[HTML][HTML] Decoding enhancer complexity with machine learning and high-throughput discovery
GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …
flexible organization and functional redundancies make deciphering their sequence-function …
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data
Abstract ChIP-Atlas (https://chip-atlas. org) is a web service providing both GUI-and API-
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
based data-mining tools to reveal the architecture of the transcription regulatory landscape …
[HTML][HTML] Neutrophils and emergency granulopoiesis drive immune suppression and an extreme response endotype during sepsis
AJ Kwok, A Allcock, RC Ferreira, E Cano-Gamez… - Nature …, 2023 - nature.com
Sepsis arises from diverse and incompletely understood dysregulated host response
processes following infection that leads to life-threatening organ dysfunction. Here we …
processes following infection that leads to life-threatening organ dysfunction. Here we …
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 …
[HTML][HTML] Liquid biopsy epigenomic profiling for cancer subtyping
SC Baca, JH Seo, MP Davidsohn, B Fortunato… - Nature medicine, 2023 - nature.com
Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical
decisions in cancer care, they have limited ability to identify the transcriptional programs that …
decisions in cancer care, they have limited ability to identify the transcriptional programs that …
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Abstract JASPAR (http://jaspar. genereg. net) is an open-access database of curated, non-
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
redundant transcription factor (TF)-binding profiles stored as position frequency matrices …
[HTML][HTML] FOXA2 drives lineage plasticity and KIT pathway activation in neuroendocrine prostate cancer
M Han, F Li, Y Zhang, P Dai, J He, Y Li, Y Zhu, J Zheng… - Cancer Cell, 2022 - cell.com
Prostate cancer adeno-to-neuroendocrine lineage transition has emerged as a mechanism
of targeted therapeutic resistance. Identifying the direct molecular drivers and developing …
of targeted therapeutic resistance. Identifying the direct molecular drivers and developing …
[HTML][HTML] Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis
Abstract The AURORA US Metastasis Project was established with the goal to identify
molecular features associated with metastasis. We assayed 55 females with metastatic …
molecular features associated with metastasis. We assayed 55 females with metastatic …
Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer
Tumor expression of prostate-specific membrane antigen (PSMA) is lost in 15–20% of men
with castration-resistant prostate cancer (CRPC), yet the underlying mechanisms remain …
with castration-resistant prostate cancer (CRPC), yet the underlying mechanisms remain …
[HTML][HTML] A sequence-based global map of regulatory activity for deciphering human genetics
Epigenomic profiling has enabled large-scale identification of regulatory elements, yet we
still lack a systematic mapping from any sequence or variant to regulatory activities. We …
still lack a systematic mapping from any sequence or variant to regulatory activities. We …