7,578 Works

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...

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...

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...

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...

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.

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 \"Connectomics and new approaches for analyzing human brain functional connectivity\"

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

Peer review of \"Connectomics and new approaches for analyzing human brain functional connectivity\"

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

Peer review of \"A genome draft of the legless anguid lizard, Ophisaurus gracilis\"

Todd Castoe
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 ???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.

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)...

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...

Supporting material for: \"Rapid detection of structural variation in a Human genome using nanochannel-based genome mapping technology\"

HZ Cao, AR Hastie, D Cao, ET Lam, Y Sun, H Huang, X Liu, L Lin, W Andrews, S Chan, S Huang, X Tong, M Requa, T Anantharaman, A Krogh, H Yang, H Cao & X Xu
The nanochannel-based Genome Mapping technology, commercialized as the Irys Platform, automatically images fluorescently labeled DNA molecules in a massively parallel nanochannel array. This technology has previously been used to map the 4.7-Mb highly variable human MHC region, as well as for de novo assembly of a 2.1-Mb region in the highly complex Aegilops tauschii genome, lending great promise for use in complete genome sequence analysis. Here, we apply this rapid and high-throughput genome mapping method...

Annotation and analysis of three crocodilian genomes

RE Green, EL Braun, J Armstrong, D Earl, N Nguyen, G Hickey, MW Vandewege, JA St John, S Capella-Gutiérrez, TA Castoe, C Kern, MK Fujita, JC Opazo, J Jurka, KK Kojima, J Caballero, RM Hubley, AF Smit, RN Platt, CA Lavoie, MP Ramakodi, , A Suh, Isberg, L Miles … & DA Ray
Crocodilians are important model organisms in fields as diverse as developmental biology, osmoregulation, cardiophysiology, paleoclimatology, sex determination, population genetics, paleobiogeography, and functional morphology. Crocodilians, birds, dinosaurs, and pterosaurs comprise a monophyletic group known as the archosaurs. Crocodilians and birds are the only extant members and thus crocodilians (alligators, caimans, crocodiles, and gharials) are the closest living relatives of all birds. To provide context for the diversifications of archosaurs, we generated draft genomes of three crocodilians,...

Supporting materials from “Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication”

CW Nossa, P Havlak, JX Yue, J Lv, KY Vincent, HJ Brockmann & NH Putnam
Atlantic horseshoe crabs (Limulus polyphemus) are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a number of ancestral arthropod traits, and are often cited as examples of “living fossils.” We constructed a genetic linkage map of this 2.7 Gbp genome by sequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and their parents at a mean redundancy of 1.1x per...

Genomic data of the Bald Eagle (Haliaeetus leucocephalus)

W Warren, ED Jarvis, RK Wilson, JT Howard, MTP Gilbert, G Zhang & The Avian Genome Consortium
The Bald Eagle (Haliaeetus leucocephalus(Linnaeus, 1766)) is the official emblem of the United States and it belongs to a group of birds known as fish eagles. They are a large bird with adults weighing upto 4kg.These data have been produced as part of the Avian Phylogenomic Project . DNA was collected from a male bird bred at the NC Raptor Center, Huntersville, North Carolina, USA. The sequencing was conducted at WUSTL. We sequenced the 1.4Gb...

Quantitative proteomics data using mTRAQ/MRM looking at human AKR family members in cancer cell lines

S Zhang, B Wen, B Zhou, L Yang, C Cha, S Xu, X Qiu, Q Wang, H Sun, X Lou, J Zi, Y Zhang, L Lin & Liu S
Members of the human aldo-keto reductase(AKR)superfamily have been reported to be involved in cancer progression, and to investigate their role further a quantitative method to measure human AKR proteins in cells using mTRAQ-based multiple reaction monitoring (MRM) has been developed. AKR peptides with multiple transitions were carefully selected upon tryptic digestion of the recombinant AKR proteins, while AKR proteins were identified by SDS-PAGE fractionation coupled with LC MS/MS. Utilizing mTRAQ triplex labeling to produce the...

Genomic data from Triticum urartu - the progenitor of wheat A genome

H-Q Ling, S Zhao, C Zhang, Y Tao, C Gao, Q Liang, D Wang, A Zhang & J Wang
The wheat A genome, as a basic genome of bread wheat and other polyploid wheats, is centrally important to the evolution, domestication, and genetic improvement of wheat. The progenitor of the A genome is the diploid wild einkorn wheat Triticum urartu. Here, we sequenced T. urartu (accession G1812) using a whole-genome shotgun strategy on the Illumina HiSeq 2000 platform, and assembled the genome using SOAPdenovo2 with 448.49 Gb of filtered high-quality sequence data. The genome...

Genomic data from Aegilops tauschii - The Progenitor of Wheat D Genome

J Jia, S Zhao, W He, Y Tao, C Zhang, C Gao, D Li, L Mao & J Wang
A spontaneous hybridization of the wild diploid grass Aegilops tauschii (2n=14, DD) with cultivated tetraploid wheat Triticum turgidum (2n=4x=28, AABB) 8,000~10,000 years ago in the Fertile Crescent resulted in the bread wheat (Triticum aestivum; 2n=6x=42, AABBDD), one of the earliest cultivated crops in modern agriculture. We sequenced the 4.36-gigabase (Gb) genome of Ae. tauschii by generating ~90x genome coverage of short reads from a series of libraries with various insert sizes. The assembled scaffolds of...

Genomic data of the chickpea (Cicer arietinum)

RK Varshney, C Song, RK Saxena, S Azam, S Yu, AG Sharpe, S Cannon, J Baek, BD Rosen, B Taran, T Millan, X Zhang, LD Ramsay, A Iwata, Y Wang, W Nelson, AD Farmer, PM Gaur, C Soderlund, RV Penmetsa, C Xu, AK Bharti, W He, P Winter, S Zhao … &
Chickpea (Cicer arietinum) is one of the world's most consumed pulses. The Chickpea plant has finely divided leaves, giving it a feathery appearance. The pods are oblong (2 to 3 by 1 to 2 cm) and contain one or two beaked seeds which may be white, yellow, red, brown, or nearly black. They do well in a cool, dry climate and are grown in India as a winter crop. The draft of the chickpea genome...

Registration Year

  • 2020
    281
  • 2019
    2,503
  • 2018
    3,456
  • 2017
    548
  • 2016
    241
  • 2015
    396
  • 2014
    91
  • 2013
    21
  • 2012
    13
  • 2011
    28

Resource Types

  • Dataset
    4,631
  • Text
    2,947