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  1. 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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  4. 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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  7. 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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  8. 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

  9. 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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  10. 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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  11. 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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  13. 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

  14. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  22. 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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  24. 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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  25. 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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  26. 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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  27. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  36. 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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  37. 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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  38. 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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  40. 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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  42. 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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  43. 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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  44. 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

  45. 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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  48. 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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  49. 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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