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  1. Research

    Draft genome of the living fossil Ginkgo biloba

    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,...

    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…

    GigaScience 2016 5:49

    Published on: 21 November 2016

  2. Meeting abstracts

    2015 Brainhack Proceedings

    I1 Introduction to the 2015 Brainhack Proceedings

    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…

    GigaScience 2016 5(Suppl 1):46

    Published on: 1 November 2016

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

  3. Data Note

    Draft genome of the leopard gecko, Eublepharis macularius

    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,...

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

    GigaScience 2016 5:47

    Published on: 26 October 2016

  4. Technical Note

    Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets

    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...

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

    GigaScience 2016 5:44

    Published on: 24 October 2016

  5. Research

    Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions

    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...

    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…

    GigaScience 2016 5:43

    Published on: 20 October 2016

  6. Data Note

    The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes

    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...

    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…

    GigaScience 2016 5:42

    Published on: 11 October 2016

  7. Data Note

    A picture is worth a thousand data points: an imagery dataset of paired shrub-open microsites within the Carrizo Plain National Monument

    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 ...

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

    GigaScience 2016 5:40

    Published on: 27 September 2016

  8. Research

    The genome of the largest bony fish, ocean sunfish (Mola mola), provides insights into its fast growth rate

    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...

    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

    GigaScience 2016 5:36

    Published on: 9 September 2016

  9. TECHNICAL NOTE

    Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences

    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...

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

    GigaScience 2016 5:38

    Published on: 22 August 2016

  10. Data Note

    High-quality genome assembly of channel catfish, Ictalurus punctatus

    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...

    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…

    GigaScience 2016 5:39

    Published on: 22 August 2016

  11. Data Note

    Improved hybrid de novo genome assembly of domesticated apple (Malus x domestica)

    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. ...

    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

    GigaScience 2016 5:35

    Published on: 8 August 2016

  12. Technical Note

    INC-Seq: accurate single molecule reads using nanopore sequencing

    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...

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

    GigaScience 2016 5:34

    Published on: 2 August 2016

  13. TECHNICAL NOTE

    Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing

    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...

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

    GigaScience 2016 5:32

    Published on: 26 July 2016

  14. Review

    Tools and techniques for computational reproducibility

    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...

    Stephen R. Piccolo and Michael B. Frampton

    GigaScience 2016 5:30

    Published on: 11 July 2016

  15. Data Note

    Genome sequence of the olive tree, Olea europaea

    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....

    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…

    GigaScience 2016 5:29

    Published on: 27 June 2016

  16. Data Note

    Sequencing, de novo assembly and annotation of a pink bollworm larval midgut transcriptome

    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...

    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

    GigaScience 2016 5:28

    Published on: 22 June 2016

  17. Technical Note

    Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets

    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...

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

    GigaScience 2016 5:27

    Published on: 13 June 2016

  18. Review

    Recommendations on e-infrastructures for next-generation sequencing

    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...

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

    GigaScience 2016 5:26

    Published on: 7 June 2016

  19. Technical Note

    Gigwa—Genotype investigator for genome-wide analyses

    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 ...

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

    GigaScience 2016 5:25

    Published on: 6 June 2016

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

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