4,110 Works

Peer review of \"Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data\"

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

Peer Review of ???A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education\".

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

Peer review of \"Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma\"

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

Peer review of \"Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma\"

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

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...

Peer review of \"Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies\"

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

Supporting data for the \"Draft genome of the Chinese mitten crab, Eriocheir sinensis\"

, Chao Bian, , , , Jia Li, Ying Qiu, , , Liang Ma, , Ying Lei, Jun Qiang, , , Alex Wong, , Qiong Shi &
Chinese mitten crab, Eriocheir sinensis, has been one of the most famous representatives of crustacean in China. Its transition from swimming type to crawling during the early development process, anadromous migration for growth, and catadromous migration for breeding have been attractive for research. However, the knowledge about the underlying molecular mechanisms to regulate these processes is still very limited. A total of 258.8-Gb raw reads for crab whole-genome sequencing were generated by the Illumina HiSeq2000...

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 \"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 \"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 \"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 \"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 \"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.

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...

Peer review of \"Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data\"

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

Peer review of \"Mitochondrial metagenomics: letting the genes out of the bottle\"

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

Supporting material for \"High throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcriptome sequencing\"

Chao Peng, Ge Yao, , , Chao Bian, , Ying Cao, Bo Wen, , , , , Jie Bai, Jia Li, , , , Ying Qiu, , Steven L Coon, , Ji-Sheng Chen & Qiong Shi
The venom of predatory marine cone snails mainly contains a diverse array of unique bioactive peptides commonly referred to as conopeptides or conotoxins. These peptides have proven to be valuable pharmacological probes and potential drugs because of their high specificity and affinity to important ion channels, receptors and transporters of the nervous system. Most of previous studies have specifically focused on the conopeptides from piscivorous and molluscivorous cone snails, but little attention has been devoted...

Peer review of \"The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes\"

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

Supporting data for \"Analyzing climate variations on multiple timescales can guide Zika virus response measures\"

Ángel GG Muñoz, Madeleine C Thomson, Lisa Goddard & Sylvain Aldighieri
The emergence of Zika virus (ZIKV) as a public health emergency in Latin America and the Caribbean (LAC) occurred during a period of severe drought and unusually high temperatures. Speculation in the literature exists that these climate conditions were associated with the 2015/2016 El Niño event and/or climate change but to date no quantitative assessment has been made. Analysis of related flaviviruses -such as dengue and chikungunya, which are transmitted by the same vectors- suggests...

Peer review of \"INC-Seq: accurate single molecule reads using nanopore sequencing\"

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

Peer review of \"Transcriptome of the Caribbean stony coral Porites astreoidesfrom three developmental stages\"

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

Peer review of \"High-quality genome assembly of channel catfish, Ictalurus punctatus\"

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

Supporting data for \"Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages\"

Tamer A Mansour, Joshua JC Rosenthal & Loretta M Roberson C Titus Brown
The coral Porites astreoides is a ubiquitous species on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most coral species. Using sequences from the Illumina platform, we have assembled and annotated a transcriptome from this coral using three different developmental stages collected over several years: free-swimming larvae, newly-settled larvae, and adults (>10 cm in diameter). This resource will aid in the understanding of coral calcification, larval...

Peer review of \"Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite\"

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

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