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  1. Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically...

    Authors: Emma K. Accorsi, Eric A. Franzosa, Tiffany Hsu, Regina Joice Cordy, Ayala Maayan-Metzger, Hanaa Jaber, Aylana Reiss-Mandel, Madeleine Kline, Casey DuLong, Marc Lipsitch, Gili Regev-Yochay and Curtis Huttenhower

    Citation: Genome Biology 2020 21:301

    Content type: Research

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  2. The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. How...

    Authors: Simon M. Hoser, Anne Hoffmann, Andreas Meindl, Maximilian Gamper, Jörg Fallmann, Stephan H. Bernhart, Lisa Müller, Melanie Ploner, Matthias Misslinger, Leopold Kremser, Herbert Lindner, Stephan Geley, Heiner Schaal, Peter F. Stadler and Alexander Huettenhofer

    Citation: Genome Biology 2020 21:299

    Content type: Research

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  3. STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is...

    Authors: Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White and Mark Gerstein

    Citation: Genome Biology 2020 21:298

    Content type: Method

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  4. Despite the long-observed correlation between H3K9me3, chromatin architecture, and transcriptional repression, how H3K9me3 regulates genome higher-order organization and transcriptional activity in living cell...

    Authors: Ying Feng, Yao Wang, Xiangnan Wang, Xiaohui He, Chen Yang, Ardalan Naseri, Thoru Pederson, Jing Zheng, Shaojie Zhang, Xiao Xiao, Wei Xie and Hanhui Ma

    Citation: Genome Biology 2020 21:296

    Content type: Research

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  5. The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-spec...

    Authors: Tao Shi and Jinming Chen

    Citation: Genome Biology 2020 21:295

    Content type: Correspondence

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    The Correspondence to this article has been published in Genome Biology 2020 21:297

  6. As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and ...

    Authors: Shuai He, Lin-He Wang, Yang Liu, Yi-Qi Li, Hai-Tian Chen, Jing-Hong Xu, Wan Peng, Guo-Wang Lin, Pan-Pan Wei, Bo Li, Xiaojun Xia, Dan Wang, Jin-Xin Bei, Xiaoshun He and Zhiyong Guo

    Citation: Genome Biology 2020 21:294

    Content type: Research

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  7. We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with an...

    Authors: Ana T. Duggan, Edward C. Holmes and Hendrik N. Poinar

    Citation: Genome Biology 2020 21:287

    Content type: Correspondence

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    The original article was published in Genome Biology 2020 21:286

  8. According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends o...

    Authors: Annika Brinkmann, Aline R. V. Souza, José Esparza, Andreas Nitsche and Clarissa R. Damaso

    Citation: Genome Biology 2020 21:286

    Content type: Correspondence

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    The Correspondence to this article has been published in Genome Biology 2020 21:287

  9. Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and res...

    Authors: Ping-Li Liu, Xi Zhang, Jian-Feng Mao, Yan-Ming Hong, Ren-Gang Zhang, Yilan E, Shuai Nie, Kaihua Jia, Chen-Kun Jiang, Jian He, Weiwei Shen, Qizouhong He, Wenqing Zheng, Samar Abbas, Pawan Kumar Jewaria, Xuechan Tian…

    Citation: Genome Biology 2020 21:291

    Content type: Research

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  10. One ongoing concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target activity is challenging....

    Authors: Ida Höijer, Josefin Johansson, Sanna Gudmundsson, Chen-Shan Chin, Ignas Bunikis, Susana Häggqvist, Anastasia Emmanouilidou, Maria Wilbe, Marcel den Hoed, Marie-Louise Bondeson, Lars Feuk, Ulf Gyllensten and Adam Ameur

    Citation: Genome Biology 2020 21:290

    Content type: Research

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  11. To meet increasing global food demand, breeders and scientists aim to improve the yield and quality of major food crops. Plant diseases threaten food security and are expected to increase because of climate ch...

    Authors: Syed Shan-e-Ali Zaidi, Ahmed Mahas, Hervé Vanderschuren and Magdy M. Mahfouz

    Citation: Genome Biology 2020 21:289

    Content type: Review

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  12. Adenosine-to-inosine (A-to-I) RNA editing plays important roles in diversifying the transcriptome and preventing MDA5 sensing of endogenous dsRNA as nonself. To date, few studies have investigated the populati...

    Authors: Hui Zhang, Qiang Fu, Xinrui Shi, Ziqing Pan, Wenbing Yang, Zichao Huang, Tian Tang, Xionglei He and Rui Zhang

    Citation: Genome Biology 2020 21:288

    Content type: Research

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  13. Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more pron...

    Authors: Pierre Bourguet, Leticia López-González, Ángeles Gómez-Zambrano, Thierry Pélissier, Amy Hesketh, Magdalena E. Potok, Marie-Noëlle Pouch-Pélissier, Magali Perez, Olivier Da Ines, David Latrasse, Charles I. White, Steven E. Jacobsen, Moussa Benhamed and Olivier Mathieu

    Citation: Genome Biology 2020 21:283

    Content type: Research

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  14. Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent...

    Authors: Inés Sentís, Santiago Gonzalez, Eulalia Genescà, Violeta García-Hernández, Ferran Muiños, Celia Gonzalez, Erika López-Arribillaga, Jessica Gonzalez, Lierni Fernandez-Ibarrondo, Loris Mularoni, Lluís Espinosa, Beatriz Bellosillo, Josep-Maria Ribera, Anna Bigas, Abel Gonzalez-Perez and Nuria Lopez-Bigas

    Citation: Genome Biology 2020 21:284

    Content type: Research

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  15. Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of g...

    Authors: Prithvi Raj, Ran Song, Honglin Zhu, Linley Riediger, Dong-Jae Jun, Chaoying Liang, Carlos Arana, Bo Zhang, Yajing Gao, Benjamin E. Wakeland, Igor Dozmorov, Jinchun Zhou, Jennifer A. Kelly, Bernard R. Lauwerys, Joel M. Guthridge, Nancy J. Olsen…

    Citation: Genome Biology 2020 21:281

    Content type: Research

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  16. Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using S...

    Authors: Xiaoming Liu and Yun-Xin Fu

    Citation: Genome Biology 2020 21:280

    Content type: Method

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    The Author Correction to this article has been published in Genome Biology 2020 21:305

  17. During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored.

    Authors: Chengchen Zhao, Naiqian Zhang, Yalin Zhang, Nuermaimaiti Tuersunjiang, Shaorong Gao, Wenqiang Liu and Yong Zhang

    Citation: Genome Biology 2020 21:277

    Content type: Research

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  18. Biological rhythms regulate the biology of most, if not all living creatures, from whole organisms to their constitutive cells, their microbiota, and also parasites. Here, we present the hypothesis that intern...

    Authors: Luis Enrique Cortés-Hernández, Zahra Eslami-S, Antoine M. Dujon, Mathieu Giraudeau, Beata Ujvari, Frédéric Thomas and Catherine Alix-Panabières

    Citation: Genome Biology 2020 21:276

    Content type: Review

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  19. The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive morta...

    Authors: Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jessica Gómez-Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo-Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, André Corvelo, Leonor Frias, Marta Gut, Toni Gabaldón, Alberto Pallavicini…

    Citation: Genome Biology 2020 21:275

    Content type: Research

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  20. Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual cu...

    Authors: Kristina Hanspers, Anders Riutta, Martina Summer-Kutmon and Alexander R. Pico

    Citation: Genome Biology 2020 21:273

    Content type: Database

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  21. Structural maintenance of chromosomes (SMC) complexes are central organizers of chromatin architecture throughout the cell cycle. The SMC family member condensin is best known for establishing long-range chrom...

    Authors: Yasutaka Kakui, Christopher Barrington, David J. Barry, Tereza Gerguri, Xiao Fu, Paul A. Bates, Bhavin S. Khatri and Frank Uhlmann

    Citation: Genome Biology 2020 21:272

    Content type: Research

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  22. Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary.

    Authors: Won-Chul Lee, Alexandre Reuben, Xin Hu, Nicholas McGranahan, Runzhe Chen, Ali Jalali, Marcelo V. Negrao, Shawna M. Hubert, Chad Tang, Chia-Chin Wu, Anthony San Lucas, Whijae Roh, Kenichi Suda, Jihye Kim, Aik-Choon Tan, David H. Peng…

    Citation: Genome Biology 2020 21:271

    Content type: Research

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  23. Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mecha...

    Authors: Ke Fang, Wei Huang, Yu-Meng Sun, Tian-Qi Chen, Zhan-Cheng Zeng, Qian-Qian Yang, Qi Pan, Cai Han, Lin-Yu Sun, Xue-Qun Luo, Wen-Tao Wang and Yue-Qin Chen

    Citation: Genome Biology 2020 21:269

    Content type: Research

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  24. RNA editing generates modifications to the RNA sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in editing levels across...

    Authors: Tracey W. Chan, Ting Fu, Jae Hoon Bahn, Hyun-Ik Jun, Jae-Hyung Lee, Giovanni Quinones-Valdez, Chonghui Cheng and Xinshu Xiao

    Citation: Genome Biology 2020 21:268

    Content type: Research

    Published on:

  25. One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes...

    Authors: Enrique Navas-Pérez, Cristina Vicente-García, Serena Mirra, Demian Burguera, Noèlia Fernàndez-Castillo, José Luis Ferrán, Macarena López-Mayorga, Marta Alaiz-Noya, Irene Suárez-Pereira, Ester Antón-Galindo, Fausto Ulloa, Carlos Herrera-Úbeda, Pol Cuscó, Rafael Falcón-Moya, Antonio Rodríguez-Moreno, Salvatore D’Aniello…

    Citation: Genome Biology 2020 21:267

    Content type: Research

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  26. CRISPR-Cas9 gene editing has transformed our ability to rapidly interrogate the functional impact of somatic mutations in human cancers. Droplet-based technology enables the analysis of Cas9-introduced gene ed...

    Authors: Elisa ten Hacken, Kendell Clement, Shuqiang Li, María Hernández-Sánchez, Robert Redd, Shu Wang, David Ruff, Michaela Gruber, Kaitlyn Baranowski, Jose Jacob, James Flynn, Keith W. Jones, Donna Neuberg, Kenneth J. Livak, Luca Pinello and Catherine J. Wu

    Citation: Genome Biology 2020 21:266

    Content type: Short Report

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  27. Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of IC...

    Authors: Shengqing Stan Gu, Xiaoqing Wang, Xihao Hu, Peng Jiang, Ziyi Li, Nicole Traugh, Xia Bu, Qin Tang, Chenfei Wang, Zexian Zeng, Jingxin Fu, Cliff Meyer, Yi Zhang, Paloma Cejas, Klothilda Lim, Jin Wang…

    Citation: Genome Biology 2020 21:263

    Content type: Research

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  28. Pooled library CRISPR/Cas9 knockout screening across hundreds of cell lines has identified genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the...

    Authors: Merve Dede, Megan McLaughlin, Eiru Kim and Traver Hart

    Citation: Genome Biology 2020 21:262

    Content type: Research

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  29. iMOKA (interactive multi-objective k-mer analysis) is a software that enables comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elem...

    Authors: Claudio Lorenzi, Sylvain Barriere, Jean-Philippe Villemin, Laureline Dejardin Bretones, Alban Mancheron and William Ritchie

    Citation: Genome Biology 2020 21:261

    Content type: Method

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  30. Stochastic changes in DNA methylation (i.e., spontaneous epimutations) contribute to methylome diversity in plants. Here, we describe AlphaBeta, a computational method for estimating the precise rate of such stoc...

    Authors: Yadollah Shahryary, Aikaterini Symeonidi, Rashmi R. Hazarika, Johanna Denkena, Talha Mubeen, Brigitte Hofmeister, Thomas van Gurp, Maria Colomé-Tatché, Koen J.F. Verhoeven, Gerald Tuskan, Robert J. Schmitz and Frank Johannes

    Citation: Genome Biology 2020 21:260

    Content type: Software

    Published on:

    The Research to this article has been published in Genome Biology 2020 21:259

  31. Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development con...

    Authors: Brigitte T. Hofmeister, Johanna Denkena, Maria Colomé-Tatché, Yadollah Shahryary, Rashmi Hazarika, Jane Grimwood, Sujan Mamidi, Jerry Jenkins, Paul P. Grabowski, Avinash Sreedasyam, Shengqiang Shu, Kerrie Barry, Kathleen Lail, Catherine Adam, Anna Lipzen, Rotem Sorek…

    Citation: Genome Biology 2020 21:259

    Content type: Research

    Published on:

    The Software to this article has been published in Genome Biology 2020 21:260

  32. Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.

    Authors: Jian Guo, Ke Cao, Cecilia Deng, Yong Li, Gengrui Zhu, Weichao Fang, Changwen Chen, Xinwei Wang, Jinlong Wu, Liping Guan, Shan Wu, Wenwu Guo, Jia-Long Yao, Zhangjun Fei and Lirong Wang

    Citation: Genome Biology 2020 21:258

    Content type: Research

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  33. Prime editing is a novel and universal CRISPR/Cas-derived precision genome-editing technology that has been recently developed. However, low efficiency of prime editing has been shown in transgenic rice lines....

    Authors: Yuan-Yuan Jiang, Yi-Ping Chai, Min-Hui Lu, Xiu-Li Han, Qiupeng Lin, Yu Zhang, Qiang Zhang, Yun Zhou, Xue-Chen Wang, Caixia Gao and Qi-Jun Chen

    Citation: Genome Biology 2020 21:257

    Content type: Short Report

    Published on:

  34. We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in computer vision, to detect blob-shape...

    Authors: Abbas Roayaei Ardakany, Halil Tuvan Gezer, Stefano Lonardi and Ferhat Ay

    Citation: Genome Biology 2020 21:256

    Content type: Method

    Published on:

  35. Chloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their o...

    Authors: Jan A. Freudenthal, Simon Pfaff, Niklas Terhoeven, Arthur Korte, Markus J. Ankenbrand and Frank Förster

    Citation: Genome Biology 2020 21:254

    Content type: Research

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  36. Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in ...

    Authors: Mikko Rautiainen and Tobias Marschall

    Citation: Genome Biology 2020 21:253

    Content type: Software

    Published on:

  37. Resolving genomes at haplotype level is crucial for understanding the evolutionary history of polyploid species and for designing advanced breeding strategies. Polyploid phasing still presents considerable cha...

    Authors: Sven D. Schrinner, Rebecca Serra Mari, Jana Ebler, Mikko Rautiainen, Lancelot Seillier, Julia J. Reimer, Björn Usadel, Tobias Marschall and Gunnar W. Klau

    Citation: Genome Biology 2020 21:252

    Content type: Method

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  38. Acquired human mitochondrial genome (mtDNA) deletions are symptoms and drivers of focal mitochondrial respiratory deficiency, a pathological hallmark of aging and late-onset mitochondrial disease.

    Authors: Scott A. Lujan, Matthew J. Longley, Margaret H. Humble, Christopher A. Lavender, Adam Burkholder, Emma L. Blakely, Charlotte L. Alston, Grainne S. Gorman, Doug M. Turnbull, Robert McFarland, Robert W. Taylor, Thomas A. Kunkel and William C. Copeland

    Citation: Genome Biology 2020 21:248

    Content type: Research

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