Page 9 of 45
Tumor-associated macrophages (TAMs) are abundant in gliomas and immunosuppressive TAMs are a barrier to emerging immunotherapies. It is unknown to what extent macrophages derived from peripheral blood adopt th...
Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that...
Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expre...
The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We...
We present the software Condition-specific Regulatory Units Prediction (CRUP) to infer from epigenetic marks a list of regulatory units consisting of dynamically changing enhancers with their target genes. The wo...
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...
Crosslinking immunoprecipitation sequencing (CLIP-seq) technologies have enabled researchers to characterize transcriptome ... soft-clustering method, RBPgroup, to various CLIP-seq datasets to group together RBPs...
The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently b...
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore ... large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin...
Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alterna...
Here, we perform formaldehyde RNA immunoprecipitation (fRIP-Seq) to survey the RNA associated with a...
Transcription factor-dependent cellular reprogramming is integral to normal development and is central to production of induced pluripotent stem cells. This process typically requires pioneer transcription fac...
Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and ...
The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild...
Accurate fusion transcript detection is essential for comprehensive characterization of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been developed to predict fusions from RNA-seq
We annotate granulocyte lncRNAs and mRNAs in RNA-seq data from 10 healthy individuals, identifying multiple...
Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in ... effective tool for differential isoform quantification between scRNA-seq data sets. BRIE, therefore, expands the scope ...
Mitochondrial heteroplasmy, the presence of more than one mitochondrial DNA (mtDNA) variant in a cell or individual, is not as uncommon as previously thought. It is mostly due to the high mutation rate of the mtD...
We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly ... . CIDANE supports the integra...
We develop a strategy to bridge the gap between measurement and function in single-cell epigenomics. Using single-cell chromatin accessibility and RNA-seq data in K562 leukemic cells, we identify...
Using a ChIP-seq time series dataset, we find that the...Stat1−/− cells.
Both imprinted domains are located within overarching topologically associating domains (TADs) that are similar on both parental chromosomes. At each domain, a single differentially methylated region is bound by ...
Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that ... years ago. With the advantages of scRNA-seq come computational challenges that are just beginning ... available for the design a...
Although scRNA-seq is now ubiquitously adopted in studies of ... mutations and inference of clonal membership from scRNA-seq is currently unreliable. We propose DENDRO, an analysis method for scRNA-seq data that ...
CTCF and BORIS (CTCFL), two paralogous mammalian proteins sharing nearly identical DNA binding domains, are thought to function in a mutually exclusive manner in DNA binding and transcriptional regulation.
RNA sequencing (RNA-seq) is the current gold-standard method to ... potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of...
There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole...
The simultaneous quantification of protein and RNA makes possible the inference of past, present, and future cell states from single experimental snapshots. To enable such temporal analysis from multimodal sin...
A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneousl...
The Author Correction to this article has been published in Genome Biology 2023 24:32
The Publisher Correction to this article has been published in Genome Biology 2021 22:177
Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylati...
We describe here a long-read proteogenomics approach for integrating sample-matched long-read RNA-seq and MS-based proteomics data to enhance...
One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging....
Using HiC-Seq, ATAC-Seq, and RNA-Seq, we first demonstrate that transcriptional and chromatin...
The three-dimensional genome organization influences diverse nuclear processes. Here we present Chromatin Interaction Predictor (ChIPr), a suite of regression models based on deep neural networks, random forest, ...
Single-cell RNA sequencing has emerged as a powerful tool for characterizing cells, but not all phenotypes of interest can be observed through changes in gene expression. Linking sequencing with optical analys...
Gene expression is epigenetically regulated by a combination of histone modifications and methylation of CpG dinucleotides in promoters. In normal cells, CpG-rich promoters are typically unmethylated, marked w...
Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput ... and states. With the cost of scRNA-seq decreasing and techniques for sample multiplexing improving, population-scale scRNA-seq,...
Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great ...
Association of chromatin with lamin proteins at the nuclear periphery has emerged as a potential mechanism to coordinate cell type-specific gene expression and maintain cellular identity via gene silencing. Un...
Epigenetic modifications of histones are associated with development and pathogenesis of disease. Existing approaches cannot provide insights into long-range interactions and represent the average chromatin state...
Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic ...
The Correspondence to this article has been published in Genome Biology 2024 25:85
Expression quantitative trait loci (eQTLs) are likely to play an important role in the genetics of complex traits; however, their functional basis remains poorly understood. Using the HapMap lymphoblastoid cel...
Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and c...
Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis.
To compare the genome-wide DNA binding profile of SVP during vegetative and reproductive development we performed ChIP-seq analyses. These ChIP-seq data were combined with tiling array expression...
With knowledge-primed neural networks (KPNNs), we exploit the ability of deep learning algorithms to assign meaningful weights in multi-layered networks, resulting in a widely applicable approach for interpretabl...
Identifying and removing multiplets are essential to improving the scalability and the reliability of single cell RNA sequencing (scRNA-seq). Multiplets create artificial cell types in ... sample barcoding, inclu...
Recent advances in single-cell biotechnologies have resulted in high-dimensional datasets with increased complexity, making feature selection an essential technique for single-cell data analysis. Here, we revi...
The rapid accumulation of single-cell RNA sequencing (scRNA-seq) data presents unique opportunities to decode the ... new method, scGWAS, which effectively leverages scRNA-seq data to achieve two goals: (1)...
By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified...cis- than by trans-genetic factors.
The Correction to this article has been published in Genome Biology 2018 19:122
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.
