mRNAs, proteins and the emerging principles of gene expression control

Quantitative Proteomics of the Cancer Cell Line Encyclopedia

(2020) David P. Nusinow et al.   CELL

Phase separation provides a mechanism to reduce noise in cells

(2020) A. Klosin et al.   SCIENCE

Keeping the Proportions of Protein Complex Components in Check

(2020) James Christopher Taggart et al.   Cell Systems

Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation

(2020) Barbora Salovska et al.   Molecular Systems Biology

Proteogenomic Characterization of Human Early-Onset Gastric Cancer

(2019) Dong-Gi Mun et al.   CANCER CELL

Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause

(2019) Christian P. Moritz et al.   JOURNAL OF NEUROCHEMISTRY

The Case for Proteomics and Phospho‐Proteomics in Personalized Cancer Medicine

(2019) Sophia Doll et al.   Proteomics Clinical Applications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues

(2019) Basak Eraslan et al.   Molecular Systems Biology

Disentangling Genetic and Environmental Effects on the Proteotypes of Individuals

(2019) Natalie Romanov et al.   CELL

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Exploiting inter-data relationships in next-generation proteomics analysis

(2019) Burcu Vitrinel et al.   MOLECULAR & CELLULAR PROTEOMICS

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Protein aggregation mediates stoichiometry of protein complexes in aneuploid cells

(2019) Christopher M. Brennan et al.   GENES & DEVELOPMENT

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Local translation in neurons: visualization and function

(2019) Christine E. Holt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

(2019) Andrea Riba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of targeted protein degradation therapeutics

(2019) Philip P. Chamberlain et al.   Nature Chemical Biology

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Context is everything: aneuploidy in cancer

(2019) Uri Ben-David et al.   NATURE REVIEWS GENETICS

Of Gene Expression and Cell Division Time: A Mathematical Framework for Advanced Differential Gene Expression and Data Analysis

(2019) Katharina Baum et al.   Cell Systems

Enamel proteome shows that Gigantopithecus was an early diverging pongine

(2019) Frido Welker et al.   NATURE

Co-regulation map of the human proteome enables identification of protein functions

(2019) Georg Kustatscher et al.   NATURE BIOTECHNOLOGY

Cellular quality control by the ubiquitin-proteasome system and autophagy

(2019) Christian Pohl et al.   SCIENCE

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Relative and Absolute Quantitation in Mass Spectrometry–Based Proteomics

(2018) J. Astor Ankney et al.   Annual Review of Analytical Chemistry

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis

(2018) Mikhail M. Savitski et al.   CELL

Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics

(2018) Jana Zecha et al.   MOLECULAR & CELLULAR PROTEOMICS

How many human proteoforms are there?

(2018) Ruedi Aebersold et al.   Nature Chemical Biology

A brave new world of RNA-binding proteins

(2018) Matthias W. Hentze et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Evolution of Gene Expression in cis and trans

(2018) Sarah A. Signor et al.   TRENDS IN GENETICS

Systematic analysis of protein turnover in primary cells

(2018) Toby Mathieson et al.   Nature Communications

The extent of ribosome queuing in budding yeast

(2018) Alon Diament et al.   PLoS Computational Biology

Local and global influences on protein turnover in neurons and glia

(2018) Aline R Dörrbaum et al.   eLife

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups

(2018) Tenley C. Archer et al.   CANCER CELL

Quality Control of Orphaned Proteins

(2018) Szymon Juszkiewicz et al.   MOLECULAR CELL

Translation deregulation in human disease

(2018) Soroush Tahmasebi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Translational Control during Developmental Transitions

(2018) Felipe Karam Teixeira et al.   Cold Spring Harbor Perspectives in Biology

Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts

(2018) Aleksej Zelezniak et al.   Cell Systems

Artificial Intelligence Understands Peptide Observability and Assists With Absolute Protein Quantification

(2018) David Zimmer et al.   Frontiers in Plant Science

Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells

(2018) Doris Popovic et al.   Cell Systems

Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes

(2018) James C. Taggart et al.   Cell Systems

Ribosome Stoichiometry: From Form to Function

(2018) Edward Emmott et al.   TRENDS IN BIOCHEMICAL SCIENCES

Quantitative body fluid proteomics in medicine — A focus on minimal invasiveness

(2017) Éva Csősz et al.   Journal of Proteomics

Pervasive coexpression of spatially proximal genes is buffered at the protein level

(2017) Georg Kustatscher et al.   Molecular Systems Biology

Revisiting biomarker discovery by plasma proteomics

(2017) Philipp E Geyer et al.   Molecular Systems Biology

Can we predict protein from mRNA levels?

(2017) Nikolaus Fortelny et al.   NATURE

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

(2017) John D Lapek et al.   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Regulation of mitochondrial biogenesis in erythropoiesis by mTORC1-mediated protein translation

(2017) Xin Liu et al.   NATURE CELL BIOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Thiol-linked alkylation of RNA to assess expression dynamics

(2017) Veronika A Herzog et al.   NATURE METHODS

UBE2O remodels the proteome during terminal erythroid differentiation

(2017) Anthony T. Nguyen et al.   SCIENCE

UBE2O is a quality control factor for orphans of multiprotein complexes

(2017) Kota Yanagitani et al.   SCIENCE

RNA localization is a key determinant of neurite-enriched proteome

(2017) Alessandra Zappulo et al.   Nature Communications

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells

(2017) Theodoros I. Roumeliotis et al.   Cell Reports

Post-transcriptional regulation across human tissues

(2017) Alexander Franks et al.   PLoS Computational Biology

Time-Resolved Proteomics Extends Ribosome Profiling-Based Measurements of Protein Synthesis Dynamics

(2017) Tzu-Yu Liu et al.   Cell Systems

Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer

(2017) Emanuel Gonçalves et al.   Cell Systems

Tracking the Missing Footprints of Idle Ribosomes

(2017) Nicholas T. Ingolia   Cell Systems

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation

(2016) Erik McShane et al.   CELL

Experiments on Plant Hybrids by Gregor Mendel

(2016) S. Abbott et al.   GENETICS

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

(2016) Jing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Eyes on Translation

(2016) Marina Chekulaeva et al.   MOLECULAR CELL

Digital Quantification of Proteins and mRNA in Single Mammalian Cells

(2016) Cem Albayrak et al.   MOLECULAR CELL

Gene‐specific correlation of RNA and protein levels in human cells and tissues

(2016) Fredrik Edfors et al.   Molecular Systems Biology

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress

(2016) Z. Cheng et al.   Molecular Systems Biology

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

(2016) Vasiliy O. Sysoev et al.   Nature Communications

The landscape of chromosomal aberrations in breast cancer mouse models reveals driver-specific routes to tumorigenesis

(2016) Uri Ben-David et al.   Nature Communications

Comprehensive Proteomic Analysis of Human Erythropoiesis

(2016) Emilie-Fleur Gautier et al.   Cell Reports

Post-transcriptional Wnt Signaling Governs Epididymal Sperm Maturation

(2015) Stefan Koch et al.   CELL

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development

(2015) Leonid Peshkin et al.   DEVELOPMENTAL CELL

Aneuploidy-induced cellular stresses limit autophagic degradation

(2015) Stefano Santaguida et al.   GENES & DEVELOPMENT

Negative feedback buffers effects of regulatory variants

(2015) D. M. Bader et al.   Molecular Systems Biology

Gene expression analysis identifies global gene dosage sensitivity in cancer

(2015) Rudolf S N Fehrmann et al.   NATURE GENETICS

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

Adding another dimension to gene regulation

(2015) Linda Koch   NATURE REVIEWS GENETICS

Pervasive robustness in biological systems

(2015) Marie-Anne Félix et al.   NATURE REVIEWS GENETICS

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Quantitative affinity purification mass spectrometry: a versatile technology to study protein–protein interactions

(2015) Katrina Meyer et al.   Frontiers in Genetics

Cellular Differences in Protein Synthesis Regulate Tissue Homeostasis

(2014) Michael Buszczak et al.   CELL

Global characterization of the oocyte-to-embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism

(2014) M. Stoeckius et al.   EMBO JOURNAL

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Comparative primate genomics: emerging patterns of genome content and dynamics

(2014) Jeffrey Rogers et al.   NATURE REVIEWS GENETICS

Coupling mRNA processing with transcription in time and space

(2014) David L. Bentley   NATURE REVIEWS GENETICS

Impact of regulatory variation from RNA to protein

(2014) A. Battle et al.   SCIENCE

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

(2014) Noah Dephoure et al.   eLife

Synthesis and degradation jointly determine the responsiveness of the cellular proteome

(2013) Björn Schwanhäusser et al.   BIOESSAYS

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

(2013) C. J. McManus et al.   GENOME RESEARCH

Evolution at two levels of gene expression in yeast

(2013) C. G. Artieri et al.   GENOME RESEARCH

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

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

High-resolution network biology: connecting sequence with function

(2013) Colm J. Ryan et al.   NATURE REVIEWS GENETICS

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

(2013) Erik Ahrné et al.   PROTEOMICS

Direct Proteomic Quantification of the Secretome of Activated Immune Cells

(2013) F. Meissner et al.   SCIENCE

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells

(2013) J. Kronke et al.   SCIENCE

The Myeloma Drug Lenalidomide Promotes the Cereblon-Dependent Destruction of Ikaros Proteins

(2013) G. Lu et al.   SCIENCE

Transcription factor binding kinetics constrain noise suppression via negative feedback

(2013) Andreas Grönlund et al.   Nature Communications

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

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

(2012) Samuel Marguerat et al.   CELL

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

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

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

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Identification of Aneuploidy-Selective Antiproliferation Compounds

(2011) Yun-Chi Tang 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

Ubiquitination of E3 ligases: self-regulation of the ubiquitin system via proteolytic and non-proteolytic mechanisms

(2011) P de Bie et al.   CELL DEATH AND DIFFERENTIATION

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

(2011) A. Schlattl et al.   GENOME 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

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Jacob and Monod: From Operons to EvoDevo

(2010) Alexander Gann   CURRENT BIOLOGY

Emerging properties of animal gene regulatory networks

(2010) Eric H. Davidson   NATURE

Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells

(2010) Tamar Geiger et al.   PLoS Genetics

Targeting Proteins for Destruction by the Ubiquitin System: Implications for Human Pathobiology

(2008) Alan L. Schwartz et al.   Annual Review of Pharmacology and Toxicology

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

(2008) Mary K. Doherty et al.   JOURNAL OF PROTEOME RESEARCH

Widespread changes in protein synthesis induced by microRNAs

(2008) Matthias Selbach et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA