[HTML][HTML] Methods for ChIP-seq analysis: A practical workflow and advanced applications
R Nakato, T Sakata - Methods, 2021 - Elsevier
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
epigenomic research. Genome-wide analysis of histone modifications, such as enhancer …
Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level
A Farmer, S Thibivilliers, KH Ryu, J Schiefelbein… - Molecular Plant, 2021 - cell.com
Similar to other complex organisms, plants consist of diverse and specialized cell types. The
gain of unique biological functions of these different cell types is the consequence of the …
gain of unique biological functions of these different cell types is the consequence of the …
Nitrogen sensing and regulatory networks: it's about time and space
A plant's response to external and internal nitrogen signals/status relies on sensing and
signaling mechanisms that operate across spatial and temporal dimensions. From a …
signaling mechanisms that operate across spatial and temporal dimensions. From a …
VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases
Interpreting the molecular mechanism of genomic variations and their causal relationship
with diseases/traits are important and challenging problems in the human genetic study. To …
with diseases/traits are important and challenging problems in the human genetic study. To …
Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution
Comparative genomic approaches have been used to identify sites where mutations are
under purifying selection and of functional consequence by searching for sequences that …
under purifying selection and of functional consequence by searching for sequences that …
VarCards2: an integrated genetic and clinical database for ACMG-AMP variant-interpretation guidelines in the human whole genome
Z Wang, G Zhao, Z Zhu, Y Wang, X Xiang… - Nucleic Acids …, 2024 - academic.oup.com
VarCards, an online database, combines comprehensive variant-and gene-level annotation
data to streamline genetic counselling for coding variants. Recognising the increasing …
data to streamline genetic counselling for coding variants. Recognising the increasing …
Extreme purifying selection against point mutations in the human genome
Large-scale genome sequencing has enabled the measurement of strong purifying
selection in protein-coding genes. Here we describe a new method, called ExtRaINSIGHT …
selection in protein-coding genes. Here we describe a new method, called ExtRaINSIGHT …
GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies
Recent advances in genome sequencing and imputation technologies provide an exciting
opportunity to comprehensively study the contribution of genetic variants to complex …
opportunity to comprehensively study the contribution of genetic variants to complex …
Performance comparison of computational methods for the prediction of the function and pathogenicity of non-coding variants
Z Wang, G Zhao, B Li, Z Fang, Q Chen… - Genomics …, 2023 - academic.oup.com
Non-coding variants in the human genome significantly influence human traits and complex
diseases via their regulation and modification effects. Hence, an increasing number of …
diseases via their regulation and modification effects. Hence, an increasing number of …
From summary statistics to gene trees: methods for inferring positive selection
Methods to detect signals of natural selection from genomic data have traditionally
emphasized the use of simple summary statistics. Here, we review a new generation of …
emphasized the use of simple summary statistics. Here, we review a new generation of …