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  1. Content type: Method

    We introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell-type composition distribution of the studied tissue...

    Authors: Elior Rahmani, Regev Schweiger, Liat Shenhav, Theodora Wingert, Ira Hofer, Eilon Gabel, Eleazar Eskin and Eran Halperin

    Citation: Genome Biology 2018 19:141

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  2. Content type: Review

    Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools...

    Authors: Mona Schreiber, Nils Stein and Martin Mascher

    Citation: Genome Biology 2018 19:140

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  3. Content type: Research

    The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eura...

    Authors: Kristiina Tambets, Bayazit Yunusbayev, Georgi Hudjashov, Anne-Mai Ilumäe, Siiri Rootsi, Terhi Honkola, Outi Vesakoski, Quentin Atkinson, Pontus Skoglund, Alena Kushniarevich, Sergey Litvinov, Maere Reidla, Ene Metspalu, Lehti Saag, Timo Rantanen, Monika Karmin…

    Citation: Genome Biology 2018 19:139

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  4. Content type: Research

    Clustered, regularly interspaced, short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) have recently opened a new avenue for gene therapy. Cas9 nuclease guided by a single-guide RNA (sgRNA) ...

    Authors: Raed Ibraheim, Chun-Qing Song, Aamir Mir, Nadia Amrani, Wen Xue and Erik J. Sontheimer

    Citation: Genome Biology 2018 19:137

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  5. Content type: Research

    The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modificatio...

    Authors: Alexis Vandenbon, Yutaro Kumagai, Mengjie Lin, Yutaka Suzuki and Kenta Nakai

    Citation: Genome Biology 2018 19:138

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  6. Content type: Research

    Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1–7-bp scale, but cis elements remain poorly characterized. Th...

    Authors: Chaorui Duan, Qing Huan, Xiaoshu Chen, Shaohuan Wu, Lucas B. Carey, Xionglei He and Wenfeng Qian

    Citation: Genome Biology 2018 19:132

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  7. Content type: Meeting report

    A meeting report on the 14th Gordon Research Conference on Meiosis, held at Colby Sawyer College, New London, NH, USA, 9–15 June 2018, chaired by Monica Colaiacovo, Harvard Medical School.

    Authors: Weronika E. Borek and Adele L. Marston

    Citation: Genome Biology 2018 19:134

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  8. Content type: Review

    “Conservation genomics” encompasses the idea that genome-scale data will improve the capacity of resource managers to protect species. Although genetic approaches have long been used in conservation research, ...

    Authors: Megan A. Supple and Beth Shapiro

    Citation: Genome Biology 2018 19:131

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  9. Content type: Method

    Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method ...

    Authors: Paul Geeleher, Aritro Nath, Fan Wang, Zhenyu Zhang, Alvaro N. Barbeira, Jessica Fessler, Robert L. Grossman, Cathal Seoighe and R. Stephanie Huang

    Citation: Genome Biology 2018 19:130

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  10. Content type: Research

    In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has...

    Authors: Yanting Shen, Jixiang Zhang, Yucheng Liu, Shulin Liu, Zhi Liu, Zongbiao Duan, Zheng Wang, Baoge Zhu, Ya-Long Guo and Zhixi Tian

    Citation: Genome Biology 2018 19:128

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  11. Content type: Research

    DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures—each representing a mutagenic process...

    Authors: Marketa Tomkova, Jakub Tomek, Skirmantas Kriaucionis and Benjamin Schuster-Böckler

    Citation: Genome Biology 2018 19:129

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  12. Content type: Research

    Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expre...

    Authors: Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jeremy Denizot, Raquel Manzano Garcia, Steven W. Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip Hawkins, Len Stephens…

    Citation: Genome Biology 2018 19:126

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  13. Content type: Research

    Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental char...

    Authors: Seunghoon Baek, Kyung Choi, Goon-Bo Kim, Hee-Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kae Sun Chang, Joo-Hwan Kim and Jeong-Hwan Mun

    Citation: Genome Biology 2018 19:127

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  14. Content type: Method

    The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and for development of new biomarkers and therapeutic targets. We develop a new method for...

    Authors: Sergio Barberán-Soler, Jenny M. Vo, Ryan E. Hogans, Anne Dallas, Brian H. Johnston and Sergei A. Kazakov

    Citation: Genome Biology 2018 19:105

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  15. Content type: Research

    Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and in...

    Authors: K. Leigh Greathouse, James R. White, Ashely J. Vargas, Valery V. Bliskovsky, Jessica A. Beck, Natalia von Muhlinen, Eric C. Polley, Elise D. Bowman, Mohammed A. Khan, Ana I. Robles, Tomer Cooks, Bríd M. Ryan, Noah Padgett, Amiran H. Dzutsev, Giorgio Trinchieri, Marbin A. Pineda…

    Citation: Genome Biology 2018 19:123

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  16. Content type: Research

    In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea ...

    Authors: Lakshmipuram Seshadri Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson and John Parkinson

    Citation: Genome Biology 2018 19:124

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  17. Content type: Software

    We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, al...

    Authors: Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H. Alver, Hanspeter Pfister, Leonid A. Mirny, Peter J. Park…

    Citation: Genome Biology 2018 19:125

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  18. Content type: Correction

    The original version [1] of this article unfortunately contained a mistake. The additive effects of the eQTLs of lncRNAs were flipped, meaning that the base allele in the contrast to derive the additive effect...

    Authors: Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng-Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Matthew M. S. Evans, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C. P. Timmermans, Nathan M. Springer…

    Citation: Genome Biology 2018 19:122

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    The original article was published in Genome Biology 2014 15:R40

  19. Content type: Method

    Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read leng...

    Authors: Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur and Alicia Oshlack

    Citation: Genome Biology 2018 19:121

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  20. Content type: Research

    Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they shoul...

    Authors: François Mallard, Viola Nolte, Ray Tobler, Martin Kapun and Christian Schlötterer

    Citation: Genome Biology 2018 19:119

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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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

  34. 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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  35. 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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  36. 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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  37. 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