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  1. Content type: Method

    We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for s...

    Authors: Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma and Caroline Gubser Keller

    Citation: Genome Biology 2019 20:142

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  2. Content type: Research

    The long introns of mammals are pools of evolutionary potential due to the multiplicity of sequences that permit the acquisition of novel exons. However, the permissibility of genes to this type of acquisition...

    Authors: Nesli Avgan, Juli I. Wang, Javier Fernandez-Chamorro and Robert J. Weatheritt

    Citation: Genome Biology 2019 20:141

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  3. Content type: Research

    Despite continual progress in the identification and characterization of trait- and disease-associated variants that disrupt transcription factor (TF)-DNA binding, little is known about the distribution of TF ...

    Authors: Shan Li, Evgeny Z. Kvon, Axel Visel, Len A. Pennacchio and Ivan Ovcharenko

    Citation: Genome Biology 2019 20:140

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  4. Content type: Research

    Bread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regul...

    Authors: Zijuan Li, Meiyue Wang, Kande Lin, Yilin Xie, Jingyu Guo, Luhuan Ye, Yili Zhuang, Wan Teng, Xiaojuan Ran, Yiping Tong, Yongbiao Xue, Wenli Zhang and Yijing Zhang

    Citation: Genome Biology 2019 20:139

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  5. Content type: Method

    Methylation datasets are affected by innumerable sources of variability, both biological (cell-type composition, genetics) and technical (batch effects). Here, we propose a reference-free method based on spars...

    Authors: Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani and Eran Halperin

    Citation: Genome Biology 2019 20:138

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  6. Content type: Method

    Systems for CRISPR-based combinatorial perturbation of two or more genes are emerging as powerful tools for uncovering genetic interactions. However, systematic identification of these relationships is complic...

    Authors: Mahdi Zamanighomi, Sidharth S. Jain, Takahiro Ito, Debjani Pal, Timothy P. Daley and William R. Sellers

    Citation: Genome Biology 2019 20:137

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  7. Content type: Research

    Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domes...

    Authors: Hong Cheng, Jing Liu, Jia Wen, Xiaojun Nie, Luohao Xu, Ningbo Chen, Zhongxing Li, Qilin Wang, Zhuqing Zheng, Ming Li, Licao Cui, Zihua Liu, Jianxin Bian, Zhonghua Wang, Shengbao Xu, Qin Yang…

    Citation: Genome Biology 2019 20:136

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  8. Content type: Research

    The importance of cell type-specific epigenetic variation of non-coding regions in neuropsychiatric disorders is increasingly appreciated, yet data from disease brains are conspicuously lacking. We generate ce...

    Authors: Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka and Soojin V. Yi

    Citation: Genome Biology 2019 20:135

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  9. Content type: Method

    We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules. Applying SMURF-seq using the Oxford Nanopore MinION yield...

    Authors: Rishvanth K. Prabakar, Liya Xu, James Hicks and Andrew D. Smith

    Citation: Genome Biology 2019 20:134

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  10. Content type: Research

    Genome-wide association studies (GWAS) have identified hundreds of loci associated with coronary artery disease (CAD) and blood pressure (BP) or hypertension. Many of these loci are not linked to traditional r...

    Authors: Simon Lalonde, Valérie-Anne Codina-Fauteux, Sébastian Méric de Bellefon, Francis Leblanc, Mélissa Beaudoin, Marie-Michelle Simon, Rola Dali, Tony Kwan, Ken Sin Lo, Tomi Pastinen and Guillaume Lettre

    Citation: Genome Biology 2019 20:133

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  11. Content type: Short Report

    CRISPR-based nucleic acid detection methods are reported to facilitate rapid and sensitive DNA detection. However, precise DNA detection at the single-base resolution and its wide applications including high-f...

    Authors: Fei Teng, Lu Guo, Tongtong Cui, Xin-Ge Wang, Kai Xu, Qingqin Gao, Qi Zhou and Wei Li

    Citation: Genome Biology 2019 20:132

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  12. Content type: Research

    For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the met...

    Authors: Céline Duc, Marianne Yoth, Silke Jensen, Nolwenn Mouniée, Casey M. Bergman, Chantal Vaury and Emilie Brasset

    Citation: Genome Biology 2019 20:127

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  13. Content type: Research

    Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary m...

    Authors: Baosheng Wang, Julius P. Mojica, Nadeesha Perera, Cheng-Ruei Lee, John T. Lovell, Aditi Sharma, Catherine Adam, Anna Lipzen, Kerrie Barry, Daniel S. Rokhsar, Jeremy Schmutz and Thomas Mitchell-Olds

    Citation: Genome Biology 2019 20:126

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  14. Content type: Review

    In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare th...

    Authors: Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul P. Gardner, Anne-Laure Boulesteix, Yvan Saeys and Mark D. Robinson

    Citation: Genome Biology 2019 20:125

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  15. Content type: Correction

    Following publication of the original article [1], the authors reported the following error in the name of the fourth author.

    Authors: Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh T. Ghanbarian, Guillem Portella and Shankar Balasubramanian

    Citation: Genome Biology 2019 20:124

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    The original article was published in Genome Biology 2018 19:229

  16. Content type: Research

    Cold stress can greatly affect plant growth and development. Plants have developed special systems to respond to and tolerate cold stress. While plant scientists have discovered numerous genes involved in resp...

    Authors: Zixian Zeng, Wenli Zhang, Alexandre P. Marand, Bo Zhu, C. Robin Buell and Jiming Jiang

    Citation: Genome Biology 2019 20:123

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  17. Content type: Correction

    Following publication of the original article [1], the authors reported that Figs. 4 and 5 had mistakenly been transposed. Please find the correct Figs. 4 and 5 below. The original article [1] has been corrected.

    Authors: Andrew N. Holding, Federico M. Giorgi, Amanda Donnelly, Amy E. Cullen, Sankari Nagarajan, Luke A. Selth and Florian Markowetz

    Citation: Genome Biology 2019 20:122

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    The original article was published in Genome Biology 2019 20:91

  18. Content type: Review

    Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-...

    Authors: Changdai Gu, Gi Bae Kim, Won Jun Kim, Hyun Uk Kim and Sang Yup Lee

    Citation: Genome Biology 2019 20:121

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  19. Content type: Research

    The uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias in regulating cell state-specific expression ...

    Authors: Susanne Bornelöv, Tommaso Selmi, Sophia Flad, Sabine Dietmann and Michaela Frye

    Citation: Genome Biology 2019 20:119

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  20. Content type: Research

    In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error rate co...

    Authors: Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm and Stephanie C. Hicks

    Citation: Genome Biology 2019 20:118

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  21. Content type: Research

    Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV det...

    Authors: Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo and Yoichiro Kamatani

    Citation: Genome Biology 2019 20:117

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  22. Content type: Method

    Current genotyping approaches for single-nucleotide variations rely on short, accurate reads from second-generation sequencing devices. Presently, third-generation sequencing platforms are rapidly becoming mor...

    Authors: Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall and Benedict Paten

    Citation: Genome Biology 2019 20:116

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  23. Content type: Research

    Genes are comprised of DNA codes and contain promoters and other control elements for reading these codes. The rapid development of clustered regularly interspaced short palindromic repeats (CRISPR) technology...

    Authors: Hengji Zhan, Qun Zhou, Qunjun Gao, Jianfa Li, Weiren Huang and Yuchen Liu

    Citation: Genome Biology 2019 20:113

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  24. Content type: Opinion

    Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference tra...

    Authors: Antonin Morillon and Daniel Gautheret

    Citation: Genome Biology 2019 20:112

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  25. Content type: Research

    DNA methylation is thought to be an important determinant of human phenotypic variation, but its inherent cell type specificity has impeded progress on this question. At exceptional genomic regions, interindiv...

    Authors: Chathura J. Gunasekara, C. Anthony Scott, Eleonora Laritsky, Maria S. Baker, Harry MacKay, Jack D. Duryea, Noah J. Kessler, Garrett Hellenthal, Alexis C. Wood, Kelly R. Hodges, Manisha Gandhi, Amy B. Hair, Matt J. Silver, Sophie E. Moore, Andrew M. Prentice, Yumei Li…

    Citation: Genome Biology 2019 20:105

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  26. Content type: Opinion

    Data science allows the extraction of practical insights from large-scale data. Here, we contextualize it as an umbrella term, encompassing several disparate subdomains. We focus on how genomics fits as a spec...

    Authors: Fábio C. P. Navarro, Hussein Mohsen, Chengfei Yan, Shantao Li, Mengting Gu, William Meyerson and Mark Gerstein

    Citation: Genome Biology 2019 20:109

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  27. Content type: Method

    The rapid increase of omic data has greatly facilitated the investigation of associations between omic profiles such as DNA methylation (DNAm) and complex traits in large cohorts. Here, we propose a mixed-line...

    Authors: Futao Zhang, Wenhan Chen, Zhihong Zhu, Qian Zhang, Marta F. Nabais, Ting Qi, Ian J. Deary, Naomi R. Wray, Peter M. Visscher, Allan F. McRae and Jian Yang

    Citation: Genome Biology 2019 20:107

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  28. Content type: Method

    The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) t...

    Authors: Laurent Gentzbittel, Cécile Ben, Mélanie Mazurier, Min-Gyoung Shin, Todd Lorenz, Martina Rickauer, Paul Marjoram, Sergey V. Nuzhdin and Tatiana V. Tatarinova

    Citation: Genome Biology 2019 20:106

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  29. Content type: Research Highlight

    A recent study on human structural variation indicates insufficiencies and errors in the human reference genome, GRCh38, and argues for the construction of a human pan-genome.

    Authors: Xiaofei Yang, Wan-Ping Lee, Kai Ye and Charles Lee

    Citation: Genome Biology 2019 20:104

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  30. Content type: Research

    Inherited factors contribute to lung cancer risk, but the mechanism is not well understood. Defining the biological consequence of GWAS hits in cancers is a promising strategy to elucidate the inherited mechan...

    Authors: Lipei Shao, Xianglin Zuo, Yin Yang, Yu Zhang, Nan Yang, Bin Shen, Jianying Wang, Xuchun Wang, Ruilei Li, Guangfu Jin, Dawei Yu, Yuan Chen, Luan Sun, Zhen Li, Qiaofen Fu, Zhibin Hu…

    Citation: Genome Biology 2019 20:103

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  31. Content type: Method

    Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin l...

    Authors: Yousra Ben Zouari, Anne M. Molitor, Natalia Sikorska, Vera Pancaldi and Tom Sexton

    Citation: Genome Biology 2019 20:102

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  32. Content type: Short Report

    Base editing installs a precise nucleotide change in specific gene loci without causing a double-strand break. Its efficiency in human embryos is generally low, limiting its utility in functional genetic studi...

    Authors: Meiling Zhang, Changyang Zhou, Yu Wei, Chunlong Xu, Hong Pan, Wenqin Ying, Yidi Sun, Yun Sun, Qingquan Xiao, Ning Yao, Wanxia Zhong, Yun Li, Keliang Wu, Gao Yuan, Shoukhrat Mitalipov, Zi-jiang Chen…

    Citation: Genome Biology 2019 20:101

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  33. Content type: Research

    The functional determinants of H3K4me3, their potential dependency on histone H2B monoubiquitination, and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in Sacc...

    Authors: Anne-Sophie Fiorucci, Clara Bourbousse, Lorenzo Concia, Martin Rougée, Anne-Flore Deton-Cabanillas, Gérald Zabulon, Elodie Layat, David Latrasse, Soon Kap Kim, Nicole Chaumont, Bérangère Lombard, David Stroebel, Sophie Lemoine, Ammara Mohammad, Corinne Blugeon, Damarys Loew…

    Citation: Genome Biology 2019 20:100

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  34. Content type: Research

    Circular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypi...

    Authors: Zelin Liu, Yuan Ran, Changyu Tao, Sichen Li, Jian Chen and Ence Yang

    Citation: Genome Biology 2019 20:99

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  35. Content type: Research

    The human genome contains “dark” gene regions that cannot be adequately assembled or aligned using standard short-read sequencing technologies, preventing researchers from identifying mutations within these ge...

    Authors: Mark T. W. Ebbert, Tanner D. Jensen, Karen Jansen-West, Jonathon P. Sens, Joseph S. Reddy, Perry G. Ridge, John S. K. Kauwe, Veronique Belzil, Luc Pregent, Minerva M. Carrasquillo, Dirk Keene, Eric Larson, Paul Crane, Yan W. Asmann, Nilufer Ertekin-Taner, Steven G. Younkin…

    Citation: Genome Biology 2019 20:97

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  36. Content type: Research

    The diversity and evolutionary success of beetles (Coleoptera) are proposed to be related to the diversity of plants on which they feed. Indeed, the largest beetle suborder, Polyphaga, mostly includes plant ea...

    Authors: Mathieu Seppey, Panagiotis Ioannidis, Brent C. Emerson, Camille Pitteloud, Marc Robinson-Rechavi, Julien Roux, Hermes E. Escalona, Duane D. McKenna, Bernhard Misof, Seunggwan Shin, Xin Zhou, Robert M. Waterhouse and Nadir Alvarez

    Citation: Genome Biology 2019 20:98

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  37. Content type: Short Report

    Whole metagenome shotgun (WMGS) sequencing is a method that provides insights into the genomic composition and arrangement of complex microbial consortia. Here, we report how WMGS coupled with a cultivation ap...

    Authors: Gabriele Andrea Lugli, Christian Milani, Sabrina Duranti, Giulia Alessandri, Francesca Turroni, Leonardo Mancabelli, Danilo Tatoni, Maria Cristina Ossiprandi, Douwe van Sinderen and Marco Ventura

    Citation: Genome Biology 2019 20:96

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  38. Content type: Short Report

    Gene co-expression networks capture biological relationships between genes and are important tools in predicting gene function and understanding disease mechanisms. We show that technical and biological artifa...

    Authors: Princy Parsana, Claire Ruberman, Andrew E. Jaffe, Michael C. Schatz, Alexis Battle and Jeffrey T. Leek

    Citation: Genome Biology 2019 20:94

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