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  1. Content type: Research

    Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives....

    Authors: Anupriya Kaur Thind, Thomas Wicker, Thomas Müller, Patrick M. Ackermann, Burkhard Steuernagel, Brande B. H. Wulff, Manuel Spannagl, Sven O. Twardziok, Marius Felder, Thomas Lux, Klaus F. X. Mayer, Beat Keller and Simon G. Krattinger

    Citation: Genome Biology 2018 19:104

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  2. Content type: Research

    Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an al...

    Authors: Thomas Wicker, Heidrun Gundlach, Manuel Spannagl, Cristobal Uauy, Philippa Borrill, Ricardo H. Ramírez-González, Romain De Oliveira, Klaus F. X. Mayer, Etienne Paux and Frédéric Choulet

    Citation: Genome Biology 2018 19:103

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  3. Content type: Research

    Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is revolutionizing our ability to achieve this task. Oncoge...

    Authors: Ruiqi Han, Li Li, Alejandro Piñeiro Ugalde, Arieh Tal, Zohar Manber, Eric Pinto Barbera, Veronica Della Chiara, Ran Elkon and Reuven Agami

    Citation: Genome Biology 2018 19:118

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  4. Content type: Research

    Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.

    Authors: Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, Kerrie Forrest, Zeev Frenkel, Abraham Korol, B. Emma Huang, Colin Cavanagh, Jen Taylor, Michael Abrouk, Andrew Sharpe, David Konkin, Pierre Sourdille, Benoît Darrier…

    Citation: Genome Biology 2018 19:112

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  5. Content type: Database

    The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome S...

    Authors: Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert…

    Citation: Genome Biology 2018 19:111

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  6. Content type: Research

    Alternative RNA processing plays an essential role in shaping cell identity and connectivity in the central nervous system. This is believed to involve differential regulation of RNA processing in various cell...

    Authors: Yuan Yuan, Shirley Xie, Jennifer C. Darnell, Andrew J. Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth A. Murphy, Chaolin Zhang, Tom Maniatis and Robert B. Darnell

    Citation: Genome Biology 2018 19:117

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  7. Content type: Method

    CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the s...

    Authors: Michael Gapinske, Alan Luu, Jackson Winter, Wendy S. Woods, Kurt A. Kostan, Nikhil Shiva, Jun S. Song and Pablo Perez-Pinera

    Citation: Genome Biology 2018 19:107

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  8. Content type: Research

    The large and highly repetitive genomes of the cultivated species Hordeum vulgare (barley), Triticum aestivum (wheat), and Secale cereale (rye) belonging to the Triticeae tribe of grasses appear to be particularl...

    Authors: Jeyaraman Rajaraman, Dimitar Douchkov, Stefanie Lück, Götz Hensel, Daniela Nowara, Maria Pogoda, Twan Rutten, Tobias Meitzel, Jonathan Brassac, Caroline Höfle, Ralph Hückelhoven, Jörn Klinkenberg, Marco Trujillo, Eva Bauer, Thomas Schmutzer, Axel Himmelbach…

    Citation: Genome Biology 2018 19:116

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  12. Content type: Research

    Cancers have long been recognized to be not only genetically but also epigenetically distinct from their tissues of origin. Although genetic alterations underlying oncogene upregulation have been well studied,...

    Authors: Jianzhong Su, Yung-Hsin Huang, Xiaodong Cui, Xinyu Wang, Xiaotian Zhang, Yong Lei, Jianfeng Xu, Xueqiu Lin, Kaifu Chen, Jie Lv, Margaret A. Goodell and Wei Li

    Citation: Genome Biology 2018 19:108

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  15. Content type: Research

    CTCF binding to DNA helps partition the mammalian genome into discrete structural and regulatory domains. Complete removal of CTCF from mammalian cells causes catastrophic genome dysregulation, likely due to w...

    Authors: Sarah J. Aitken, Ximena Ibarra-Soria, Elissavet Kentepozidou, Paul Flicek, Christine Feig, John C. Marioni and Duncan T. Odom

    Citation: Genome Biology 2018 19:106

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  19. Content type: Research

    Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and neg...

    Authors: Stefano G. Manzo, Stella R. Hartono, Lionel A. Sanz, Jessica Marinello, Sara De Biasi, Andrea Cossarizza, Giovanni Capranico and Frederic Chedin

    Citation: Genome Biology 2018 19:100

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  21. Content type: Research

    What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of geno...

    Authors: Ildikó M. L. Somorjai, Josep Martí-Solans, Miriam Diaz-Gracia, Hiroki Nishida, Kaoru S. Imai, Hector Escrivà, Cristian Cañestro and Ricard Albalat

    Citation: Genome Biology 2018 19:98

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  22. Content type: Correspondence

    In a recent publication, Sood et al. (Genome Biol 16:185, 2015) presented a set of 150 probe sets that could be used in the diagnosis of Alzheimer’s disease (AD) based on gene expression. We reproduce some of ...

    Authors: Laurent Jacob and Terence P. Speed

    Citation: Genome Biology 2018 19:97

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    The Research to this article has been published in Genome Biology 2015 16:185

  23. Content type: Review

    Cancer arises through the accumulation of somatic mutations over time. An understanding of the sequence of events during this process should allow both earlier diagnosis and better prediction of cancer progres...

    Authors: Clemency Jolly and Peter Van Loo

    Citation: Genome Biology 2018 19:95

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  24. Content type: Research

    Long non-coding RNAs (lncRNAs) are typically expressed at low levels and are inherently highly variable. This is a fundamental challenge for differential expression (DE) analysis. In this study, the performanc...

    Authors: Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas and Jo Vandesompele

    Citation: Genome Biology 2018 19:96

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  25. Content type: Research

    Fitness costs imposed on bacteria by antibiotic resistance mechanisms are believed to hamper their dissemination. The scale of these costs is highly variable. Some, including resistance of Staphylococcus aureus t...

    Authors: Maho Yokoyama, Emily Stevens, Maisem Laabei, Leann Bacon, Kate Heesom, Sion Bayliss, Nicola Ooi, Alex J. O’Neill, Ewan Murray, Paul Williams, Anneke Lubben, Shaun Reeksting, Guillaume Meric, Ben Pascoe, Samuel K. Sheppard, Mario Recker…

    Citation: Genome Biology 2018 19:94

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  27. Content type: Software

    Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized gen...

    Authors: Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng and Sheng Zhong

    Citation: Genome Biology 2018 19:92

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    The Research Highlight to this article has been published in Genome Biology 2018 19:93

  28. Content type: Research

    Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac functio...

    Authors: Bram P. Prins, Timothy J. Mead, Jennifer A. Brody, Gardar Sveinbjornsson, Ioanna Ntalla, Nathan A. Bihlmeyer, Marten van den Berg, Jette Bork-Jensen, Stefania Cappellani, Stefan Van Duijvenboden, Nikolai T. Klena, George C. Gabriel, Xiaoqin Liu, Cagri Gulec, Niels Grarup, Jeffrey Haessler…

    Citation: Genome Biology 2018 19:87

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  30. Content type: Research

    DNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5m...

    Authors: Tianpeng Gu, Xueqiu Lin, Sean M. Cullen, Min Luo, Mira Jeong, Marcos Estecio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Stanley Qi, Jia-Jia Chen, Michael Kyba…

    Citation: Genome Biology 2018 19:88

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  31. Content type: Research

    Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We...

    Authors: Karol Szlachta, Ryan G. Thys, Naomi D. Atkin, Levi C. T. Pierce, Stefan Bekiranov and Yuh-Hwa Wang

    Citation: Genome Biology 2018 19:89

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  32. Content type: Opinion

    Single-cell analyses have revealed a tremendous variety among cells in the abundance and chemical composition of RNA. Much of this heterogeneity is due to alternative splicing by the spliceosome. Little is kno...

    Authors: Yihan Wan and Daniel R. Larson

    Citation: Genome Biology 2018 19:86

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  33. Content type: Research

    Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a ...

    Authors: Atma M. Ivancevic, R. Daniel Kortschak, Terry Bertozzi and David L. Adelson

    Citation: Genome Biology 2018 19:85

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  34. Content type: Research

    Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) ...

    Authors: Xu Tang, Guanqing Liu, Jianping Zhou, Qiurong Ren, Qi You, Li Tian, Xuhui Xin, Zhaohui Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn, Zhiyun Gong, Yiping Qi, Tao Zhang and Yong Zhang

    Citation: Genome Biology 2018 19:84

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  36. Content type: Software

    Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational ta...

    Authors: Qi Zheng, Casey Bartow-McKenney, Jacquelyn S. Meisel and Elizabeth A. Grice

    Citation: Genome Biology 2018 19:82

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  38. Content type: Method

    A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized desi...

    Authors: Guohui Chuai, Hanhui Ma, Jifang Yan, Ming Chen, Nanfang Hong, Dongyu Xue, Chi Zhou, Chenyu Zhu, Ke Chen, Bin Duan, Feng Gu, Sheng Qu, Deshuang Huang, Jia Wei and Qi Liu

    Citation: Genome Biology 2018 19:80

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  39. Content type: Research

    Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats...

    Authors: Francis W. B. Sanders, Animesh Acharjee, Celia Walker, Luke Marney, Lee D. Roberts, Fumiaki Imamura, Benjamin Jenkins, Jack Case, Sumantra Ray, Samuel Virtue, Antonio Vidal-Puig, Diana Kuh, Rebecca Hardy, Michael Allison, Nita Forouhi, Andrew J. Murray…

    Citation: Genome Biology 2018 19:79

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  40. Content type: Software

    Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing c...

    Authors: Viktor Petukhov, Jimin Guo, Ninib Baryawno, Nicolas Severe, David T. Scadden, Maria G. Samsonova and Peter V. Kharchenko

    Citation: Genome Biology 2018 19:78

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  41. Content type: Research

    Pear (Pyrus) is a globally grown fruit, with thousands of cultivars in five domesticated species and dozens of wild species. However, little is known about the evolutionary history of these pear species and what ...

    Authors: Jun Wu, Yingtao Wang, Jiabao Xu, Schuyler S. Korban, Zhangjun Fei, Shutian Tao, Ray Ming, Shuaishuai Tai, Awais M. Khan, Joseph D. Postman, Chao Gu, Hao Yin, Danman Zheng, Kaijie Qi, Yong Li, Runze Wang…

    Citation: Genome Biology 2018 19:77

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  43. Content type: Research

    Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino ...

    Authors: Raphaël Méheust, Andrew K. Watson, François-Joseph Lapointe, R. Thane Papke, Philippe Lopez and Eric Bapteste

    Citation: Genome Biology 2018 19:75

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  44. Content type: Research Highlight

    We discuss a recent study that has identified and validated the link between a type-2 diabetes (T2D) association and human adipose biology by means of KLF14 gene expression. In addition to being maternally imprin...

    Authors: Kim Lorenz and Benjamin F. Voight

    Citation: Genome Biology 2018 19:74

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  45. Content type: Method

    We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-s...

    Authors: Mahmoud N. Abdelmoez, Kei Iida, Yusuke Oguchi, Hidekazu Nishikii, Ryuji Yokokawa, Hidetoshi Kotera, Sotaro Uemura, Juan G. Santiago and Hirofumi Shintaku

    Citation: Genome Biology 2018 19:66

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  46. Content type: Method

    Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumori...

    Authors: Yin Tong, Jianlong Sun, Chi Fat Wong, Qingzheng Kang, Beibei Ru, Ching Ngar Wong, April Sheila Chan, Suet Yi Leung and Jiangwen Zhang

    Citation: Genome Biology 2018 19:73

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  47. Content type: Research

    The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits ...

    Authors: Jing Wang, Jihua Ding, Biyue Tan, Kathryn M. Robinson, Ingrid H. Michelson, Anna Johansson, Björn Nystedt, Douglas G. Scofield, Ove Nilsson, Stefan Jansson, Nathaniel R. Street and Pär K. Ingvarsson

    Citation: Genome Biology 2018 19:72

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  49. 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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  50. 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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