System wide analyses have underestimated protein abundances and the importance of transcription in mammals

Poly(A)-tail profiling reveals an embryonic switch in translational control

(2014) Alexander O. Subtelny et al.   NATURE

Protein synthesis rate is the predominant regulator of protein expression during differentiation

(2013) A. R. Kristensen et al.   Molecular Systems Biology

Parallel measurement of dynamic changes in translation rates in single cells

(2013) Kyuho Han et al.   NATURE METHODS

Critical assessment of proteome-wide label-free absolute abundance estimation strategies

(2013) Erik Ahrné et al.   PROTEOMICS

A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways

(2013) Paul Michael Loriaux et al.   PLoS Computational Biology

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

(2012) Marcus Bantscheff et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells

(2012) Daniel Hebenstreit et al.   CURRENT OPINION IN CELL BIOLOGY

Identification of microRNA-regulated gene networks by expression analysis of target genes

(2012) Vincenzo Alessandro Gennarino et al.   GENOME RESEARCH

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

(2012) Jacek R Wiśniewski et al.   Molecular Systems Biology

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

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

(2011) Nicholas T. Ingolia et al.   CELL

MicroRNAs and developmental timing

(2011) Victor Ambros   CURRENT OPINION IN GENETICS & DEVELOPMENT

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

microRNAs and the Operon Paper

(2011) Nikolaus Rajewsky   JOURNAL OF MOLECULAR BIOLOGY

Systems-wide Proteomic Analysis in Mammalian Cells Reveals Conserved, Functional Protein Turnover

(2011) Sidney B. Cambridge 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

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

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

The quantitative proteome of a human cell line

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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Cdc45 Limits Replicon Usage from a Low Density of preRCs in Mammalian Cells

(2011) Philip G. Wong et al.   PLoS One

Proteome Half-Life Dynamics in Living Human Cells

(2011) E. Eden et al.   SCIENCE

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Mammalian microRNAs predominantly act to decrease target mRNA levels

(2010) Huili Guo et al.   NATURE

Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe

(2010) Dong-Uk Kim et al.   NATURE BIOTECHNOLOGY

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

(2009) Srilatha Kuntumalla et al.   Proteome Science

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

The impact of microRNAs on protein output

(2008) Daehyun Baek et al.   NATURE

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

LNA-mediated microRNA silencing in non-human primates

(2008) Joacim Elmén et al.   NATURE

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Gene Regulation by Transcription Factors and MicroRNAs

(2008) O. Hobert   SCIENCE