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  1. Data Note

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

    Schistocephalus solidus is a well-established model organism for studying the complex life cycle of cestodes and the mechanisms underlying host-parasite interactions. However, very few...

    François Olivier Hébert, Stephan Grambauer, Iain Barber, Christian R. Landry and Nadia Aubin-Horth

    GigaScience 2016 5:24

    Published on: 2 June 2016

  2. Data Note

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

    The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans and mange in other animal species. Scabies infections are a major health problem, particular...

    Ehtesham Mofiz, Deborah C. Holt, Torsten Seemann, Bart J. Currie, Katja Fischer and Anthony T. Papenfuss

    GigaScience 2016 5:23

    Published on: 2 June 2016

  3. Data Note

    Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

    Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) ...

    Andrew Bissett, Anna Fitzgerald, Thys Meintjes, Pauline M. Mele, Frank Reith, Paul G. Dennis, Martin F. Breed, Belinda Brown, Mark V. Brown, Joel Brugger, Margaret Byrne, Stefan Caddy-Retalic, Bernie Carmody, David J. Coates, Carolina Correa, Belinda C. Ferrari…

    GigaScience 2016 5:21

    Published on: 18 May 2016

  4. COMMENTARY

    Recommendations for open data science

    Life science research increasingly relies on large-scale computational analyses. However, the code and data used for these analyses are often lacking in publications. To maximize scientific impact, reproducibi...

    Melissa Gymrek and Yossi Farjoun

    GigaScience 2016 5:22

    Published on: 18 May 2016

  5. Data Note

    Low coverage sequencing of three echinoderm genomes: the brittle star Ophionereis fasciata, the sea star Patiriella regularis, and the sea cucumber Australostichopus mollis

    There are five major extant groups of Echinodermata: Crinoidea (feather stars and sea lillies), Ophiuroidea (brittle stars and basket stars), Asteroidea (sea stars), Echinoidea (sea urchins, sea biscuits, and ...

    Kyle A. Long, Carlos W. Nossa, Mary A. Sewell, Nicholas H. Putnam and Joseph F. Ryan

    GigaScience 2016 5:20

    Published on: 10 May 2016

  6. Commentary

    Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies

    Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in ‘omics studies. ...

    Ying Sun, Yu Huang, Xiaofeng Li, Carole C. Baldwin, Zhuocheng Zhou, Zhixiang Yan, Keith A. Crandall, Yong Zhang, Xiaomeng Zhao, Min Wang, Alex Wong, Chao Fang, Xinhui Zhang, Hai Huang, Jose V. Lopez, Kirk Kilfoyle…

    GigaScience 2016 5:18

    Published on: 3 May 2016

  7. Research

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

    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 pharmacologi...

    Chao Peng, Ge Yao, Bing-Miao Gao, Chong-Xu Fan, Chao Bian, Jintu Wang, Ying Cao, Bo Wen, Yabing Zhu, Zhiqiang Ruan, Xiaofei Zhao, Xinxin You, Jie Bai, Jia Li, Zhilong Lin, Shijie Zou…

    GigaScience 2016 5:17

    Published on: 14 April 2016

  8. Review

    Brainhack: a collaborative workshop for the open neuroscience community

    Brainhack events offer a novel workshop format with participant-generated content that caters to the rapidly growing open neuroscience community. Including components from hackathons and unconferences, as well...

    R. Cameron Craddock, Daniel S. Margulies, Pierre Bellec, B. Nolan Nichols, Sarael Alcauter, Fernando A. Barrios, Yves Burnod, Christopher J. Cannistraci, Julien Cohen-Adad, Benjamin De Leener, Sebastien Dery, Jonathan Downar, Katharine Dunlop, Alexandre R. Franco, Caroline Seligman Froehlich, Andrew J. Gerber…

    GigaScience 2016 5:16

    Published on: 31 March 2016

  9. Review

    Mitochondrial metagenomics: letting the genes out of the bottle

    ‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to...

    Alex Crampton-Platt, Douglas W. Yu, Xin Zhou and Alfried P. Vogler

    GigaScience 2016 5:15

    Published on: 22 March 2016

  10. Commentary

    Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

    Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science i...

    Neil Davies, Dawn Field, David Gavaghan, Sally J. Holbrook, Serge Planes, Matthias Troyer, Michael Bonsall, Joachim Claudet, George Roderick, Russell J. Schmitt, Linda Amaral Zettler, Véronique Berteaux, Hervé C. Bossin, Charlotte Cabasse, Antoine Collin, John Deck…

    GigaScience 2016 5:14

    Published on: 17 March 2016

  11. TECHNICAL NOTE

    Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

    With next-generation sequencing (NGS) technologies, the life sciences face a deluge of raw data. Classical analysis processes for such data often begin with an assembly step, needing large amounts of computing...

    Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru and Pierre Peterlongo

    GigaScience 2016 5:9

    Published on: 11 February 2016

  12. Data Note

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

    The cell line BT-474 is a popular cell line for studying the biology of cancer and developing novel drugs. However, there is no complete, published genome sequence for this highly utilized scientific resource....

    Serban Ciotlos, Qing Mao, Rebecca Yu Zhang, Zhenyu Li, Robert Chin, Natali Gulbahce, Sophie Jia Liu, Radoje Drmanac and Brock A. Peters

    GigaScience 2016 5:8

    Published on: 9 February 2016

  13. Data Note

    Draft genome of the Chinese mitten crab, Eriocheir sinensis

    The Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, a...

    Linsheng Song, Chao Bian, Yongju Luo, Lingling Wang, Xinxin You, Jia Li, Ying Qiu, Xingyu Ma, Zhifei Zhu, Liang Ma, Zhaogen Wang, Ying Lei, Jun Qiang, Hongxia Li, Juhua Yu, Alex Wong…

    GigaScience 2016 5:5

    Published on: 28 January 2016

  14. Research

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

    Esophageal squamous cell carcinoma (ESCC) is the sixth most lethal cancer worldwide and the fourth most lethal cancer in China. Genomic characterization of tumors, particularly those of different stages, is li...

    Caixia Cheng, Heyang Cui, Ling Zhang, Zhiwu Jia, Bin Song, Fang Wang, Yaoping Li, Jing Liu, Pengzhou Kong, Ruyi Shi, Yanghui Bi, Bin Yang, Juan Wang, Zhenxiang Zhao, Yanyan Zhang, Xiaoling Hu…

    GigaScience 2016 5:1

    Published on: 11 January 2016

  15. Technical Note

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

    Comprehensive recognition of genomic variation in one individual is important for understanding disease and developing personalized medication and treatment. Many tools based on DNA re-sequencing exist for ide...

    Siyang Liu, Shujia Huang, Junhua Rao, Weijian Ye, Anders Krogh and Jun Wang

    GigaScience 2015 4:64

    Published on: 24 December 2015

  16. Data Note

    Spatially transformed fluorescence image data for ERK-MAPK and selected proteins within human epidermis

    Phosphoprotein signalling pathways have been intensively studied in vitro, yet their role in regulating tissue homeostasis is not fully understood. In the skin, interfollicular keratinocytes differentiate over...

    Joseph Cursons, Catherine E. Angel, Daniel G. Hurley, Cristin G. Print, P. Rod Dunbar, Marc D. Jacobs and Edmund J. Crampin

    GigaScience 2015 4:63

    Published on: 14 December 2015

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