Page 36 of 45
The Integrative Genomics Viewer (IGV) for iPad, based on the popular IGV application for desktop and laptop computers, supports researchers who wish to take advantage of the mobility of today’s tablet computers t...
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
Millions of small open reading frames exist in eukaryotes. We do not know how many, or which are translated, but bioinformatics is getting us closer to the answer.
Alu elements can integrate into human genes and lead to the generation of primate-specific isoforms. A new study examines their contribution to the human proteome.
A new study investigates how microRNAs affect the binding of proteins to RNA.
Histone variants constitute a fundamental feature of the epigenome. However, their dynamics during normal and challenged DNA replication and their distribution in the three-dimensional space of the nucleus rem...
A recent study using massive parallel sequencing demonstrates unequivocally that alternative tandem acceptor splicing is tissue-specifically regulated.
Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifa...
Chromosome folding can reinforce the demarcation between euchromatin and heterochromatin. Two new studies show how epigenetic data, including DNA methylation, can accurately predict chromosome folding in three...
A report on the Second Aegean International Conference on the Long and the Short of Non-Coding RNAs, held in Heraklion, Greece, 9–14 June 2017.
Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces...
Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purp...
Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases...
N 6 -methyladenosine (m6A) modification in mRNAs was recently shown to be dynamically regulated, indicating a pivotal role in multiple developmental processes. Most recently,...
Gene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the ...
Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.
Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective con...
The origin of new genes with novel functions creates genetic and phenotypic diversity in organisms. To acquire functional roles, new genes must integrate into ancestral gene-gene interaction (GGI) networks. Th...
Gene expression is controlled at multiple levels, including transcription, stability, translation, and degradation. Over the years, it has become apparent that Plasmodium falciparum exerts limited transcriptional...
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more ...
The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...
CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functiona...
Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ...
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the dive...
Network analysis is a powerful way of modeling chromatin interactions. Assortativity is a network property used in social sciences to identify factors affecting how people establish social ties. We propose a n...
Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-...
DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, ...
The Protocol to this article has been published in Nature Protocols 2020 15:s41596-020-0369-6
Establishing a link between RNA structure and function remains a great challenge in RNA biology. The emergence of high-throughput structure profiling experiments is revolutionizing our ability to decipher stru...
CpG islands and nucleosome-free regions are both found in promoters. However, their association has never been studied. On the other hand, DNA methylation is absent in promoters but is enriched in gene bodies....
Interactive graphical genome browsers are essential tools in genomics, but they do not contain all the recent genome assemblies. We create Genome Archive (GenArk) collection of UCSC Genome Browsers from NCBI a...
The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence ...
Machine learning models that predict genomic activity are most useful when they make accurate predictions across cell types. Here, we show that when the training and test sets contain the same genomic loci, th...
Gene regulatory networks (GRNs) are rapidly being delineated, but their quality and biological meaning are often questioned. Here, I argue that biological meaning is challenging to define and discuss reasons w...
The use of genomic technologies for the molecular characterization of tumors has propelled our understanding of cancer biology and is transforming the way patients with cancer are diagnosed and treated.
Processing of pre-miRNAs by Dicer is regulated by its dsRNA-binding protein partner, and leads to the generation of alternative miRNA forms with distinct target sets.
The Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface.
Mapping of 5-hydroxylmethylcytosine in mammalian genomes has unveiled its unique role in the epigenetic regulation of gene expression.
A report on the Cold Spring Harbor Laboratory 27th annual meeting on the Biology of Genomes, held in Cold Spring Harbor, New York, USA, 6-10 May 2014.
A report of the meeting 'Gene Expression and Signaling in the Immune System', Cold Spring Harbor, USA, 22-26 April 2008.
Three recent studies have altered thinking on the role of TIMING OF CAB EXPRESSION 1 (TOC1), a core element in the plant circadian oscillator.
A report on the Keystone Symposium 'Cancer Genomics and Epigenomics', Taos, USA, 19-24 February 2008.
Studies describing intricate patterns of DNA methylation in nematode and ciliate are controversial due to the uncertainty of genomic evolutionary conservation of DNA methylation enzymes.
Two new studies imply that the reprogramming of 5-methylcytosine via TET- and TDG-family enzymes is both widespread throughout the genome and functionally significant.
A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013.
A report on the Plant and Animal Genome XXII meeting held in San Diego, California, USA, January 11–15, 2014.
The original article was published in Genome Biology 2021 22:163
A genetic study in Drosophila gives important insights into the epigenetic control of gene expression implicated in a human mental retardation syndrome.
DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation.
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.
