Dynamic profiling of the protein life cycle in response to pathogens

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Rapid Temporal Dynamics of Transcription, Protein Synthesis, and Secretion during Macrophage Activation

(2014) Katrin Eichelbaum et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

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

(2014) Alexander O. Subtelny et al.   NATURE

TLR-driven early glycolytic reprogramming via the kinases TBK1-IKKɛ supports the anabolic demands of dendritic cell activation

(2014) Bart Everts et al.   NATURE IMMUNOLOGY

Genetic Influences on Translation in Yeast

(2014) Frank W. Albert et al.   PLoS Genetics

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

(2014) Jingyi Jessica Li et al.   PeerJ

Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation

(2013) R. Aviner et al.   GENES & DEVELOPMENT

Metabolic Pathways in Immune Cell Activation and Quiescence

(2013) Erika L. Pearce et al.   IMMUNITY

Quantitative Proteomics Reveals the Induction of Mitophagy in Tumor Necrosis Factor-α-activated (TNFα) Macrophages

(2013) Christina Bell et al.   MOLECULAR & CELLULAR PROTEOMICS

Initial Quantitative Proteomic Map of 28 Mouse Tissues Using the SILAC Mouse

(2013) Tamar Geiger et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Receptor interacting protein kinase 2–mediated mitophagy regulates inflammasome activation during virus infection

(2013) Christopher Lupfer et al.   NATURE IMMUNOLOGY

Integrated proteomic analysis of post-translational modifications by serial enrichment

(2013) Philipp Mertins et al.   NATURE METHODS

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

(2013) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Erik Ahrné et al.   PROTEOMICS

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

RNA-binding proteins in Mendelian disease

(2013) Alfredo Castello et al.   TRENDS IN GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Commitment to glycolysis sustains survival of NO-producing inflammatory dendritic cells

(2012) B. Everts et al.   BLOOD

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

Collective transport of coupled particles

(2012) D. Hennig et al.   EUROPEAN PHYSICAL JOURNAL B

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

Selective enrichment of newly synthesized proteins for quantitative secretome analysis

(2012) Katrin Eichelbaum et al.   NATURE BIOTECHNOLOGY

Protease bias in absolute protein quantitation

(2012) Mao Peng et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Decoding Human Cytomegalovirus

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

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

(2011) Nicolas Chevrier et al.   CELL

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef 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

Protein Expression Regulation under Oxidative Stress

(2011) Christine Vogel et al.   MOLECULAR & CELLULAR PROTEOMICS

Initial genome sequencing and analysis of multiple myeloma

(2011) Michael A. Chapman et al.   NATURE

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

Toll-like receptor-induced changes in glycolytic metabolism regulate dendritic cell activation

(2010) C. M. Krawczyk et al.   BLOOD

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

Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome

(2010) Manuel Weiss et al.   PROTEOMICS

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

DNA extraction procedures meaningfully influence qPCR-based mtDNA copy number determination

(2009) Wen Guo et al.   MITOCHONDRION

Global signatures of protein and mRNA expression levels

(2009) Raquel de Sousa Abreu et al.   Molecular BioSystems

SUnSET, a nonradioactive method to monitor protein synthesis

(2009) Enrico K Schmidt et al.   NATURE METHODS

Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses

(2009) I. Amit et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL

FLN29 Deficiency Reveals Its Negative Regulatory Role in the Toll-like Receptor (TLR) and Retinoic Acid-inducible Gene I (RIG-I)-like Helicase Signaling Pathway

(2008) Takahito Sanada et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Coupling and coordination in gene expression processes: a systems biology view

(2007) Suzanne Komili et al.   NATURE REVIEWS GENETICS