Gene regulatory network inference in the era of single-cell multi-omics
P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
Targeting transcription factors in cancer—from undruggable to reality
JH Bushweller - Nature Reviews Cancer, 2019 - nature.com
Mutated or dysregulated transcription factors represent a unique class of drug targets that
mediate aberrant gene expression, including blockade of differentiation and cell death gene …
mediate aberrant gene expression, including blockade of differentiation and cell death gene …
cGAS–STING drives the IL-6-dependent survival of chromosomally instable cancers
Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy
resistance, and is associated with poor prognosis. CIN leads to micronuclei that release …
resistance, and is associated with poor prognosis. CIN leads to micronuclei that release …
[HTML][HTML] Effective drug combinations in breast, colon and pancreatic cancer cells
Combinations of anti-cancer drugs can overcome resistance and provide new treatments,.
The number of possible drug combinations vastly exceeds what could be tested clinically …
The number of possible drug combinations vastly exceeds what could be tested clinically …
[HTML][HTML] SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids
Kidney failure is frequently observed during and after COVID-19, but it remains elusive
whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects …
whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects …
[HTML][HTML] Pan-cancer proteomic map of 949 human cell lines
The proteome provides unique insights into disease biology beyond the genome and
transcriptome. A lack of large proteomic datasets has restricted the identification of new …
transcriptome. A lack of large proteomic datasets has restricted the identification of new …
Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
Functional genomics approaches can overcome limitations—such as the lack of
identification of robust targets and poor clinical efficacy—that hamper cancer drug …
identification of robust targets and poor clinical efficacy—that hamper cancer drug …
ChEA3: transcription factor enrichment analysis by orthogonal omics integration
AB Keenan, D Torre, A Lachmann… - Nucleic acids …, 2019 - academic.oup.com
Identifying the transcription factors (TFs) responsible for observed changes in gene
expression is an important step in understanding gene regulatory networks. ChIP-X …
expression is an important step in understanding gene regulatory networks. ChIP-X …
Benchmark and integration of resources for the estimation of human transcription factor activities
The prediction of transcription factor (TF) activities from the gene expression of their targets
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …
Analysis of single-cell RNA-seq identifies cell-cell communication associated with tumor characteristics
Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor
interactions. Targeting ligand-receptor interactions (for instance, with immune checkpoint …
interactions. Targeting ligand-receptor interactions (for instance, with immune checkpoint …