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To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural pa...
It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. However, the level of conservation of gene expression patt...
Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.
Recent work has used a family-based approach and whole-exome sequencing to identify de novo mutations in sporadic cases of mental retardation.
A recent study has generated blood cell progenitors with therapeutic potential by direct lineage conversion of human fibroblasts, thus circumventing reprogramming to pluripotent stem cells.
We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this m...
A report on the meeting 'Beyond the Genome', Boston, USA, 11-13 October 2010.
Recent research shows that declining oocyte quality with age is not inevitable in nematodes, and similar signals might regulate reproductive aging in women.
Recent studies have implicated the microRNA biogenesis enzyme Dicer as a suppressor of breast carcinoma metastasis and elucidated upstream signaling pathways that control Dicer levels.
We propose definitions and procedures for comparing nucleosome maps and discuss current agreement and disagreement on the effect of histone sequence preferences on nucleosome organization in vivo.
Targeted re-sequencing of candidate genes in individuals at the extremes of a quantitative phenotype distribution is a method of choice to gain information on the contribution of rare variants to disease susce...
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies ...
We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the hi...
We report the construction of a genome-wide fish metabolic network model, MetaFishNet, and its application to analyzing high throughput gene expression data. This model is a stepping stone to broader applicati...
To identify potential tumor suppressor genes, genome-wide data from exome and transcriptome sequencing were combined to search for genes with loss of heterozygosity and allele-specific expression. The analysis...
Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale ...
Recent research has revealed complex heterogeneous genomic landscapes in human cancers. However, mutations tend to occur within a core group of pathways and biological processes that can be grouped into gene s...
Inbred individuals reared in controlled environments display considerable variance in many complex traits but the underlying cause of this intangible variation has been an enigma. Here we show that two modifie...
Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for...
Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley's most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solel...
This article is part of a Supplement: Volume 11 Supplement 1
Hapi is a new dynamic programming algorithm that ignores uninformative states and state transitions in order to efficiently compute minimum-recombinant and maximum likelihood haplotypes. When applied to a data...
Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptoco...
The Erratum to this article has been published in Genome Biology 2011 12:140
A report on the joint Cold Spring Harbor Laboratory/Wellcome Trust Conference 'Genome Informatics', 15-19 September 2010, Hinxton, Cambridge, UK.
Under starvation conditions, the soil bacterium Sinorhizobium meliloti divides into two types of daughter cell: one suited to short-term and the other to long-term starvation.
High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statis...
Gene expression is a dynamic trait, and the evolution of gene regulation can dramatically alter the timing of gene expression without greatly affecting mean expression levels. Moreover, modules of co-regulated...
We have developed FusionSeq to identify fusion transcripts from paired-end RNA-sequencing. FusionSeq includes filters to remove spurious candidate fusions with artifacts, such as misalignment or random pairing...
Meiotic recombination events tend to cluster into narrow spans of a few kilobases long, called recombination hotspots. Such hotspots are not conserved between human and chimpanzee and vary between different hu...
A comprehensive transcriptome survey, or gene atlas, provides information essential for a complete understanding of the genomic biology of an organism. We present an atlas of RNA abundance for 92 adult, juveni...
Molecular genetic studies of floral development have concentrated on several core eudicots and grasses (monocots), which have canalized floral forms. Basal eudicots possess a wider range of floral morphologies...
Here we present the first paired-end sequencing of tumors from genetically engineered mouse models of cancer to determine how faithfully these models recapitulate the landscape of somatic rearrangements found ...
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
This article is part of a Supplement: Volume 11 Supplement 1
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