[HTML][HTML] Integrative dissection of gene regulatory elements at base resolution

Z Chen, N Javed, M Moore, J Wu, G Sun, M Vinyard… - Cell Genomics, 2023 - cell.com
Although vast numbers of putative gene regulatory elements have been cataloged, the
sequence motifs and individual bases that underlie their functions remain largely unknown …

[HTML][HTML] Accelerated DNA methylation age plays a role in the impact of cardiovascular risk factors on the human heart

CC Topriceanu, E Dev, M Ahmad, R Hughes… - Clinical …, 2023 - Springer
Background DNA methylation (DNAm) age acceleration (AgeAccel) and cardiac age by 12-
lead advanced electrocardiography (A-ECG) are promising biomarkers of biological and …

[HTML][HTML] Microhomology-mediated end joining drives complex rearrangements and overexpression of MYC and PVT1 in multiple myeloma

A Mikulasova, C Ashby, RG Tytarenko, P Qu… - …, 2020 - ncbi.nlm.nih.gov
MYC is a widely acting transcription factor and its deregulation is a crucial event in many
human cancers. MYC is important biologically and clinically in multiple myeloma, but the …

Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex

M Fujita, Z Gao, L Zeng, C McCabe, CC White, B Ng… - bioRxiv, 2022 - biorxiv.org
The relationship between genetic variation and gene expression in individual brain cell
types and subtypes has remained elusive. Here, we generated single-nucleus RNA …

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) …

[HTML][HTML] tidybulk: an R tidy framework for modular transcriptomic data analysis

S Mangiola, R Molania, R Dong, MA Doyle… - Genome biology, 2021 - Springer
Recently, efforts have been made toward the harmonization of transcriptomic data structures
and workflows using the concept of data tidiness, to facilitate modularisation. We present …

The European Bioinformatics Institute in 2017: data coordination and integration

CE Cook, MT Bergman, G Cochrane… - Nucleic acids …, 2018 - academic.oup.com
Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research
throughout the world by providing open data, open-source software and analytical tools, and …

[HTML][HTML] Methylation-based therapies for colorectal cancer

K Cervena, A Siskova, T Buchler, P Vodicka… - Cells, 2020 - mdpi.com
Colorectal carcinogenesis (CRC) is caused by the gradual long-term accumulation of both
genetic and epigenetic changes. Recently, epigenetic alterations have been included in the …

scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets

H Liu, H Li, A Sharma, W Huang, D Pan… - Briefings in …, 2023 - academic.oup.com
Undoubtedly, single-cell RNA sequencing (scRNA-seq) has changed the research
landscape by providing insights into heterogeneous, complex and rare cell populations …

[HTML][HTML] Human monocyte-to-macrophage differentiation involves highly localized gain and loss of DNA methylation at transcription factor binding sites

KF Dekkers, AE Neele, JW Jukema, BT Heijmans… - Epigenetics & …, 2019 - Springer
Background Macrophages and their precursors monocytes play a key role in inflammation
and chronic inflammatory disorders. Monocyte-to-macrophage differentiation and activation …