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Dissemination of metabolomics results: role of MetaboLights and COSMOS
Reza M Salek, Kenneth Haug, Christoph Steinbeck GigaScience 2013, 2:8 (17 May 2013)
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There is a need to disseminate the increasing amount of metabolomic data in standard reproducible ways. Hosted and coordinated by the EBI, the open source MetaboLights repository, and COSMOS community standards consortium tackle this
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Quantifying the use of bioresources for promoting their sharing in scientific research
Laurence Mabile, Raymond Dalgleish, Gudmundur A Thorisson, Mylène Deschênes, Robert Hewitt, Jane Carpenter, Elena Bravo, Mirella Filocamo, Pierre Gourraud, Jennifer R Harris, Paul Hofman, Francine Kauffmann, Maria Muñoz-Fernàndez, Markus Pasterk, Anne Cambon-Thomsen, BRIF working group GigaScience 2013, 2:7 (1 May 2013)
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The Bioresource Research Impact Factor (BRIF) aims to address the lack of recognition for the sharing of bioresources such as databases and biobanks, enabling crediting and measurement of their impact and use |
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A test-retest fMRI dataset for motor, language and spatial attention functions
Krzysztof J Gorgolewski, Amos Storkey, Mark E Bastin, Ian R Whittle, Joanna M Wardlaw, Cyril R Pernet GigaScience 2013, 2:6 (29 April 2013)
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Presented here is test-retest functional MRI dataset for motor, language and spatial attention functions to validate fMRI tasks used in pre-surgical planning for tumor resection, and providing a resource for new methods and algorithms
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Sequence squeeze: an open contest for sequence compression
Richard CG Holland, Nick Lynch GigaScience 2013, 2:5 (18 April 2013)
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Aiming to tackle the genomics data-deluge, the sequence squeeze challenge was an open innovation contest to find sequence compression algorithms that used a novel dynamic leaderboard and cloud computing to assess entries in real-time
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Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
Xin Zhou, Yiyuan Li, Shanlin Liu, Qing Yang, Xu Su, Lili Zhou, Min Tang, Ribei Fu, Jiguang Li, Quanfei Huang GigaScience 2013, 2:4 (27 March 2013)
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A new PCR-free sequencing-based method for metabarcoding provides new tools for studying eukaryotic biodiversity and gain quantitative taxonomic information from a DNA-soup extracted from bulk arthropod samples
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AXIOME: automated exploration of microbial diversity
Michael DJ Lynch, Andre P Masella, Michael W Hall, Andrea K Bartram, Josh D Neufeld GigaScience 2013, 2:3 (13 March 2013)
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AXIOME (Automated and eXtensible Integration Of Microbial Ecology) is a highly flexible and extensible management tool for a number of popular microbial ecology analysis packages
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Crowdsourcing genomic analyses of ash and ash dieback – power to the people
Dan MacLean, Kentaro Yoshida, Anne Edwards, Lisa Crossman, Bernardo Clavijo, Matt Clark, David Swarbreck, Matthew Bashton, Patrick Chapman, Mark Gijzen, Mario Caccamo, Allan Downie, Sophien Kamoun, Diane GO Saunders GigaScience 2013, 2:2 (12 February 2013)
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We present a call to arms for the genomics community to join in an open-source collaborative project using GitHub to fight Ash Dieback, a devastating disease of ash trees that has swept across Europe
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Peering into peer-review at GigaScience
Scott C Edmunds GigaScience 2013, 2:1 (24 January 2013)
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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Ruibang Luo, Binghang Liu, Yinlong Xie, Zhenyu Li, Weihua Huang, Jianying Yuan, Guangzhu He, Yanxiang Chen, Qi Pan, Yunjie Liu, Jingbo Tang, Gengxiong Wu, Hao Zhang, Yujian Shi, Yong Liu, Chang Yu, Bo Wang, Yao Lu, Changlei Han, David W Cheung, Siu-Ming Yiu, Shaoliang Peng, Zhu Xiaoqian, Guangming Liu, Xiangke Liao, Yingrui Li, Huanming Yang, Jian Wang, Tak-Wah Lam, Jun Wang et al.
GigaScience 2012, 1:18 (27 December 2012)
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The latest version of BGI's popular SOAPdenovo assembler is designed with a new algorithm optimized for larger genomes, and is competitive with other short-read de novo assemblers on both assembly length and accuracy
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Correction: Genome empowerment for the Puerto Rican parrot – Amazona vittata
Stephen J O’Brien GigaScience 2012, 1:17 (27 November 2012)
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The sequence and analysis of a Chinese pig genome
Xiaodong Fang, Yulian Mou, Zhiyong Huang, Yong Li, Lijuan Han, Yanfeng Zhang, Yue Feng, Yuanxin Chen, Xuanting Jiang, Wei Zhao, Xiaoqing Sun, Zhiqiang Xiong, Lan Yang, Huan Liu, Dingding Fan, Likai Mao, Lijie Ren, Chuxin Liu, Juan Wang, Kui Li, Guangbiao Wang, Shulin Yang, Liangxue Lai, Guojie Zhang, Yingrui Li, Jun Wang, Lars Bolund, Huanming Yang, Jian Wang, Shutang Feng, Songgang Li, Yutao Du et al.
GigaScience 2012, 1:16 (15 November 2012)
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An important model organism for medical research, the genome of the Wuzhishan inbred miniature pig is presented along with analysis of its unusual genetic features
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A genome blogger manifesto
Manuel Corpas GigaScience 2012, 1:15 (26 October 2012)
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A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education
Taras K Oleksyk, Jean-Francois Pombert, Daniel Siu, Anyimilehidi Mazo-Vargas, Brian Ramos, Wilfried Guiblet, Yashira Afanador, Christina T Ruiz-Rodriguez, Michael L Nickerson, David M Logue, Michael Dean, Luis Figueroa, Ricardo Valentin, Juan-Carlos Martinez-Cruzado GigaScience 2012, 1:14 (28 September 2012)
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Community funded with an innovative approach to assembly, the critically endangered Puerto Rican Parrot (Amazona vittata) genome is presented here for the first time
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Genome empowerment for the Puerto Rican parrot – Amazona vittata
Stephen J O’Brien GigaScience 2012, 1:13 (28 September 2012)
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Stephen O'Brien discusses our recent publication of the Puerto Rican Parrot (Amazona vittata), highlighting its example as a completely community funded and annotated genome project
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Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer
Yingrui Li, Xun Xu, Luting Song, Yong Hou, Zesong Li, Shirley Tsang, Fuqiang Li, Kate Im, Kui Wu, Hanjie Wu, Xiaofei Ye, Guibo Li, Linlin Wang, Bo Zhang, Jie Liang, Wei Xie, Renhua Wu, Hui Jiang, Xiao Liu, Chang Yu, Hancheng Zheng, Min Jian, Liping Nie, Lei Wan, Min Shi, Xiaojuan Sun, Aifa Tang, Guangwu Guo, Yaoting Gui, Zhiming Cai, Jingxiang Li, Wen Wang, Zuhong Lu, Xiuqing Zhang, Lars Bolund, Karsten Kristiansen, Jian Wang, Huanming Yang, Michael Dean, Jun Wang et al.
GigaScience 2012, 1:12 (14 August 2012)
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Single-cell exome sequencing provides a detailed look at both local genetic changes and tumor evolution in bladder transitional cell carcinoma
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Data sharing and publishing in the field of neuroimaging
Janis L Breeze, Jean-Baptiste Poline, David N Kennedy GigaScience 2012, 1:9 (12 July 2012)
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Tissue sampling methods and standards for vertebrate genomics
Pamela BY Wong, Edward O Wiley, Warren E Johnson, Oliver A Ryder, Stephen J O’Brien, David Haussler, Klaus-Peter Koepfli, Marlys L Houck, Polina Perelman, Gabriela Mastromonaco, Andrew C Bentley, Byrappa Venkatesh, Ya-ping Zhang, Robert W Murphy, G10KCOS GigaScience 2012, 1:8 (12 July 2012)
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The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle, Folker Meyer, Rob Knight, J Caporaso GigaScience 2012, 1:7 (12 July 2012)
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Badomics words and the power and peril of the ome-meme
Jonathan A Eisen GigaScience 2012, 1:6 (12 July 2012)
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Jonathan Eisen discusses good omes, badomes — and how to tell the difference |
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A call for an international network of genomic observatories (GOs)
Neil Davies, Chris Meyer, Jack A Gilbert, Linda Amaral-Zettler, John Deck, Mesude Bicak, Philippe Rocca-Serra, Susanna Assunta-Sansone, Kathy Willis, Dawn Field GigaScience 2012, 1:5 (12 July 2012)
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The Genomic Observatories network plans to digitally characterize whole ecosystems of specific ‘research hotspots’, with the aim of better enabling predictive modeling of biodiversity dynamics |
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The rise of a digital immune system
Michael C Schatz, Adam M Phillippy GigaScience 2012, 1:4 (12 July 2012)
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Mike Schatz and Adam Phillippy feel the time is right for developing a sequencing-based pathogen surveillance system, and discuss the idea of a "digital immune system"
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Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers
Gareth A Wilson, Pawandeep Dhami, Andrew Feber, Daniel Cortázar, Yuka Suzuki, Reiner Schulz, Primo Schär, Stephan Beck GigaScience 2012, 1:3 (12 July 2012)
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MeDUSA is a novel MeDIP-seq-based methylation analysis pipeline, and all the tools and 18 mouse methylomes are available at GigaDB to test it out yourselves
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The future of DNA sequence archiving
Guy Cochrane, Charles E Cook, Ewan Birney GigaScience 2012, 1:2 (12 July 2012)
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Sustainable DNA archiving will depend on the understanding that not all data is created - or preserved - equally
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GigaDB: announcing the GigaScience database
Tam P Sneddon, Peter Li, Scott C Edmunds GigaScience 2012, 1:11 (12 July 2012)
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On the evolving portfolio of community-standards and data sharing policies: turning challenges into new opportunities
Susanna-Assunta Sansone, Philippe Rocca-Serra GigaScience 2012, 1:10 (12 July 2012)
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