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  1. Content type: Research

    Ginkgo biloba L. (Ginkgoaceae) is one of the most distinctive plants. It possesses a suite of fascinating characteristics including a large genome, outstanding resistance/tolerance to abiotic and biotic stresses,...

    Authors: Rui Guan, Yunpeng Zhao, He Zhang, Guangyi Fan, Xin Liu, Wenbin Zhou, Chengcheng Shi, Jiahao Wang, Weiqing Liu, Xinming Liang, Yuanyuan Fu, Kailong Ma, Lijun Zhao, Fumin Zhang, Zuhong Lu, Simon Ming-Yuen Lee…

    Citation: GigaScience 2016 5:49

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  2. Content type: Meeting abstracts

    I1 Introduction to the 2015 Brainhack Proceedings

    Authors: R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean-Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel Clark, Krzysztof J. Gorgolewski, R. Cameron Craddock, R. Cameron Craddock, Daniel J. Clark…

    Citation: GigaScience 2016 5(Suppl 1):46

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    This article is part of a Supplement: Volume 5 Supplement 1

  3. Content type: Data Note

    Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity,...

    Authors: Zijun Xiong, Fang Li, Qiye Li, Long Zhou, Tony Gamble, Jiao Zheng, Ling Kui, Cai Li, Shengbin Li, Huanming Yang and Guojie Zhang

    Citation: GigaScience 2016 5:47

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  4. Content type: DATA NOTE

    Skull-stripping is the procedure of removing non-brain tissue from anatomical MRI data. This procedure can be useful for calculating brain volume and for improving the quality of other image processing steps. ...

    Authors: Benjamin Puccio, James P. Pooley, John S. Pellman, Elise C. Taverna and R. Cameron Craddock

    Citation: GigaScience 2016 5:45

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  5. Content type: Technical Note

    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 an...

    Authors: Apurva Narechania, Richard Baker, Rob DeSalle, Barun Mathema, Sergios-Orestis Kolokotronis, Barry Kreiswirth and Paul J. Planet

    Citation: GigaScience 2016 5:44

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  6. Content type: Research

    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 regu...

    Authors: Víctor Resco de Dios, 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, Serajis Salekin…

    Citation: GigaScience 2016 5:43

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  7. Content type: Data Note

    Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. Ho...

    Authors: Qing Mao, Serban Ciotlos, Rebecca Yu Zhang, Madeleine P. Ball, Robert Chin, Paolo Carnevali, Nina Barua, Staci Nguyen, Misha R. Agarwal, Tom Clegg, Abram Connelly, Ward Vandewege, Alexander Wait Zaranek, Preston W. Estep, George M. Church, Radoje Drmanac…

    Citation: GigaScience 2016 5:42

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  8. Content type: Data Note

    Carrizo Plain National Monument (San Joaquin Desert, California, USA) is home to many threatened and endangered species including the blunt-nosed leopard lizard (Gambelia sila). Vegetation is dominated by annual ...

    Authors: Taylor J. Noble, Christopher J. Lortie, Michael Westphal and H. Scott Butterfield

    Citation: GigaScience 2016 5:40

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  9. Content type: Research

    The ocean sunfish (Mola mola), which can grow up to a length of 2.7 m and weigh 2.3 tons, is the world’s largest bony fish. It has an extremely fast growth rate and its endoskeleton is mainly composed of cartilag...

    Authors: Hailin Pan, Hao Yu, Vydianathan Ravi, Cai Li, Alison P. Lee, Michelle M. Lian, Boon-Hui Tay, Sydney Brenner, Jian Wang, Huanming Yang, Guojie Zhang and Byrappa Venkatesh

    Citation: GigaScience 2016 5:36

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  10. Content type: Data Note

    The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world, especially in the United States’ aquaculture industry. Since its...

    Authors: Xiaohui Chen, Liqiang Zhong, Chao Bian, Pao Xu, Ying Qiu, Xinxin You, Shiyong Zhang, Yu Huang, Jia Li, Minghua Wang, Qin Qin, Xiaohua Zhu, Chao Peng, Alex Wong, Zhifei Zhu, Min Wang…

    Citation: GigaScience 2016 5:39

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  11. Content type: TECHNICAL NOTE

    As the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts...

    Authors: Gaik Tamazian, Pavel Dobrynin, Ksenia Krasheninnikova, Aleksey Komissarov, Klaus-Peter Koepfli and Stephen J. O’Brien

    Citation: GigaScience 2016 5:38

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  12. Content type: Technical Note

    High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic varian...

    Authors: Zongji Wang, Jinmin Lian, Qiye Li, Pei Zhang, Yang Zhou, Xiaoyu Zhan and Guojie Zhang

    Citation: GigaScience 2016 5:37

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  13. Content type: Data Note

    Domesticated apple (Malus × domestica Borkh) is a popular temperate fruit with high nutrient levels and diverse flavors. In 2012, global apple production accounted for at least one tenth of all harvested fruits. ...

    Authors: Xuewei Li, Ling Kui, Jing Zhang, Yinpeng Xie, Liping Wang, Yan Yan, Na Wang, Jidi Xu, Cuiying Li, Wen Wang, Steve van Nocker, Yang Dong, Fengwang Ma and Qingmei Guan

    Citation: GigaScience 2016 5:35

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  14. Content type: Technical Note

    Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relatively high single-read err...

    Authors: Chenhao Li, Kern Rei Chng, Esther Jia Hui Boey, Amanda Hui Qi Ng, Andreas Wilm and Niranjan Nagarajan

    Citation: GigaScience 2016 5:34

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  15. Content type: Data Note

    Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral speci...

    Authors: Tamer A. Mansour, Joshua J. C. Rosenthal, C. Titus Brown and Loretta M. Roberson

    Citation: GigaScience 2016 5:33

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  16. Content type: TECHNICAL NOTE

    The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid dia...

    Authors: Minh Duc Cao, Devika Ganesamoorthy, Alysha G. Elliott, Huihui Zhang, Matthew A. Cooper and Lachlan J.M. Coin

    Citation: GigaScience 2016 5:32

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  17. Content type: Review

    When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can re...

    Authors: Stephen R. Piccolo and Michael B. Frampton

    Citation: GigaScience 2016 5:30

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  18. Content type: Data Note

    The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil....

    Authors: Fernando Cruz, Irene Julca, Jèssica Gómez-Garrido, Damian Loska, Marina Marcet-Houben, Emilio Cano, Beatriz Galán, Leonor Frias, Paolo Ribeca, Sophia Derdak, Marta Gut, Manuel Sánchez-Fernández, Jose Luis García, Ivo G. Gut, Pablo Vargas, Tyler S. Alioto…

    Citation: GigaScience 2016 5:29

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  19. Content type: Data Note

    The pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is one of the world’s most important pests of cotton. Insecticide sprays and transgenic cotton producing toxins of the bacterium Ba...

    Authors: Erica E. Tassone, Gina Zastrow-Hayes, John Mathis, Mark E. Nelson, Gusui Wu, J. Lindsey Flexner, Yves Carrière, Bruce E. Tabashnik and Jeffrey A. Fabrick

    Citation: GigaScience 2016 5:28

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  20. Content type: Technical Note

    Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, wh...

    Authors: Jai Ram Rideout, John H. Chase, Evan Bolyen, Gail Ackermann, Antonio González, Rob Knight and J. Gregory Caporaso

    Citation: GigaScience 2016 5:27

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  21. Content type: Review

    With ever-increasing amounts of data being produced by next-generation sequencing (NGS) experiments, the requirements placed on supporting e-infrastructures have grown. In this work, we provide recommendations...

    Authors: Ola Spjuth, Erik Bongcam-Rudloff, Johan Dahlberg, Martin Dahlö, Aleksi Kallio, Luca Pireddu, Francesco Vezzi and Eija Korpelainen

    Citation: GigaScience 2016 5:26

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  22. Content type: Technical Note

    Exploring the structure of genomes and analyzing their evolution is essential to understanding the ecological adaptation of organisms. However, with the large amounts of data being produced by next-generation ...

    Authors: Guilhem Sempéré, Florian Philippe, Alexis Dereeper, Manuel Ruiz, Gautier Sarah and Pierre Larmande

    Citation: GigaScience 2016 5:25

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    The Erratum to this article has been published in GigaScience 2016 5:48

  23. Content type: Data Note

    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...

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

    Citation: GigaScience 2016 5:24

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  24. Content type: Data Note

    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...

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

    Citation: GigaScience 2016 5:23

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  25. Content type: COMMENTARY

    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...

    Authors: Melissa Gymrek and Yossi Farjoun

    Citation: GigaScience 2016 5:22

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  26. Content type: Data Note

    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) ...

    Authors: 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…

    Citation: GigaScience 2016 5:21

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  27. Content type: Data Note

    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 ...

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

    Citation: GigaScience 2016 5:20

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  28. Content type: Commentary

    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. ...

    Authors: 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…

    Citation: GigaScience 2016 5:18

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  29. Content type: Research

    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...

    Authors: 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…

    Citation: GigaScience 2016 5:17

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  30. Content type: Review

    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...

    Authors: 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…

    Citation: GigaScience 2016 5:16

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  31. Content type: Review

    ‘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...

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

    Citation: GigaScience 2016 5:15

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  32. Content type: Commentary

    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...

    Authors: 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…

    Citation: GigaScience 2016 5:14

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  33. Content type: Data Note

    We investigated whether images obtained through X-ray micro-computed tomography (μCT) can be used in conjunction with traditional methods for morphological studies of soft-bodied land planarians. μCT is non-in...

    Authors: Fernando Carbayo and Jennifer Winifred Lenihan

    Citation: GigaScience 2016 5:13

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  34. Content type: Technical Note

    Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potent...

    Authors: Robert L. Davidson, Ralf J. M. Weber, Haoyu Liu, Archana Sharma-Oates and Mark R. Viant

    Citation: GigaScience 2016 5:10

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  35. Content type: TECHNICAL NOTE

    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...

    Authors: 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

    Citation: GigaScience 2016 5:9

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  36. Content type: Data Note

    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....

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

    Citation: GigaScience 2016 5:8

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  37. Content type: Data Note

    The plant bug Lygus hesperus Knight is a polyphagous pest of many economically important crops. Despite its pest status, little is known about the molecular mechanisms responsible for much of the biology of this ...

    Authors: Erica E. Tassone, Scott M. Geib, Brian Hall, Jeffrey A. Fabrick, Colin S. Brent and J. Joe Hull

    Citation: GigaScience 2016 5:6

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  38. Content type: Data Note

    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...

    Authors: 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…

    Citation: GigaScience 2016 5:5

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  39. Content type: Research

    The miniaturised and portable DNA sequencer MinION™ has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic app...

    Authors: Alfonso Benítez-Páez, Kevin J. Portune and Yolanda Sanz

    Citation: GigaScience 2016 5:4

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  40. Content type: Data Note

    Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields ar...

    Authors: Hui Liu, Xiao Ma, Haiqin Yu, Dunhuang Fang, Yongping Li, Xiao Wang, Wen Wang, Yang Dong and Bingguang Xiao

    Citation: GigaScience 2016 5:3

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  41. Content type: Research

    Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies...

    Authors: Davide Verzotto, Audrey S. M. Teo, Axel M. Hillmer and Niranjan Nagarajan

    Citation: GigaScience 2016 5:2

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  42. Content type: Research

    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...

    Authors: 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…

    Citation: GigaScience 2016 5:1

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  43. Content type: Data Note

    Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with rea...

    Authors: Audrey S. M. Teo, Davide Verzotto, Fei Yao, Niranjan Nagarajan and Axel M. Hillmer

    Citation: GigaScience 2015 4:65

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  44. Content type: Technical Note

    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...

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

    Citation: GigaScience 2015 4:64

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