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 …
functions. When cells do not properly interact or improperly decode molecular messages …
A guide to conquer the biological network era using graph theory
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …
of binary interactions or relations between different bioentities. In this article, we discuss the …
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Background RNA-seq is widely used for transcriptomic profiling, but the bioinformatics
analysis of resultant data can be time-consuming and challenging, especially for biologists …
analysis of resultant data can be time-consuming and challenging, especially for biologists …
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins
AD Rouillard, GW Gundersen, NF Fernandez… - Database, 2016 - academic.oup.com
Genomics, epigenomics, transcriptomics, proteomics and metabolomics efforts rapidly
generate a plethora of data on the activity and levels of biomolecules within mammalian …
generate a plethora of data on the activity and levels of biomolecules within mammalian …
Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities
S Müller-Dott, E Tsirvouli, M Vazquez… - Nucleic acids …, 2023 - academic.oup.com
Gene regulation plays a critical role in the cellular processes that underlie human health and
disease. The regulatory relationship between transcription factors (TFs), key regulators of …
disease. The regulatory relationship between transcription factors (TFs), key regulators of …
Mitochondrial control of microglial phagocytosis by the translocator protein and hexokinase 2 in Alzheimer's disease
Microglial phagocytosis is an energetically demanding process that plays a critical role in
the removal of toxic protein aggregates in Alzheimer's disease (AD). Recent evidence …
the removal of toxic protein aggregates in Alzheimer's disease (AD). Recent evidence …
Gene essentiality and synthetic lethality in haploid human cells
Although the genes essential for life have been identified in less complex model organisms,
their elucidation in human cells has been hindered by technical barriers. We used extensive …
their elucidation in human cells has been hindered by technical barriers. We used extensive …
Identification of cancer driver genes based on nucleotide context
Cancer genomes contain large numbers of somatic mutations but few of these mutations
drive tumor development. Current approaches either identify driver genes on the basis of …
drive tumor development. Current approaches either identify driver genes on the basis of …
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions
PM Müller, J Rademacher, RD Bagshaw… - Nature cell …, 2020 - nature.com
Rho GTPases are central regulators of the cytoskeleton and, in humans, are controlled by
145 multidomain guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating …
145 multidomain guanine nucleotide exchange factors (RhoGEFs) and GTPase-activating …
NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data
Meta-analysis of gene expression data sets is increasingly performed to help identify robust
molecular signatures and to gain insights into underlying biological processes. The …
molecular signatures and to gain insights into underlying biological processes. The …