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  1. Content type: Research

    Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential sourc...

    Authors: Hadas Hezroni, Rotem Ben-Tov Perry, Zohar Meir, Gali Housman, Yoav Lubelsky and Igor Ulitsky

    Citation: Genome Biology 2017 18:162

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  2. Content type: Research

    Soybean (Glycine max [L.] Merr.) is one of the most important oil and protein crops. Ever-increasing soybean consumption necessitates the improvement of varieties for more efficient production. However, both corr...

    Authors: Chao Fang, Yanming Ma, Shiwen Wu, Zhi Liu, Zheng Wang, Rui Yang, Guanghui Hu, Zhengkui Zhou, Hong Yu, Min Zhang, Yi Pan, Guoan Zhou, Haixiang Ren, Weiguang Du, Hongrui Yan, Yanping Wang…

    Citation: Genome Biology 2017 18:161

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  3. Content type: Research

    As key regulators of gene expression in eukaryotes, small RNAs have been characterized in many seed plants, and pathways for their biogenesis, degradation, and action have been defined in model angiosperms. Ho...

    Authors: Chenjiang You, Jie Cui, Hui Wang, Xinping Qi, Li-Yaung Kuo, Hong Ma, Lei Gao, Beixin Mo and Xuemei Chen

    Citation: Genome Biology 2017 18:158

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  4. Content type: Research

    The merging of two diverged genomes can result in hybrid offspring that phenotypically differ greatly from both parents. In plants, interspecific hybridization plays important roles in evolution and speciation...

    Authors: Wangsheng Zhu, Bo Hu, Claude Becker, Ezgi Süheyla Doğan, Kenneth Wayne Berendzen, Detlef Weigel and Chang Liu

    Citation: Genome Biology 2017 18:157

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  5. Content type: Research

    Differences in DNA methylation can arise as epialleles, which are loci that differ in chromatin state and are inherited over generations. Epialleles offer an additional source of variation that can affect phen...

    Authors: Brigitte T. Hofmeister, Kevin Lee, Nicholas A. Rohr, David W. Hall and Robert J. Schmitz

    Citation: Genome Biology 2017 18:155

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  6. Content type: Research

    Identification of genes whose basal mRNA expression predicts the sensitivity of tumor cells to cytotoxic treatments can play an important role in individualized cancer medicine. It enables detailed characteriz...

    Authors: Amin Emad, Junmei Cairns, Krishna R. Kalari, Liewei Wang and Saurabh Sinha

    Citation: Genome Biology 2017 18:153

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  7. Content type: Method

    Deep mutational scanning is a widely used method for multiplex measurement of functional consequences of protein variants. We developed a new deep mutational scanning statistical model that generates error est...

    Authors: Alan F. Rubin, Hannah Gelman, Nathan Lucas, Sandra M. Bajjalieh, Anthony T. Papenfuss, Terence P. Speed and Douglas M. Fowler

    Citation: Genome Biology 2017 18:150

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    The Correction to this article has been published in Genome Biology 2018 19:17

  8. Content type: Method

    RNA sequencing studies with complex designs and transcript-resolution analyses involve multiple hypotheses per gene; however, conventional approaches fail to control the false discovery rate (FDR) at gene leve...

    Authors: Koen Van den Berge, Charlotte Soneson, Mark D. Robinson and Lieven Clement

    Citation: Genome Biology 2017 18:151

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  9. Content type: Research

    The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activat...

    Authors: Pierre J. Fabre, Marion Leleu, Benjamin H. Mormann, Lucille Lopez-Delisle, Daan Noordermeer, Leonardo Beccari and Denis Duboule

    Citation: Genome Biology 2017 18:149

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  10. Content type: Method

    Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTran...

    Authors: Nadia M. Davidson, Anthony D. K. Hawkins and Alicia Oshlack

    Citation: Genome Biology 2017 18:148

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    The Erratum to this article has been published in Genome Biology 2017 18:160

  11. Content type: Research

    Immunometabolism plays a central role in many cardiometabolic diseases. However, a robust map of immune-related gene networks in circulating human cells, their interactions with metabolites, and their genetic ...

    Authors: Artika P. Nath, Scott C. Ritchie, Sean G. Byars, Liam G. Fearnley, Aki S. Havulinna, Anni Joensuu, Antti J. Kangas, Pasi Soininen, Annika Wennerström, Lili Milani, Andres Metspalu, Satu Männistö, Peter Würtz, Johannes Kettunen, Emma Raitoharju, Mika Kähönen…

    Citation: Genome Biology 2017 18:146

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  12. Content type: Research

    Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate a...

    Authors: Qingjiao Li, Harianto Tjong, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo and Frank Alber

    Citation: Genome Biology 2017 18:145

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  13. Content type: Research

    Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations as...

    Authors: Nisha Patel, Arif O. Khan, Maher Al-Saif, Walid N. Moghrabi, Balsam M. AlMaarik, Niema Ibrahim, Firdous Abdulwahab, Mais Hashem, Tarfa Alshidi, Eman Alobeid, Rana A. Alomar, Saad Al-Harbi, Mohamed Abouelhoda, Khalid S. A. Khabar and Fowzan S. Alkuraya

    Citation: Genome Biology 2017 18:144

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  14. Content type: Research

    A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism f...

    Authors: Eddie Park, Jiguang Guo, Shihao Shen, Levon Demirdjian, Ying Nian Wu, Lan Lin and Yi Xing

    Citation: Genome Biology 2017 18:143

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  15. Content type: Method

    Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequen...

    Authors: Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp and Sohrab P. Shah

    Citation: Genome Biology 2017 18:140

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    The Correction to this article has been published in Genome Biology 2017 18:188

  16. Content type: Research

    The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence show...

    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 18:142

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    The Correction to this article has been published in Genome Biology 2017 18:214

  17. Content type: Method

    We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation ch...

    Authors: Priyanka Dhingra, Alexander Martinez-Fundichely, Adeline Berger, Franklin W. Huang, Andre Neil Forbes, Eric Minwei Liu, Deli Liu, Andrea Sboner, Pablo Tamayo, David S. Rickman, Mark A. Rubin and Ekta Khurana

    Citation: Genome Biology 2017 18:141

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  18. Content type: Research

    Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are charact...

    Authors: Gahee Park, Joo Kyung Park, Seung-Ho Shin, Hyo-Jeong Jeon, Nayoung K. D. Kim, Yeon Jeong Kim, Hyun-Tae Shin, Eunjin Lee, Kwang Hyuck Lee, Dae-Soon Son, Woong-Yang Park and Donghyun Park

    Citation: Genome Biology 2017 18:136

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  19. Content type: Research

    While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part,...

    Authors: Rurika Oka, Johan Zicola, Blaise Weber, Sarah N. Anderson, Charlie Hodgman, Jonathan I. Gent, Jan-Jaap Wesselink, Nathan M. Springer, Huub C. J. Hoefsloot, Franziska Turck and Maike Stam

    Citation: Genome Biology 2017 18:137

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  20. Content type: Research

    The spread of drug-resistant bacterial pathogens poses a major threat to global health. It is widely recognised that the widespread use of antibiotics has generated selective pressures that have driven the eme...

    Authors: Catriona P. Harkins, Bruno Pichon, Michel Doumith, Julian Parkhill, Henrik Westh, Alexander Tomasz, Herminia de Lencastre, Stephen D. Bentley, Angela M. Kearns and Matthew T. G. Holden

    Citation: Genome Biology 2017 18:130

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  21. Content type: Research

    Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanism...

    Authors: Michael Thieme, Sophie Lanciano, Sandrine Balzergue, Nicolas Daccord, Marie Mirouze and Etienne Bucher

    Citation: Genome Biology 2017 18:134

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  22. Content type: Research

    Microbial-associated molecular patterns activate several MAP kinases, which are major regulators of the innate immune response in Arabidopsis thaliana that induce large-scale changes in gene expression. Here, we ...

    Authors: David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling…

    Citation: Genome Biology 2017 18:131

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  23. Content type: Correspondence

    Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Bio...

    Authors: Siyuan Zheng

    Citation: Genome Biology 2017 18:129

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  24. Content type: Correspondence

    In a recently published article in Genome Biology, Li and colleagues introduced TIMER, a gene expression deconvolution approach for studying tumor-infiltrating leukocytes (TILs) in 23 cancer types profiled by The...

    Authors: Aaron M. Newman, Andrew J. Gentles, Chih Long Liu, Maximilian Diehn and Ash A. Alizadeh

    Citation: Genome Biology 2017 18:128

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  25. Content type: Research

    The mapping resolution of genome-wide association studies (GWAS) is limited by historic recombination events and effects are often assigned to haplotype blocks rather than individual SNPs. It is not clear how ...

    Authors: Jean-Michel Gibert, Jorge Blanco, Marlies Dolezal, Viola Nolte, Frédérique Peronnet and Christian Schlötterer

    Citation: Genome Biology 2017 18:126

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  26. Content type: Method

    Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell...

    Authors: V. K. Chaithanya Ponnaluri, Guoqiang Zhang, Pierre-Olivier Estève, George Spracklin, Stephanie Sian, Shuang-yong Xu, Touati Benoukraf and Sriharsa Pradhan

    Citation: Genome Biology 2017 18:122

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  27. Content type: Method

    Chromosomal rearrangements occur constitutionally in the general population and somatically in the majority of cancers. Detection of balanced rearrangements, such as reciprocal translocations and inversions, i...

    Authors: Louise Harewood, Kamal Kishore, Matthew D. Eldridge, Steven Wingett, Danita Pearson, Stefan Schoenfelder, V. Peter Collins and Peter Fraser

    Citation: Genome Biology 2017 18:125

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  28. Content type: Research

    Paradoxically, centromeres are known both for their characteristic repeat sequences (satellite DNA) and for being epigenetically defined. Maize (Zea mays mays) is an attractive model for studying centromere posit...

    Authors: Jonathan I. Gent, Na Wang and R. Kelly Dawe

    Citation: Genome Biology 2017 18:121

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  29. Content type: Review

    Studies on genetic–epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in ...

    Authors: Catherine Do, Alyssa Shearer, Masako Suzuki, Mary Beth Terry, Joel Gelernter, John M. Greally and Benjamin Tycko

    Citation: Genome Biology 2017 18:120

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  30. Content type: Research Highlight

    Epigenetic profiling in diploid, allopolyploid, and domesticated cotton shows that despite most DNA methylation being conserved and stably inherited, alterations likely due to hybridization and domestication a...

    Authors: Scott A. Jackson

    Citation: Genome Biology 2017 18:117

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  31. Content type: Research

    The daily gene expression oscillations that underlie mammalian circadian rhythms show striking differences between tissues and involve post-transcriptional regulation. Both aspects remain poorly understood. We...

    Authors: Violeta Castelo-Szekely, Alaaddin Bulak Arpat, Peggy Janich and David Gatfield

    Citation: Genome Biology 2017 18:116

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  32. 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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  33. Content type: Research

    Post-transcriptional regulation of gene expression can be achieved through the control of mRNA stability, cytoplasmic compartmentalization, 3′ UTR length and translational efficacy. Spermiogenesis, a process t...

    Authors: Ying Zhang, Chong Tang, Tian Yu, Ruirui Zhang, Huili Zheng and Wei Yan

    Citation: Genome Biology 2017 18:105

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