Standout Papers
- High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells (2005)
- Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants (2001)
- edgeR : a Bioconductor package for differential expression analysis of digital gene expression data (2009)
- A scaling normalization method for differential expression analysis of RNA-seq data (2010)
Citation Impact
Citing Papers
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
2005 Standout
HTSeq—a Python framework to work with high-throughput sequencing data
2014 Standout
DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging
2014
Gene essentiality and synthetic lethality in haploid human cells
2015 Science
A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients
2023 StandoutNobel
New tools for studying microglia in the mouse and human CNS
2016
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
2014 Standout
The microbiota regulates type 2 immunity through RORγt + T cells
2015 StandoutScienceNobel
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
2010
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
2014 Standout
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
2005
Gene ontology analysis for RNA-seq: accounting for selection bias
2010 Standout
How to decide which are the most pertinent overly-represented features during gene set enrichment analysis
2007
On-target efficacy of a HIF-2α antagonist in preclinical kidney cancer models
2016 StandoutNatureNobel
Hallmarks of Cancer: The Next Generation
2011 Standout
Differential expression analysis for sequence count data
2010 Standout
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
2011 Standout
Reconsidering Movement of Eukaryotic mRNAs between Polysomes and P Bodies
2011 StandoutNobel
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
2013
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
2013
Interferon-γ regulates cellular metabolism and mRNA translation to potentiate macrophage activation
2015 StandoutNobel
GOToolBox: functional analysis of gene datasets based on Gene Ontology
2004
Comparing functional annotation analyses with Catmap
2004
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
2010
The promise and challenge of therapeutic genome editing
2020 StandoutNatureNobel
Guide: a desktop application for analysing gene expression data
2013
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
2014 Standout
Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo
2003 Nature
Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity
2020 StandoutNobel
The Concept of Synthetic Lethality in the Context of Anticancer Therapy
2005 StandoutNobel
Differential analysis of gene regulation at transcript resolution with RNA-seq
2012 Standout
BIND--The Biomolecular Interaction Network Database
2001
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
2012 Standout
Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
2014 Standout
Mutation load, functional overlap, and synthetic lethality in the evolution and treatment of cancer
2003
De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
2014
CD22 blockade restores homeostatic microglial phagocytosis in ageing brains
2019 StandoutNatureNobel
Human ADAR1 Prevents Endogenous RNA from Triggering Translational Shutdown
2018 StandoutNobel
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
2003 Standout
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
2013 StandoutNobel
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia
2017 StandoutNobel
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes
2017 StandoutNobel
Epithelial-Mesenchymal Transition: At the Crossroads of Development and Tumor Metastasis
2008 Standout
Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity
2013
Differential L1 regulation in pluripotent stem cells of humans and apes
2013 Nature
The genomic landscape of Neanderthal ancestry in present-day humans
2014 StandoutNatureNobel
Pathways to the analysis of microarray data
2005
An RNA-seq based comparative approach reveals the transcriptome-wide interplay between 3′-to-5′ exoRNases and RNase Y
2020 StandoutNobel
From large networks to small molecules
2003
Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis
2013 Standout
FUS(1-359) transgenic mice as a model of ALS: pathophysiological and molecular aspects of the proteinopathy
2018
Characterizing gene sets with FuncAssociate
2003
Transformation by the (R)-enantiomer of 2-hydroxyglutarate linked to EGLN activation
2012 StandoutNatureNobel
Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps
2014
Developmental Heterogeneity of Microglia and Brain Myeloid Cells Revealed by Deep Single-Cell RNA Sequencing
2018
Removing technical variability in RNA-seq data using conditional quantile normalization
2012
RNA regulons: coordination of post-transcriptional events
2007
A Genomic and Functional Inventory of Deubiquitinating Enzymes
2005 Standout
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
2012 StandoutNature
Complex networks orchestrate epithelial–mesenchymal transitions
2006 Standout
Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome
2007
Assigning Function to Yeast Proteins by Integration of Technologies
2003 StandoutNobel
TGFβ: the molecular Jekyll and Hyde of cancer
2006
Global Changes in the Mammary Epigenome Are Induced by Hormonal Cues and Coordinated by Ezh2
2013
Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer
2013
Quantitative phenotyping via deep barcode sequencing
2009
GC-Content Normalization for RNA-Seq Data
2011
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
2008 Standout
Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors
2012
Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation
2014
Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling
2019
T-profiler: scoring the activity of predefined groups of genes using gene expression data
2005
RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
2008 Standout
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments
2010
Structural organization of the tight junctions
2007
Enrichment or depletion of a GO category within a class of genes: which test?
2006
Human occludin is a hepatitis C virus entry factor required for infection of mouse cells
2009 StandoutNatureNobel
The GRID: The General Repository for Interaction Datasets
2003
An enteric virus can replace the beneficial function of commensal bacteria
2014 Nature
limma powers differential expression analyses for RNA-sequencing and microarray studies
2015 Standout
Defining transcription modules using large-scale gene expression data
2004
Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis
2019 Nature
Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry
2007 StandoutNatureNobel
The microglial sensome revealed by direct RNA sequencing
2013
Normalization, testing, and false discovery rate estimation for RNA-sequencing data
2011
Fast gapped-read alignment with Bowtie 2
2012 Standout
Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer
2012
Surrogate Wnt agonists that phenocopy canonical Wnt and β-catenin signalling
2017 StandoutNatureNobel
Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome
2010
Global analysis of protein localization in budding yeast
2003 StandoutNature
Transmembrane proteins of tight junctions
2007
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
2004 Standout
Comparative assessment of large-scale data sets of protein–protein interactions
2002 StandoutNature
The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA
2016 Nature
Cloud-scale RNA-sequencing differential expression analysis with Myrna
2010
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
2012
Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy
2017 Standout
Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis
2011
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
2004
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
2008
Maintenance of Low Histone Ubiquitylation by Ubp10 Correlates with Telomere-Proximal Sir2 Association and Gene Silencing
2005
Detecting differential usage of exons from RNA-seq data
2012
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
Lysosome-targeting chimaeras for degradation of extracellular proteins
2020 StandoutNatureNobel
Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation
2018
Evolution of the Human Nervous System Function, Structure, and Development
2017
Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays
2011
Stem cell-derived polarized hepatocytes
2020 StandoutNobel
A Combination of Ontogeny and CNS Environment Establishes Microglial Identity
2018
Organoid single-cell genomic atlas uncovers human-specific features of brain development
2019 StandoutNatureNobel
The evolution of gene expression levels in mammalian organs
2011 StandoutNatureNobel
Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development
2015
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
2015
Hepatitis C Virus RNA Functionally Sequesters miR-122
2015 StandoutNobel
In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes
2018 StandoutNobel
MEGO: Gene Functional Module Expression Based on Gene Ontology
2005
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
2009 Standout
A powerful and flexible approach to the analysis of RNA sequence count data
2011
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments
2013
Independent filtering increases detection power for high-throughput experiments
2010
Clustering by Passing Messages Between Data Points
2007 StandoutScience
CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine
2017
CLAUDINS AND EPITHELIAL PARACELLULAR TRANSPORT
2005
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation
2012 Standout
DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray
2003
Computational methods for transcriptome annotation and quantification using RNA-seq
2011
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote
2013 Standout
RNA-dependent RNA targeting by CRISPR-Cas9
2018 StandoutNobel
easyRNASeq: a bioconductor package for processing RNA-Seq data
2012
Global Gene Expression Profiling Reveals Widespread yet Distinctive Translational Responses to Different Eukaryotic Translation Initiation Factor 2B-Targeting Stress Pathways
2005
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data
2012
Live cell micropatterning reveals the dynamics of signaling complexes at the plasma membrane
2014
RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself
2015 Science
Late Cytoplasmic Maturation of the Small Ribosomal Subunit Requires RIO Proteins in Saccharomyces cerevisiae
2003
Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data
2011
A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA
2022 StandoutNobel
Differential Oestrogen Receptor Binding is Associated with Clinical Outcome in Breast Cancer
2012
Identifying differentially expressed transcripts from RNA-seq data with biological variation
2012
Design and Analysis of Bar-seq Experiments
2013
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
2012
CRISPR-Cas guides the future of genetic engineering
2018 StandoutScienceNobel
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
2013 Standout
Comparative ribosome profiling reveals extensive translational complexity in differentTrypanosoma bruceilife cycle stages
2014
Combining biological networks to predict genetic interactions
2004
Accurate proteome-wide missense variant effect prediction with AlphaMissense
2023 StandoutScienceNobel
Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain
2010
Yeast genome-wide drug-induced haploinsufficiency screen to determine drug mode of action
2004
CLUSTERING BIOLOGICAL ANNOTATIONS AND GENE EXPRESSION DATA TO IDENTIFY PUTATIVELY CO-REGULATED BIOLOGICAL PROCESSES
2006
Works of Mark D. Robinson being referenced
High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells
2005 StandoutScience
Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants
2001 StandoutScience
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
2009 Standout
A scaling normalization method for differential expression analysis of RNA-seq data
2010 Standout
Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
2010
FunSpec: a web-based cluster interpreter for yeast
2002
A comparison of Affymetrix gene expression arrays
2007
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
2002
diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering
2019
Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
2015
Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry
2018
Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
2005
Treatment of a metabolic liver disease by in vivo genome base editing in adult mice
2018
From RNA-seq reads to differential expression results
2010
Copy-number-aware differential analysis of quantitative DNA sequencing data
2012
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
2013
Small-sample estimation of negative binomial dispersion, with applications to SAGE data
2007
Robustly detecting differential expression in RNA sequencing data using observation weights
2014
Repitools: an R package for the analysis of enrichment-based epigenomic data
2010
FIRMA: a method for detection of alternative splicing from exon array data
2008
Genome-Wide Analysis of mRNA Stability Using Transcription Inhibitors and Microarrays Reveals Posttranscriptional Control of Ribosome Biogenesis Factors
2004
Moderated statistical tests for assessing differences in tag abundance
2007