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  1. Content type: Research

    Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and tem...

    Authors: Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz…

    Citation: Genome Biology 2017 18:114

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  2. Content type: Research

    The genetic relationships reported by recent studies between Sherpas and Tibetans are controversial. To gain insights into the population history and the genetic basis of high-altitude adaptation of the two gr...

    Authors: Chao Zhang, Yan Lu, Qidi Feng, Xiaoji Wang, Haiyi Lou, Jiaojiao Liu, Zhilin Ning, Kai Yuan, Yuchen Wang, Ying Zhou, Lian Deng, Lijun Liu, Yajun Yang, Shilin Li, Lifeng Ma, Zhiying Zhang…

    Citation: Genome Biology 2017 18:115

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  3. Content type: Research

    The organisation of vertebrate genomes into topologically associating domains (TADs) is believed to facilitate the regulation of the genes located within them. A remaining question is whether TAD organisation ...

    Authors: Cristina Vicente-García, Barbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter W. J. Rigby, Damien P. Devos, Jose L. Gómez-Skarmeta and Jaime J. Carvajal

    Citation: Genome Biology 2017 18:106

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  4. Content type: Research

    The functional divergence of duplicate genes (ohnologues) retained from whole genome duplication (WGD) is thought to promote evolutionary diversification. However, species radiation and phenotypic diversificat...

    Authors: Fiona M. Robertson, Manu Kumar Gundappa, Fabian Grammes, Torgeir R. Hvidsten, Anthony K. Redmond, Sigbjørn Lien, Samuel A. M. Martin, Peter W. H. Holland, Simen R. Sandve and Daniel J. Macqueen

    Citation: Genome Biology 2017 18:111

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  5. Content type: Research

    The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations...

    Authors: Gyaneshwer Chaubey, Qasim Ayub, Niraj Rai, Satya Prakash, Veena Mushrif-Tripathy, Massimo Mezzavilla, Ajai Kumar Pathak, Rakesh Tamang, Sadaf Firasat, Maere Reidla, Monika Karmin, Deepa Selvi Rani, Alla G. Reddy, Jüri Parik, Ene Metspalu, Siiri Rootsi…

    Citation: Genome Biology 2017 18:110

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  6. Content type: Method

    CRISPR is widely used to disrupt gene function by inducing small insertions and deletions. Here, we show that some single-guide RNAs (sgRNAs) can induce exon skipping or large genomic deletions that delete exo...

    Authors: Haiwei Mou, Jordan L. Smith, Lingtao Peng, Hao Yin, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Qiongqiong Wu, Deniz M. Ozata, Yingxiang Li, Daniel G. Anderson, Charles P. Emerson, Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng…

    Citation: Genome Biology 2017 18:108

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  7. Content type: Correspondence

    Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that hav...

    Authors: Susanne Bornelöv, Eyal Seroussi, Sara Yosefi, Ken Pendavis, Shane C. Burgess, Manfred Grabherr, Miriam Friedman-Einat and Leif Andersson

    Citation: Genome Biology 2017 18:112

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  8. Content type: Research Highlight

    Epigenetic clocks provide powerful tools to evaluate nutritional, hormonal, and genetic effects on aging. What can we learn from differences between species in how these clocks tick?

    Authors: Wolfgang Wagner

    Citation: Genome Biology 2017 18:107

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  9. Content type: Correspondence

    While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that ...

    Authors: Peter V. Lovell and Claudio V. Mello

    Citation: Genome Biology 2017 18:113

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  10. Content type: Research

    Long-term evolution of sex chromosomes is a dynamic process shaped by gene gain and gene loss. Sex chromosome gene traffic has been studied in XY and ZW systems but no detailed analyses have been carried out f...

    Authors: Agnieszka P. Lipinska, Nicholas R. T. Toda, Svenja Heesch, Akira F. Peters, J. Mark Cock and Susana M. Coelho

    Citation: Genome Biology 2017 18:104

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  11. Content type: Research

    The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and...

    Authors: Rong Yang, Zhimin Zheng, Qing Chen, Lan Yang, Huan Huang, Daisuke Miki, Wenwu Wu, Liang Zeng, Jun Liu, Jin-Xing Zhou, Joe Ogas, Jian-Kang Zhu, Xin-Jian He and Heng Zhang

    Citation: Genome Biology 2017 18:103

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  12. Content type: Research

    Polyploidy is a pervasive evolutionary feature of all flowering plants and some animals, leading to genetic and epigenetic changes that affect gene expression and morphology. DNA methylation changes can produc...

    Authors: Qingxin Song, Tianzhen Zhang, David M. Stelly and Z. Jeffrey Chen

    Citation: Genome Biology 2017 18:99

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  13. Content type: Method

    We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide m...

    Authors: Gleb Kuznetsov, Daniel B. Goodman, Gabriel T. Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J. Lajoie and George M. Church

    Citation: Genome Biology 2017 18:100

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  14. Content type: Software

    Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a...

    Authors: Daniel B. Goodman, Gleb Kuznetsov, Marc J. Lajoie, Brian W. Ahern, Michael G. Napolitano, Kevin Y. Chen, Changping Chen and George M. Church

    Citation: Genome Biology 2017 18:101

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  15. Content type: Research

    Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that ...

    Authors: Isidore Rigoutsos, Sang Kil Lee, Su Youn Nam, Simone Anfossi, Barbara Pasculli, Martin Pichler, Yi Jing, Cristian Rodriguez-Aguayo, Aristeidis G. Telonis, Simona Rossi, Cristina Ivan, Tina Catela Ivkovic, Linda Fabris, Peter M. Clark, Hui Ling, Masayoshi Shimizu…

    Citation: Genome Biology 2017 18:98

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  16. Content type: Research Highlight

    Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer.

    Authors: Gabriel J. Sandoval and William C. Hahn

    Citation: Genome Biology 2017 18:95

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  17. Content type: Research

    Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enri...

    Authors: Heike Wollmann, Hume Stroud, Ramesh Yelagandula, Yoshiaki Tarutani, Danhua Jiang, Li Jing, Bhagyshree Jamge, Hidenori Takeuchi, Sarah Holec, Xin Nie, Tetsuji Kakutani, Steven E. Jacobsen and Frédéric Berger

    Citation: Genome Biology 2017 18:94

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  18. Content type: Research

    Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Condit...

    Authors: Rolen M. Quadros, Hiromi Miura, Donald W. Harms, Hisako Akatsuka, Takehito Sato, Tomomi Aida, Ronald Redder, Guy P. Richardson, Yutaka Inagaki, Daisuke Sakai, Shannon M. Buckley, Parthasarathy Seshacharyulu, Surinder K. Batra, Mark A. Behlke, Sarah A. Zeiner, Ashley M. Jacobi…

    Citation: Genome Biology 2017 18:92

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  19. Content type: Open Letter

    Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...

    Authors: Guo-Cheng Yuan, Long Cai, Michael Elowitz, Tariq Enver, Guoping Fan, Guoji Guo, Rafael Irizarry, Peter Kharchenko, Junhyong Kim, Stuart Orkin, John Quackenbush, Assieh Saadatpour, Timm Schroeder, Ramesh Shivdasani and Itay Tirosh

    Citation: Genome Biology 2017 18:84

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  20. Content type: Review

    High-throughput technologies have revolutionized medical research. The advent of genotyping arrays enabled large-scale genome-wide association studies and methods for examining global transcript levels, which ...

    Authors: Yehudit Hasin, Marcus Seldin and Aldons Lusis

    Citation: Genome Biology 2017 18:83

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  21. Content type: Research

    The structure and mechanical properties of chromatin impact DNA functions and nuclear architecture but remain poorly understood. In budding yeast, a simple polymer model with minimal sequence-specific constrai...

    Authors: Jean-Michel Arbona, Sébastien Herbert, Emmanuelle Fabre and Christophe Zimmer

    Citation: Genome Biology 2017 18:81

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  22. Content type: Research

    Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which marks many transcriptionally silent genes throughout the mammalian genome. Although H3K27me3 is associated with silenced gene expression b...

    Authors: Emily Maclary, Michael Hinten, Clair Harris, Shriya Sethuraman, Srimonta Gayen and Sundeep Kalantry

    Citation: Genome Biology 2017 18:82

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  23. Content type: Research

    Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arab...

    Authors: Fernando A. Rabanal, Terezie Mandáková, Luz M. Soto-Jiménez, Robert Greenhalgh, David L. Parrott, Stefan Lutzmayer, Joshua G. Steffen, Viktoria Nizhynska, Richard Mott, Martin A. Lysak, Richard M. Clark and Magnus Nordborg

    Citation: Genome Biology 2017 18:75

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  24. Content type: Research

    The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridipl...

    Authors: Adam J. Bewick, Chad E. Niederhuth, Lexiang Ji, Nicholas A. Rohr, Patrick T. Griffin, Jim Leebens-Mack and Robert J. Schmitz

    Citation: Genome Biology 2017 18:65

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  25. Content type: Research

    Artemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutatio...

    Authors: Gustavo C. Cerqueira, Ian H. Cheeseman, Steve F. Schaffner, Shalini Nair, Marina McDew-White, Aung Pyae Phyo, Elizabeth A. Ashley, Alexandre Melnikov, Peter Rogov, Bruce W. Birren, François Nosten, Timothy J. C. Anderson and Daniel E. Neafsey

    Citation: Genome Biology 2017 18:78

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  26. Content type: Research

    Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates ...

    Authors: Andrej Trauner, Qingyun Liu, Laura E. Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England…

    Citation: Genome Biology 2017 18:71

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  27. Content type: Q & A

    In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biol...

    Authors: Robert Lowe

    Citation: Genome Biology 2017 18:72

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  28. Content type: Research

    The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finni...

    Authors: Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J. Kangas, Pasi Soininen, Zeneng Wang, Mika Ala-Korpela, Stanley L. Hazen, Markku Laakso and Aldons J. Lusis

    Citation: Genome Biology 2017 18:70

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  29. Content type: Research

    Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recrui...

    Authors: Yue Zhou, Francisco J. Romero-Campero, Ángeles Gómez-Zambrano, Franziska Turck and Myriam Calonje

    Citation: Genome Biology 2017 18:69

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  30. Content type: Method

    Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methyl...

    Authors: Christof Angermueller, Heather J. Lee, Wolf Reik and Oliver Stegle

    Citation: Genome Biology 2017 18:67

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    The Erratum to this article has been published in Genome Biology 2017 18:90

  31. Content type: Research

    DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an un...

    Authors: Thomas M. Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, Ferdinand von Meyenn, Oliver Stegle and Wolf Reik

    Citation: Genome Biology 2017 18:68

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  32. Content type: Method

    Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues...

    Authors: Grace O. Silva, Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou and Mengjie Chen

    Citation: Genome Biology 2017 18:66

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