241 Works

Supporting data for \"The genome of Antarctic-endemic Copepod, Tigriopus kingsejongensis\"

, Do Hwan Ahn, Jun Hyuck Lee, Sung Gu Lee, Seung Chul Shin, , Gi Sik Min, , Hyun Woo Kim, & Hyun Park
The Antarctic intertidal zone is continuously subject to extreme fluctuations in biotic and abiotic stressors, and the West Antarctic Peninsula is the most rapidly warming region on earth. Organisms living in Antarctic intertidal pools are therefore of great interest for research on topics such as evolutionary adaptation to extreme environments and the effects of climate change. Here, we report the whole-genome sequence of the Antarctic endemic Harpacticoid copepod, Tigriopus kingsejongensis with a total of 37...

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 \"Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets\"

, Richard Baker, Rob DeSalle, , , Barry Kreiswirth & Paul J Planet
Collective animal behavior such as the flocking of birds or the shoaling of fish has inspired a class of algorithms designed to optimize distance-based clusters in various applications including document analysis and DNA microarrays. In the flocking model, individual agents respond only to their immediate environment and move according to a few simple rules. After several iterations the agents self-organize and clusters emerge without the need for partitional seeds. In addition to their unsupervised nature,...

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...

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...

Supporting information for \"Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)\"

, , Ling Kui, Jing Zhang, , , Yan Yan, Na Wang, , , Wen Wang, Yang Dong &
Domesticated apple (Malus domestica Borkh) is a popular temperate fruit with high levels of nutrients and a diversity of flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. A high-quality apple genome assembly is crucial for the selection and breeding of new cultivars. Currently, there is only a single genome reference available for apple, assembled from 16.9 genome coverage short reads via Sanger and 454 sequencing technologies. Although...

Software and supporting material for: \"RES-Scanner: a software package for genome-wide identification of RNA-editing sites\"

, , , Pei Zhang, Yang Zhou, &
High-throughput sequencing (HTS) provides a powerful resolution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to discriminate RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors. Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-Seq and DNA-Seq data from the same individuals or samples. RES-Scanner allows using both raw HTS reads and pre-aligned reads in...

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 \"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...

Supporting data for \"Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions\"

, Arthur Gessler, Juan Pedro Ferrio, Josu G Alday, Michael Bahn, Jorge Del Castillo, Sébastien Devidal, Sonia García-Muñoz, Zachary Kayler, Damien Landais, Paula Martín-Gómez, Alexandru Milcu, Clément Piel, Karin Pirhofer-Walzl, Olivier Ravel, , David T Tissue, Mark G Tjoelker, Jordi Voltas & Jacques Roy
Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance and other cell and leaf level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regulation over whole-canopy fluxes remains uncertain and diurnal CO2 and H2O vapor flux dynamics in the field are currently interpreted as resulting almost exclusively from direct physiological responses to variations in light, temperature and other environmental factors. We tested whether circadian regulation would affect plant and canopy...

Calculating the Laterality Index Using FSL for Stroke Neuroimaging Data

Kaori L Ito & Sook-Lei Liew
The laterality index (LI) is one way to assess hemispheric dominance in a variety of tasks, such as language, cognitive functions, and changes in laterality in clinical populations, such as after stroke. In stroke neuroimaging, however, an optimal method of calculating the LI remains controversial, largely due to lesion variability in post-stroke brains.Two main methods of calculating LI have evolved in neuroimaging literature The first, more traditional approach counts the number of active voxels in...

Supporting data for \"Genome sequencing of the winged midge, Parochlus steinenii, from the Antarctic Peninsula\"

, , , , & Seung Chul Shin
In the Antarctic, only two species of Chironomidae occur naturally—the wingless midge, Belgica antarctica, and the winged midge, Parochlus steinenii. B. antarctica is an extremophile with unusual adaptations. The larvae of B. antarctica are desiccation- and freeze-tolerant and the adults are wingless. Recently, the compact genome of B. antarctica was reported and it is the first Antarctic eukaryote to be sequenced. Although they occur naturally in the Antarctic with B. antarctica, the larvae of P....

Supporting data for \"Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants\"

, , Hyun Gwan Lee, Hyun Hee Hong, Sung Gwon Lee, , Elizabeth MA Kern, , Sung Jin Cho, Joong Ki Park &
The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic disease have generated increasing conservation concern. Here we present a total of 312 gigabases (Gb) of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb which...

Peer review of \"Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets\"

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

Peer review of \"Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets\"

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

Peer review of \"Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets\"

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

Supporting data for \"Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius\"

Kai Liu, , Jia Li, Chao Bian, , , , , Yang You, , Hui Yu, , , Jun Qiang, , Jie He, , Qiong Shi, &
Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic values in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to the Sinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and...

LORIS: DICOM anonymizer

Samir Das, Cécile Madjar, Ayan Sengupta & Zia Mohades
The purpose of this Brainhack project was to create a simple application, with the least dependencies, for anonymization of DICOM files directly on a workstation. Anonymization of DICOM datasets is a requirement before an imaging study can be uploaded in a web-based database system, such as LORIS. Currently, a simple and efficient interface for the anonymization of such imaging datasets, which works on all operating systems and is very light in terms of dependencies, is...

Generating music with resting-state fMRI data

Caroline Froehlich, Gil Dekel, Daniel S Margulies & R Cameron Craddock
Resting-state fMRI (rsfMRI) data generates time courses with unpredictable hills and valleys. People with musical training may notice that, to some degree, it resemble the notes of a musical scale. Taking advantage of these similarities, and using only rsfMRI data as input, we use basic rules of music theory to transform the data into musical form. Our project is implemented in Python using the midiutil library. We used open rsfMRI from the ABIDE dataset preprocessed...

BGISEQ-500 sequencer first reference dataset

Jie Huang, , , , , , , , , Ting Yu, Nan Sun, , , , Ying Chen, Sha Liao, Hui Jiang, Xin Liu, , Feng Mu &
BGISEQ-500 sequencer is a new desktop sequencer developed by BGI. Using DNA nanoballs (DNB) and combinational probe-anchor synthesis (cPAS) developed from Complete Genomics(TM) sequencing technology, it generates short reads at a large scale, which can help fulfill the growing demands for sequencing. Here, we present the first human whole genome sequencing dataset from the BGISEQ-500. The dataset was generated by sequencing the widely used Genome in a Bottle Consortium cell line, HG001 (NA12878) in one...

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.

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.

Peer review of \"Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis\"

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

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

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

Peer review of \"Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads\"

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

Registration Year

  • 2016
    241

Resource Types

  • Text
    156
  • Dataset
    85