Deciphering cell–cell interactions and communication from gene expression

E Armingol, A Officer, O Harismendy… - Nature Reviews …, 2021 - nature.com
Cell–cell interactions orchestrate organismal development, homeostasis and single-cell
functions. When cells do not properly interact or improperly decode molecular messages …

Pathway and network analysis of cancer genomes

Nature methods, 2015 - nature.com
Genomic information on tumors from 50 cancer types cataloged by the International Cancer
Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently …

g: Profiler—interoperable web service for functional enrichment analysis and gene identifier map** (2023 update)

L Kolberg, U Raudvere, I Kuzmin, P Adler… - Nucleic acids …, 2023 - academic.oup.com
Abstract g: Profiler is a reliable and up-to-date functional enrichment analysis tool that
supports various evidence types, identifier types and organisms. The toolset integrates many …

[HTML][HTML] gprofiler2--an R package for gene list functional enrichment analysis and namespace conversion toolset g: Profiler

L Kolberg, U Raudvere, I Kuzmin, J Vilo… - …, 2020 - ncbi.nlm.nih.gov
Abstract g: Profiler (https://biit. cs. ut. ee/gprofiler) is a widely used gene list functional
profiling and namespace conversion toolset that has been contributing to reproducible …

Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes

J Humphrey, S Venkatesh, R Hasan, JT Herb… - Nature …, 2023 - nature.com
Amyotrophic lateral sclerosis (ALS) is a progressively fatal neurodegenerative disease
affecting motor neurons in the brain and spinal cord. In this study, we investigated gene …

g: Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

U Raudvere, L Kolberg, I Kuzmin, T Arak… - Nucleic acids …, 2019 - academic.oup.com
Biological data analysis often deals with lists of genes arising from various studies. The g:
Profiler toolset is widely used for finding biological categories enriched in gene lists …

Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap

J Reimand, R Isserlin, V Voisin, M Kucera… - Nature protocols, 2019 - nature.com
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …

Potential roles of gut microbiome and metabolites in modulating ALS in mice

E Blacher, S Bashiardes, H Shapiro, D Rothschild… - Nature, 2019 - nature.com
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disorder, in which the
clinical manifestations may be influenced by genetic and unknown environmental factors …

[HTML][HTML] Transient naive reprogramming corrects hiPS cells functionally and epigenetically

S Buckberry, X Liu, D Poppe, JP Tan, G Sun, J Chen… - Nature, 2023 - nature.com
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced
pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human …

Failure of human rhombic lip differentiation underlies medulloblastoma formation

LD Hendrikse, P Haldipur, O Saulnier, J Millman… - Nature, 2022 - nature.com
Medulloblastoma (MB) comprises a group of heterogeneous paediatric embryonal
neoplasms of the hindbrain with strong links to early development of the hindbrain 1, 2, 3, 4 …