Citation Impact
Citing Papers
The human disease network
2007 Standout
Constitutive AP-1 Activity and EBV Infection Induce PD-L1 in Hodgkin Lymphomas and Posttransplant Lymphoproliferative Disorders: Implications for Targeted Therapy
2012
A noninflammatory mRNA vaccine for treatment of experimental autoimmune encephalomyelitis
2021 StandoutScienceNobel
Sample processing obscures cancer-specific alterations in leukemic transcriptomes
2014
A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients
2023 StandoutNobel
Epidermal progenitors give rise to Merkel cells during embryonic development and adult homeostasis
2009
Pan-cancer single-cell landscape of tumor-infiltrating T cells
2021 Science
Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA
2011 StandoutScience
Par3 cooperates with Sanpodo for the assembly of Notch clusters following asymmetric division of Drosophila sensory organ precursor cells
2021
Integrating sequence, evolution and functional genomics in regulatory genomics
2009
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging
2015
Integrative approaches to the prediction of protein functions based on the feature selection
2009
Genome-wide features of neuroendocrine regulation in Drosophila by the basic helix-loop-helix transcription factor DIMMED
2015 StandoutNobel
Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons
2013 StandoutNobel
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
2019 Standout
Platelet factor 4–induced T H 1-T reg polarization suppresses antitumor immunity
2024 StandoutScienceNobel
Old and new functions of proneural factors revealed by the genome-wide characterization of their transcriptional targets
2011
Determining cell type abundance and expression from bulk tissues with digital cytometry
2019 Standout
Merkel Cells Activate Sensory Neural Pathways through Adrenergic Synapses
2018 StandoutNobel
A microRNA family exerts maternal control on sex determination in C. elegans
2017 StandoutNobel
Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy
2020
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
2015
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity
2008 StandoutNobel
MEME SUITE: tools for motif discovery and searching
2009 Standout
Large-scale structure of genomic methylation patterns
2005
Host tissue determinants of tumour immunity
2019
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia
2017 StandoutNobel
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
2007 StandoutNobel
Advances in autism genetics: on the threshold of a new neurobiology
2008
Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease
2019
Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
2012
Chemotherapy-induced complement signaling modulates immunosuppression and metastatic relapse in breast cancer
2022
Predicting cell-type–specific gene expression from regions of open chromatin
2012
Hallmarks of aging: An expanding universe
2023 Standout
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
2005
Tissue-specific tumorigenesis: context matters
2017
Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family
2007
Clinical and therapeutic relevance of cancer-associated fibroblasts
2021
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama
2019
The Human Transcription Factors
2018 Standout
The changing landscape of atherosclerosis
2021 StandoutNature
Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity
2022
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
2016 Standout
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
2011
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
2014 StandoutNobel
The landscape of cell–cell communication through single-cell transcriptomics
2021
Hippo Pathway in Organ Size Control, Tissue Homeostasis, and Cancer
2015 Standout
Biological Functions of Autophagy Genes: A Disease Perspective
2019 Standout
Decoding ALS: from genes to mechanism
2016 StandoutNature
Super-Enhancers in the Control of Cell Identity and Disease
2013 Standout
Cytosine Methylation and DNA Repair
2006
Hypoxia and the extracellular matrix: drivers of tumour metastasis
2014 StandoutNobel
The Cellular Phase of Alzheimer’s Disease
2016
Alzheimer Disease: An Update on Pathobiology and Treatment Strategies
2019 Standout
Detection of functional DNA motifs via statistical over-representation
2004
Spermine synthase deficiency causes lysosomal dysfunction and oxidative stress in models of Snyder-Robinson syndrome
2017
The Mammalian Epigenome
2007 Standout
A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells
2021
miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity
2015 StandoutNobel
Mammary Epithelial-Specific Disruption of Focal Adhesion Kinase Retards Tumor Formation and Metastasis in a Transgenic Mouse Model of Human Breast Cancer
2008
Synthetic Par polarity induces cytoskeleton asymmetry in unpolarized mammalian cells
2023 StandoutNobel
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
2016 Standout
Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding
2019
On the Dependency of Cellular Protein Levels on mRNA Abundance
2016 Standout
A comparison of single-cell trajectory inference methods
2019
RSAT 2011: regulatory sequence analysis tools
2011
Cancer-associated fibroblasts in the single-cell era
2022
Alzheimer's disease
2016 Standout
The Classical Complement Cascade Mediates CNS Synapse Elimination
2007 Standout
Cancer-Associated Fibroblasts Build and Secure the Tumor Microenvironment
2019
Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy
2017 Standout
The evolving tumor microenvironment: From cancer initiation to metastatic outgrowth
2023 Standout
Global Coevolution of Human MicroRNAs and Their Target Genes
2014
Combinatorial function of transcription factors and cofactors
2017
Unraveling transcription regulatory networks by protein–DNA and protein–protein interaction mapping
2006
Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
2020 Standout
Macrophage diversity in cancer revisited in the era of single-cell omics
2022
Quantifying similarity between motifs
2007
Dimensionality reduction for visualizing single-cell data using UMAP
2018 Standout
Immunomodulation by endothelial cells — partnering up with the immune system?
2022
Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues
2005
Oncofetal reprogramming in tumour development and progression
2022
Axonal Transport of TDP-43 mRNA Granules Is Impaired by ALS-Causing Mutations
2014
Absence of a simple code: how transcription factors read the genome
2014
Widespread transcription at neuronal activity-regulated enhancers
2010 StandoutNature
The Hallmarks of Aging
2013 Standout
Fibroblasts as immune regulators in infection, inflammation and cancer
2021
A Neuroligin-4 Missense Mutation Associated with Autism Impairs Neuroligin-4 Folding and Endoplasmic Reticulum Export
2009 StandoutNobel
Comprehensive Integration of Single-Cell Data
2019 Standout
Matrix Crosslinking Forces Tumor Progression by Enhancing Integrin Signaling
2009 Standout
Applied bioinformatics for the identification of regulatory elements
2004
Single-cell transcriptomic analysis of Alzheimer’s disease
2019 StandoutNature
PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles
2015 StandoutNobel
Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth
2020
Tumour-infiltrating B cells: immunological mechanisms, clinical impact and therapeutic opportunities
2022
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
2009 Standout
Macrophages as tools and targets in cancer therapy
2022
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
2013 Standout
Single Cell RNA Sequencing in Atherosclerosis Research
2020
Advances in skin grafting and treatment of cutaneous wounds
2014 StandoutScience
Diversity and Biology of Cancer-Associated Fibroblasts
2020
Application of Single-Cell Multi-Omics in Dissecting Cancer Cell Plasticity and Tumor Heterogeneity
2021
Comprehensive comparison of large-scale tissue expression datasets
2015
oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets
2012
Discovering disease-genes by topological features in human protein–protein interaction network
2006
DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
2009 Standout
Meta-analysis of age-related gene expression profiles identifies common signatures of aging
2009
A Genome-Wide Survey of Sexually Dimorphic Expression of Drosophila miRNAs Identifies the Steroid Hormone-Induced miRNA let-7 as a Regulator of Sexual Identity
2014
PD-1 Blockade with Nivolumab in Relapsed or Refractory Hodgkin's Lymphoma
2014 Standout
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal
2012 StandoutNobel
Molecular signature of late-stage human ALS revealed by expression profiling of postmortem spinal cord gray matter
2004
Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma
2010
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles
2008
Plasticity of epithelial stem cells in tissue regeneration
2014 Science
Works of Stein Aerts being referenced
Robust Target Gene Discovery through Transcriptome Perturbations and Genome-Wide Enhancer Predictions in Drosophila Uncovers a Regulatory Basis for Sensory Specification
2010
Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization
2013
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
2014
Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
2016
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state
2015
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
2005
Comprehensive analysis of the base composition around the transcription start site in Metazoa
2004
SCENIC: single-cell regulatory network inference and clustering
2017 Standout
Gene prioritization through genomic data fusion
2006
Comprehensive Analysis of Transcriptome Variation Uncovers Known and Novel Driver Events in T-Cell Acute Lymphoblastic Leukemia
2013
Adult interfollicular tumour-initiating cells are reprogrammed into an embryonic hair follicle progenitor-like fate during basal cell carcinoma initiation
2012
Text-mining assisted regulatory annotation
2008
Phenotype molding of stromal cells in the lung tumor microenvironment
2018
Comparison and meta-analysis of microarray data: from the bench to the computer desk
2003
Male-Specific Fruitless Isoforms Target Neurodevelopmental Genes to Specify a Sexually Dimorphic Nervous System
2014
The Atonal Proneural Transcription Factor Links Differentiation and Tumor Formation in Drosophila
2009
Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma
2020
ENDEAVOUR update: a web resource for gene prioritization in multiple species
2008
TDP-43 Loss-of-Function Causes Neuronal Loss Due to Defective Steroid Receptor-Mediated Gene Program Switching in Drosophila
2013
Toucan: deciphering the cis-regulatory logic of coregulated genes
2003
Alteration of the micro RNA network during the progression of Alzheimer's disease
2013
Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
2020
COMPARISON OF DIFFERENT METHODOLOGIES TO IDENTIFY DIFFERENTIALLY EXPRESSED GENES IN TWO-SAMPLE cDNA MICROARRAYS
2002
Reduced synaptic vesicle protein degradation at lysosomes curbs TBC1D24/sky-induced neurodegeneration
2014
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules
2012
Computational detection of cis -regulatory modules
2003