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JournalISSN: 2041-2649

Briefings in Functional Genomics 

Oxford University Press
About: Briefings in Functional Genomics is an academic journal published by Oxford University Press. The journal publishes majorly in the area(s): Medicine & Biology. It has an ISSN identifier of 2041-2649. Over the lifetime, 658 publications have been published receiving 20573 citations.
Topics: Medicine, Biology, Genomics, Genome, Epigenetics


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Journal ArticleDOI
TL;DR: Genome selection (GS) as discussed by the authors uses all marker data as predictors of performance and consequently delivers more accurate predictions, potentially leading to more rapid and lower cost gains from breeding. But these traits are complex and affected by many genes, each with small effect.
Abstract: We intuitively believe that the dramatic drop in the cost of DNA marker information we have experienced should have immediate benefits in accelerating the delivery of crop varieties with improved yield, quality and biotic and abiotic stress tolerance. But these traits are complex and affected by many genes, each with small effect. Traditional marker-assisted selection has been ineffective for such traits. The introduction of genomic selection (GS), however, has shifted that paradigm. Rather than seeking to identify individual loci significantly associated with a trait, GS uses all marker data as predictors of performance and consequently delivers more accurate predictions. Selection can be based on GS predictions, potentially leading to more rapid and lower cost gains from breeding. The objectives of this article are to review essential aspects of GS and summarize the important take-home messages from recent theoretical, simulation and empirical studies. We then look forward and consider research needs surrounding methodological questions and the implications of GS for long-term selection.

986 citations

Journal ArticleDOI
TL;DR: Banerjee et al. as mentioned in this paper proposed Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promising to deliver high resolution population genomic data-thousands of sequenced markers across many individuals at reasonable costs.
Abstract: Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis of genetic diversity in populations. However, genome-scale population genetic studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, a method that samples at reduced complexity across target genomes, promises to deliver high resolution population genomic data-thousands of sequenced markers across many individuals-for any organism at reasonable costs. It has found application in wild populations and non-traditional study species, and promises to become an important technology for ecological population genomics.

662 citations

Journal ArticleDOI
TL;DR: From the cataloguing of the in vivo genomic targets of STAT3 (the transcription factor downstream of IL-10) to the identification of specific co-factors that endow STAT3 with genomic-binding specificity, and how genomic and computational methods are being used to elucidate the regulatory mechanisms of this essential physiological response in macrophages are reviewed.
Abstract: Inflammation is a fundamental response of the immune system whose successful termination involves the elimination of the invading pathogens, the resolution of inflammation and the repair of the local damaged tissue. In this context, the interleukin 10 (IL-10)-mediated anti-inflammatory response (AIR) represents an essential homeostatic mechanism that controls the degree and duration of inflammation. Here, we review recent work on the mechanistic characterization of the IL-10-mediated AIR on multiple levels: from the cataloguing of the in vivo genomic targets of STAT3 (the transcription factor downstream of IL-10) to the identification of specific co-factors that endow STAT3 with genomic-binding specificity, and how genomic and computational methods are being used to elucidate the regulatory mechanisms of this essential physiological response in macrophages.

295 citations

Journal ArticleDOI
TL;DR: This review discusses the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis and concludes that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.
Abstract: In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.

259 citations

Journal ArticleDOI
TL;DR: A detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph is made, from how they match the Lander-Waterman model, to the required sequencing depth and reads length.
Abstract: Since the completion of the cucumber and panda genome projects using Illumina sequencing in 2009, the global scientific community has had to pay much more attention to this new cost-effective approach to generate the draft sequence of large genomes. To allow new users to more easily understand the assembly algorithms and the optimum software packages for their projects, we make a detailed comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph, from how they match the Lander-Waterman model, to the required sequencing depth and reads length. We also discuss the computational efficiency of each class of algorithm, the influence of repeats and heterozygosity and points of note in the subsequent scaffold linkage and gap closure steps. We hope this review can help further promote the application of second-generation de novo sequencing, as well as aid the future development of assembly algorithms.

238 citations

Performance
Metrics
No. of papers from the Journal in previous years
YearPapers
202339
202253
202152
202037
201933
201855