NicheNet: modeling intercellular communication by linking ligands to target genes

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

(2019) Johnny Bonnardel et al.   IMMUNITY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Mapping the physical network of cellular interactions

(2018) Jean-Charles Boisset et al.   NATURE METHODS

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface

(2017) Mihaela Pavličev et al.   GENOME RESEARCH

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

OmniPath: guidelines and gateway for literature-curated signaling pathway resources

(2016) Dénes Türei et al.   NATURE METHODS

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

Writ large: Genomic dissection of the effect of cellular environment on immune response

(2016) N. Yosef et al.   SCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

TRRUST: a reference database of human transcriptional regulatory interactions

(2015) Heonjong Han et al.   Scientific Reports

Transcriptome Analysis of Individual Stromal Cell Populations Identifies Stroma-Tumor Crosstalk in Mouse Lung Cancer Model

(2015) Hyejin Choi et al.   Cell Reports

The human DEPhOsphorylation database DEPOD: a 2015 update

(2014) Guangyou Duan et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape

(2014) Aurélien Griffon et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands

(2013) Adam J. Pawson et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

(2013) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Modeling community-wide molecular networks of multicellular systems

(2012) K. Komurov   BIOINFORMATICS

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

(2012) Luiz A Bovolenta et al.   BMC GENOMICS

The ConsensusPathDB interaction database: 2013 update

(2012) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

KEA: kinase enrichment analysis

(2009) A. Lachmann et al.   BIOINFORMATICS

Integrative analysis of RUNX1 downstream pathways and target genes

(2009) Joëlle Michaud et al.   BMC GENOMICS

MotifMap: a human genome-wide map of candidate regulatory motif sites

(2008) Xiaohui Xie et al.   BIOINFORMATICS

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY