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Single-cell chromosome conformations vary significantly among individual cells. We introduce a two-step dimensionality reduction method for density-based, unsupervised clustering of single-cell 3D chromosome s...
The history of human populations has been strongly shaped by admixture events, contributing to patterns of observed genetic diversity across populations. In this study, we introduce the Principal component Anc...
Chromatin higher-order structure plays an important role in genome stability maintenance and gene transcriptional regulation; however, the dynamics of the three-dimensional (3D) chromatin in male gametophytes ...
Genome-wide association studies (GWAS) have uncovered the genetic basis behind many diseases and conditions. However, most of these genetic loci affect regulatory regions, making the interpretation challenging...
Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yi...
Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Leiden clus...
While CENP-A is the epigenetic determinant of the centromeric function, the role of CENP-B, a centromeric protein binding a specific DNA sequence, the CENP-B-box, remains elusive. In the few mammalian species ...
SETD2 is the sole epigenetic factor responsible for catalyzing histone 3, lysine 36, tri-methylation (H3K36me3) in mammals. Its role in regulating cellular processes such as RNA splicing, DNA repair, and spuri...
Transcriptome-wide association study (TWAS) has emerged as a powerful tool for translating the myriad variations identified by genome-wide association studies (GWAS) into regulated genes in the post-GWAS era. ...
Plant residue microbial decomposition, subject to significant environmental regulation, represents a crucial ecological process shaping and cycling the largest terrestrial soil organic carbon pool. However, th...
We present multi-integration of transcriptome-wide association studies and colocalization (Multi-INTACT), an algorithm that models multiple “gene products” (e.g., encoded RNA transcript and protein levels) to ...
Base editors are precise editing tools that employ deaminases to modify target DNA bases. The DYW-family of cytosine deaminases is structurally and phylogenetically distinct and might be harnessed for genome e...
We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. “EA78” (2n ...
The original article was published in Genome Biology 2025 26:15
Sequence alignment is foundational to many bioinformatic analyses. Many aligners start by splitting sequences into contiguous, fixed-length seeds, called k-mers. Alignment is faster with longer, unique seeds, ...
The Author Correction to this article has been published in Genome Biology 2025 26:16
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have b...
Multiplexed assays of variant effect (MAVEs) are a critical tool for researchers and clinicians to understand genetic variants. Here we describe the 2024 update to MaveDB (
The original article was published in Genome Biology 2024 25:296
The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammal...
Genetic studies have associated thousands of enhancers with breast cancer (BC). However, the vast majority have not been functionally characterized. Thus, it remains unclear how BC-associated enhancers contrib...
Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or n...
Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial population...
Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations...
We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sit...
Biological data visualization is challenged by the growing complexity of datasets. Traditional single-data plots or simple juxtapositions often fail to fully capture dataset intricacies and interrelations. To ...
Genetic variation in the non-recombining part of the human Y chromosome has provided important insight into the paternal history of human populations. However, a significant and yet unexplained branch length v...
Deciphering the link between tissue architecture and function requires methods to identify and interpret patterns in spatial arrangement of cells. We present SMORE, an approach to detect patterns in sequential...
In humans and other mammals, the process of oogenesis initiates asynchronously in specific ovarian regions, leading to the localization of dormant and growing follicles in the cortex and medulla, respectively;...
We present SiCLAT, which introduces a dCas9-dCas13d cassette into the mouse genome. This model enables the stable expression of both dCas9 and dCas13 proteins in diverse cell populations, facilitating concurre...
Promoters serve as key elements in the regulation of gene transcription. In mammals, loop interactions between promoters and enhancers increase the complexity of the promoter-based regulatory networks. However...
DNA damage tolerance (DDT) enables replication to continue in the presence of fork stalling lesions. In mammalian cells, DDT is regulated by two independent pathways, controlled by the polymerase REV1 and ubiq...
Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heteroge...
Single-cell DNA methylation measurements reveal genome-scale inter-cellular epigenetic heterogeneity, but extreme sparsity and noise challenges rigorous analysis. Previous methods to detect variably methylated...
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through...
The fatal diffuse midline gliomas (DMG) are characterized by an undruggable H3K27M mutation in H3.1 or H3.3. K27M impairs normal development by stalling differentiation. The identification of targetable pathwa...
Plasma cell-free DNA (cfDNA) is derived from cellular death in various tissues. Investigating the tissue origin of cfDNA through cell type deconvolution, we can detect changes in tissue homeostasis that occur ...
Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method fo...
Single-cell DNA sequencing (scDNA-seq) enables decoding somatic cancer variation. Existing methods are hampered by low throughput or cannot be combined with transcriptome sequencing in the same cell. We propos...
We present GenomeDelta, a novel tool for identifying sample-specific sequences, such as recent transposable element (TE) invasions, without requiring a repeat library. GenomeDelta compares high-quality assembl...
Cloud computing allows storing the ever-growing genotype-phenotype datasets crucial for precision medicine. Due to the sensitive nature of this data and varied laws and regulations, additional security measure...
Transcription factors (TFs) bind regulatory genomic regions to orchestrate spatio-temporal expression of target genes. Global dissection of the cistrome is critical for elucidating transcriptional networks und...
Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite...
Synthetic CRISPR-Cas9 gene drive has been developed to control harmful species. However, resistance to Cas9 gene drive can be acquired easily when DNA repair mechanisms patch up the genetic insults introduced ...
The inherent similarities between natural language and biological sequences have inspired the use of large language models in genomics, but current models struggle to incorporate chromatin interactions or pred...
The accuracy of machine learning methods is often limited by the amount of training data that is available. We proposed to improve machine learning training regimes by augmenting datasets with synthetically ge...
Immunotherapy has improved survival for patients with advanced clear cell renal cell carcinoma (ccRCC), but resistance to therapy develops in most patients. We use cellular-resolution spatial transcriptomics i...
CRISPR/Cas13 system, recognized for its compact size and specificity in targeting RNA, is currently employed for RNA degradation. However, the potential of various CRISPR/Cas13 subtypes, particularly concernin...
Plants respond to environmental stimuli by altering gene transcription that is highly related with chromatin status, including histone modification, chromatin accessibility, and three-dimensional chromatin int...
Epigenetic heterogeneity is a fundamental property of biological systems and is recognized as a potential driver of tumor plasticity and therapy resistance. Single-cell epigenomics technologies have been widel...
We present MoCHI, a tool to fit interpretable models using deep mutational scanning data. MoCHI infers free energy changes, as well as interaction terms (energetic couplings) for specified biophysical models, ...
Citation Impact 2023
Journal Impact Factor: 10.1
5-year Journal Impact Factor: 16.5
Source Normalized Impact per Paper (SNIP): 2.521
SCImago Journal Rank (SJR): 7.197
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