549 Works

Supporting data for \"Draft genome of the milu (Elaphurus davidianus)\"

Zhang Chenzhou, Zhang Guojie, Wang Kun, Chen Lei, , Ryder A Oliver, Qiu Qiang, Wang Wen & Zhou Yang
Milu, also known as Père David’s deer (Elaphurus davidianus), was widely distributed in East Asia but recently experienced a severe bottleneck. Only 18 survived by the end of the 19th century, and the current population of 4500 individuals was propagated from just 11 kept by the 11th British Duke of Bedford. This species is known for its distinguishable appearance, the driving force behind which is still a mystery. To aid efforts to explore these phenomena...

Supporting data for \"drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes\"

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Virus discovery using high-throughput next-generation sequencing (NGS) has become more commonplace. However, although analysis of deep NGS data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Here we present a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes),...

Peer review of \"Genomes and virulence difference between two physiological races of Phytophthora nicotianae\"

Kentaro Yoshida
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Genomes and virulence difference between two physiological races of Phytophthora nicotianae\"

Leila Blackman
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"The healthy brain network serial scanning initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions\"

Karl Helmer
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"The healthy brain network serial scanning initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions\"

Karl Helmer
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Estimating the total number of phosphoproteins and phosphorylation sites in eukaryotic proteomes\"

Luca Freschi
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for \"SOAPnuke: A MapReduce Acceleration supported Software for integrated Quality Control and Preprocessing of High-Throughput Sequencing Data\"

Yu Chang, Shi Chunmei, Yang Huanming, Ye Jia, Wang Jian, Fang Lin, Chen Qiang, Li Shengkang, Zhang Xiuqing, Li Yan, Zhang Yong, Chen Yongsheng, Chen Yuxin, Huang Zhibo & Li Zhuo
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a ‘QC-Preprocess-QC’ workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE)...

Peer review of \"HOMINID: A framework for identifying associations between host genetic variation and microbiome composition\"

Jun Chen
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for \"funRiceGenes dataset for comprehensive understanding and application of rice functional genes\"

Li Guangwei, Yao Wen, Ouyang Yidan & Yu Yiming
As a main staple food, rice is also a model plant for functional genomics researches of monocots. Decoding of every DNA element of the rice genome is essential for genetic improvement to address the increasing food demands. The past 15 years have witnessed extraordinary advances in rice functional genomics. Systematic characterization and proper deposition of every rice gene are vital for both functional studies and crop genetic improvement. We built a comprehensive and accurate dataset...

Supporting data for \"Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data\"

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Genome sequences for hundreds of mammalian species are available, but an understanding of their genomic regulatory regions, which control gene expression, is only beginning. A comprehensive prediction of potential active regulatory regions is necessary to functionally study the roles of the majority of genomic variants in evolution, domestication, and animal production. We developed a computational method to predict regulatory DNA sequences (promoters, enhancers and transcription factor binding sites) in production animals (cows and pigs) and...

Peer review of \"The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum \"

David Edwards
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum \"

Takashi Gojobori
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Draft genome of the Reindeer (Rangifer tarandus) \"

John McEwan
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Draft genome of the Marco Polo Sheep (Ovis ammon polii)\"

Jon Slate
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Full Genome Survey and Dynamics of Gene Expression in the Greater Amberjack Seriola dumerili\"

Benjamin Reading
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Genome sequence of the small brown planthopper Laodelphax striatellus\"

Denis Tagu
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies\"

Andrew Adey
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Sim3C: simulation of Hi-C and Meta4C proximity ligation sequencing technologies\"

Ming Hu
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Comparative transcriptomics of five high-altitude vertebrates and their low-altitude relatives\"

Christopher Tuggle
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Large scale phylogenomic analysis resolves a backbone phylogeny in ferns \"

This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome\"

Stephen Richards
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"ProphTools: General Prioritization Tools for Heterogeneous Biological Networks\"

Joseph J. Nalluri
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Improving amphibian genomic resources: a multi-tissue reference transcriptome of an iconic invader\"

Masanori Taira
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of \"Genome sequence of Japanese oak silk moth, Antheraea yamamai : the first draft genome in family Saturniidae \"

Reuben William Nowell
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Registration Year

  • 2017
    549

Resource Types

  • Text
    432
  • Dataset
    117