396 Works

Supporting material for \"Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data\"

Robert L Davidson, Ralf JM Weber, Archana Sharma-Oates, & Mark R Viant
Metabolomics is increasingly recognised as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other ‘omics fields, specifically genomics and transcriptomics. To achieve its full potential, including the integration of multiple ‘omics modalities, the accessibility, standardisation and reproducibility of computational metabolomics tools must to be improved significantly. Here we present an end-to-end metabolomics analysis pipeline that has been developed for both direct infusion mass spectrometry (DIMS) and...

Supporting data and materials for \"Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat\"

Nicholas C Wong, Bernard J Pope, Ida Candiloro, Darren Korbie, Matt Trau, Stephen Q Wong, Thomas Mikeska, Bryce J Van Denderen, Erik W Thompson, Stefanie Eggers, Stephen Doyle & Alexander Dobrovic
DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. We created a program called Methpat that...

The genome of the Australian dragon lizard Pogona vitticeps

Arthur Georges, , , Denis OMeally, Janine Deakin, , Pei Zhang, Matthew Fujita, Hardip R Patel, Clare E Holleley, Yang Zhou, , Kazumi Matsubara, Paul Waters, Jennifer AM Graves, Stephen D Sarre &
We present a genomic resource for a wild-caught male ZZ Central Bearded Dragon Pogona vitticeps, from Australia. The genomic sequence, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (185x raw read depth) from 13 insert libraries ranging from 250 bp to 40 Kbp. After filtering for low quality and duplicated reads, a total of 146 Gbp of data (86x) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % SNP plus indels)...

Supporting data for \"Evaluating a multigene environmental DNAapproach for comprehensive biodiversityassessment\"

Alexei J Drummond, Richard D Newcomb, Thomas R Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A Ross, Leah Tooman, Stefanie Grosser, , Nicholas J Demetras, Mark I Stevens, James C Russell, Sandra H Anderson, Anna Carter & Nicola Nelson
There is increasing demand for rapid biodiversity assessment tools that have broad taxonomic coverage. Traditional approaches typically rely on specialists for identification and only evaluate small subsets of biodiversity. Environmental DNA (eDNA) approaches are being promoted as a solution to these limitations, but questions remain unresolved. Here we evaluate a suite of DNA markers coupled with next generation sequencing (NGS) that span the tree of life. We compare these data to traditional biodiversity monitoring tools,...

Gene-set of brown planthopper genome

Wang Zhuo, Yu Li-Li, Zhou Xin & Zhang Chuan-Xi
The brown planthopper, Nilaparvata lugens, the most destructive pest of rice, is a typical monophagous herbivore that feeds exclusively on rice sap, which migrates over long distances. Outbreaks of it have re-occurred approximately every three years in Asia. It has also been used as a model system for ecological studies and for developing effective pest management. The N. lugens population sequenced in the present study was originally collected in Hangzhou, China, in 2008 and had...

Supporting materials for: \"VirAmp: A Galaxy-based viral genome assembly pipeline\".

Y Wan, DW Renner, I Albert & ML Szpara
We have developed a multi-step viral genome assembly pipeline named VirAmp, that combines existing tools and techniques and presents them to end users via a web-enabled Galaxy interface. Our pipeline allows users to assemble, analyze and interpret high coverage viral sequencing data with an ease and efficiency that was not possible previously. Our software makes a large number of genome assembly and related tools available to life scientists and automates the currently recommended best practices...

Supporting materials for \"BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ\"

Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai & Olivier Collin
Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. The Galaxy web-based platform for data intensive biomedical research (http://usegalaxy.org/) offers multiple ways to give access to this data through its web interface. However, the process of adding new reference data was customarily manual and time consuming, even more so when this data needed to be indexed in a variety of formats (e.g. Blast, Bowtie, BWA, or 2bit). BioMAJ is a widely...

The colorectal adenoma-carcinoma microbiome

Qiang Feng, , , Andreas Stadlmayr, , Zhou Lan, , , , , Lili Su, , Xin Li, , Liang Xiao, Ursula Huber-Schonauer, David Niederseer, Xun Xu, Jumana Yousuf Al-Aama, , Jian Wang, Karsten Kristiansen, , Herbert Tilg, Christian Datz … & Jun Wang
Colorectal cancer, a commonly diagnosed cancer in the elderly, often develops slowly from benign polyps called adenoma. The gut microbiota is believed to be directly involved in colorectal carcinogenesis. The identity and functional capacity of the adenoma- or carcinoma-related gutmicrobe(s), however, have not been surveyed in a comprehensive manner. Here we perform a metagenome-wide association study (MGWAS) on stools from advanced adenoma and carcinoma patients and from healthy subjects, revealing microbial genes, strains and functions...

RNA-Seq analysis and annotation of a draft blueberry genome assembly.

V Gupta, AD Estrada, I Blakley, R Reid, K Patel, , SU Andersen, AF Brown, MA Lila & AE Loraine
Blueberries are a popular and commercially important fruit, rich in antioxidants and other beneficial compounds that can protect against disease. To understand and identify genes involved in synthesis of bioactive compounds that could enable breeding berry varieties with enhanced health benefits, a draft blueberry genome assembly was produced using RNA-Seq data from five stages of berry fruit development and ripening. Libraries were prepared from samples of green and ripe fruit from plants of the O’Neal...

Peer review of \"Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples \"

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

Peer review of \"Multi-platform microRNA profiling of hepatoblastoma patients using formalin fixed paraffin embedded archival samples\"

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

Peer review of \"Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat\"

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

Peer review of \"A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data\"

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

Peer review of \"A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data\"

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

Peer review of \"Enhanced reproducibility of SADI web service workflows with Galaxy and Docker\"

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

Peer review of \"Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale\"

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

Peer review of \"Hybrid de novo genome assembly of the Chinese herbal plant danshen (Salvia miltiorrhiza Bunge)\"

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

Peer review of \"Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis\"

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

Peer review of \"VirAmp: a galaxy-based viral genome assembly pipeline\"

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

Peer review of \"VirAmp: a galaxy-based viral genome assembly pipeline\"

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

Peer review of \"VirAmp: a galaxy-based viral genome assembly pipeline\"

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

Peer review of \"Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome\"

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

Peer review of \"Large-scale analysis of the evolutionary histories of phosphorylation motifs in the human genome\"

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

Peer review of \"Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears\"

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

Peer review of \"SmileFinder: a resampling-based approach to evaluate signatures of selection from genome-wide sets of matching allele frequency data in two or more diploid populations\"

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

Registration Year

  • 2015
    396

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  • Text
    341
  • Dataset
    55