Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

(2012) C. Fritsch et al.   GENOME RESEARCH

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

(2012) Kang Ning et al.   JOURNAL OF PROTEOME RESEARCH

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

(2012) Nicholas T Ingolia et al.   Nature Protocols

LNCipedia: a database for annotated human lncRNA transcript sequences and structures

(2012) Pieter-Jan Volders et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution

(2012) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding Human Cytomegalovirus

(2012) N. Stern-Ginossar et al.   SCIENCE

Translational Control via Protein-Regulated Upstream Open Reading Frames

(2011) Jan Medenbach et al.   CELL

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

(2011) Nicholas T. Ingolia et al.   CELL

Improvements in Proteomic Metrics of Low Abundance Proteins through Proteome Equalization Using ProteoMiner Prior to MudPIT

(2011) Bryan R. Fonslow et al.   JOURNAL OF PROTEOME RESEARCH

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

Bioinformatics Analysis of aSaccharomyces cerevisiaeN-Terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-Translational N-Terminal Acetylation

(2011) Kenny Helsens et al.   JOURNAL OF PROTEOME RESEARCH

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

(2011) François-Michel Boisvert et al.   MOLECULAR & CELLULAR PROTEOMICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Selecting protein N-terminal peptides by combined fractional diagonal chromatography

(2011) An Staes et al.   Nature Protocols

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA

(2011) F. Zhang et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Hundreds of putatively functional small open reading frames in Drosophila

(2011) Emmanuel Ladoukakis et al.   GENOME BIOLOGY

Prediction of novel miRNAs and associated target genes in Glycine max

(2010) Trupti Joshi et al.   BMC BIOINFORMATICS

C/EBP  uORF mice--a genetic model for uORF-mediated translational control in mammals

(2010) K. Wethmar et al.   GENES & DEVELOPMENT

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

Expanding the Dipeptidyl Peptidase 4-Regulated Peptidome via an Optimized Peptidomics Platform

(2010) Arthur D. Tinoco et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Complementary positional proteomics for screening substrates of endo- and exoproteases

(2010) Petra Van Damme et al.   NATURE METHODS

Expanding the mouse embryonic stem cell proteome: Combining three proteomic approaches

(2010) Rebekah L. Gundry et al.   PROTEOMICS

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

The Proteomics Identifications database: 2010 update

(2009) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

(2009) T. Arnesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Alternative Translation Initiation in Rat Brain Yields K2P2.1 Potassium Channels Permeable to Sodium

(2008) Dierk Thomas et al.   NEURON

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC)

(2008) An Staes et al.   PROTEOMICS