Standout Papers
Citation Impact
Citing Papers
Analytical distributions for stochastic gene expression
2008
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells
2010 StandoutScience
Ribosome Profiling Shows That miR-430 Reduces Translation Before Causing mRNA Decay in Zebrafish
2012 Science
RNAi in Budding Yeast
2009 Science
Dynamic profiling of the protein life cycle in response to pathogens
2015 Science
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes
2012
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
De novo design of self-assembling helical protein filaments
2018 StandoutScienceNobel
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans
2009
Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression
2008 Science
The Myeloma Drug Lenalidomide Promotes the Cereblon-Dependent Destruction of Ikaros Proteins
2013 StandoutScienceNobel
Counting Low-Copy Number Proteins in a Single Cell
2007 StandoutScienceNobel
Next-generation analysis of gene expression regulation – comparing the roles of synthesis and degradation
2015
Global signatures of protein and mRNA expression levels
2009
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
2014 Standout
Rate-Limiting Steps in Yeast Protein Translation
2013
A dynamic model of proteome changes reveals new roles for transcript alteration in yeast
2011
Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons
2013 StandoutNobel
Reconsidering Movement of Eukaryotic mRNAs between Polysomes and P Bodies
2011 StandoutNobel
Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation
2015 StandoutNobel
Negative feedback buffers effects of regulatory variants
2015
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
2011 Standout
Stochastic mRNA Synthesis in Mammalian Cells
2006
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
2015
The translational landscape of mTOR signalling steers cancer initiation and metastasis
2012 Nature
Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins
2013
Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression
2006
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
2012 Standout
nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs
2016
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
2012
Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources
2014
Ribosome profiling: new views of translation, from single codons to genome scale
2014
Antecedent- and response-focused emotion regulation: Divergent consequences for experience, expression, and physiology.
1998 Standout
Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock
2007 Nature
Modular and tunable biological feedback control using a de novo protein switch
2019 StandoutNatureNobel
Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
2009
Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown
2018 StandoutNobel
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
2003 Standout
Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
2009
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
2013 StandoutNobel
CRISPR interference (CRISPRi) for sequence-specific control of gene expression
2013
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
2008 Standout
Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans
2014
Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
2015
N6-methyladenosine Modulates Messenger RNA Translation Efficiency
2015 Standout
Reading RNA methylation codes through methyl-specific binding proteins
2014
Design of protein-interaction specificity gives selective bZIP-binding peptides
2009 Nature
Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
2012 StandoutNatureNobel
Protein interaction databases
2001
Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats
2015
Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway
2010
Comprehensive comparative analysis of strand-specific RNA sequencing methods
2010
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features
2013 Nature
Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions
2012
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
2006
Optimization of specificity in a cellular protein interaction network by negative selection
2003 Nature
Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution
2012 StandoutNobel
Mammalian microRNAs predominantly act to decrease target mRNA levels
2010 StandoutNature
Quantitative profiling of initiating ribosomes in vivo
2014
Translational control of immune responses: from transcripts to translatomes
2014
Evolution at two levels of gene expression in yeast
2013
Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation
2013
Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)
2014
Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates
2015
‘Ribozoomin’ – Translation Initiation from the Perspective of the Ribosome-bound Eukaryotic Initiation Factors (eIFs)
2012
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
2015
Coupling and coordination in gene expression processes: a systems biology view
2007
Posttranscriptional Expression Regulation: What Determines Translation Rates?
2007
The coming of age of de novo protein design
2016 StandoutNatureNobel
Universally increased mRNA stability downstream of the translation initiation site in eukaryotes and prokaryotes
2013
Reducing ligation bias of small RNAs in libraries for next generation sequencing
2012
The Perseus computational platform for comprehensive analysis of (prote)omics data
2016 Standout
Phenotypic Consequences of Promoter-Mediated Transcriptional Noise
2006
An efficient and sensitive method for preparing cDNA libraries from scarce biological samples
2014 StandoutNobel
Atlas of Subcellular RNA Localization Revealed by APEX-Seq
2019
Structure of mammalian eIF3 in the context of the 43S preinitiation complex
2015 StandoutNatureNobel
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
2011 Standout
Fiji: an open-source platform for biological-image analysis
2012 Standout
On the Dependency of Cellular Protein Levels on mRNA Abundance
2016 Standout
Diversifying microRNA sequence and function
2013
RNA-guided genetic silencing systems in bacteria and archaea
2012 StandoutNatureNobel
Insights into RNA structure and function from genome-wide studies
2014 StandoutNobel
Variability and memory of protein levels in human cells
2006 Nature
A unifying model for mTORC1-mediated regulation of mRNA translation
2012 Nature
Heritable Stochastic Switching Revealed by Single-Cell Genealogy
2007
Structural specificity in coiled-coil interactions
2008
Protein binding specificity versus promiscuity
2010
Mass spectrometry in high-throughput proteomics: ready for the big time
2010
De novo design of bioactive protein switches
2019 StandoutNatureNobel
Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells
2012
Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
2013
Transcription of functionally related constitutive genes is not coordinated
2010
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
2012
Evolution of chromosome organization driven by selection for reduced gene expression noise
2007
Single-RNA counting reveals alternative modes of gene expression in yeast
2008
Principles of Translational Control: An Overview
2012
Nascent transcript sequencing visualizes transcription at nucleotide resolution
2011 Nature
An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation
2010
Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition
2013 Nature
Deriving Heterospecific Self-Assembling Protein–Protein Interactions Using a Computational Interactome Screen
2015
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences
2011
Genome-wide measurement of RNA secondary structure in yeast
2010 Nature
Genome-Wide Translational Profiling by Ribosome Footprinting
2010
Imaging in Systems Biology
2007
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
2012 Standout
Control of Transcript Variability in Single Mammalian Cells
2015
N6-methyladenosine-dependent regulation of messenger RNA stability
2013 StandoutNature
Upstream open reading frames: Molecular switches in (patho)physiology
2010
Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo
2013 Nature
Rewiring the Specificity of Two-Component Signal Transduction Systems
2008
Programmable design of orthogonal protein heterodimers
2018 StandoutNatureNobel
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
2008
CasX enzymes comprise a distinct family of RNA-guided genome editors
2019 StandoutNatureNobel
Global quantification of mammalian gene expression control
2011 StandoutNature
lincRNAs act in the circuitry controlling pluripotency and differentiation
2011 StandoutNature
Lysosome-targeting chimaeras for degradation of extracellular proteins
2020 StandoutNatureNobel
Computational design of ligand-binding proteins with high affinity and selectivity
2013 StandoutNatureNobel
Evolution of Gene Regulation during Transcription and Translation
2015
Multistate approaches in computational protein design
2012
Structure-based Prediction of bZIP Partnering Specificity
2005
Correlation of mRNA and protein in complex biological samples
2009
Interplay between gene expression noise and regulatory network architecture
2012
Small RNAs are modified with N-glycans and displayed on the surface of living cells
2021 StandoutNobel
Risk Perception and Communication
1993
Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments
2013
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
2013 StandoutNobel
Hepatitis C Virus RNA Functionally Sequesters miR-122
2015 StandoutNobel
Strong association between mRNA folding strength and protein abundance in S. cerevisiae
2012
Synthetic protein–protein interaction domains created by shuffling Cys 2 His 2 zinc‐fingers
2006
The Struggle to Govern the Commons
2003 StandoutScienceNobel
A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly
2015
Increasing the affinity of selective bZIP‐binding peptides through surface residue redesign
2014
eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation
2016 StandoutNatureNobel
Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
2011 StandoutNobel
Networks of bZIP Protein-Protein Interactions Diversified Over a Billion Years of Evolution
2013 Science
Intermediate Filaments: Molecular Structure, Assembly Mechanism, and Integration Into Functionally Distinct Intracellular Scaffolds
2004
Monitoring cotranslational protein folding in mammalian cells at codon resolution
2012
Efficient translation initiation dictates codon usage at gene start
2013
Sequence signatures and mRNA concentration can explain two‐thirds of protein abundance variation in a human cell line
2010
Colored extrinsic fluctuations and stochastic gene expression
2008
Global Protein Stability Profiling in Mammalian Cells
2008 Science
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
2016 StandoutScienceNobel
A comprehensive two-hybrid analysis to explore the yeast protein interactome
2001 Standout
Genetic Determinants and Cellular Constraints in Noisy Gene Expression
2013 Science
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
2003 StandoutScienceNobel
Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils
2001
Translation efficiency is determined by both codon bias and folding energy
2010
Regulation of mRNA translation during mitosis
2015
Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks
2009
Impact of regulatory variation from RNA to protein
2014 Science
A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering
2010
Combinatorial promoter design for engineering noisy gene expression
2007
Comparative ribosome profiling reveals extensive translational complexity in differentTrypanosoma bruceilife cycle stages
2014
Tunable protein synthesis by transcript isoforms in human cells
2016 StandoutNobel
Reconfigurable asymmetric protein assemblies through implicit negative design
2022 StandoutScienceNobel
High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling
2011 Science
De novo design of protein logic gates
2020 StandoutScienceNobel
Works of J. Robert Newman being referenced
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
2009 StandoutScience
Comprehensive Identification of Human bZIP Interactions with Coiled-Coil Arrays
2003 Science
Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise
2006 Nature
Empirical scaling of common verbal phrases associated with numerical probabilities
1967
A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae
2000
Self-regulation of mood: Strategies for changing a bad mood, raising energy, and reducing tension.
1994