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  1. Content type: Research

    The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with...

    Authors: Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau and Jane A. Skok

    Citation: Genome Biology 2018 19:216

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  2. Content type: Research

    Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is kn...

    Authors: Naifei Chen, Gang Zhao, Xu Yan, Zheng Lv, Hongmei Yin, Shilin Zhang, Wei Song, Xueli Li, Lingyu Li, Zhonghua Du, Lin Jia, Lei Zhou, Wei Li, Andrew R. Hoffman, Ji-Fan Hu and Jiuwei Cui

    Citation: Genome Biology 2018 19:218

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  3. Content type: Research

    Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple spe...

    Authors: Marie Zufferey, Daniele Tavernari, Elisa Oricchio and Giovanni Ciriello

    Citation: Genome Biology 2018 19:217

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  4. Content type: Research

    The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild...

    Authors: Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Paul D. Donohoue, Alexander H. Settle, Alexandra M. Lied, Kyle McGovern, Chris K. Fuller, Peter Cameron, Thomas G. Fazzio…

    Citation: Genome Biology 2018 19:214

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  5. Content type: Research

    Recently, DNA methylation was proposed to regulate fleshy fruit ripening. Fleshy fruits can be distinguished by their ripening process as climacteric fruits, such as tomatoes, or non-climacteric fruits, such a...

    Authors: Jingfei Cheng, Qingfeng Niu, Bo Zhang, Kunsong Chen, Ruihua Yang, Jian-Kang Zhu, Yijing Zhang and Zhaobo Lang

    Citation: Genome Biology 2018 19:212

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  6. Content type: Method

    We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and re...

    Authors: Wenjing Kang, Yrin Eldfjell, Bastian Fromm, Xavier Estivill, Inna Biryukova and Marc R. Friedländer

    Citation: Genome Biology 2018 19:213

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  7. Content type: Review

    Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism’s genome. Genome-editing systems have been utilized in a wide variet...

    Authors: Yi Zhang, Karen Massel, Ian D. Godwin and Caixia Gao

    Citation: Genome Biology 2018 19:210

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  8. Content type: Database

    We assembled the sequences from deep RNA sequencing experiments by the Genotype-Tissue Expression (GTEx) project, to create a new catalog of human genes and transcripts, called CHESS. The new database contains...

    Authors: Mihaela Pertea, Alaina Shumate, Geo Pertea, Ales Varabyou, Florian P. Breitwieser, Yu-Chi Chang, Anil K. Madugundu, Akhilesh Pandey and Steven L. Salzberg

    Citation: Genome Biology 2018 19:208

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  9. Content type: Method

    Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and ...

    Authors: Robert J. Kimmerling, Sanjay M. Prakadan, Alejandro J. Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Olcum, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek and Scott R. Manalis

    Citation: Genome Biology 2018 19:207

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  10. Content type: Editorial

    We describe the results of our year-long trial of transparent peer review and announce the adoption of transparent review as permanent policy.

    Authors: Andrew Cosgrove and Barbara Cheifet

    Citation: Genome Biology 2018 19:206

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  11. Content type: Method

    High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead ...

    Authors: Yuchao Jiang, Rujin Wang, Eugene Urrutia, Ioannis N. Anastopoulos, Katherine L. Nathanson and Nancy R. Zhang

    Citation: Genome Biology 2018 19:202

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  12. Content type: Method

    Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heter...

    Authors: Jun Wang, Li Zhao, Xia Wang, Yong Chen, Mingchu Xu, Zachry T. Soens, Zhongqi Ge, Peter Ronghan Wang, Fei Wang and Rui Chen

    Citation: Genome Biology 2018 19:203

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  13. Content type: Review

    The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impa...

    Authors: Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J. McGrew, Alan L. Archibald, Helen M. Sang, Ross D. Houston, C. Bruce Whitelaw and Mick Watson

    Citation: Genome Biology 2018 19:204

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  14. Content type: Research Highlight

    The study of the evolution of chromosomal number and structure has long been of interest to evolutionary biologists. However, this research has been hindered by the lack of chromosome-level genome assemblies f...

    Authors: Guojie Zhang

    Citation: Genome Biology 2018 19:201

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  15. 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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  16. Content type: Review

    Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of geno...

    Authors: Guillaume Bourque, Kathleen H. Burns, Mary Gehring, Vera Gorbunova, Andrei Seluanov, Molly Hammell, Michaël Imbeault, Zsuzsanna Izsvák, Henry L. Levin, Todd S. Macfarlan, Dixie L. Mager and Cédric Feschotte

    Citation: Genome Biology 2018 19:199

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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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