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This article is part of a Supplement: Volume 11 Supplement 1
The original article was published in Genome Biology 2022 23:227
This article is part of a Supplement: Volume 11 Supplement 1
The original article was published in Genome Biology 2023 24:107
This article is part of a Supplement: Volume 12 Supplement 1
An amendment to this paper has been published and can be accessed via the original article.
The original article was published in Genome Biology 2019 20:134
This article is part of a Supplement: Volume 12 Supplement 1
An amendment to this paper has been published and can be accessed via the original article.
The original article was published in Genome Biology 2019 20:295
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
The original article was published in Genome Biology 2016 17:74
The original article was published in Genome Biology 2013 14:3097
This article is part of a Supplement: Volume 12 Supplement 1
The original article was published in Genome Biology 2015 16:149
This article is part of a Supplement: Volume 12 Supplement 1
In our recent article [1], it has come to our attention that the sample labels are not consistent between Table 1, the data labels deposited in the Sequence Read Archive, and Additional file 1: Table S2. We ar...
The original article was published in Genome Biology 2017 18:12
Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely used in studying chromatin biology ... , we discuss the major steps in ATAC-seq data analysis, including pre-analysis (quality ... we desc...
Single-cell RNA-sequencing (scRNA-seq) measures gene expression in single cells, while single-nucleus ATAC-sequencing (snATAC-seq) quantifies chromatin accessibility in single nuclei....
Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both ... for integr...
Identifying genomic regions with hypervariable ChIP-seq or ATAC-seq signals across given samples is essential for...
CRISPR-based genome perturbation provides a new avenue to conveniently change DNA sequences, transcription, and epigenetic modifications in genetic screens. However, it remains challenging to assay the complex mo...
The recently developed method TEA-seq and similar DOGMA-seq single cell trimodal omics assays provide unprecedented ... lacking. We explore the utility of DOGMA-seq compared to the bimodal CITE-seq assay in activ...
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology ... landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing...
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 pe...
DNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes: N6-methyladenine (6mA), N4...-methylcytosine (4mC), and 5-methylcytosine (5mC). Altho...
We present a novel genome-wide off-target prediction method named Extru-seq and compare it with cell-based (GUIDE-seq), in vitro (Digenome-seq), and in silico methods using promiscuous ... numbers of valid off-ta...
It is a challenging task to integrate scRNA-seq and scATAC-seq data obtained from different batches. Existing methods ... defined gene activity matrix to convert the scATAC-seq data into scRNA-seq data. The pre-d...
Here, we applied STARR-seq, a genome-wide plasmid-based assay, ... mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq librari...
Gene expression microarray has been the primary biomarker platform ubiquitously applied in biomedical research, resulting in enormous data, predictive models, and biomarkers accrued. Recently, RNA-seq has looked ...
RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the ... the composition of bulk...
Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler (scMVP), which is designed for handling sequencing data that simultaneously measure gene expression and chromatin accessib...
We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated ... MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the ... predictions. MACS compares favorab...
The Related Article to this article has been published in Nature Protocols 2012 7:nprot.2012.101
The ChIP-chip and ChIP-seq techniques enable genome-wide mapping of in vivo...protein-DNA interactions and chromatin states. The cross-platform and between-laboratory variation poses a challenge to the comparison...
Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling...Oryz...
Existing methods for computational prediction of transcription factor (TF) binding sites evaluate genomic regions with similarity to known TF sequence preferences. Most TF binding sites, however, do not resemble ...
Single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the ... evaluation is critical to the development of scATAC-seq pipelines, wh...
The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our...
Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and samples. We pres...
The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq). A large number of algorithms and com...
We developed Lisa (http://lisa.cistrome.org/...) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on th...
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological...
Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method — multiple genetic abnormality sequencing (MGA-Seq) — to simultaneously detect st...
Single-cell ATAC-seq has emerged as a powerful approach for ... we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing ... indexing step with droplet-based ...
Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possibl...
ZINBA (Zero-Inflated Negative Binomial Algorithm) identifies genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes ......
Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) ... detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome ...
The global effort to annotate the non-coding portion of the human genome relies heavily on chromatin immunoprecipitation data generated with high-throughput DNA sequencing (ChIP-seq). ChIP-seq is generally succes...
The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughpu...
We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-sp...
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing...−/−) model. Our study of CC16−/− nuclei uncovers previously underappreciated technical artifacts derived from remnant 129...
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