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

Reconstruction of protein networks from an atlas of maize seed proteotypes

(2013) J. W. Walley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

False discovery rates in spectral identification

(2012) Kyowon Jeong et al.   BMC BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Building and Searching Tandem Mass Spectral Libraries for Peptide Identification

(2011) Henry Lam   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis ofMycobacterium tuberculosisBy High Resolution Mass Spectrometry

(2011) Dhanashree S. Kelkar et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis of Bacteria and Archaea: A 46 Organism Case Study

(2011) Eli Venter et al.   PLoS One

Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

(2011) Rebecca M. Davidson et al.   Plant Genome

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Overlapping genes in the human and mouse genomes

(2008) Chaitanya R Sanna et al.   BMC GENOMICS

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

(2008) G. E. Merrihew et al.   GENOME RESEARCH

Ortho-proteogenomics: Multiple proteomes investigation through orthology and a new MS-based protocol

(2008) S. Gallien et al.   GENOME RESEARCH

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

(2008) N. Gupta et al.   GENOME RESEARCH

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

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