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• W2390422268 abstract "Recent advances in quantitative biology has attested the important roles bioinformatics play in biological sciences as well as the great expansion of the scope of next-generation bioinformatics to all areas of systems biology. From the last issue of Quantitative Biology, we started to publish a special collection of reviews and research articles on next-generation bioinformatics to reflect this trend. The collection is dedicated to the completion of the 5-year center grant (#2012CB316500) on next-generation bioinformatics under the National Basic Research Program of China or the “973 Program”. The project aims to advance research on basic bioinformatics methodologies for processing next-generation biological data especially multiple types of sequencing data, and for converting the information buried in the data into quantitative understanding of important biological processes. The papers in the special collection were selected from submissions by the principle investigators and their collaborators of this project, after the standard peer-review procedure of Quantitative Biology. They reflect current progresses from the team and the whole community in several major directions that the project covers. The special collection will be continued in this issue and the next issue. Four papers are published in this issue. In the last issue, Zhao et al. reviewed methods for processing RNA-sequencing data for transcriptomes for which the reference genome is available. In this issue, Li et al. from the subproject 1 told the other aspect of the story by reviewing methods for processing RNA-sequencing data when the reference genome is not available or complete. The title of the paper is “De novo assembly of transcriptome from next-generation sequencing data”. In genomic sequencing analysis for genetics studies, obtaining haplotype data is an important and difficult task. In the paper “Comparison of the experimental methods in haplotype sequencing via next generation sequencing”, Tu et al. from subproject 1 reviewed major technologies for haplotype sequencing, and compared their performances and characteristics. Wu et al. from subproject 4 reviewedmajor sequencing platforms and bioinformatics strategies and methods for medical genetics studies based on nextgeneration sequencing, with the title “Whole genome sequencing and its applications in medical genetics”. It provided a rich source for bioinformatics tools available in this field and discussed existing open issues and possible future directions for dealing with the issues. Genomes are organized in three-dimensional space rather than one-dimensional linear space. Although analyzing the 1D genome sequence is fundamental in genetics studies, obtaining the 3D structure is crucial for understanding many key aspects of the genome organization and its relation to higher order gene regulation. In the paper “Developing bioimaging and quantitative methods to study 3D genome”, Gao et al. from subproject 3 reviewed existing knowledge on the structural organization of genomes, and the advances in super-resolution microscopy techniques for directly detecting 3D structure of a genome. Progresses on software for processing and visualizing Hi-C sequencing data are also introduced, followed by discussions on future trends for integrating image-based approaches and sequencing-based approaches for better understanding the 3D genome organization. Another four papers of the special collection will be published in the next issue. In the paper “An overview of" @default.
• W2390422268 created "2016-06-24" @default.
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• W2390422268 date "2016-05-14" @default.
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• W2390422268 title "Special collection of recent advances in next-generation bioinformatics, part II" @default.
• W2390422268 doi "https://doi.org/10.1007/s40484-016-0072-3" @default.
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