(2017) Juan Antonio Vizcaíno et al.   MOLECULAR & CELLULAR PROTEOMICS

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards

(2014) Fawaz Ghali et al.   PROTEOMICS

Analysis of phosphoproteome in rice pistil

(2014) Kun Wang et al.   PROTEOMICS

The 3,000 rice genomes project: new opportunities and challenges for future rice research

(2014) Jia-Yang Li et al.   GigaScience

The 3,000 rice genomes project

(2014)   GigaScience

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

(2013) Jainab Khatun et al.   BMC GENOMICS

Deep Coverage of theEscherichia coliProteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments

(2013) Karsten Krug et al.   MOLECULAR & CELLULAR PROTEOMICS

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Stress Responsive Proteins Are Actively Regulated during Rice (Oryza sativa) Embryogenesis as Indicated by Quantitative Proteomics Analysis

(2013) Jin Zi et al.   PLoS One

Identification of Proteins Enriched in Rice Egg or Sperm Cells by Single-Cell Proteomics

(2013) Mafumi Abiko et al.   PLoS One

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics

(2011) Mohamed Helmy et al.   BMC PLANT BIOLOGY

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

PeaksPTM: Mass Spectrometry-Based Identification of Peptides with Unspecified Modifications

(2011) Xi Han et al.   JOURNAL OF PROTEOME RESEARCH

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA