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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: 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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  11. 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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  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

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