GTRD: an integrated view of transcription regulation
S Kolmykov, I Yevshin, M Kulyashov… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Gene Transcription Regulation Database (GTRD; http://gtrd. biouml. org/)
contains uniformly annotated and processed NGS data related to gene transcription …
contains uniformly annotated and processed NGS data related to gene transcription …
Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens
Most variants associated with complex traits and diseases identified by genome-wide
association studies (GWAS) map to noncoding regions of the genome with unknown effects …
association studies (GWAS) map to noncoding regions of the genome with unknown effects …
Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers
A Karollus, T Mauermeier, J Gagneur - Genome biology, 2023 - Springer
Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …
obtained by predicting genome-wide gene regulatory assays across the human genome …
Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH
Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is
challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment …
challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment …
HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …
Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe
Ancient genomics can directly detect human genetic adaptation to environmental cues.
However, it remains unclear how pathogens have exerted selective pressures on human …
However, it remains unclear how pathogens have exerted selective pressures on human …
Functional characterization of genetic variant effects on expression
ED Flynn, T Lappalainen - Annual Review of Biomedical Data …, 2022 - annualreviews.org
Thousands of common genetic variants in the human population have been associated with
disease risk and phenotypic variation by genome-wide association studies (GWAS) …
disease risk and phenotypic variation by genome-wide association studies (GWAS) …
Hidden modes of DNA binding by human nuclear receptors
D Bhimsaria, JA Rodríguez-Martínez… - Nature …, 2023 - nature.com
Human nuclear receptors (NRs) are a superfamily of ligand-responsive transcription factors
that have central roles in cellular function. Their malfunction is linked to numerous diseases …
that have central roles in cellular function. Their malfunction is linked to numerous diseases …
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases
Interpreting the molecular mechanism of genomic variations and their causal relationship
with diseases/traits are important and challenging problems in the human genetic study. To …
with diseases/traits are important and challenging problems in the human genetic study. To …
Complex regulatory networks influence pluripotent cell state transitions in human iPSCs
TD Arthur, JP Nguyen, A D'Antonio-Chronowska… - Nature …, 2024 - nature.com
Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing
hundreds of hiPSCs derived from different individuals, we show the proportions of these …
hundreds of hiPSCs derived from different individuals, we show the proportions of these …