A Proteogenomic Survey of theMedicago truncatulaGenome

Comparative Large Scale Characterization of PlantversusMammal Proteins Reveals Similar and IdiosyncraticN-α-Acetylation Features

(2012) Willy V. Bienvenut et al.   MOLECULAR & CELLULAR PROTEOMICS

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana

(2011) Katja Baerenfaller et al.   Integrative Biology

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A non-canonical start codon in the Drosophila fragile X gene yields two functional isoforms

(2011) R.W. Beerman et al.   NEUROSCIENCE

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

(2011) Ivaylo P. Ivanov et al.   NUCLEIC ACIDS RESEARCH

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

COMPASS: A suite of pre- and post-search proteomics software tools for OMSSA

(2011) Craig D. Wenger et al.   PROTEOMICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Noncanonical Translation Initiation of the Arabidopsis Flowering Time and Alternative Polyadenylation Regulator FCA

(2010) G. G. Simpson et al.   PLANT CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

(2009) James C Wright et al.   BMC GENOMICS

CUG Start Codon Generates Thioredoxin/Glutathione Reductase Isoforms in Mouse Testes

(2009) Maxim V. Gerashchenko et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Large-Scale Phosphoprotein Analysis in Medicago truncatula Roots Provides Insight into in Vivo Kinase Activity in Legumes

(2009) P. A. Grimsrud et al.   PLANT PHYSIOLOGY

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

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

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE