HOCOMOCO in 2024: a rebuild of the curated collection of binding models for human and mouse transcription factors

IE Vorontsov, IA Eliseeva, A Zinkevich… - Nucleic Acids …, 2024 - academic.oup.com
We present a major update of the HOCOMOCO collection that provides DNA binding
specificity patterns of 949 human transcription factors and 720 mouse orthologs. To make …

Methods for functional characterization of genetic polymorphisms of non-coding regulatory regions of the human genome

AN Uvarova, EA Tkachenko, EM Stasevich… - Biochemistry …, 2024 - Springer
Currently, numerous associations between genetic polymorphisms and various diseases
have been characterized through the Genome-Wide Association Studies. Majority of the …

Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits

J Wan, A van Ouwerkerk, JC Mouren… - Nucleic Acids …, 2024 - academic.oup.com
There is growing evidence that a wide range of human diseases and physiological traits are
influenced by genetic variation of cis-regulatory elements. We and others have shown that a …

[HTML][HTML] Decoding Non-coding Variants: Recent Approaches to Studying Their Role in Gene Regulation and Human Diseases

EG Peña-Martínez… - Frontiers in bioscience …, 2024 - ncbi.nlm.nih.gov
Genome-wide association studies (GWAS) have mapped over 90% of disease-and
quantitative-trait-associated variants within the non-coding genome. Non-coding regulatory …

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression of RUVBL1 and prostate cancer progression

Y Tian, D Dong, Z Wang, L Wu, JY Park, GH Wei… - The American Journal of …, 2023 - cell.com
Genome-wide association studies along with expression quantitative trait locus (eQTL)
mapping have identified hundreds of single-nucleotide polymorphisms (SNPs) and their …

Identifying genetic variants associated with chromatin looping and genome function

S Bhattacharyya, F Ay - Nature Communications, 2024 - nature.com
Here we present a comprehensive HiChIP dataset on naïve CD4 T cells (nCD4) from 30
donors and identify QTLs that associate with genotype-dependent and/or allele-specific …

rs71327024 Associated with COVID-19 Hospitalization Reduces CXCR6 Promoter Activity in Human CD4+ T Cells via Disruption of c-Myb Binding

AN Uvarova, EM Stasevich, AS Ustiugova… - International Journal of …, 2023 - mdpi.com
Single-nucleotide polymorphism rs71327024 located in the human 3p21. 31 locus has been
associated with an elevated risk of hospitalization upon SARS-CoV-2 infection. The 3p21 …

Integration of risk variants from GWAS with SARS-CoV-2 RNA interactome prioritizes FUBP1 and RAB2A as risk genes for COVID-19

W Shi, M Chen, T Pan, M Chen, Y Cheng, Y Hao… - Scientific Reports, 2023 - nature.com
The role of host genetic factors in COVID-19 outcomes remains unclear despite various
genome-wide association studies (GWAS). We annotate all significant variants and those …

[HTML][HTML] Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response

IS Damarov, EE Korbolina, EY Rykova… - International Journal of …, 2024 - mdpi.com
The goal of our study was to identify and assess the functionally significant SNPs with
potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their …

Bioinformatics in Russia: history and present-day landscape

MA Nawaz, IE Pamirsky… - Briefings in …, 2024 - academic.oup.com
Bioinformatics has become an interdisciplinary subject due to its universal role in molecular
biology research. The current status of Russia's bioinformatics research in Russia is not …