Page 12 of 150
Technological development has enabled the profiling of gene expression and chromatin accessibility from the same cell. We develop scREG, a dimension reduction methodology, based on the concept of cis-regulatory p...
The Author Correction to this article has been published in Genome Biology 2022 23:213
Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironmen...
The Author Correction to this article has been published in Genome Biology 2022 23:156
Integration of single-cell multiomics profiles generated by different single-cell technologies from the same biological sample is still challenging. Previous approaches based on shared features have only provi...
Recent proteogenomic studies revealed extensive translation outside of annotated protein coding regions, such as non-coding RNAs and untranslated regions of mRNAs. This non-canonical translation is largely due...
Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for e...
The precise spatiotemporal gene expression is orchestrated by enhancers that lack general sequence features and thus are difficult to be computationally identified. By nascent RNA sequencing combined with epig...
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts i...
The original article was published in Genome Biology 2018 19:37
Patient-derived organoid culture is a powerful system for studying the molecular mechanisms of cancers, especially colorectal cancer (CRC), one of the most prevalent cancers worldwide. There are two main types...
Revealing the gene targets of distal regulatory elements is challenging yet critical for interpreting regulome data. Experiment-derived enhancer-gene links are restricted to a small set of enhancers and/or cel...
The original article was published in Genome Biology 2022 23:82
Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pan...
Integrative analysis of large-scale single-cell RNA sequencing (scRNA-seq) datasets can aggregate complementary biological information from different datasets. However, most existing methods fail to efficientl...
Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on tr...
Scaling scRNA-seq to profile millions of cells is crucial for constructing high-resolution maps of transcriptional manifolds. Current analysis strategies, in particular dimensionality reduction and two-phase c...
Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-thro...
Multiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning experiments on proteins and massively parallel reporter assays on gene regulatory sequences. Despite th...
The advancement of highly multiplexed spatial technologies requires scalable methods that can leverage spatial information. We present MISTy, a flexible, scalable, and explainable machine learning framework fo...
Genome-wide association studies have identified 3p21.31 as the main risk locus for severe COVID-19, although underlying mechanisms remain elusive. We perform an epigenomic dissection of 3p21.31, identifying a ...
Differential abundance analysis is at the core of statistical analysis of microbiome data. The compositional nature of microbiome sequencing data makes false positive control challenging. Here, we show that th...
The analysis of microbiome data has several technical challenges. In particular, count matrices contain a large proportion of zeros, some of which are biological, whereas others are technical. Furthermore, the...
The Author Correction to this article has been published in Genome Biology 2023 24:84
Biases of DNA repair can shape the nucleotide landscape of genomes at evolutionary timescales. The molecular mechanisms of those biases are still poorly understood because it is difficult to isolate the contri...
Prime editing can induce a desired base substitution, insertion, or deletion in a target gene using reverse transcriptase after nick formation by CRISPR nickase. In this study, we develop a technology that can...
Interactions of chromatin with the nuclear lamina via lamina-associated domains (LADs) confer structural stability to the genome. The dynamics of positioning of LADs during differentiation, and how LADs imping...
Cardiac differentiation of human-induced pluripotent stem (hiPS) cells consistently produces a mixed population of cardiomyocytes and non-cardiac cell types, even when using well-characterized protocols. We so...
Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed tu...
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it...
Vascular invasion with tumor thrombus frequently occurs in advanced renal cell carcinoma (RCC). Thrombectomy is one of the most challenging surgeries with high rate of perioperative morbidity and mortality. Ho...
Brassica napus is an important vegetable oil source worldwide. Seed coat content is a complex quantitative trait that negatively correlates with the seed oil content in B. napus.
Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees...
Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust ...
The recent advancement in spatial transcriptomics technology has enabled multiplexed profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the experimental technologies ...
The increasing number of scRNA-seq data emphasizes the need for integrative analysis to interpret similarities and differences between single-cell samples. Although different batch effect removal methods have ...
The Author Correction to this article has been published in Genome Biology 2022 23:104
Cleavage Under Targets and Tagmentation (CUT&Tag) is an antibody-directed transposase tethering strategy for in situ chromatin profiling in small samples and single cells. We describe a modified CUT&Tag protoc...
Genomic prediction in crop breeding is hindered by modeling on limited phenotypic traits. We propose an integrative multi-trait breeding strategy via machine learning algorithm, target-oriented prioritization ...
When identifying differentially expressed genes between two conditions using human population RNA-seq samples, we found a phenomenon by permutation analysis: two popular bioinformatics methods, DESeq2 and edge...
Paralogs that arise from gene duplications during genome evolution enable genetic redundancy and phenotypic robustness. Variation in the coding or regulatory sequence of paralogous transcriptional regulators d...
DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown.
The original article was published in Genome Biology 2021 22:332
Spinach (Spinacia oleracea L.) is a dioecious species with an XY sex chromosome system, but its Y chromosome has not been fully characterized. Our knowledge about the history of its domestication and improvement ...
Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamic...
A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ordering and trajectories for cells. Here we present TraSig, a computational method for improving the i...
Host-microbe interactions are crucial for normal physiological and immune system development and are implicated in a variety of diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), ob...
Neuroblastoma is a pediatric malignancy with a high frequency of metastatic disease at initial diagnosis. Neuroblastoma tumors have few recurrent protein-coding mutations but contain extensive somatic copy num...
Cohesin is a chromosome-associated SMC–kleisin complex that mediates sister chromatid cohesion, recombination, and most chromosomal processes during mitosis and meiosis. However, it remains unclear whether mei...
The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but is...
Structural variants (SVs) are a major source of human genetic diversity and have been associated with different diseases and phenotypes. The detection of SVs is difficult, and a diverse range of detection meth...
The Author Correction to this article has been published in Genome Biology 2022 23:198
Few methods have been developed to investigate copy number variants (CNVs) based on their predicted pathogenicity. We introduce TADA, a method to prioritise pathogenic CNVs through assisted manual filtering an...
Vaginal bacterial communities dominated by Lactobacillus species are associated with a reduced risk of various adverse health outcomes. However, somewhat unexpectedly, many healthy women have microbiota that are ...
Nucleomorphs are remnants of secondary endosymbiotic events between two eukaryote cells wherein the endosymbiont has retained its eukaryotic nucleus. Nucleomorphs have evolved at least twice independently, in ...
2022 Citation Impact
12.3 - 2-year Impact Factor
17.4 - 5-year Impact Factor
3.476 - SNIP (Source Normalized Impact per Paper)
9.249 - SJR (SCImago Journal Rank)
2023 Speed
21 days submission to first editorial decision for all manuscripts (Median)
277 days submission to accept (Median)
2023 Usage
6,688,476 downloads
12,515 Altmetric mentions
This journal is participating in a pilot of NISO/STM's Working Group on Peer Review Taxonomy, to identify and standardize definitions and terminology in peer review practices in order to make the peer review process for articles and journals more transparent. Further information on the pilot is available here.
The following summary describes the peer review process for this journal:
We welcome your feedback on this Peer Review Taxonomy Pilot. Please can you take the time to complete this short survey.
