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  1. Content type: Research

    Diverse molecular alterations associated with smoking in normal and precursor lung cancer cells have been reported, yet their role in lung cancer etiology remains unclear. A prominent example is hypomethylatio...

    Authors: Yuting Chen, Martin Widschwendter and Andrew E. Teschendorff

    Citation: Genome Biology 2017 18:236

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  2. Content type: Software

    The increase in available sequence data has advanced the field of microbiology; however, making sense of these data without bioinformatics skills is still problematic. We describe MICRA, an automatic pipeline,...

    Authors: Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert and David Hot

    Citation: Genome Biology 2017 18:233

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  3. Content type: Research Highlight

    Balancing selection maintains variation for evolution. A recent study investigated the extent of balancing selection in two Brassicaceae species and highlighted its importance for adaptation.

    Authors: Baosheng Wang and Thomas Mitchell-Olds

    Citation: Genome Biology 2017 18:231

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  4. Content type: Method

    We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, a...

    Authors: Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu…

    Citation: Genome Biology 2017 18:230

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  5. Content type: Review

    Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the res...

    Authors: Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan and Curtis Huttenhower

    Citation: Genome Biology 2017 18:228

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  6. Content type: Research

    The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an en...

    Authors: Erwei Zuo, Xiaona Huo, Xuan Yao, Xinde Hu, Yidi Sun, Jianhang Yin, Bingbing He, Xing Wang, Linyu Shi, Jie Ping, Yu Wei, Wenqin Ying, Wei Wei, Wenjia Liu, Cheng Tang, Yixue Li…

    Citation: Genome Biology 2017 18:224

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  7. Content type: Comment

    The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by ...

    Authors: Itai Yanai and Eva Chmielnicki

    Citation: Genome Biology 2017 18:223

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  8. Content type: Research

    Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, be...

    Authors: Yuwen Liu, Shan Yu, Vineet K. Dhiman, Tonya Brunetti, Heather Eckart and Kevin P. White

    Citation: Genome Biology 2017 18:219

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  9. Content type: Research

    Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution...

    Authors: Stefan M. Berger, Iván Fernández-Lamo, Kai Schönig, Sandra M. Fernández Moya, Janina Ehses, Rico Schieweck, Stefano Clementi, Thomas Enkel, Sascha Grothe, Oliver von Bohlen und Halbach, Inmaculada Segura, José María Delgado-García, Agnès Gruart, Michael A. Kiebler and Dusan Bartsch

    Citation: Genome Biology 2017 18:222

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  10. Content type: Research

    While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of ...

    Authors: Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J. Lieschke, Justin J-L Wong and John E. J. Rasko

    Citation: Genome Biology 2017 18:216

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  11. Content type: Research

    In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adapta...

    Authors: Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu and Ya-Long Guo

    Citation: Genome Biology 2017 18:217

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  12. Content type: Comment

    Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it i...

    Authors: Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann…

    Citation: Genome Biology 2017 18:221

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  13. Content type: Research

    The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay be...

    Authors: Li Wang, Timothy M. Beissinger, Anne Lorant, Claudia Ross-Ibarra, Jeffrey Ross-Ibarra and Matthew B. Hufford

    Citation: Genome Biology 2017 18:215

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  14. Content type: Correction

    Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.

    Authors: Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai…

    Citation: Genome Biology 2017 18:214

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    The original article was published in Genome Biology 2017 18:142

  15. Content type: Method

    Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing source...

    Authors: Florian Buettner, Naruemon Pratanwanich, Davis J. McCarthy, John C. Marioni and Oliver Stegle

    Citation: Genome Biology 2017 18:212

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  16. Content type: Research

    Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-r...

    Authors: Seungill Kim, Jieun Park, Seon-In Yeom, Yong-Min Kim, Eunyoung Seo, Ki-Tae Kim, Myung-Shin Kim, Je Min Lee, Kyeongchae Cheong, Ho-Sub Shin, Saet-Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyun-Ah Lee, Hye-Young Lee…

    Citation: Genome Biology 2017 18:210

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  17. Content type: Review

    A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (ln...

    Authors: Francesco P. Marchese, Ivan Raimondi and Maite Huarte

    Citation: Genome Biology 2017 18:206

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  18. Content type: Research

    Herpesviruses can infect a wide range of animal species. Herpes simplex virus 1 (HSV-1) is one of the eight herpesviruses that can infect humans and is prevalent worldwide. Herpesviruses have evolved multiple ...

    Authors: Emanuel Wyler, Jennifer Menegatti, Vedran Franke, Christine Kocks, Anastasiya Boltengagen, Thomas Hennig, Kathrin Theil, Andrzej Rutkowski, Carmelo Ferrai, Laura Baer, Lisa Kermas, Caroline Friedel, Nikolaus Rajewsky, Altuna Akalin, Lars Dölken, Friedrich Grässer…

    Citation: Genome Biology 2017 18:209

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  19. Content type: Research

    Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of their in vivo binding targets and binding land...

    Authors: Katja Meyer, Tino Köster, Christine Nolte, Claus Weinholdt, Martin Lewinski, Ivo Grosse and Dorothee Staiger

    Citation: Genome Biology 2017 18:204

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  20. Content type: Research

    Polycomb Repressive Complexes 2 (PRC2) are multi-protein chromatin modifiers that are evolutionarily conserved among eukaryotes and play key roles in the regulation of gene expression, notably through the trim...

    Authors: Claudia Chica, Alexandra Louis, Hugues Roest Crollius, Vincent Colot and François Roudier

    Citation: Genome Biology 2017 18:207

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  21. Content type: Research

    All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, ...

    Authors: Olivia S. Rissland, Alexander O. Subtelny, Miranda Wang, Andrew Lugowski, Beth Nicholson, John D. Laver, Sachdev S. Sidhu, Craig A. Smibert, Howard D. Lipshitz and David P. Bartel

    Citation: Genome Biology 2017 18:211

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  22. Content type: Research

    Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few...

    Authors: Alexandre P. Marand, Shelley H. Jansky, Hainan Zhao, Courtney P. Leisner, Xiaobiao Zhu, Zixian Zeng, Emily Crisovan, Linsey Newton, Andy J. Hamernik, Richard E. Veilleux, C. Robin Buell and Jiming Jiang

    Citation: Genome Biology 2017 18:203

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  23. Content type: Research

    Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of protein variants or to the regulation of gene expression via nonsense-mediated messenger RNA (mRNA) dec...

    Authors: Baptiste Saudemont, Alexandra Popa, Joanna L. Parmley, Vincent Rocher, Corinne Blugeon, Anamaria Necsulea, Eric Meyer and Laurent Duret

    Citation: Genome Biology 2017 18:208

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  24. Content type: Research

    Translation factors eIF4E and eIF4G form eIF4F, which interacts with the messenger RNA (mRNA) 5′ cap to promote ribosome recruitment and translation initiation. Variations in the association of eIF4F with indi...

    Authors: Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Christopher M. Grant, Simon J. Hubbard and Graham D. Pavitt

    Citation: Genome Biology 2017 18:201

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  25. Content type: Research

    It is now obvious that the majority of cellular transcripts do not code for proteins, and a significant subset of them are long non-coding RNAs (lncRNAs). Many lncRNAs show aberrant expression in cancer, and s...

    Authors: Oskar Marín-Béjar, Aina M. Mas, Jovanna González, Dannys Martinez, Alejandro Athie, Xabier Morales, Mikel Galduroz, Ivan Raimondi, Elena Grossi, Shuling Guo, Ana Rouzaut, Igor Ulitsky and Maite Huarte

    Citation: Genome Biology 2017 18:202

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  26. Content type: Method

    The interaction between a pathogen and a host is a highly dynamic process in which both agents activate complex programs. Here, we introduce a single-cell RNA-sequencing method, scDual-Seq, that simultaneously...

    Authors: Gal Avital, Roi Avraham, Amy Fan, Tamar Hashimshony, Deborah T. Hung and Itai Yanai

    Citation: Genome Biology 2017 18:200

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  27. Content type: Method

    Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning a...

    Authors: Dina Hafez, Aslihan Karabacak, Sabrina Krueger, Yih-Chii Hwang, Li-San Wang, Robert P. Zinzen and Uwe Ohler

    Citation: Genome Biology 2017 18:199

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  28. Content type: Research

    Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates. A relatively recent vertebrate genome duplication is that in Xenopus laevis, which resulted fr...

    Authors: Dei M. Elurbe, Sarita S. Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Ozren Bogdanovic, Romain Gibeaux, Rebecca Heald, Ryan Lister, Martijn A. Huynen, Simon J. van Heeringen and Gert Jan C. Veenstra

    Citation: Genome Biology 2017 18:198

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  29. Content type: Review

    RNA contains over 150 types of chemical modifications. Although many of these chemical modifications were discovered several decades ago, their functions were not immediately apparent. Discoveries of RNA demet...

    Authors: Phillip J. Hsu, Hailing Shi and Chuan He

    Citation: Genome Biology 2017 18:197

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  30. Content type: Research

    Most cancer risk-associated single nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) are noncoding and it is challenging to assess their functional impacts. To systematically...

    Authors: Song Liu, Yuwen Liu, Qin Zhang, Jiayu Wu, Junbo Liang, Shan Yu, Gong-Hong Wei, Kevin P. White and Xiaoyue Wang

    Citation: Genome Biology 2017 18:194

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  31. Content type: Research Highlight

    Concentration is important and not only while driving; a new study indicates how an adjacent genomic element helps to increase the efficiency of a specific adenosine to inosine RNA editing reaction, by providi...

    Authors: Miri Danan-Gotthold and Erez Y. Levanon

    Citation: Genome Biology 2017 18:196

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  32. Content type: Research

    Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, ...

    Authors: Yaping Liu, Abhishek Sarkar, Pouya Kheradpour, Jason Ernst and Manolis Kellis

    Citation: Genome Biology 2017 18:193

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  33. Content type: Research

    There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits.

    Authors: Hung-ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J. Scanlon, Dan Nettleton and Patrick S. Schnable

    Citation: Genome Biology 2017 18:192

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  34. Content type: Method

    High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of S...

    Authors: Dingbo Zhang, Huawei Zhang, Tingdong Li, Kunling Chen, Jin-Long Qiu and Caixia Gao

    Citation: Genome Biology 2017 18:191

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  35. Content type: Research

    The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of...

    Authors: Péter István Kulcsár, András Tálas, Krisztina Huszár, Zoltán Ligeti, Eszter Tóth, Nóra Weinhardt, Elfrieda Fodor and Ervin Welker

    Citation: Genome Biology 2017 18:190

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  36. Content type: Research

    The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene r...

    Authors: Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A. Nyman…

    Citation: Genome Biology 2017 18:189

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  37. Content type: Review

    Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of ...

    Authors: Andrzej Zielezinski, Susana Vinga, Jonas Almeida and Wojciech M. Karlowski

    Citation: Genome Biology 2017 18:186

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  38. Content type: Research

    Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by the ADAR (adenosine deaminase that acts on RNA) enzymes, which are ubiquitously expressed among metazoans. Technica...

    Authors: Hagit T. Porath, Binyamin A. Knisbacher, Eli Eisenberg and Erez Y. Levanon

    Citation: Genome Biology 2017 18:185

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