Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation
R Nakato, K Shirahige - Briefings in bioinformatics, 2017 - academic.oup.com
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect
protein/DNA-binding and histone-modification sites across an entire genome. Recent …
protein/DNA-binding and histone-modification sites across an entire genome. Recent …
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments
F Hammal, P De Langen, A Bergon… - Nucleic acids …, 2022 - academic.oup.com
Abstract ReMap (https://remap. univ-amu. fr) aims to provide manually curated, high-quality
catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA …
catalogs of regulatory regions resulting from a large-scale integrative analysis of DNA …
NicheNet: modeling intercellular communication by linking ligands to target genes
Computational methods that model how gene expression of a cell is influenced by
interacting cells are lacking. We present NicheNet (https://github. com/saeyslab/nichenetr), a …
interacting cells are lacking. We present NicheNet (https://github. com/saeyslab/nichenetr), a …
CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication
Y Zhang, T Liu, X Hu, M Wang, J Wang… - Nucleic acids …, 2021 - academic.oup.com
With the dramatic development of single-cell RNA sequencing (scRNA-seq) technologies,
the systematic decoding of cell-cell communication has received great research interest. To …
the systematic decoding of cell-cell communication has received great research interest. To …
[HTML][HTML] Mechanism of action for HDAC inhibitors—insights from omics approaches
W Li, Z Sun - International journal of molecular sciences, 2019 - mdpi.com
Histone deacetylase inhibitors (HDIs) are a class of prominent epigenetic drugs that are
currently being tested in hundreds of clinical trials against a variety of diseases. A few …
currently being tested in hundreds of clinical trials against a variety of diseases. A few …
Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function
We determined the relationships between DNA sequence variation and DNA methylation
using blood samples from 3,799 Europeans and 3,195 South Asians. We identify …
using blood samples from 3,799 Europeans and 3,195 South Asians. We identify …
[HTML][HTML] Transcription factor IRF4 promotes CD8+ T cell exhaustion and limits the development of memory-like T cells during chronic infection
During chronic stimulation, CD8+ T cells acquire an exhausted phenotype characterized by
expression of inhibitory receptors, down-modulation of effector function, and metabolic …
expression of inhibitory receptors, down-modulation of effector function, and metabolic …
Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity
Explaining the genetics of many diseases is challenging because most associations localize
to incompletely characterized regulatory regions. Using new computational methods, we …
to incompletely characterized regulatory regions. Using new computational methods, we …
[HTML][HTML] SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits
Local genetic correlation quantifies the genetic similarity of complex traits in specific
genomic regions. However, accurate estimation of local genetic correlation remains …
genomic regions. However, accurate estimation of local genetic correlation remains …
A common haplotype lowers PU. 1 expression in myeloid cells and delays onset of Alzheimer's disease
A genome-wide survival analysis of 14,406 Alzheimer's disease (AD) cases and 25,849
controls identified eight previously reported AD risk loci and 14 novel loci associated with …
controls identified eight previously reported AD risk loci and 14 novel loci associated with …