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  2. Content type: Method

    Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis c...

    Authors: Lynn Yi, Harold Pimentel, Nicolas L. Bray and Lior Pachter

    Citation: Genome Biology 2018 19:53

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  3. Content type: Research article

    Early life exposure to adverse environments affects cardiovascular and metabolic systems in the offspring. These programmed effects are transmissible to a second generation through both male and female lines, ...

    Authors: Jessy Cartier, Thomas Smith, John P. Thomson, Catherine M. Rose, Batbayar Khulan, Andreas Heger, Richard R. Meehan and Amanda J. Drake

    Citation: Genome Biology 2018 19:50

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  6. Content type: Correction

    In our recent article [1], it has come to our attention that the sample labels are not consistent between Table 1, the data labels deposited in the Sequence Read Archive, and Additional file 1: Table S2. We ar...

    Authors: Agata Wesolowska-Andersen, Jamie L. Everman, Rebecca Davidson, Cydney Rios, Rachelle Herrin, Celeste Eng, William J. Janssen, Andrew H. Liu, Sam S. Oh, Rajesh Kumar, Tasha E. Fingerlin, Jose Rodriguez-Santana, Esteban G. Burchard and Max A. Seibold

    Citation: Genome Biology 2018 19:49

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    The original article was published in Genome Biology 2017 18:12

  7. Content type: Research

    Human pluripotent stem cells (hPSCs) provide powerful models for studying cellular differentiations and unlimited sources of cells for regenerative medicine. However, a comprehensive single-cell level differen...

    Authors: Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo-Cheng Yuan and Guoji Guo

    Citation: Genome Biology 2018 19:47

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  8. Content type: Research

    The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription initiat...

    Authors: Seyed Yahya Anvar, Guy Allard, Elizabeth Tseng, Gloria M. Sheynkman, Eleonora de Klerk, Martijn Vermaat, Raymund H. Yin, Hans E. Johansson, Yavuz Ariyurek, Johan T. den Dunnen, Stephen W. Turner and Peter A. C. ‘t Hoen

    Citation: Genome Biology 2018 19:46

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  10. Content type: Method

    3′ Untranslated regions (3' UTRs) length is regulated in relation to cellular state. To uncover key regulators of poly(A) site use in specific conditions, we have developed PAQR, a method for quantifying poly(...

    Authors: Andreas J. Gruber, Ralf Schmidt, Souvik Ghosh, Georges Martin, Andreas R. Gruber, Erik van Nimwegen and Mihaela Zavolan

    Citation: Genome Biology 2018 19:44

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  11. Content type: Research

    Glioma stem cells (GSCs) are a subpopulation of stem-like cells that contribute to glioblastoma (GBM) aggressiveness, recurrence, and resistance to radiation and chemotherapy. Therapeutically targeting the GSC...

    Authors: Dan Zhou, Bonnie M. Alver, Shuang Li, Ryan A. Hlady, Joyce J. Thompson, Mark A. Schroeder, Jeong-Heon Lee, Jingxin Qiu, Philip H. Schwartz, Jann N. Sarkaria and Keith D. Robertson

    Citation: Genome Biology 2018 19:43

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  13. Content type: Correction

    In the recent Research Highlight [1], it has been highlighted that part b of Fig. 1 was incorrectly labelled as “sgRNA + tracrRNA” instead of “sgRNA (crRNA + tracrRNA)”. An updated Figure 1, including also the...

    Authors: Gaetan Burgio

    Citation: Genome Biology 2018 19:41

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    The original article was published in Genome Biology 2018 19:27

  14. 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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  16. 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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  17. 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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  18. 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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  20. 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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  21. 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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  22. 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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  24. 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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