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  1. Content type: Research

    The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ to act as a...

    Authors: Andy Kilianski, Jamie L Haas, Elizabeth J Corriveau, Alvin T Liem, Kristen L Willis, Dana R Kadavy, C Nicole Rosenzweig and Samuel S Minot

    Citation: GigaScience 2015 4:12

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  2. Content type: DATA NOTE

    Acute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% tod...

    Authors: Nicholas CL Wong, Gavin D Meredith, George Marnellos, Miroslav Dudas, Mandy Parkinson-Bates, Minhee Suh Halemba, Zac Chatterton, Jovana Maksimovic, David M Ashley, Francoise Mechinaud, Jeffrey M Craig and Richard Saffery

    Citation: GigaScience 2015 4:11

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  3. Content type: Technical note

    PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequ...

    Authors: Christopher C Chang, Carson C Chow, Laurent CAM Tellier, Shashaank Vattikuti, Shaun M Purcell and James J Lee

    Citation: GigaScience 2015 4:7

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  4. Content type: Data Note

    The wound healing assay is the common method to study collective cell migration in vitro. Computational analyses of live imaging exploit the rich temporal information and significantly improve understanding of co...

    Authors: Assaf Zaritsky, Sari Natan, Doron Kaplan, Eshel Ben-Jacob and Ilan Tsarfaty

    Citation: GigaScience 2015 4:8

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  5. Content type: Research

    Blueberries are a rich source of antioxidants and other beneficial compounds that can protect against disease. Identifying genes involved in synthesis of bioactive compounds could enable the breeding of berry ...

    Authors: Vikas Gupta, April D Estrada, Ivory Blakley, Rob Reid, Ketan Patel, Mason D Meyer, Stig Uggerhøj Andersen, Allan F Brown, Mary Ann Lila and Ann E Loraine

    Citation: GigaScience 2015 4:5

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  6. Content type: Data Note

    Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genome...

    Authors: Erich D Jarvis, Siavash Mirarab, Andre J Aberer, Bo Li, Peter Houde, Cai Li, Simon Y W Ho, Brant C Faircloth, Benoit Nabholz, Jason T Howard, Alexander Suh, Claudia C Weber, Rute R da Fonseca, Alonzo Alfaro-Núñez, Nitish Narula, Liang Liu…

    Citation: GigaScience 2015 4:4

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  7. Content type: Review

    Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline. Optical mapping provides long-rang...

    Authors: Haibao Tang, Eric Lyons and Christopher D Town

    Citation: GigaScience 2015 4:3

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  8. Content type: Technical Note

    Adaptive alleles may rise in frequency as a consequence of positive selection, creating a pattern of decreased variation in the neighboring loci, known as a selective sweep. When the region containing this pat...

    Authors: Wilfried M Guiblet, Kai Zhao, Stephen J O’Brien, Steven E Massey, Alfred L Roca and Taras K Oleksyk

    Citation: GigaScience 2015 4:1

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  9. Content type: Research

    Structural variants (SVs) are less common than single nucleotide polymorphisms and indels in the population, but collectively account for a significant fraction of genetic polymorphism and diseases. Base pair ...

    Authors: Hongzhi Cao, Alex R Hastie, Dandan Cao, Ernest T Lam, Yuhui Sun, Haodong Huang, Xiao Liu, Liya Lin, Warren Andrews, Saki Chan, Shujia Huang, Xin Tong, Michael Requa, Thomas Anantharaman, Anders Krogh, Huanming Yang…

    Citation: GigaScience 2014 3:34

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  10. Content type: Review

    Optical mapping and newer genome mapping technologies based on nicking enzymes provide low resolution but long-range genomic information. The optical mapping technique has been successfully used for assessing ...

    Authors: Lee Mendelowitz and Mihai Pop

    Citation: GigaScience 2014 3:33

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  11. Content type: Research

    We provide common datasets (which we call the CORT dataset: common optimization for radiation therapy) that researchers can use when developing and contrasting radiation treatment planning optimization algorit...

    Authors: David Craft, Mark Bangert, Troy Long, Dávid Papp and Jan Unkelbach

    Citation: GigaScience 2014 3:37

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  12. Content type: Research

    Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them ha...

    Authors: Cai Li, Yong Zhang, Jianwen Li, Lesheng Kong, Haofu Hu, Hailin Pan, Luohao Xu, Yuan Deng, Qiye Li, Lijun Jin, Hao Yu, Yan Chen, Binghang Liu, Linfeng Yang, Shiping Liu, Yan Zhang…

    Citation: GigaScience 2014 3:27

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  13. Content type: Data Note

    The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the g...

    Authors: Guojie Zhang, Bo Li, Cai Li, M Thomas P Gilbert, Erich D Jarvis and Jun Wang

    Citation: GigaScience 2014 3:26

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  14. Content type: Commentary

    Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers – both amateurs and professionals - have marveled for centuries at t...

    Authors: Stephen J OBrien, David Haussler and Oliver Ryder

    Citation: GigaScience 2014 3:32

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  15. Content type: Research

    Next generation sequencing (NGS) is now being used for detecting chromosomal abnormalities in blastocyst trophectoderm (TE) cells from in vitro fertilized embryos. However, few data are available regarding the cl...

    Authors: Yueqiu Tan, Xuyang Yin, Shuoping Zhang, Hui Jiang, Ke Tan, Jian Li, Bo Xiong, Fei Gong, Chunlei Zhang, Xiaoyu Pan, Fang Chen, Shengpei Chen, Chun Gong, Changfu Lu, Keli Luo, Yifan Gu…

    Citation: GigaScience 2014 3:30

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  16. Content type: Commentary

    Research in the context of data-driven science requires a backbone of well-written software, but scientific researchers are typically not trained at length in software engineering, the principles for creating ...

    Authors: Janna Hastings, Kenneth Haug and Christoph Steinbeck

    Citation: GigaScience 2014 3:31

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  17. Content type: Review

    From the initial arguments over whether 12 to 20 subjects were sufficient for an fMRI study, sample sizes in psychiatric neuroimaging studies have expanded into the tens of thousands. These large-scale imaging...

    Authors: Jessica A Turner

    Citation: GigaScience 2014 3:29

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  18. Content type: Review

    Functional brain images are rich and noisy data that can capture indirect signatures of neural activity underlying cognition in a given experimental setting. Can data mining leverage them to build models of co...

    Authors: Gael Varoquaux and Bertrand Thirion

    Citation: GigaScience 2014 3:28

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  19. Content type: Technical Note

    As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associati...

    Authors: Anton Svitin, Sergey Malov, Nikolay Cherkasov, Paul Geerts, Mikhail Rotkevich, Pavel Dobrynin, Andrey Shevchenko, Li Guan, Jennifer Troyer, Sher Hendrickson, Holli Hutcheson Dilks, Taras K Oleksyk, Sharyne Donfield, Edward Gomperts, Douglas A Jabs, Efe Sezgin…

    Citation: GigaScience 2014 3:18

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  20. Content type: Review

    Genetic modification has long provided an approach for “reverse genetics”, analyzing gene function and linking DNA sequence to phenotype. However, traditional genome editing technologies have not kept pace wit...

    Authors: Lei Chen, Linyi Tang, Hui Xiang, Lijun Jin, Qiye Li, Yang Dong, Wen Wang and Guojie Zhang

    Citation: GigaScience 2014 3:24

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  21. Content type: Data Note

    Tuber melanosporum, also known in the gastronomic community as “truffle”, features one of the largest fungal genomes (125 Mb) with an exceptionally high transposable element (TE) and repetitive DNA content (>58%...

    Authors: Pao-Yang Chen, Barbara Montanini, Wen-Wei Liao, Marco Morselli, Artur Jaroszewicz, David Lopez, Simone Ottonello and Matteo Pellegrini

    Citation: GigaScience 2014 3:25

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  22. Content type: Review

    The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridi...

    Authors: Naim Matasci, Ling-Hong Hung, Zhixiang Yan, Eric J Carpenter, Norman J Wickett, Siavash Mirarab, Nam Nguyen, Tandy Warnow, Saravanaraj Ayyampalayam, Michael Barker, J Gordon Burleigh, Matthew A Gitzendanner, Eric Wafula, Joshua P Der, Claude W dePamphilis, Béatrice Roure…

    Citation: GigaScience 2014 3:17

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  23. Content type: Data Note

    The MinION™ is a new, portable single-molecule sequencer developed by Oxford Nanopore Technologies. It measures four inches in length and is powered from the USB 3.0 port of a laptop computer. The MinION™ meas...

    Authors: Joshua Quick, Aaron R Quinlan and Nicholas J Loman

    Citation: GigaScience 2014 3:22

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    The Erratum to this article has been published in GigaScience 2015 4:6

  24. Content type: Data Note

    Apart from its application in human diagnostics, magnetic resonance imaging (MRI) can also be used to study the internal anatomy of zoological specimens. As a non-invasive imaging technique, MRI has several ad...

    Authors: Alexander Ziegler, Cornelius Faber, Susanne Mueller, Nina Nagelmann and Leif Schröder

    Citation: GigaScience 2014 3:21

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  25. Content type: Technical Note

    Understanding the biological roles of microRNAs (miRNAs) is a an active area of research that has produced a surge of publications in PubMed, particularly in cancer research. Along with this increasing interes...

    Authors: Regina Z Cer, J Enrique Herrera-Galeano, Joseph J Anderson, Kimberly A Bishop-Lilly and Vishwesh P Mokashi

    Citation: GigaScience 2014 3:20

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  26. Content type: Technical Note

    Galaxy offers a number of visualisation options with components, such as Trackster, Circster and Galaxy Charts, but currently lacks the ability to easily combine outputs from different tools into a single view...

    Authors: Saskia Hiltemann, Youri Hoogstrate, Peter van der Spek, Guido Jenster and Andrew Stubbs

    Citation: GigaScience 2014 3:19

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  27. Content type: Review

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genom...

    Authors: Emily B Sessa, Jo Ann Banks, Michael S Barker, Joshua P Der, Aaron M Duffy, Sean W Graham, Mitsuyasu Hasebe, Jane Langdale, Fay-Wei Li, D Blaine Marchant, Kathleen M Pryer, Carl J Rothfels, Stanley J Roux, Mari L Salmi, Erin M Sigel, Douglas E Soltis…

    Citation: GigaScience 2014 3:15

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  28. Content type: Data Note

    Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque, the common ...

    Authors: Mnirnal D Maudhoo, Dongren Ren, Julien S Gradnigo, Robert M Gibbs, Austin C Lubker, Etsuko N Moriyama, Jeffrey A French and Robert B Norgren Jr

    Citation: GigaScience 2014 3:14

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  29. Content type: Data Note

    Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly h...

    Authors: Gaik Tamazian, Serguei Simonov, Pavel Dobrynin, Alexey Makunin, Anton Logachev, Aleksey Komissarov, Andrey Shevchenko, Vladimir Brukhin, Nikolay Cherkasov, Anton Svitin, Klaus-Peter Koepfli, Joan Pontius, Carlos A Driscoll, Kevin Blackistone, Cristina Barr, David Goldman…

    Citation: GigaScience 2014 3:13

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  30. Content type: Data Note

    Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movem...

    Authors: Ganeshkumar Ganapathy, Jason T Howard, James M Ward, Jianwen Li, Bo Li, Yingrui Li, Yingqi Xiong, Yong Zhang, Shiguo Zhou, David C Schwartz, Michael Schatz, Robert Aboukhalil, Olivier Fedrigo, Lisa Bukovnik, Ty Wang, Greg Wray…

    Citation: GigaScience 2014 3:11

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  31. Content type: Research

    The aim of a genome-wide association study (GWAS) is to isolate DNA markers for variants affecting phenotypes of interest. This is constrained by the fact that the number of markers often far exceeds the numbe...

    Authors: Shashaank Vattikuti, James J Lee, Christopher C Chang, Stephen D H Hsu and Carson C Chow

    Citation: GigaScience 2014 3:10

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  32. Content type: Data Note

    Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated g...

    Authors:

    Citation: GigaScience 2014 3:7

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  33. Content type: Data Note

    Although molecular tools are increasingly employed to decipher invertebrate systematics, earthworm (Annelida: Clitellata: ‘Oligochaeta’) taxonomy is still largely based on conventional dissection, resulting in...

    Authors: Jennifer Lenihan, Sebastian Kvist, Rosa Fernández, Gonzalo Giribet and Alexander Ziegler

    Citation: GigaScience 2014 3:6

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  34. Content type: Research

    Horseshoe crabs are marine arthropods with a fossil record extending back approximately 450 million years. They exhibit remarkable morphological stability over their long evolutionary history, retaining a numb...

    Authors: Carlos W Nossa, Paul Havlak, Jia-Xing Yue, Jie Lv, Kimberly Y Vincent, H Jane Brockmann and Nicholas H Putnam

    Citation: GigaScience 2014 3:9

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  35. Content type: Research

    During early development, neural circuits fire spontaneously, generating activity episodes with complex spatiotemporal patterns. Recordings of spontaneous activity have been made in many parts of the nervous s...

    Authors: Stephen John Eglen, Michael Weeks, Mark Jessop, Jennifer Simonotto, Tom Jackson and Evelyne Sernagor

    Citation: GigaScience 2014 3:3

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  36. Content type: Commentary

    The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic...

    Authors: Neil Davies, Dawn Field, Linda Amaral-Zettler, Melody S Clark, John Deck, Alexei Drummond, Daniel P Faith, Jonathan Geller, Jack Gilbert, Frank Oliver Glöckner, Penny R Hirsch, Jo-Ann Leong, Chris Meyer, Matthias Obst, Serge Planes, Chris Scholin…

    Citation: GigaScience 2014 3:2

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  37. Content type: Technical Note

    Complete Genomics provides an open-source suite of command-line tools for the analysis of their CG-formatted mapped sequencing files. Determination of; for example, the functional impact of detected variants, ...

    Authors: Saskia Hiltemann, Hailiang Mei, Mattias de Hollander, Ivo Palli, Peter van der Spek, Guido Jenster and Andrew Stubbs

    Citation: GigaScience 2014 3:1

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  38. Content type: Research

    Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for...

    Authors: Oscar C Bedoya-Reina, Aakrosh Ratan, Richard Burhans, Hie Lim Kim, Belinda Giardine, Cathy Riemer, Qunhua Li, Thomas L Olson, Thomas P Loughran Jr, Bridgett M vonHoldt, George H Perry, Stephan C Schuster and Webb Miller

    Citation: GigaScience 2013 2:17

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