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  1. Content type: Method

    Despite the many approaches to study differential splicing from RNA-seq, many challenges remain unsolved, including computing capacity and sequencing depth requirements. Here we present SUPPA2, a new method th...

    Authors: Juan L. Trincado, Juan C. Entizne, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott and Eduardo Eyras

    Citation: Genome Biology 2018 19:40

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  2. Content type: Method

    Comprehensive and accurate identification of structural variations (SVs) from next generation sequencing data remains a major challenge. We develop FusorSV, which uses a data mining approach to assess performance...

    Authors: Timothy Becker, Wan-Ping Lee, Joseph Leone, Qihui Zhu, Chengsheng Zhang, Silvia Liu, Jack Sargent, Kritika Shanker, Adam Mil-homens, Eliza Cerveira, Mallory Ryan, Jane Cha, Fabio C. P. Navarro, Timur Galeev, Mark Gerstein, Ryan E. Mills…

    Citation: Genome Biology 2018 19:38

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  3. Content type: Research

    Genomic instability promotes evolution and heterogeneity of tumors. Unraveling its mechanistic basis is essential for the design of appropriate therapeutic strategies. In a previous study, we reported an unexp...

    Authors: Panagiotis Galanos, George Pappas, Alexander Polyzos, Athanassios Kotsinas, Ioanna Svolaki, Nickolaos N. Giakoumakis, Christina Glytsou, Ioannis S. Pateras, Umakanta Swain, Vassilis L. Souliotis, Alexandros G. Georgakilas, Nicholas Geacintov, Luca Scorrano, Claudia Lukas, Jiri Lukas, Zvi Livneh…

    Citation: Genome Biology 2018 19:37

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  4. Content type: Research

    Ovarian cancer constitutes one of the most lethal gynecologic malignancies for females. Currently, early detection strategies and therapeutic options for ovarian cancer are far from satisfactory, leading to hi...

    Authors: Linjie Zhao, Wei Wang, Shuang Huang, Zhengnan Yang, Lian Xu, Qilian Yang, Xiu Zhou, Jinjin Wang, Qiuhong Shen, Chenlu Wang, Xiaobing Le, Min Feng, Nianxin Zhou, Wayne Bond Lau, Bonnie Lau, Shaohua Yao…

    Citation: Genome Biology 2018 19:35

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  5. Content type: Research

    Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of ...

    Authors: Nelly Olova, Felix Krueger, Simon Andrews, David Oxley, Rebecca V. Berrens, Miguel R. Branco and Wolf Reik

    Citation: Genome Biology 2018 19:33

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  6. Content type: Research

    The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and l...

    Authors: Paulo P. Amaral, Tommaso Leonardi, Namshik Han, Emmanuelle Viré, Dennis K. Gascoigne, Raúl Arias-Carrasco, Magdalena Büscher, Luca Pandolfini, Anda Zhang, Stefano Pluchino, Vinicius Maracaja-Coutinho, Helder I. Nakaya, Martin Hemberg, Ramin Shiekhattar, Anton J. Enright and Tony Kouzarides

    Citation: Genome Biology 2018 19:32

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  7. Content type: Research article

    Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this pro...

    Authors: Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen and Fuchou Tang

    Citation: Genome Biology 2018 19:31

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  8. Content type: Method

    High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus...

    Authors: Yohei Sasagawa, Hiroki Danno, Hitomi Takada, Masashi Ebisawa, Kaori Tanaka, Tetsutaro Hayashi, Akira Kurisaki and Itoshi Nikaido

    Citation: Genome Biology 2018 19:29

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  9. Content type: Research

    Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, ...

    Authors: David V. Dylus, Anna Czarkwiani, Liisa M. Blowes, Maurice R. Elphick and Paola Oliveri

    Citation: Genome Biology 2018 19:26

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  10. Content type: Method

    We present a robust method called improved-Genome editing via Oviductal Nucleic Acids Delivery (i-GONAD) that delivers CRISPR ribonucleoproteins to E0.7 embryos via in situ electroporation. The method generates m...

    Authors: Masato Ohtsuka, Masahiro Sato, Hiromi Miura, Shuji Takabayashi, Makoto Matsuyama, Takayuki Koyano, Naomi Arifin, Shingo Nakamura, Kenta Wada and Channabasavaiah B. Gurumurthy

    Citation: Genome Biology 2018 19:25

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  11. Content type: Method

    Dropout events in single-cell RNA sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This...

    Authors: Koen Van den Berge, Fanny Perraudeau, Charlotte Soneson, Michael I. Love, Davide Risso, Jean-Philippe Vert, Mark D. Robinson, Sandrine Dudoit and Lieven Clement

    Citation: Genome Biology 2018 19:24

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  12. Content type: Research

    The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that ...

    Authors: Paul C. Bailey, Christian Schudoma, William Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew Moscou and Ksenia V. Krasileva

    Citation: Genome Biology 2018 19:23

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  13. Content type: Research

    Mammalian species exhibit a wide range of lifespans. To date, a robust and dynamic molecular readout of these lifespan differences has not yet been identified. Recent studies have established the existence of ...

    Authors: Robert Lowe, Carl Barton, Christopher A. Jenkins, Christina Ernst, Oliver Forman, Denise S. Fernandez-Twinn, Christoph Bock, Stephen J. Rossiter, Chris G. Faulkes, Susan E. Ozanne, Lutz Walter, Duncan T. Odom, Cathryn Mellersh and Vardhman K. Rakyan

    Citation: Genome Biology 2018 19:22

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  14. Content type: Open Letter

    The accurate description of ancestry is essential to interpret, access, and integrate human genomics data, and to ensure that these benefit individuals from all ancestral backgrounds. However, there are no est...

    Authors: Joannella Morales, Danielle Welter, Emily H. Bowler, Maria Cerezo, Laura W. Harris, Aoife C. McMahon, Peggy Hall, Heather A. Junkins, Annalisa Milano, Emma Hastings, Cinzia Malangone, Annalisa Buniello, Tony Burdett, Paul Flicek, Helen Parkinson, Fiona Cunningham…

    Citation: Genome Biology 2018 19:21

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  15. Content type: Method

    High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq an...

    Authors: Serghei Mangul, Harry Taegyun Yang, Nicolas Strauli, Franziska Gruhl, Hagit T. Porath, Kevin Hsieh, Linus Chen, Timothy Daley, Stephanie Christenson, Agata Wesolowska-Andersen, Roberto Spreafico, Cydney Rios, Celeste Eng, Andrew D. Smith, Ryan D. Hernandez, Roel A. Ophoff…

    Citation: Genome Biology 2018 19:36

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  16. Content type: Research

    Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment.

    Authors: Eugenia D’Atanasio, Beniamino Trombetta, Maria Bonito, Andrea Finocchio, Genny Di Vito, Mara Seghizzi, Rita Romano, Gianluca Russo, Giacomo Maria Paganotti, Elizabeth Watson, Alfredo Coppa, Paolo Anagnostou, Jean-Michel Dugoujon, Pedro Moral, Daniele Sellitto, Andrea Novelletto…

    Citation: Genome Biology 2018 19:20

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  17. Content type: Method

    We developed a chemical cleavage method that releases single nucleosome dyad-containing fragments, allowing us to precisely map both single nucleosomes and linkers with high accuracy genome-wide in yeast. Our ...

    Authors: Răzvan V. Chereji, Srinivas Ramachandran, Terri D. Bryson and Steven Henikoff

    Citation: Genome Biology 2018 19:19

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  18. Content type: Research

    Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large ...

    Authors: Yuanyuan Li, Hui Zheng, Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang and Wei Xie

    Citation: Genome Biology 2018 19:18

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  19. Content type: Correction

    After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an ove...

    Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

    Citation: Genome Biology 2018 19:17

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    The original article was published in Genome Biology 2017 18:150

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