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  1. Content type: Method

    To fully utilize the power of single-cell RNA sequencing (scRNA-seq) technologies for identifying cell lineages and bona fide transcriptional signals, it is necessary to combine data from multiple experiments....

    Authors: Tongxin Wang, Travis S. Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang and Kun Huang

    Citation: Genome Biology 2019 20:165

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  2. Content type: Research

    Like many bacteria, Vibrio cholerae deploys a harpoon-like type VI secretion system (T6SS) to compete against other microbes in environmental and host settings. The T6SS punctures adjacent cells and delivers toxi...

    Authors: Cristian V. Crisan, Aroon T. Chande, Kenneth Williams, Vishnu Raghuram, Lavanya Rishishwar, Gabi Steinbach, Samit S. Watve, Peter Yunker, I. King Jordan and Brian K. Hammer

    Citation: Genome Biology 2019 20:163

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  3. Content type: Correction

    Following publication of the original article [1], the authors reported that the Availability of data and materials section required updating. The updated text reads as follows:

    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 20:161

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    The original article was published in Genome Biology 2019 20:126

  4. Content type: Correction

    Following publication of the original article [1], the following error was reported: The actin control panel in Fig. 3 of this paper is reproduced from Fig. 7 of Touré et al, 2004 [2] by kind permission of the...

    Authors: Aminata Touré, Emily J. Clemente, Peter J. I. Ellis, Shantha K. Mahadevaiah, Obah A. Ojarikre, Penny A. F. Ball, Louise Reynard, Kate L. Loveland, Paul S. Burgoyne and Nabeel A. Affara

    Citation: Genome Biology 2019 20:160

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    The original article was published in Genome Biology 2005 6:R102

  5. Content type: Opinion

    The use of the human reference genome has shaped methods and data across modern genomics. This has offered many benefits while creating a few constraints. In the following opinion, we outline the history, prop...

    Authors: Sara Ballouz, Alexander Dobin and Jesse A. Gillis

    Citation: Genome Biology 2019 20:159

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  6. Content type: Research

    Chromatin provides a tunable platform for gene expression control. Besides the well-studied core nucleosome, H1 linker histones are abundant chromatin components with intrinsic potential to influence chromatin...

    Authors: Kinga Rutowicz, Maciej Lirski, Benoît Mermaz, Gianluca Teano, Jasmin Schubert, Imen Mestiri, Magdalena A. Kroteń, Tohnyui Ndinyanka Fabrice, Simon Fritz, Stefan Grob, Christoph Ringli, Lusik Cherkezyan, Fredy Barneche, Andrzej Jerzmanowski and Célia Baroux

    Citation: Genome Biology 2019 20:157

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  7. Content type: Method

    We describe a highly sensitive, quantitative, and inexpensive technique for targeted sequencing of transcript cohorts or genomic regions from thousands of bulk samples or single cells in parallel. Multiplexing...

    Authors: Fatma Uzbas, Florian Opperer, Can Sönmezer, Dmitry Shaposhnikov, Steffen Sass, Christian Krendl, Philipp Angerer, Fabian J. Theis, Nikola S. Mueller and Micha Drukker

    Citation: Genome Biology 2019 20:155

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  8. Content type: Method

    We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read ...

    Authors: Derek M. Bickhart, Mick Watson, Sergey Koren, Kevin Panke-Buisse, Laura M. Cersosimo, Maximilian O. Press, Curtis P. Van Tassell, Jo Ann S. Van Kessel, Bradd J. Haley, Seon Woo Kim, Cheryl Heiner, Garret Suen, Kiranmayee Bakshy, Ivan Liachko, Shawn T. Sullivan, Phillip R. Myer…

    Citation: Genome Biology 2019 20:153

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  9. Content type: Correspondence

    Jacob and Speed did not identify even a single example of a ‘150-gene-set’ that was statistically significant at classifying Alzheimer’s disease (AD) samples, or age in independent studies. We attempt to clari...

    Authors: James A. Timmons, Iain J. Gallagher, Sanjana Sood, Bethan Phillips, Hannah Crossland, Robert Howard, William E. Kraus and Philip J. Atherton

    Citation: Genome Biology 2019 20:152

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    The Research to this article has been published in Genome Biology 2015 16:185

  10. Content type: Research

    In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life c...

    Authors: Lee M. Yeoh, Christopher D. Goodman, Vanessa Mollard, Emma McHugh, V. Vern Lee, Angelika Sturm, Anton Cozijnsen, Geoffrey I. McFadden and Stuart A. Ralph

    Citation: Genome Biology 2019 20:151

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  11. Content type: Method

    The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPA...

    Authors: Zhongqu Duan, Yuyang Qiao, Jinyuan Lu, Huimin Lu, Wenmin Zhang, Fazhe Yan, Chen Sun, Zhiqiang Hu, Zhen Zhang, Guichao Li, Hongzhuan Chen, Zhen Xiang, Zhenggang Zhu, Hongyu Zhao, Yingyan Yu and Chaochun Wei

    Citation: Genome Biology 2019 20:149

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  12. Content type: Research

    The number of reported examples of chromatin architecture alterations involved in the regulation of gene transcription and in disease is increasing. However, no genome-wide testing has been performed to assess...

    Authors: Michal Sadowski, Agnieszka Kraft, Przemyslaw Szalaj, Michal Wlasnowolski, Zhonghui Tang, Yijun Ruan and Dariusz Plewczynski

    Citation: Genome Biology 2019 20:148

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    The Correction to this article has been published in Genome Biology 2019 20:188

  13. Content type: Method

    The CRISPR/Cas9 system is unable to edit all targetable genomic sites with full efficiency in vivo. We show that Cas9-mediated editing is more efficient in open chromatin regions than in closed chromatin regio...

    Authors: Guanwen Liu, Kangquan Yin, Qianwei Zhang, Caixia Gao and Jin-Long Qiu

    Citation: Genome Biology 2019 20:145

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  14. Content type: Research

    Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined be...

    Authors: Andrzej Zielezinski, Hani Z. Girgis, Guillaume Bernard, Chris-Andre Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S. Waterman, Matteo Comin, Sung-Hou Kim, Susana Vinga, Jonas S. Almeida, Cheong Xin Chan, Benjamin T. James…

    Citation: Genome Biology 2019 20:144

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  15. Content type: Method

    While genetic relatedness, usually manifested as segments identical by descent (IBD), is ubiquitous in modern large biobanks, current IBD detection methods are not efficient at such a scale. Here, we describe ...

    Authors: Ardalan Naseri, Xiaoming Liu, Kecong Tang, Shaojie Zhang and Degui Zhi

    Citation: Genome Biology 2019 20:143

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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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    The Correction to this article has been published in Genome Biology 2019 20:161

  29. 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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  30. 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

  31. 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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  32. 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

  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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