Chromatin-state discovery and genome annotation with ChromHMM

J Ernst, M Kellis - Nature protocols, 2017 - nature.com
Noncoding DNA regions have central roles in human biology, evolution, and disease.
ChromHMM helps to annotate the noncoding genome using epigenomic information across …

RNA splicing factors as oncoproteins and tumour suppressors

H Dvinge, E Kim, O Abdel-Wahab… - Nature Reviews Cancer, 2016 - nature.com
The recent genomic characterization of cancers has revealed recurrent somatic point
mutations and copy number changes affecting genes encoding RNA splicing factors. Initial …

[HTML][HTML] Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration

V Moiseeva, A Cisneros, V Sica, O Deryagin, Y Lai… - Nature, 2023 - nature.com
Tissue regeneration requires coordination between resident stem cells and local niche
cells,. Here we identify that senescent cells are integral components of the skeletal muscle …

[HTML][HTML] Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy

X Hong, J Isern, S Campanario, E Perdiguero… - Cell Stem Cell, 2022 - cell.com
Skeletal muscle regeneration depends on the correct expansion of resident quiescent stem
cells (satellite cells), a process that becomes less efficient with aging. Here, we show that …

Mutational signature in colorectal cancer caused by genotoxic pks+E. coli

C Pleguezuelos-Manzano, J Puschhof… - Nature, 2020 - nature.com
Various species of the intestinal microbiota have been associated with the development of
colorectal cancer,, but it has not been demonstrated that bacteria have a direct role in the …

[HTML][HTML] OrthoFinder: phylogenetic orthology inference for comparative genomics

DM Emms, S Kelly - Genome biology, 2019 - Springer
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder's
high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted …

[HTML][HTML] Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer

AF Aissa, AB Islam, MM Ariss, CC Go, AE Rader… - Nature …, 2021 - nature.com
Tyrosine kinase inhibitors were found to be clinically effective for treatment of patients with
certain subsets of cancers carrying somatic mutations in receptor tyrosine kinases. However …

The GeneCards suite: from gene data mining to disease genome sequence analyses

G Stelzer, N Rosen, I Plaschkes… - Current protocols in …, 2016 - Wiley Online Library
GeneCards, the human gene compendium, enables researchers to effectively navigate and
inter‐relate the wide universe of human genes, diseases, variants, proteins, cells, and …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

AF Pardiñas, P Holmans, AJ Pocklington… - Nature …, 2018 - nature.com
Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life
and decreased life expectancy. Lack of progress in improving treatment outcomes has been …