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  1. Content type: Research

    N6-methyladenosine (m6A) is an important epitranscriptomic mark with high abundance in the brain. Recently, it has been found to be involved in the regulation of memory formation and mammalian cortical neurogenes...

    Authors: Chunhui Ma, Mengqi Chang, Hongyi Lv, Zhi-Wei Zhang, Weilong Zhang, Xue He, Gaolang Wu, Shunli Zhao, Yao Zhang, Di Wang, Xufei Teng, Chunying Liu, Qing Li, Arne Klungland, Yamei Niu, Shuhui Song…

    Citation: Genome Biology 2018 19:68

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  2. Content type: Research

    Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somat...

    Authors: Luis Zapata, Oriol Pich, Luis Serrano, Fyodor A. Kondrashov, Stephan Ossowski and Martin H. Schaefer

    Citation: Genome Biology 2018 19:67

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  3. Content type: Research

    N 6 -methyladenosine (m6A) modification in mRNAs was recently shown to be dynamically regulated, indicating a pivotal role in multiple developmental processes. Most recently,...

    Authors: Miaomiao Li, Xu Zhao, Wei Wang, Hailing Shi, Qingfei Pan, Zhike Lu, Sonia Peña Perez, Rajikala Suganthan, Chuan He, Magnar Bjørås and Arne Klungland

    Citation: Genome Biology 2018 19:69

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  4. Content type: Method

    Genome-wide methylation arrays are powerful tools for assessing cell composition of complex mixtures. We compare three approaches to select reference libraries for deconvoluting neutrophil, monocyte, B-lymphoc...

    Authors: Lucas A. Salas, Devin C. Koestler, Rondi A. Butler, Helen M. Hansen, John K. Wiencke, Karl T. Kelsey and Brock C. Christensen

    Citation: Genome Biology 2018 19:64

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  5. Content type: Research

    While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homol...

    Authors: Yuanming Wang, Kaiwen Ivy Liu, Norfala-Aliah Binte Sutrisnoh, Harini Srinivasan, Junyi Zhang, Jia Li, Fan Zhang, Charles Richard John Lalith, Heyun Xing, Raghuvaran Shanmugam, Jia Nee Foo, Hwee Ting Yeo, Kean Hean Ooi, Tore Bleckwehl, Yi Yun Rachel Par, Shi Mun Lee…

    Citation: Genome Biology 2018 19:62

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  6. Content type: Method

    Nucleotide base editors in plants have been limited to conversion of cytosine to thymine. Here, we describe a new plant adenine base editor based on an evolved tRNA adenosine deaminase fused to the nickase CRI...

    Authors: Chao Li, Yuan Zong, Yanpeng Wang, Shuai Jin, Dingbo Zhang, Qianna Song, Rui Zhang and Caixia Gao

    Citation: Genome Biology 2018 19:59

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  7. Content type: Correction

    Upon publication of the original article [1] it was highlighted by the authors that a transposition error affected Additional file 1, causing the misplacement of several columns and rendering the table difficu...

    Authors: Anthony S. Zannas, Janine Arloth, Tania Carrillo-Roa, Stella Iurato, Simone Röh, Kerry J. Ressler, Charles B. Nemeroff, Alicia K. Smith, Bekh Bradley, Christine Heim, Andreas Menke, Jennifer F. Lange, Tanja Brückl, Marcus Ising, Naomi R. Wray, Angelika Erhardt…

    Citation: Genome Biology 2018 19:61

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    The original article was published in Genome Biology 2015 16:266

  8. Content type: Meeting report

    The Annual Advances in Genome Biology and Technology (AGBT) General Meeting was held in Orlando, Florida, USA, on the 12–15 February 2018. Professors Ami S. Bhatt and Christina Curtis from Stanford University,...

    Authors: Ami S. Bhatt and Christina Curtis

    Citation: Genome Biology 2018 19:60

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  9. Content type: Method

    Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produ...

    Authors: Tom Aharon Hait, David Amar, Ron Shamir and Ran Elkon

    Citation: Genome Biology 2018 19:56

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  10. Content type: Research

    Animals can show very different behaviors even in isogenic populations, but the underlying mechanisms to generate this variability remain elusive. We use the zebrafish (Danio rerio) as a model to test the influen...

    Authors: Angel-Carlos Román, Julián Vicente-Page, Alfonso Pérez-Escudero, Jose M. Carvajal-González, Pedro M. Fernández-Salguero and Gonzalo G. de Polavieja

    Citation: Genome Biology 2018 19:55

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  11. 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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  12. 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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  13. 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

  14. 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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  15. 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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  16. 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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  17. 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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  18. 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

  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. Content type: Research Highlight

    The generation of genetically modified alleles in mice using conventional transgenesis technologies is a long and inefficient process. A new study shows that the in situ delivery of CRISPR/Cas9 reagents into p...

    Authors: Gaetan Burgio

    Citation: Genome Biology 2018 19:27

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    The Correction to this article has been published in Genome Biology 2018 19:41

  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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