Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …
Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease
The human immune system displays substantial variation between individuals, leading to
differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing …
differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing …
Epigenetics, DNA organization, and inflammatory bowel disease
G Ray, MS Longworth - Inflammatory bowel diseases, 2019 - academic.oup.com
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders affecting the
gastrointestinal tract. The incidence of IBD is increasing, with more cases occurring in …
gastrointestinal tract. The incidence of IBD is increasing, with more cases occurring in …
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation
LM Pikkupeura, RB Bressan, J Guiu, Y Chen… - Science …, 2023 - science.org
During intestinal organogenesis, equipotent epithelial progenitors mature into
phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue …
phenotypically distinct stem cells that are responsible for lifelong maintenance of the tissue …
iEnhancer-5Step: identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding
An enhancer is a short (50–1500bp) region of DNA that plays an important role in gene
expression and the production of RNA and proteins. Genetic variation in enhancers has …
expression and the production of RNA and proteins. Genetic variation in enhancers has …
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome
Enhancers are deoxyribonucleic acid (DNA) fragments which when bound by transcription
factors enhance the transcription of related genes. Due to its sporadic distribution and …
factors enhance the transcription of related genes. Due to its sporadic distribution and …
Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning
Gene transcription is regulated through complex mechanisms involving non-coding RNAs
(ncRNAs). As the transcription of ncRNAs, especially of enhancer RNAs, is often low and …
(ncRNAs). As the transcription of ncRNAs, especially of enhancer RNAs, is often low and …
iEnhancer-ECNN: identifying enhancers and their strength using ensembles of convolutional neural networks
Background Enhancers are non-coding DNA fragments which are crucial in gene regulation
(eg transcription and translation). Having high locational variation and free scattering in 98 …
(eg transcription and translation). Having high locational variation and free scattering in 98 …
piEnPred: a bi-layered discriminative model for enhancers and their subtypes via novel cascade multi-level subset feature selection algorithm
Enhancers are short DNA cis-elements that can be bound by proteins (activators) to
increase the possibility that transcription of a particular gene will occur. The Enhancers …
increase the possibility that transcription of a particular gene will occur. The Enhancers …
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Genome-wide association studies (GWASs) have uncovered hundreds of autoimmune
disease-associated loci; however, the causal genetic variants within each locus are mostly …
disease-associated loci; however, the causal genetic variants within each locus are mostly …