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  1. Content type: Research

    Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV det...

    Authors: Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo and Yoichiro Kamatani

    Citation: Genome Biology 2019 20:117

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  2. Content type: Research

    Genes are comprised of DNA codes and contain promoters and other control elements for reading these codes. The rapid development of clustered regularly interspaced short palindromic repeats (CRISPR) technology...

    Authors: Hengji Zhan, Qun Zhou, Qunjun Gao, Jianfa Li, Weiren Huang and Yuchen Liu

    Citation: Genome Biology 2019 20:113

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  3. Content type: Research

    DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, interindiv...

    Authors: Chathura J. Gunasekara, C. Anthony Scott, Eleonora Laritsky, Maria S. Baker, Harry MacKay, Jack D. Duryea, Noah J. Kessler, Garrett Hellenthal, Alexis C. Wood, Kelly R. Hodges, Manisha Gandhi, Amy B. Hair, Matt J. Silver, Sophie E. Moore, Andrew M. Prentice, Yumei Li…

    Citation: Genome Biology 2019 20:105

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  4. Content type: Opinion

    Data science allows the extraction of practical insights from large-scale data. Here, we contextualize it as an umbrella term, encompassing several disparate subdomains. We focus on how genomics fits as a spec...

    Authors: Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson and Mark Gerstein

    Citation: Genome Biology 2019 20:109

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  5. Content type: Method

    The rapid increase of omic data has greatly facilitated the investigation of associations between omic profiles such as DNA methylation (DNAm) and complex traits in large cohorts. Here, we propose a mixed-line...

    Authors: Futao Zhang, Wenhan Chen, Zhihong Zhu, Qian Zhang, Marta F. Nabais, Ting Qi, Ian J. Deary, Naomi R. Wray, Peter M. Visscher, Allan F. McRae and Jian Yang

    Citation: Genome Biology 2019 20:107

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  6. Content type: Method

    The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) t...

    Authors: Laurent Gentzbittel, Cécile Ben, Mélanie Mazurier, Min-Gyoung Shin, Todd Lorenz, Martina Rickauer, Paul Marjoram, Sergey V. Nuzhdin and Tatiana V. Tatarinova

    Citation: Genome Biology 2019 20:106

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  7. Content type: Research Highlight

    A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome.

    Authors: Xiaofei Yang, Wan-Ping Lee, Kai Ye and Charles Lee

    Citation: Genome Biology 2019 20:104

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  8. Content type: Research

    Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechan...

    Authors: Lipei Shao, Xianglin Zuo, Yin Yang, Yu Zhang, Nan Yang, Bin Shen, Jianying Wang, Xuchun Wang, Ruilei Li, Guangfu Jin, Dawei Yu, Yuan Chen, Luan Sun, Zhen Li, Qiaofen Fu, Zhibin Hu…

    Citation: Genome Biology 2019 20:103

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  9. Content type: Method

    Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin l...

    Authors: Yousra Ben Zouari, Anne M. Molitor, Natalia Sikorska, Vera Pancaldi and Tom Sexton

    Citation: Genome Biology 2019 20:102

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  10. Content type: Short Report

    Base editing installs a precise nucleotide change in specific gene loci without causing a double-strand break. Its efficiency in human embryos is generally low, limiting its utility in functional genetic studi...

    Authors: Meiling Zhang, Changyang Zhou, Yu Wei, Chunlong Xu, Hong Pan, Wenqin Ying, Yidi Sun, Yun Sun, Qingquan Xiao, Ning Yao, Wanxia Zhong, Yun Li, Keliang Wu, Gao Yuan, Shoukhrat Mitalipov, Zi-jiang Chen…

    Citation: Genome Biology 2019 20:101

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  11. Content type: Research

    The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Sacc...

    Authors: Anne-Sophie Fiorucci, Clara Bourbousse, Lorenzo Concia, Martin Rougée, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Elodie Layat, David Latrasse, Soon Kap Kim, Nicole Chaumont, Bérangère Lombard, David Stroebel, Sophie Lemoine, Ammara Mohammad, Corinne Blugeon, Damarys Loew…

    Citation: Genome Biology 2019 20:100

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  12. Content type: Research

    Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypi...

    Authors: Zelin Liu, Yuan Ran, Changyu Tao, Sichen Li, Jian Chen and Ence Yang

    Citation: Genome Biology 2019 20:99

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  13. Content type: Research

    The human genome contains “dark” gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these ge...

    Authors: Mark T. W. Ebbert, Tanner D. Jensen, Karen Jansen-West, Jonathon P. Sens, Joseph S. Reddy, Perry G. Ridge, John S. K. Kauwe, Veronique Belzil, Luc Pregent, Minerva M. Carrasquillo, Dirk Keene, Eric Larson, Paul Crane, Yan W. Asmann, Nilufer Ertekin-Taner, Steven G. Younkin…

    Citation: Genome Biology 2019 20:97

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  14. Content type: Research

    The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant ea...

    Authors: Mathieu Seppey, Panagiotis Ioannidis, Brent C. Emerson, Camille Pitteloud, Marc Robinson-Rechavi, Julien Roux, Hermes E. Escalona, Duane D. McKenna, Bernhard Misof, Seunggwan Shin, Xin Zhou, Robert M. Waterhouse and Nadir Alvarez

    Citation: Genome Biology 2019 20:98

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  15. Content type: Short Report

    Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation ap...

    Authors: Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Giulia Alessandri, Francesca Turroni, Leonardo Mancabelli, Danilo Tatoni, Maria Cristina Ossiprandi, Douwe van Sinderen and Marco Ventura

    Citation: Genome Biology 2019 20:96

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  16. Content type: Short Report

    Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifa...

    Authors: Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis Battle and Jeffrey T. Leek

    Citation: Genome Biology 2019 20:94

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  17. Content type: Research

    VirtUaL ChIP-seq Analysis through Networks (VULCAN) infers regulatory interactions of transcription factors by overlaying networks generated from publicly available tumor expression data onto ChIP-seq data. We...

    Authors: Andrew N. Holding, Federico M. Giorgi, Amanda Donnelly, Amy E. Cullen, Sankari Nagarajan, Luke A. Selth and Florian Markowetz

    Citation: Genome Biology 2019 20:91

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    The Correction to this article has been published in Genome Biology 2019 20:122

  18. Content type: Method

    High-throughput single-cell assays increasingly require special consideration in experimental design, sample multiplexing, batch effect removal, and data interpretation. Here, we describe a lentiviral barcode-...

    Authors: Chuner Guo, Wenjun Kong, Kenji Kamimoto, Guillermo C. Rivera-Gonzalez, Xue Yang, Yuhei Kirita and Samantha A. Morris

    Citation: Genome Biology 2019 20:90

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  19. Content type: Correction

    Following publication of the original article [1], the authors reported an error in Additional file 1.

    Authors: Warren A. Cheung, Xiaojian Shao, Andréanne Morin, Valérie Siroux, Tony Kwan, Bing Ge, Dylan Aïssi, Lu Chen, Louella Vasquez, Fiona Allum, Frédéric Guénard, Emmanuelle Bouzigon, Marie-Michelle Simon, Elodie Boulier, Adriana Redensek, Stephen Watt…

    Citation: Genome Biology 2019 20:89

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    The original article was published in Genome Biology 2017 18:50

  20. Content type: Research

    The nuclear envelope not only serves as a physical barrier separating nuclear content from the cytoplasm but also plays critical roles in modulating the three-dimensional organization of genomic DNA. For both ...

    Authors: Bo Hu, Nan Wang, Xiuli Bi, Ezgi Süheyla Karaaslan, Anna-Lena Weber, Wangsheng Zhu, Kenneth Wayne Berendzen and Chang Liu

    Citation: Genome Biology 2019 20:87

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  21. Content type: Research Highlight

    A proof-of-concept study has demonstrated the application of CRISPR-Cas9 for directed evolution in rice, engineering crops for desired traits.

    Authors: Yingxiao Zhang and Yiping Qi

    Citation: Genome Biology 2019 20:83

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  22. Content type: Method

    Increasing genetic diversity via directed evolution holds great promise to accelerate trait development and crop improvement. We developed a CRISPR/Cas-based directed evolution platform in plants to evolve the...

    Authors: Haroon Butt, Ayman Eid, Afaque A. Momin, Jeremie Bazin, Martin Crespi, Stefan T. Arold and Magdy M. Mahfouz

    Citation: Genome Biology 2019 20:73

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  23. Content type: Method

    Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR follo...

    Authors: Daryl M. Gohl, Alessandro Magli, John Garbe, Aaron Becker, Darrell M. Johnson, Shea Anderson, Benjamin Auch, Bradley Billstein, Elyse Froehling, Shana L. McDevitt and Kenneth B. Beckman

    Citation: Genome Biology 2019 20:85

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  24. Content type: Research

    Circular RNAs are a class of regulatory RNA transcripts, which are ubiquitously expressed in eukaryotes. In the current study, we evaluate the function of a novel circRNA derived from the β-catenin gene locus,...

    Authors: Wei-Cheng Liang, Cheuk-Wa Wong, Pu-Ping Liang, Mai Shi, Ye Cao, Shi-Tao Rao, Stephen Kwok-Wing Tsui, Mary Miu-Yee Waye, Qi Zhang, Wei-Ming Fu and Jin-Fang Zhang

    Citation: Genome Biology 2019 20:84

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  25. Content type: Research

    Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 ...

    Authors: Shaohua Fan, Derek E. Kelly, Marcia H. Beltrame, Matthew E. B. Hansen, Swapan Mallick, Alessia Ranciaro, Jibril Hirbo, Simon Thompson, William Beggs, Thomas Nyambo, Sabah A. Omar, Dawit Wolde Meskel, Gurja Belay, Alain Froment, Nick Patterson, David Reich…

    Citation: Genome Biology 2019 20:82

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    The Correction to this article has been published in Genome Biology 2019 20:204

  26. Content type: Research

    Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.

    Authors: Belen Lorente-Galdos, Oscar Lao, Gerard Serra-Vidal, Gabriel Santpere, Lukas F. K. Kuderna, Lara R. Arauna, Karima Fadhlaoui-Zid, Ville N. Pimenoff, Himla Soodyall, Pierre Zalloua, Tomas Marques-Bonet and David Comas

    Citation: Genome Biology 2019 20:77

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  27. Content type: Research

    Geminiviruses cause damaging diseases in several important crop species. However, limited progress has been made in developing crop varieties resistant to these highly diverse DNA viruses. Recently, the bacter...

    Authors: Devang Mehta, Alessandra Stürchler, Ravi B. Anjanappa, Syed Shan-e-Ali Zaidi, Matthias Hirsch-Hoffmann, Wilhelm Gruissem and Hervé Vanderschuren

    Citation: Genome Biology 2019 20:80

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  28. Content type: Research

    Plant domestication provides a unique model to study genome evolution. Many studies have been conducted to examine genes, genetic diversity, genome structure, and epigenome changes associated with domesticatio...

    Authors: Jinyu Wang, Xianran Li, Kyung Do Kim, Michael J. Scanlon, Scott A. Jackson, Nathan M. Springer and Jianming Yu

    Citation: Genome Biology 2019 20:74

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  29. Content type: Method

    Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing t...

    Authors: Daniel Alpern, Vincent Gardeux, Julie Russeil, Bastien Mangeat, Antonio C. A. Meireles-Filho, Romane Breysse, David Hacker and Bart Deplancke

    Citation: Genome Biology 2019 20:71

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  30. Content type: Research

    Pistachio (Pistacia vera), one of the most important commercial nut crops worldwide, is highly adaptable to abiotic stresses and is tolerant to drought and salt stresses.

    Authors: Lin Zeng, Xiao-Long Tu, He Dai, Feng-Ming Han, Bing-She Lu, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiao-Long Li, Li-Li Ji, David M. Irwin, Hong Zhou, Min Liu, Hong-Kun Zheng, Ali Esmailizadeh…

    Citation: Genome Biology 2019 20:79

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  31. Content type: Editorial

    Machine learning has demonstrated potential in analyzing large, complex biological data. In practice, however, biological information is required in addition to machine learning for successful application.

    Authors: Chunming Xu and Scott A. Jackson

    Citation: Genome Biology 2019 20:76

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  32. Content type: Research

    Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. A lack of recombination ...

    Authors: Laura-Jayne Gardiner, Luzie U. Wingen, Paul Bailey, Ryan Joynson, Thomas Brabbs, Jonathan Wright, James D. Higgins, Neil Hall, Simon Griffiths, Bernardo J. Clavijo and Anthony Hall

    Citation: Genome Biology 2019 20:69

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  33. Content type: Short Report

    Single-cell RNA-seq technologies require library preparation prior to sequencing. Here, we present the first report to compare the cheaper BGISEQ-500 platform to the Illumina HiSeq platform for scRNA-seq. We g...

    Authors: Kedar Nath Natarajan, Zhichao Miao, Miaomiao Jiang, Xiaoyun Huang, Hongpo Zhou, Jiarui Xie, Chunqing Wang, Shishang Qin, Zhikun Zhao, Liang Wu, Naibo Yang, Bo Li, Yong Hou, Shiping Liu and Sarah A. Teichmann

    Citation: Genome Biology 2019 20:70

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  34. Content type: Correction

    Following publication of the original article [1], the authors would like to highlight the following two corrections.

    Authors: Alexa B. R. McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J. Prill, Elizabeth Hénaff, Noah Alexander, Samuel S. Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A. Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi…

    Citation: Genome Biology 2019 20:72

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    The original article was published in Genome Biology 2017 18:182

  35. Content type: Research

    The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of...

    Authors: Kristen A. Panfilio, Iris M. Vargas Jentzsch, Joshua B. Benoit, Deniz Erezyilmaz, Yuichiro Suzuki, Stefano Colella, Hugh M. Robertson, Monica F. Poelchau, Robert M. Waterhouse, Panagiotis Ioannidis, Matthew T. Weirauch, Daniel S. T. Hughes, Shwetha C. Murali, John H. Werren, Chris G. C. Jacobs, Elizabeth J. Duncan…

    Citation: Genome Biology 2019 20:64

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  36. Content type: Software

    Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell ...

    Authors: Joanna Hård, Ezeddin Al Hakim, Marie Kindblom, Åsa K. Björklund, Bengt Sennblad, Ilke Demirci, Marta Paterlini, Pedro Reu, Erik Borgström, Patrik L. Ståhl, Jakob Michaelsson, Jeff E. Mold and Jonas Frisén

    Citation: Genome Biology 2019 20:68

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  37. Content type: Method

    Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purp...

    Authors: Paul F. Harrison, Andrew D. Pattison, David R. Powell and Traude H. Beilharz

    Citation: Genome Biology 2019 20:67

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