Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Integrative Genomics Identifies the Corepressor SMRT as a Gatekeeper of Adipogenesis through the Transcription Factors C/EBPβ and KAISO

(2012) Sunil K. Raghav et al.   MOLECULAR CELL

Mass spectrometry-based absolute protein quantification: PSAQ™ strategy makes use of “noncanonical” proteotypic peptides

(2012) Michel Jaquinod et al.   PROTEOMICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

(2011) Rasmus Siersbaek et al.   EMBO JOURNAL

The importance of the digest: Proteolysis and absolute quantification in proteomics

(2011) Philip Brownridge et al.   METHODS

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

(2011) Suman S. Thakur et al.   MOLECULAR & CELLULAR PROTEOMICS

Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma

(2011) Eric Kuhn et al.   MOLECULAR & CELLULAR PROTEOMICS

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines

(2011) Marlis Zeiler et al.   MOLECULAR & CELLULAR PROTEOMICS

A targeted proteomics–based pipeline for verification of biomarkers in plasma

(2011) Jeffrey R Whiteaker et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Rapid empirical discovery of optimal peptides for targeted proteomics

(2011) Andrew B Stergachis et al.   NATURE METHODS

Automated protein-DNA interaction screening of Drosophila regulatory elements

(2011) Korneel Hens et al.   NATURE METHODS

Genome-Wide and Phase-Specific DNA-Binding Rhythms of BMAL1 Control Circadian Output Functions in Mouse Liver

(2011) Guillaume Rey et al.   PLOS BIOLOGY

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

(2011) Tommy Kaplan et al.   PLoS Genetics

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

A Quantitative Study of the Effects of Chaotropic Agents, Surfactants, and Solvents on the Digestion Efficiency of Human Plasma Proteins by Trypsin

(2010) Jennifer L. Proc et al.   JOURNAL OF PROTEOME RESEARCH

Stoichiometry Determination of the MP1−p14 Complex Using a Novel and Cost-Efficient Method To Produce an Equimolar Mixture of Standard Peptides

(2009) Johann Holzmann et al.   ANALYTICAL CHEMISTRY

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development

(2009) Amol Prakash et al.   JOURNAL OF PROTEOME RESEARCH

FLEXIQuant: A Novel Tool for the Absolute Quantification of Proteins, and the Simultaneous Identification and Quantification of Potentially Modified Peptides

(2009) Sasha Singh et al.   JOURNAL OF PROTEOME RESEARCH

DNA-centered approaches to characterize regulatory protein–DNA interaction complexes

(2009) Jovan Simicevic et al.   Molecular BioSystems

Quantitative interaction proteomics using mass spectrometry

(2009) Alexander Wepf et al.   NATURE METHODS

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes

(2009) Paola Picotti et al.   NATURE METHODS

From DNA sequence to transcriptional behaviour: a quantitative approach

(2009) Eran Segal et al.   NATURE REVIEWS GENETICS

Insights from genomic profiling of transcription factors

(2009) Peggy J. Farnham   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Proteomic Analysis of Human Adipose Tissue After Rosiglitazone Treatment Shows Coordinated Changes to Promote Glucose Uptake

(2009) Meftun Ahmed et al.   Obesity

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

Absolute SILAC for Accurate Quantitation of Proteins in Complex Mixtures Down to the Attomole Level

(2008) Stefan Hanke et al.   JOURNAL OF PROTEOME RESEARCH

Temporal Profiling of the Adipocyte Proteome during Differentiation Using a Five-Plex SILAC Based Strategy

(2008) Henrik Molina et al.   JOURNAL OF PROTEOME RESEARCH

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks

(2008) Alain Dupuis et al.   PROTEOMICS