The 2022 Nucleic Acids Research database issue and the online molecular biology database collection

DJ Rigden, XM Fernández - Nucleic acids research, 2022 - academic.oup.com
Abstract The 2022 Nucleic Acids Research Database Issue contains 185 papers, including
87 papers reporting on new databases and 85 updates from resources previously published …

[HTML][HTML] Integrated multimodal cell atlas of Alzheimer's disease

MI Gabitto, KJ Travaglini, VM Rachleff… - Research …, 2023 - ncbi.nlm.nih.gov
Alzheimer's disease (AD) is the most common cause of dementia in older adults.
Neuropathological and imaging studies have demonstrated a progressive and stereotyped …

Molecular regulation of PPARγ/RXRα signaling by the novel cofactor ZFP407

A Charrier, J Ockunzzi, L Main, SV Ghanta… - Plos one, 2024 - journals.plos.org
Cofactors interacting with PPARγ can regulate adipogenesis and adipocyte metabolism by
modulating the transcriptional activity and selectivity of PPARγ signaling. ZFP407 was …

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 …

SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells

D Sun, Y Zhu, W Peng, S Zheng, J Weng, S Dong, J Li… - Genome Biology, 2024 - Springer
Background Transposable elements play a critical role in maintaining genome architecture
during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of …

[HTML][HTML] Functional dissection of complex and molecular trait variants at single nucleotide resolution

L Siraj, RI Castro, H Dewey, S Kales, TTL Nguyen… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Identifying the causal variants and mechanisms that drive complex traits and diseases
remains a core problem in human genetics. The majority of these variants have individually …

A Vago-like gene enhances dengue and Zika virus dissemination in Aedes aegypti

E Couderc, AB Crist, J Daron, H Varet, FAH Van Hout… - bioRxiv, 2024 - biorxiv.org
Arthropod-borne viruses (arboviruses) such as dengue virus (DENV) and Zika virus (ZIKV)
pose a significant threat to global health. Novel approaches to control the spread of …

Human transcription factor combinations mapped by footprinting with deaminase

R He, W Dong, W Ma, Z Wang, L Gao, C Xie, D Li… - bioRxiv, 2024 - biorxiv.org
An individual's somatic cells have the same genome but exhibit cell-type-specific
transcriptome regulated by a combination of transcription factors (TFs) for each gene …

Scalable ultra-high-throughput single-cell chromatin and RNA sequencing reveals gene regulatory dynamics linking macrophage polarization to autoimmune disease

S Lobato-Moreno, U Yildiz, A Claringbould… - bioRxiv, 2023 - biorxiv.org
Enhancers and transcription factors (TFs) are crucial in regulating cellular processes,
including disease-associated cell states. Current multiomic technologies to study these …

Genomic background sequences systematically outperform synthetic ones in de novo motif discovery for ChIP-seq data

VV Raditsa, AV Tsukanov, AG Bogomolov, VG Levitsky - bioRxiv, 2024 - biorxiv.org
Efficient de novo motif discovery from the results of wide-genome mapping of transcription
factor binding sites (ChIP-seq) is dependent on the choice of background nucleotide …