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  1. Content type: Research

    N6-methyldeoxyadenosine (6mA or m6dA) was shown more than 40 years ago in simple eukaryotes. Recent studies revealed the presence of 6mA in more prevalent eukaryotes, even in vertebrates. However, functional char...

    Authors: Guan-Zheng Luo, Ziyang Hao, Liangzhi Luo, Mingren Shen, Daniela Sparvoli, Yuqing Zheng, Zijie Zhang, Xiaocheng Weng, Kai Chen, Qiang Cui, Aaron P. Turkewitz and Chuan He

    Citation: Genome Biology 2018 19:200

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  2. Content type: Short report

    The CRISPR/Cas9 system has recently been engineered to confer resistance to geminiviruses in plants. However, we show here that the usefulness of this antiviral strategy is undermined by off-target effects ide...

    Authors: Xiang Ji, Xiaomin Si, Yi Zhang, Huawei Zhang, Feng Zhang and Caixia Gao

    Citation: Genome Biology 2018 19:197

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  3. Content type: Research

    Integrating demography and adaptive evolution is pivotal to understanding the evolutionary history and conservation of great apes. However, little is known about the adaptive evolution of our closest relatives...

    Authors: Maja P. Mattle-Greminger, Tugce Bilgin Sonay, Alexander Nater, Marc Pybus, Tariq Desai, Guillem de Valles, Ferran Casals, Aylwyn Scally, Jaume Bertranpetit, Tomas Marques-Bonet, Carel P. van Schaik, Maria Anisimova and Michael Krützen

    Citation: Genome Biology 2018 19:193

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  4. Content type: Research

    Accurate assessment of health disparities requires unbiased knowledge of genetic risks in different populations. Unfortunately, most genome-wide association studies use genotyping arrays and European samples. ...

    Authors: Michelle S. Kim, Kane P. Patel, Andrew K. Teng, Ali J. Berens and Joseph Lachance

    Citation: Genome Biology 2018 19:179

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    The Research Highlight to this article has been published in Genome Medicine 2018 10:100

  5. Content type: Research

    Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding...

    Authors: Ting Zhao, Xiaoyuan Tao, Shouli Feng, Luyao Wang, Hui Hong, Wei Ma, Guandong Shang, Shisong Guo, Yuxin He, Baoliang Zhou and Xueying Guan

    Citation: Genome Biology 2018 19:195

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  6. Content type: Research

    Genetic influences on gene expression in the human fetal brain plausibly impact upon a variety of postnatal brain-related traits, including susceptibility to neuropsychiatric disorders. However, to date, there...

    Authors: Heath E. O’Brien, Eilis Hannon, Matthew J. Hill, Carolina C. Toste, Matthew J. Robertson, Joanne E. Morgan, Gemma McLaughlin, Cathryn M. Lewis, Leonard C. Schalkwyk, Lynsey S. Hall, Antonio F. Pardiñas, Michael J. Owen, Michael C. O’Donovan, Jonathan Mill and Nicholas J. Bray

    Citation: Genome Biology 2018 19:194

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  7. Content type: Short report

    CRISPR/dCas9 is a versatile tool that can be used to recruit various effectors and fluorescent molecules to defined genome regions where it can modulate genetic and epigenetic markers, or track the chromatin d...

    Authors: Jinzhi Duan, Guangqing Lu, Yu Hong, Qingtao Hu, Xueying Mai, Jing Guo, Xiaofang Si, Fengchao Wang and Yu Zhang

    Citation: Genome Biology 2018 19:192

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  8. Content type: Research

    The mutational processes underlying non-coding cancer mutations and their biological significance in tumor evolution are poorly understood. To get better insights into the biological mechanisms of mutational p...

    Authors: Jiekun Yang, Xiaolong Wei, Turan Tufan, Cem Kuscu, Hayrunnisa Unlu, Saadia Farooq, Elif Demirtas, Bryce M. Paschal and Mazhar Adli

    Citation: Genome Biology 2018 19:190

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  9. Content type: Research

    The decline of hematopoietic stem cell (HSC) function upon aging contributes to aging-associated immune remodeling and leukemia pathogenesis. Aged HSCs show changes to their epigenome, such as alterations in D...

    Authors: Ani Grigoryan, Novella Guidi, Katharina Senger, Thomas Liehr, Karin Soller, Gina Marka, Angelika Vollmer, Yolanda Markaki, Heinrich Leonhardt, Christian Buske, Daniel B. Lipka, Christoph Plass, Yi Zheng, Medhanie A. Mulaw, Hartmut Geiger and Maria Carolina Florian

    Citation: Genome Biology 2018 19:189

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  10. Content type: Research

    The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness, and provide unique therapeutic opportunities. Whole-geno...

    Authors: Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, Shadrielle Melijah G. Espiritu, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend…

    Citation: Genome Biology 2018 19:188

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  11. Content type: Research

    Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their ...

    Authors: Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin Huttley, Eldon E. Ball, Sylvain Forêt and David J. Miller

    Citation: Genome Biology 2018 19:175

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  12. Content type: Research Highlight

    Histone variants constitute a fundamental feature of the epigenome. However, their dynamics during normal and challenged DNA replication and their distribution in the three-dimensional space of the nucleus rem...

    Authors: Stella Maxouri, Stavros Taraviras and Zoi Lygerou

    Citation: Genome Biology 2018 19:182

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  13. Content type: Research

    Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome archit...

    Authors: Han Chen, Haidong Shu, Liyuan Wang, Fan Zhang, Xi Li, Sylvans Ochieng Ochola, Fei Mao, Hongyu Ma, Wenwu Ye, Tingting Gu, Lubin Jiang, Yufeng Wu, Yuanchao Wang, Sophien Kamoun and Suomeng Dong

    Citation: Genome Biology 2018 19:181

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  14. Content type: Open Letter

    In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k-mer-based lowest common ancestor taxonomic classification. We present t...

    Authors: Daniel J. Nasko, Sergey Koren, Adam M. Phillippy and Todd J. Treangen

    Citation: Genome Biology 2018 19:165

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  15. Content type: Q and A

    As part of our Q&A series, Genome Biology spoke to four scientists about their personal experiences as parents in their careers to highlight the challenges of researchers having children and the support they need...

    Authors: Emily Perry, Kristin Tessmar-Raible and Florian Raible

    Citation: Genome Biology 2018 19:180

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  16. Content type: Research

    In response to a wound, fibroblasts are activated to migrate toward the wound, to proliferate and to contribute to the wound healing process. We hypothesize that changes in pre-mRNA processing occurring as fib...

    Authors: Mithun Mitra, Elizabeth L Johnson, Vinay S Swamy, Lois E Nersesian, David C Corney, David G Robinson, Daniel G Taylor, Aaron M Ambrus, David Jelinek, Wei Wang, Sandra L Batista and Hilary A Coller

    Citation: Genome Biology 2018 19:176

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  17. Content type: Research

    Transcription factor (TF) binding to regulatory DNA sites is a key determinant of cell identity within multi-cellular organisms and has been studied extensively in relation to site affinity and chromatin modif...

    Authors: Xiaoyan Ma, Daphne Ezer, Boris Adryan and Tim J. Stevens

    Citation: Genome Biology 2018 19:174

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  18. Content type: Software

    Functional characterization of the noncoding genome is essential for biological understanding of gene regulation and disease. Here, we introduce the computational framework PINES (Phenotype-Informed Noncoding ...

    Authors: Corneliu A. Bodea, Adele A. Mitchell, Alex Bloemendal, Aaron G. Day-Williams, Heiko Runz and Shamil R. Sunyaev

    Citation: Genome Biology 2018 19:173

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  19. Content type: Research

    The number of de novo genome sequence assemblies is increasing exponentially; however, relatively few contain one scaffold/contig per chromosome. Such assemblies are essential for studies of genotype-to-phenot...

    Authors: Rebecca E O’Connor, Marta Farré, Sunitha Joseph, Joana Damas, Lucas Kiazim, Rebecca Jennings, Sophie Bennett, Eden A Slack, Emily Allanson, Denis M Larkin and Darren K Griffin

    Citation: Genome Biology 2018 19:171

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  20. Content type: Method

    Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to...

    Authors: Bogdan Budnik, Ezra Levy, Guillaume Harmange and Nikolai Slavov

    Citation: Genome Biology 2018 19:161

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  21. Content type: Research

    Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA dou...

    Authors: Tao Guo, Yi-Li Feng, Jing-Jing Xiao, Qian Liu, Xiu-Na Sun, Ji-Feng Xiang, Na Kong, Si-Cheng Liu, Guo-Qiao Chen, Yue Wang, Meng-Meng Dong, Zhen Cai, Hui Lin, Xiu-Jun Cai and An-Yong Xie

    Citation: Genome Biology 2018 19:170

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  22. Content type: Method

    CRISPR/Cas9 pooled screening permits parallel evaluation of comprehensive guide RNA libraries to systematically perturb protein coding sequences in situ and correlate with functional readouts. For the analysis...

    Authors: Vivien A. C. Schoonenberg, Mitchel A. Cole, Qiuming Yao, Claudio Macias-Treviño, Falak Sher, Patrick G. Schupp, Matthew C. Canver, Takahiro Maeda, Luca Pinello and Daniel E. Bauer

    Citation: Genome Biology 2018 19:169

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  23. Content type: Research

    Cytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by...

    Authors: Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm-Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang…

    Citation: Genome Biology 2018 19:168

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  24. Content type: Method

    We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB mem...

    Authors: Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian and Jinze Liu

    Citation: Genome Biology 2018 19:167

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  25. Content type: Research

    It has been proposed that more than 450 million years ago, two successive whole genome duplications took place in a marine chordate lineage before leading to the common ancestor of vertebrates. A precise recon...

    Authors: Christine Sacerdot, Alexandra Louis, Céline Bon, Camille Berthelot and Hugues Roest Crollius

    Citation: Genome Biology 2018 19:166

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  26. Content type: Short report

    In previous studies, CRISPR/Cas9 was shown to induce unexpected exon skipping; however, the mechanism by which this phenomenon is triggered is controversial. By analyzing 22 gene-edited rabbit lines generated ...

    Authors: Tingting Sui, Yuning Song, Zhiquan Liu, Mao Chen, Jichao Deng, Yuanyuan Xu, Liangxue Lai and Zhanjun Li

    Citation: Genome Biology 2018 19:164

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  27. Content type: Method

    Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a sin...

    Authors: Zhengyun Xiao, Guo Cheng, Yang Jiao, Chen Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng and Junling Jia

    Citation: Genome Biology 2018 19:163

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  28. Content type: Research

    There is substantial interest in the evolutionary forces that shaped the regulatory framework in early human development. Progress in this area has been slow because it is difficult to obtain relevant biologic...

    Authors: Lauren E. Blake, Samantha M. Thomas, John D. Blischak, Chiaowen Joyce Hsiao, Claudia Chavarria, Marsha Myrthil, Yoav Gilad and Bryan J. Pavlovic

    Citation: Genome Biology 2018 19:162

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  29. Content type: Research

    Recent genome-wide association studies (GWAS) have identified more than 100 loci associated with increased risk of prostate cancer, most of which are in non-coding regions of the genome. Understanding the func...

    Authors: Yu Guo, Andrew A. Perez, Dennis J. Hazelett, Gerhard A. Coetzee, Suhn Kyong Rhie and Peggy J. Farnham

    Citation: Genome Biology 2018 19:160

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  30. Content type: Method

    Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortuna...

    Authors: Timothy P. Daley, Zhixiang Lin, Xueqiu Lin, Yanxia Liu, Wing Hung Wong and Lei S. Qi

    Citation: Genome Biology 2018 19:159

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  31. Content type: Method

    Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe PHLI-seq, a novel approach that enables hi...

    Authors: Sungsik Kim, Amos Chungwon Lee, Han-Byoel Lee, Jinhyun Kim, Yushin Jung, Han Suk Ryu, Yongju Lee, Sangwook Bae, Minju Lee, Kyungmin Lee, Ryong Nam Kim, Woong-Yang Park, Wonshik Han and Sunghoon Kwon

    Citation: Genome Biology 2018 19:158

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  32. Content type: Research

    The patterns of gene expression on highly differentiated sex chromosomes differ drastically from those on autosomes, due to sex-specific patterns of selection and inheritance. As a result, X chromosomes are of...

    Authors: Wen-Juan Ma, Paris Veltsos, Roberto Sermier, Darren J Parker and Nicolas Perrin

    Citation: Genome Biology 2018 19:156

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  33. Content type: Research

    Reconstruction of ancestral karyotypes is critical for our understanding of genome evolution, allowing for the identification of the gross changes that shaped extant genomes. The identification of such changes...

    Authors: Joana Damas, Jaebum Kim, Marta Farré, Darren K Griffin and Denis M Larkin

    Citation: Genome Biology 2018 19:155

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  34. Content type: Research

    Recently, increasing evidence shows that long noncoding RNAs (lncRNAs) play a significant role in human tumorigenesis. However, the function of lncRNAs in human gastric cancer remains largely unknown.

    Authors: Erbao Zhang, Xuezhi He, Chongguo Zhang, Jun Su, Xiyi Lu, Xinxin Si, Jinfei Chen, Dandan Yin, Liang Han and Wei De

    Citation: Genome Biology 2018 19:154

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  35. Content type: Software

    SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit shows that SKESA produces assemblies that have ...

    Authors: Alexandre Souvorov, Richa Agarwala and David J. Lipman

    Citation: Genome Biology 2018 19:153

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  36. Content type: Research

    MicroRNAs (miRNAs) are short regulatory RNAs that derive from hairpin precursors. Important for understanding the functional roles of miRNAs is the ability to predict the messenger RNA (mRNA) targets most resp...

    Authors: Vikram Agarwal, Alexander O. Subtelny, Prathapan Thiru, Igor Ulitsky and David P. Bartel

    Citation: Genome Biology 2018 19:152

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  37. Content type: Method

    Here, we introduce the 3D Genome Browser, http://​3dgenome.​org, which allows users to conveniently explore both their own and over 300 publicly available chro...

    Authors: Yanli Wang, Fan Song, Bo Zhang, Lijun Zhang, Jie Xu, Da Kuang, Daofeng Li, Mayank N. K. Choudhary, Yun Li, Ming Hu, Ross Hardison, Ting Wang and Feng Yue

    Citation: Genome Biology 2018 19:151

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