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  1. Content type: Research

    Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid ...

    Authors: A. P. Lipinska, M. L. Serrano-Serrano, A. Cormier, A. F. Peters, K. Kogame, J. M. Cock and S. M. Coelho

    Citation: Genome Biology 2019 20:35

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  2. Content type: Research

    Adenosine-to-inosine (A-to-I) RNA editing is an essential post-transcriptional mechanism mediated by ADAR enzymes that have been recently associated with cancer.

    Authors: Domenico Alessandro Silvestris, Ernesto Picardi, Valeriana Cesarini, Bruno Fosso, Nicolò Mangraviti, Luca Massimi, Maurizio Martini, Graziano Pesole, Franco Locatelli and Angela Gallo

    Citation: Genome Biology 2019 20:33

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  3. Content type: Method

    The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short...

    Authors: Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna and Siavash Mirarab

    Citation: Genome Biology 2019 20:34

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  4. Content type: Research

    Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied ...

    Authors: Stephanie M. Linker, Lara Urban, Stephen J. Clark, Mariya Chhatriwala, Shradha Amatya, Davis J. McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle and Marc Jan Bonder

    Citation: Genome Biology 2019 20:30

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  5. Content type: Method

    State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study...

    Authors: Barthélémy Caron, Yufei Luo and Antonio Rausell

    Citation: Genome Biology 2019 20:32

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  6. Content type: Opinion

    How contemporary plant genomes originated and evolved is a fascinating question. One approach uses reference genomes from extant species to reconstruct the sequence and structure of their common ancestors over...

    Authors: Caroline Pont, Stefanie Wagner, Antoine Kremer, Ludovic Orlando, Christophe Plomion and Jerome Salse

    Citation: Genome Biology 2019 20:29

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  7. Content type: Research

    Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the...

    Authors: Tracy J. Ballinger, Britta A. M. Bouwman, Reza Mirzazadeh, Silvano Garnerone, Nicola Crosetto and Colin A. Semple

    Citation: Genome Biology 2019 20:28

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  8. Content type: Research

    CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functiona...

    Authors: Emanuel Gonçalves, Fiona M. Behan, Sandra Louzada, Damien Arnol, Euan A. Stronach, Fengtang Yang, Kosuke Yusa, Oliver Stegle, Francesco Iorio and Mathew J. Garnett

    Citation: Genome Biology 2019 20:27

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  9. Content type: Short Report

    CRISPR-Cas12a/Cpf1, a single RNA-guided endonuclease system, provides a promising tool for genome engineering. However, only three Cas12a orthologs have been employed for mammalian genome editing, and the edit...

    Authors: Fei Teng, Jing Li, Tongtong Cui, Kai Xu, Lu Guo, Qingqin Gao, Guihai Feng, Chuanyuan Chen, Dali Han, Qi Zhou and Wei Li

    Citation: Genome Biology 2019 20:15

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  10. Content type: Research

    Recent studies have revealed thousands of A-to-I RNA editing events in primates, but the origination and general functions of these events are not well addressed.

    Authors: Ni A. An, Wanqiu Ding, Xin-Zhuang Yang, Jiguang Peng, Bin Z. He, Qing Sunny Shen, Fujian Lu, Aibin He, Yong E. Zhang, Bertrand Chin-Ming Tan, Jia-Yu Chen and Chuan-Yun Li

    Citation: Genome Biology 2019 20:24

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  11. Content type: Research

    Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, ap...

    Authors: Nur Diana Anuar, Sebastian Kurscheid, Matt Field, Lei Zhang, Edward Rebar, Philip Gregory, Thierry Buchou, Josephine Bowles, Peter Koopman, David J. Tremethick and Tatiana A. Soboleva

    Citation: Genome Biology 2019 20:23

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  12. Content type: Research

    Genome-wide loss-of-function screens using the CRISPR/Cas9 system allow the efficient discovery of cancer cell vulnerabilities. While several studies have focused on correcting for DNA cleavage toxicity biases...

    Authors: Jean-Philippe Fortin, Jenille Tan, Karen E. Gascoigne, Peter M. Haverty, William F. Forrest, Michael R. Costa and Scott E. Martin

    Citation: Genome Biology 2019 20:21

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  13. Content type: Method

    We report a new method using re-designed guide RNAs with internal barcodes (iBARs) embedded in their loop regions. Our iBAR approach outperforms the conventional method by producing screening results with much...

    Authors: Shiyou Zhu, Zhongzheng Cao, Zhiheng Liu, Yuan He, Yinan Wang, Pengfei Yuan, Wei Li, Feng Tian, Ying Bao and Wensheng Wei

    Citation: Genome Biology 2019 20:20

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  14. Content type: Short Report

    Trim-Away is a recent technique to rapidly deplete a protein from any cell type. Guided by antibodies, TRIM21 selects proteins for destruction. However, the applicability of this method in model organisms has ...

    Authors: Xiao Chen, Mi Liu, Hongyan Lou, Yiyi Lu, Meng-Tao Zhou, Rongying Ou, Yunsheng Xu and Kai-Fu Tang

    Citation: Genome Biology 2019 20:19

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  15. Content type: Research

    Gut microbiota from individuals in rural, non-industrialized societies differ from those in individuals from industrialized societies. Here, we use 16S rRNA sequencing to survey the gut bacteria of seven non-i...

    Authors: Matthew E. B. Hansen, Meagan A. Rubel, Aubrey G. Bailey, Alessia Ranciaro, Simon R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe G. Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian Abnet, Stephen J. Chanock, Frederic D. Bushman and Sarah A. Tishkoff

    Citation: Genome Biology 2019 20:16

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  16. Content type: Editorial

    We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses.

    Authors: Barbara Cheifet

    Citation: Genome Biology 2019 20:17

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  17. Content type: Short Report

    Genome engineering methods have advanced greatly with the development of programmable nucleases, but methods for quantifying on- and off-target cleavage sites and associated deletions remain nascent. Here, we ...

    Authors: Christopher L. Nobles, Shantan Reddy, January Salas-McKee, Xiaojun Liu, Carl H. June, J. Joseph Melenhorst, Megan M. Davis, Yangbing Zhao and Frederic D. Bushman

    Citation: Genome Biology 2019 20:14

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  18. Content type: Research

    Cisplatin resistance is a major challenge for advanced head and neck cancer (HNC). Understanding the underlying mechanisms and developing effective strategies against cisplatin resistance are highly desired in...

    Authors: Xing Qin, Haiyan Guo, Xiaoning Wang, Xueqin Zhu, Ming Yan, Xu Wang, Qin Xu, Jianbo Shi, Eryi Lu, Wantao Chen and Jianjun Zhang

    Citation: Genome Biology 2019 20:12

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  19. 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 20:11

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

  20. Content type: Method

    How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentra...

    Authors: Nathan D. Grubaugh, Karthik Gangavarapu, Joshua Quick, Nathaniel L. Matteson, Jaqueline Goes De Jesus, Bradley J. Main, Amanda L. Tan, Lauren M. Paul, Doug E. Brackney, Saran Grewal, Nikos Gurfield, Koen K. A. Van Rompay, Sharon Isern, Scott F. Michael, Lark L. Coffey, Nicholas J. Loman…

    Citation: Genome Biology 2019 20:8

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  21. Content type: Research

    Long intergenic RNAs (lincRNAs) play critical roles in eukaryotic cells, but systematic analyses of the lincRNAs of an animal for phenotypes are lacking. We generate CRISPR knockout strains for Caenorhabditis ele...

    Authors: Shuai Wei, He Chen, Emmanuel Enoch Dzakah, Bin Yu, Xiaolin Wang, Tao Fu, Jingxin Li, Lei Liu, Shucheng Fang, Weihong Liu and Ge Shan

    Citation: Genome Biology 2019 20:7

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  22. Content type: Research

    The nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in d...

    Authors: Paulina Bolívar, Laurent Guéguen, Laurent Duret, Hans Ellegren and Carina F. Mugal

    Citation: Genome Biology 2019 20:5

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  23. Content type: Software

    Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there a...

    Authors: Stuart Lee, Dianne Cook and Michael Lawrence

    Citation: Genome Biology 2019 20:4

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  24. Content type: Database

    The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, inclu...

    Authors: Dimitra Repana, Joel Nulsen, Lisa Dressler, Michele Bortolomeazzi, Santhilata Kuppili Venkata, Aikaterini Tourna, Anna Yakovleva, Tommaso Palmieri and Francesca D. Ciccarelli

    Citation: Genome Biology 2019 20:1

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  25. Content type: Research

    Maintenance of physiological circadian rhythm plays a crucial role in human health. Numerous studies have shown that disruption of circadian rhythm may increase risk for malignant, psychiatric, metabolic, and ...

    Authors: Gabriel Oh, Karolis Koncevičius, Sasha Ebrahimi, Matthew Carlucci, Daniel Erik Groot, Akhil Nair, Aiping Zhang, Algimantas Kriščiūnas, Edward S. Oh, Viviane Labrie, Albert H. C. Wong, Juozas Gordevičius, Peixin Jia, Miki Susic and Art Petronis

    Citation: Genome Biology 2019 20:2

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  26. Content type: Research

    Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 a...

    Authors: Marcus M. Dillon, Shalabh Thakur, Renan N. D. Almeida, Pauline W. Wang, Bevan S. Weir and David S. Guttman

    Citation: Genome Biology 2019 20:3

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  27. Content type: Research

    RNA secondary structures in the 5′-untranslated regions (5′-UTR) of mRNAs are key to the post-transcriptional regulation of gene expression. While it is evident that non-canonical Hoogsteen-paired G-quadruplex...

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

    Citation: Genome Biology 2018 19:229

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    The Correction to this article has been published in Genome Biology 2019 20:11

  28. Content type: Opinion

    Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay betwee...

    Authors: Cheryl Chan, Phuong Pham, Peter C. Dedon and Thomas J. Begley

    Citation: Genome Biology 2018 19:228

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  29. Content type: Short Report

    Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133...

    Authors: Jason G. Fleischer, Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin W. Hetzer and Saket Navlakha

    Citation: Genome Biology 2018 19:221

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  30. Content type: Method

    Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where o...

    Authors: Marlon Stoeckius, Shiwei Zheng, Brian Houck-Loomis, Stephanie Hao, Bertrand Z. Yeung, William M. Mauck III, Peter Smibert and Rahul Satija

    Citation: Genome Biology 2018 19:224

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  31. Content type: Research

    DNA methylation is influenced by both environmental and genetic factors and is increasingly thought to affect variation in complex traits and diseases. Yet, the extent of ancestry-related differences in DNA me...

    Authors: Lucas T. Husquin, Maxime Rotival, Maud Fagny, Hélène Quach, Nora Zidane, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Hugues Aschard, Etienne Patin and Lluis Quintana-Murci

    Citation: Genome Biology 2018 19:222

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  32. Content type: Software

    There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a v...

    Authors: Jacob Pritt, Nae-Chyun Chen and Ben Langmead

    Citation: Genome Biology 2018 19:220

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  33. Content type: Research

    The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with...

    Authors: Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey, Emily R. Miraldi, Edward B. Chuong, Cédric Feschotte, Richard Bonneau and Jane A. Skok

    Citation: Genome Biology 2018 19:216

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  34. Content type: Research

    Friend leukemia virus integration 1 (FLI1), an ETS transcription factor family member, acts as an oncogenic driver in hematological malignancies and promotes tumor growth in solid tumors. However, little is kn...

    Authors: Naifei Chen, Gang Zhao, Xu Yan, Zheng Lv, Hongmei Yin, Shilin Zhang, Wei Song, Xueli Li, Lingyu Li, Zhonghua Du, Lin Jia, Lei Zhou, Wei Li, Andrew R. Hoffman, Ji-Fan Hu and Jiuwei Cui

    Citation: Genome Biology 2018 19:218

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  35. Content type: Research

    Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple spe...

    Authors: Marie Zufferey, Daniele Tavernari, Elisa Oricchio and Giovanni Ciriello

    Citation: Genome Biology 2018 19:217

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