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  1. Content type: Data Note

    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...

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

    Citation: GigaScience 2015 4:63

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  2. Content type: Data Note

    Danshen (Salvia miltiorrhiza Bunge), also known as Chinese red sage, is a member of Lamiaceae family. It is valued in traditional Chinese medicine, primarily for the treatment of cardiovascular and cerebrovascula...

    Authors: Guanghui Zhang, Yang Tian, Jing Zhang, Liping Shu, Shengchao Yang, Wen Wang, Jun Sheng, Yang Dong and Wei Chen

    Citation: GigaScience 2015 4:62

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  3. Content type: Data Note

    Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but resu...

    Authors: Judith Risse, Marian Thomson, Sheila Patrick, Garry Blakely, Georgios Koutsovoulos, Mark Blaxter and Mick Watson

    Citation: GigaScience 2015 4:60

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  4. Content type: Technical Note

    It remains a challenge to perform de novo assembly using next-generation sequencing (NGS). Despite the availability of multiple sequencing technologies and tools (e.g., assemblers) it is still difficult to ass...

    Authors: Remi-Andre Olsen, Ignas Bunikis, Ievgeniia Tiukova, Kicki Holmberg, Britta Lötstedt, Olga Vinnere Pettersson, Volkmar Passoth, Max Käller and Francesco Vezzi

    Citation: GigaScience 2015 4:56

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  5. Content type: Review

    Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex geno...

    Authors: Prabu Ravindran and Aditya Gupta

    Citation: GigaScience 2015 4:57

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  6. Content type: Data Note

    DNA methylation is a complex epigenetic marker that can be analyzed using a wide variety of methods. Interpretation and visualization of DNA methylation data can mask complexity in terms of methylation status ...

    Authors: Nicholas C. Wong, Bernard J. Pope, Ida Candiloro, Darren Korbie, Matt Trau, Stephen Q. Wong, Thomas Mikeska, Bryce J. W. van Denderen, Erik W. Thompson, Stefanie Eggers, Stephen R. Doyle and Alexander Dobrovic

    Citation: GigaScience 2015 4:55

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  7. Content type: Data Note

    Formalin fixed paraffin embedded (FFPE) samples are a valuable resource in cancer research and have the potential to be extensively used. However, they are often underused because of degradation and chemical m...

    Authors: Anna L. Leichter, Rachel V. Purcell, Michael J. Sullivan, Michael R. Eccles and Aniruddha Chatterjee

    Citation: GigaScience 2015 4:54

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  8. Content type: Data Note

    Brooding brittle stars have a special mode of reproduction whereby they retain their eggs and juveniles inside respiratory body sacs called bursae. In the past, studying this phenomenon required disturbance of...

    Authors: Jannes Landschoff, Anton Du Plessis and Charles L. Griffiths

    Citation: GigaScience 2015 4:52

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  9. Content type: Research

    Viral infection causes multiple forms of human cancer, and HPV infection is the primary factor in cervical carcinomas. Recent single-cell RNA-seq studies highlight the tumor heterogeneity present in most cance...

    Authors: Liang Wu, Xiaolong Zhang, Zhikun Zhao, Ling Wang, Bo Li, Guibo Li, Michael Dean, Qichao Yu, Yanhui Wang, Xinxin Lin, Weijian Rao, Zhanlong Mei, Yang Li, Runze Jiang, Huan Yang, Fuqiang Li…

    Citation: GigaScience 2015 4:51

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  10. Content type: Research

    Germline mutations in the BRCA1 and BRCA2 genes account for 20–25 % of inherited breast cancers and about 10 % of all breast cancer cases. Detection of BRCA mutation carriers can lead to therapeutic interventions...

    Authors: Michael Dean, Joseph Boland, Meredith Yeager, Kate M. Im, Lisa Garland, Maria Rodriguez-Herrera, Mylen Perez, Jason Mitchell, David Roberson, Kristine Jones, Hyo Jung Lee, Rebecca Eggebeen, Julie Sawitzke, Sara Bass, Xijun Zhang, Vivian Robles…

    Citation: GigaScience 2015 4:50

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  11. Content type: Data Note

    The Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequ...

    Authors: Paul Stothard, Xiaoping Liao, Adriano S. Arantes, Mary De Pauw, Colin Coros, Graham S. Plastow, Mehdi Sargolzaei, John J. Crowley, John A. Basarab, Flavio Schenkel, Stephen Moore and Stephen P. Miller

    Citation: GigaScience 2015 4:49

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  12. Content type: Commentary

    Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplifi...

    Authors: Peter Belmann, Johannes Dröge, Andreas Bremges, Alice C. McHardy, Alexander Sczyrba and Michael D. Barton

    Citation: GigaScience 2015 4:47

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  13. Content type: Research

    There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing ...

    Authors: Alexei J. Drummond, Richard D. Newcomb, Thomas R. Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A. Ross, Leah Tooman, Stefanie Grosser, Duckchul Park, Nicholas J. Demetras, Mark I. Stevens, James C. Russell, Sandra H. Anderson, Anna Carter…

    Citation: GigaScience 2015 4:46

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  14. Content type: Data Note

    The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Po...

    Authors: Arthur Georges, Qiye Li, Jinmin Lian, Denis O’Meally, Janine Deakin, Zongji Wang, Pei Zhang, Matthew Fujita, Hardip R. Patel, Clare E. Holleley, Yang Zhou, Xiuwen Zhang, Kazumi Matsubara, Paul Waters, Jennifer A. Marshall Graves, Stephen D. Sarre…

    Citation: GigaScience 2015 4:45

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  15. Content type: Research

    The recently held Critical Assessment of Function Annotation challenge (CAFA2) required its participants to submit predictions for a large number of target proteins regardless of whether they have previous ann...

    Authors: Indika Kahanda, Christopher S Funk, Fahad Ullah, Karin M Verspoor and Asa Ben-Hur

    Citation: GigaScience 2015 4:41

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  16. Content type: Research

    Functional annotation of novel proteins is one of the central problems in bioinformatics. With the ever-increasing development of genome sequencing technologies, more and more sequence information is becoming ...

    Authors: Ishita K. Khan, Qing Wei, Samuel Chapman, Dukka B. KC and Daisuke Kihara

    Citation: GigaScience 2015 4:43

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  17. Content type: TECHNICAL NOTE

    In metagenomics, microbial communities are sequenced at increasingly high resolution, generating datasets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of seque...

    Authors: Fredrik Boulund, Anders Sjögren and Erik Kristiansson

    Citation: GigaScience 2015 4:40

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  18. Content type: Review

    “Α picture is worth a thousand words.” This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of ...

    Authors: Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright and Ioannis Iliopoulos

    Citation: GigaScience 2015 4:38

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  19. Content type: Technical Note

    The NCBI BLAST suite has become ubiquitous in modern molecular biology and is used for small tasks such as checking capillary sequencing results of single PCR products, genome annotation or even larger scale p...

    Authors: Peter J. A. Cock, John M. Chilton, Björn Grüning, James E. Johnson and Nicola Soranzo

    Citation: GigaScience 2015 4:39

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  20. Content type: Research

    Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used ...

    Authors: Yong Hou, Kui Wu, Xulian Shi, Fuqiang Li, Luting Song, Hanjie Wu, Michael Dean, Guibo Li, Shirley Tsang, Runze Jiang, Xiaolong Zhang, Bo Li, Geng Liu, Niharika Bedekar, Na Lu, Guoyun Xie…

    Citation: GigaScience 2015 4:37

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  21. Content type: Research

    Owing to the complexity of the assembly problem, we do not yet have complete genome sequences. The difficulty in assembling reads into finished genomes is exacerbated by sequence repeats and the inability of s...

    Authors: René L. Warren, Chen Yang, Benjamin P. Vandervalk, Bahar Behsaz, Albert Lagman, Steven J. M. Jones and Inanç Birol

    Citation: GigaScience 2015 4:35

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  22. Content type: Data Note

    The Braconid wasp Fopius arisanus (Sonan) has been utilized for biological control of the Mediterranean fruit fly (Ceratitis capitata), and the oriental fruit fly (Bactrocera dorsalis), both of which are phytopha...

    Authors: Bernarda Calla, Sheina B. Sim, Brian Hall, Theodore DeRego, Guang Hong Liang and Scott M. Geib

    Citation: GigaScience 2015 4:36

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  23. Content type: Commentary

    High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers...

    Authors: Leho Tedersoo, Kelly S. Ramirez, R Henrik Nilsson, Aivi Kaljuvee, Urmas Kõljalg and Kessy Abarenkov

    Citation: GigaScience 2015 4:34

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  24. Content type: DATA NOTE

    The production of biogas takes place under anaerobic conditions and involves microbial decomposition of organic matter. Most of the participating microbes are still unknown and non-cultivable. Accordingly, sho...

    Authors: Andreas Bremges, Irena Maus, Peter Belmann, Felix Eikmeyer, Anika Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter and Alexander Sczyrba

    Citation: GigaScience 2015 4:33

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  25. Content type: Review

    Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. A...

    Authors: Patricia A. Soranno, Edward G. Bissell, Kendra S. Cheruvelil, Samuel T. Christel, Sarah M. Collins, C. Emi Fergus, Christopher T. Filstrup, Jean-Francois Lapierre, Noah R. Lottig, Samantha K. Oliver, Caren E. Scott, Nicole J. Smith, Scott Stopyak, Shuai Yuan, Mary Tate Bremigan, John A. Downing…

    Citation: GigaScience 2015 4:28

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  26. Content type: Technical Note

    DNA methylation has important roles in the regulation of gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has prevailed in methylation studies due to its cost-effe...

    Authors: Shengjie Gao, Dan Zou, Likai Mao, Quan Zhou, Wenlong Jia, Yi Huang, Shancen Zhao, Gang Chen, Song Wu, Dongdong, Li, Fei Xia, Huafeng Chen, Maoshan Chen, Torben F Ørntoft, Lars Bolund and Karina D Sørensen

    Citation: GigaScience 2015 4:29

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  27. Content type: Commentary

    Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the w...

    Authors: Anna Kopf, Mesude Bicak, Renzo Kottmann, Julia Schnetzer, Ivaylo Kostadinov, Katja Lehmann, Antonio Fernandez-Guerra, Christian Jeanthon, Eyal Rahav, Matthias Ullrich, Antje Wichels, Gunnar Gerdts, Paraskevi Polymenakou, Giorgos Kotoulas, Rania Siam, Rehab Z Abdallah…

    Citation: GigaScience 2015 4:27

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  28. Content type: Research

    New high-throughput technologies, such as massively parallel sequencing, have transformed the life sciences into a data-intensive field. The most common e-infrastructure for analyzing this data consists of bat...

    Authors: Alexey Siretskiy, Tore Sundqvist, Mikhail Voznesenskiy and Ola Spjuth

    Citation: GigaScience 2015 4:26

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    The Erratum to this article has been published in GigaScience 2015 4:61

  29. Content type: Research

    Extracting important descriptors and features from images of biological specimens is an ongoing challenge. Features are often defined using landmarks and semi-landmarks that are determined a priori based on crite...

    Authors: Anne Sonnenschein, David VanderZee, William R Pitchers, Sudarshan Chari and Ian Dworkin

    Citation: GigaScience 2015 4:25

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  30. Content type: Technical Note

    Many bioinformatics tools use reference data, such as genome assemblies or sequence databanks. Galaxy offers multiple ways to give access to this data through its web interface. However, the process of adding ...

    Authors: Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai and Olivier Collin

    Citation: GigaScience 2015 4:22

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  31. Content type: Data Note

    Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging M...

    Authors: Janina Oetjen, Kirill Veselkov, Jeramie Watrous, James S McKenzie, Michael Becker, Lena Hauberg-Lotte, Jan Hendrik Kobarg, Nicole Strittmatter, Anna K Mróz, Franziska Hoffmann, Dennis Trede, Andrew Palmer, Stefan Schiffler, Klaus Steinhorst, Michaela Aichler, Robert Goldin…

    Citation: GigaScience 2015 4:20

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  32. Content type: Technical Note

    Advances in next generation sequencing make it possible to obtain high-coverage sequence data for large numbers of viral strains in a short time. However, since most bioinformatics tools are developed for comm...

    Authors: Yinan Wan, Daniel W Renner, Istvan Albert and Moriah L Szpara

    Citation: GigaScience 2015 4:19

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  33. Content type: Data Note

    Transition from a lizard-like to a snake-like body form is one of the most important transformations in reptilian evolution. The increasing number of sequenced reptilian genomes is enabling a deeper understand...

    Authors: Bo Song, Shifeng Cheng, Yanbo Sun, Xiao Zhong, Jieqiong Jin, Rui Guan, Robert W Murphy, Jing Che, Yaping Zhang and Xin Liu

    Citation: GigaScience 2015 4:17

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  34. Content type: Data Note

    Metabolomics has the potential to be a powerful and sensitive approach for investigating the low molecular weight metabolite profiles present in maternal fluids and their role in pregnancy.

    Authors: Hemi Luan, Nan Meng, Ping Liu, Jin Fu, Xiaomin Chen, Weiqiao Rao, Hui Jiang, Xun Xu, Zongwei Cai and Jun Wang

    Citation: GigaScience 2015 4:16

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  35. Content type: Data Note

    Bactrocera cucurbitae is a serious global agricultural pest. Basic genomic information is lacking for this species, and this would be useful to inform methods of control, damage mitigation, and eradication effort...

    Authors: Sheina B Sim, Bernarda Calla, Brian Hall, Theodore DeRego and Scott M Geib

    Citation: GigaScience 2015 4:14

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