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

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

(2011) Nicholas T. Ingolia et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

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

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

(2011) A. G. Hinnebusch   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The quantitative proteome of a human cell line

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

Mapping intact protein isoforms in discovery mode using top-down proteomics

(2011) John C. Tran et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

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

Novel Application of Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) in Shotgun Proteomics: Comprehensive Profiling of Rat Kidney Proteome

(2010) Piliang Hao et al.   JOURNAL OF PROTEOME RESEARCH

Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics

(2010) Danielle L. Swaney et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

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

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Mapping of the Topography and Magnitude of Proteolytic Events in Apoptosis

(2008) Melissa M. Dix et al.   CELL

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

Silencing a Candidate Nematode Effector Gene Corresponding to the Tomato Resistance Gene Mi-1 Leads to Acquisition of Virulence

(2008) Cynthia A. Gleason et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Pyruvate kinase M2 is a phosphotyrosine-binding protein

(2008) Heather R. Christofk et al.   NATURE

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

Peptidase substrates via global peptide profiling

(2008) Debarati M Tagore et al.   Nature Chemical Biology

Electrostatic Repulsion Hydrophilic Interaction Chromatography for Isocratic Separation of Charged Solutes and Selective Isolation of Phosphopeptides

(2007) Andrew J. Alpert   ANALYTICAL CHEMISTRY