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DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromat...
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow (http://github.com/liulab-dfci/MAESTRO....
Early single-cell RNA-seq (scRNA-seq) studies suggested that it was unusual to ... multiple isoforms were detected in matched bulk RNA-seq samples. However, these studies generally did...
We present a new and comprehensive Arabidopsis thaliana...Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including o...
STARR-seq technology has employed progressively more complex genomic ... and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and ... , such as GC content. Furthermore, STARR-seq
The original article was published in Genome Biology 2013 14:3158
New methods for simultaneously quantifying protein and gene expression at the single-cell level have the power to identify cell types and to classify cell populations.
The Related Article to this article has been published in Nature Methods 2017 14:nmeth.4380
Single-cell ATAC-seq detects open chromatin in individual cells. Currently...
Following publication of the original article [1], the authors reported that Figs. 4 and 5 had mistakenly been transposed. Please find the correct Figs. 4 and 5 below. The original article [1] has been corrected.
The original article was published in Genome Biology 2019 20:91
A large-scale single-cell RNA-seq analysis of tumor-associated macrophages in gliomas...
The original article was published in Genome Biology 2016 17:74
Optically decodable beads link the identity of a sample to a measurement through an optical barcode, enabling libraries of biomolecules to be captured on beads in solution and decoded by fluorescence. This approa...
The original article was published in Genome Biology 2016 17:13
Activation of regulatory elements is thought to be inversely correlated with DNA methylation levels. However, it is difficult to determine whether DNA methylation is compatible with chromatin accessibility or tra...
DNase-seq and ATAC-seq are broadly used methods to assay open ... -wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription ... bias have not been extensively studied ...
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell nu...
Single-cell RNA-seq data contain a large proportion of zeros...
Chromatin accessibility captures in vivo protein-chromosome binding status, and is considered an informative proxy for protein-DNA interactions. DNase I and Tn5 transposase assays require thousands to millions of...
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss ... a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative a...
Development of a highly reproducible and sensitive single-cell RNA sequencing (RNA-seq) method would facilitate the understanding of the ... , we report a novel single-cell RNA-seq method called Quartz-Seq that h...
The Erratum to this article has been published in Genome Biology 2017 18:9
Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of ... factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering...
Advances in droplet-based single-cell RNA-sequencing (scRNA-seq) have dramatically increased throughput, allowing tens...
We have developed a new strategy for de novo...prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing ... chimeric transcripts. When tested on mouse RNA-seq data, >31,...
With the number of cells measured in single-cell RNA sequencing (scRNA-seq) datasets increasing exponentially and concurrent increased sparsity ... also highlight the possibilities provided by binarized scRNA-seq
De novo RNA-Seq assembly facilitates the study of transcriptomes for...http://deweylab.biostat.wisc.edu/detonate.
Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of...
A large number of RNA-sequencing studies set out to predict mutations, splice junctions or fusion RNAs. We propose a method, CRAC, that integrates genomic locations and local coverage to enable such predictions t...
A major advantage of single cell RNA-sequencing (scRNA-Seq) data is the ability to reconstruct continuous ... the inference of cell-cell interactions in scRNA-Seq studies that utilizes the dynamic information to ...
Cell clustering is one of the most common routines in single cell RNA-seq data analyses, for which a number of...
Scaling scRNA-seq to profile millions of cells is crucial ... and-conquer algorithm allowing efficient decomposition of scRNA-seq datasets of any size into small and...
RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible...
Although transcriptional elongation by RNA polymerase II is coupled with many RNA-related processes, genomewide elongation rates remain unknown. We describe a method, called 4sUDRB-seq, based on reversible inhibi...
The Related Article to this article has been published in Nature Protocols 2015 10:nprot.2015.035
Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to...
The ChIP-seq technique enables genome-wide mapping of in vivo...protein-DNA interactions and chromatin states. Current analytical approaches for ChIP-seq analysis are largely geared towards single-sample ... meth...
CLIP-seq is widely used to study genome-wide ... there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the ... of data generated by three types of CLIP-seq protocol: HITS-CLIP, PAR...
ChIP-seq is a powerful method for obtaining genome- ... DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq quality control an...
Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification methods...
Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication...Saccharomyces cerevisiae..., we orien...
We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the...
The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated...
Although long-read RNA-seq is increasingly applied to characterize full-length ... analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively ... and read biases. Applied to PacBio RNA-
The fine detail provided by sequencing-based transcriptome surveys suggests that RNA-seq is likely to become the platform of...
Droplet-based microfluidic devices have become widely used to perform single-cell RNA sequencing (scRNA-seq). However, ambient RNA present in the ... compare the contamination levels between four different scRNA-
Most single-cell RNA sequencing (scRNA-seq) analyses begin with cell clustering; thus, ... . We conduct in silico and experimental scRNA-seq studies to show that CDI can select...
ChIP-seq is an established manually-performed method for ... protocol for automated high-throughput (AHT) ChIP-seq. To demonstrate the quality of data obtained using AHT-ChIP-seq, we applied it to five proteins i...
Detecting multiplets in single nucleus (sn)ATAC-seq data is challenging due to data sparsity and limited dynamic range. AMULET (ATAC-seq MULtiplet Estimation Tool) enumerates regions with greater ... . We evaluat...
In droplet-based single-cell and single-nucleus RNA-seq assays, systematic contamination of ambient RNA molecules...
Comprehensive characterisation of genome engineering technologies is relevant for their development and safe use in human gene therapy. Short-read based methods can overlook insertion events in repetitive regions...
The Author Correction to this article has been published in Genome Biology 2023 24:137
Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, ... importance and utility of count models for scRNA-seq analysis, but there is a lack of...
We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We appli...
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