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Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat
Tartary buckwheat, Fagopyrum tataricum, is a pseudocereal crop with worldwide distribution and high nutritional value. How...
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Rapid and sensitive detection of genome contamination at scale with FCS-GX
Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBI’s Foreig...
HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells
HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells
Recent developments in auxin-inducible degron (AID) technology have increased its popularity for chemogenetic control of p...
Precise fine-turning of GhTFL1 by base editing tools defines ideal cotton plant architecture
Precise fine-turning of GhTFL1 by base editing tools defines ideal cotton plant architecture
CRISPR/Cas-derived base editor enables precise editing of target sites and has been widely used for basic research and cro...
scGIST: gene panel design for spatial transcriptomics with prioritized gene sets
scGIST: gene panel design for spatial transcriptomics with prioritized gene sets
A critical challenge of single-cell spatial transcriptomics (sc-ST) technologies is their panel size. Being based on fluor...
A comparison of marker gene selection methods for single-cell RNA sequencing data
A comparison of marker gene selection methods for single-cell RNA sequencing data
The development of single-cell RNA sequencing (scRNA-seq) has enabled scientists to catalog and probe the transcr...
SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data
SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data
Multi-omic single-cell technologies, which simultaneously measure the transcriptional and epigenomic state of the same cel...
Structured 3′ UTRs destabilize mRNAs in plants
Structured 3′ UTRs destabilize mRNAs in plants
RNA secondary structure (RSS) can influence the regulation of transcription, RNA processing, and protein synthesis, among ...
DNA satellite and chromatin organization at mouse centromeres and pericentromeres
DNA satellite and chromatin organization at mouse centromeres and pericentromeres
Centromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of sat...
Undetectable off-target effects induced by FokI catalytic domain in mouse embryos
Undetectable off-target effects induced by FokI catalytic domain in mouse embryos
The FokI catalytic domain can be fused to various DNA binding architectures to improve the precision of genome editing too...
Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids
Dissecting the sequence and structural determinants guiding m6A deposition and evolution via inter- and intra-species hybrids
N6-methyladenosine (m6A) is the most abundant mRNA modification, and controls mRNA stability. m6A distribution varies cons...
RUBICON: a framework for designing efficient deep learning-based genomic basecallers
RUBICON: a framework for designing efficient deep learning-based genomic basecallers
Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide ...
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ab...
SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites
SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites
Single-strand breaks are the major DNA damage in the genome and serve a crucial role in various biological processes. To r...
IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy
IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy
Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients r...
The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer
The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer
The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in som...
Simple but powerful interactive data analysis in R with R/LinekdCharts
Simple but powerful interactive data analysis in R with R/LinekdCharts
In research involving data-rich assays, exploratory data analysis is a crucial step. Typically, this involves jumping back...
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites
BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites
Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the ...
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
RExPRT: a machine learning tool to predict pathogenicity of tandem repeat loci
Expansions of tandem repeats (TRs) cause approximately 60 monogenic diseases. We expect that the discovery of additional p...
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing ...
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding
AnnoPRO: a strategy for protein function annotation based on multi-scale protein representation and a hybrid deep learning of dual-path encoding
Protein function annotation has been one of the longstanding issues in biological sciences, and various computational meth...
Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
Mapping the functional impact of non-coding regulatory elements in primary T cells through single-cell CRISPR screens
Drug targets with genetic evidence are expected to increase clinical success by at least twofold. Yet, translating disease...
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and...
Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions
Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions
Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particu...
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells
In non-polarized cells, nonsense-mediated mRNA decay (NMD) generally begins during the translation of newly synthesized mR...
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective in...
The unusual gene architecture of polyubiquitin is created by dual-specific splice sites
The unusual gene architecture of polyubiquitin is created by dual-specific splice sites
The removal of introns occurs through the splicing of a 5′ splice site (5′ss) with a 3′ splice site (3&#...
Gene panel selection for targeted spatial transcriptomics
Gene panel selection for targeted spatial transcriptomics
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure...
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cel...