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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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

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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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

  21. 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

  22. 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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  23. 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:

  24. 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:

  25. 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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  26. 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

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  27. 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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  28. Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development...

    Authors: Ranjith K. Papareddy, Katalin Páldi, Subramanian Paulraj, Ping Kao, Stefan Lutzmayer and Michael D. Nodine

    Citation: Genome Biology 2020 21:251

    Content type: Research

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  29. During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short ...

    Authors: Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica and Richard Durbin

    Citation: Genome Biology 2020 21:250

    Content type: Research

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  30. 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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  31. The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characteri...

    Authors: Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, Maria E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos and Chongzhi Zang

    Citation: Genome Biology 2020 21:247

    Content type: Research

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  32. To provide a comprehensive mechanistic interpretation of how known trait-associated SNPs affect complex traits, we propose a method, Primo, for integrative analysis of GWAS summary statistics with multiple set...

    Authors: Kevin J. Gleason, Fan Yang, Brandon L. Pierce, Xin He and Lin S. Chen

    Citation: Genome Biology 2020 21:236

    Content type: Method

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  33. Genetic regulation of gene expression, revealed by expression quantitative trait loci (eQTLs), exhibits complex patterns of tissue-specific effects. Characterization of these patterns may allow us to better un...

    Authors: Yuan He, Surya B. Chhetri, Marios Arvanitis, Kaushik Srinivasan, François Aguet, Kristin G. Ardlie, Alvaro N. Barbeira, Rodrigo Bonazzola, Hae Kyung Im, Christopher D. Brown and Alexis Battle

    Citation: Genome Biology 2020 21:235

    Content type: Method

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  34. Allele expression (AE) analysis robustly measures cis-regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from the GTEx v8 release, containing 15,253 samples spanning ...

    Authors: Stephane E. Castel, François Aguet, Pejman Mohammadi, Kristin G. Ardlie and Tuuli Lappalainen

    Citation: Genome Biology 2020 21:234

    Content type: Short Report

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  35. Population structure among study subjects may confound genetic association studies, and lack of proper correction can lead to spurious findings. The Genotype-Tissue Expression (GTEx) project largely contains i...

    Authors: Nicole R. Gay, Michael Gloudemans, Margaret L. Antonio, Nathan S. Abell, Brunilda Balliu, YoSon Park, Alicia R. Martin, Shaila Musharoff, Abhiram S. Rao, François Aguet, Alvaro N. Barbeira, Rodrigo Bonazzola, Farhad Hormozdiari, Kristin G. Ardlie, Christopher D. Brown, Hae Kyung Im…

    Citation: Genome Biology 2020 21:233

    Content type: Research

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  36. We propose a new computational framework, probabilistic transcriptome-wide association study (PTWAS), to investigate causal relationships between gene expressions and complex traits. PTWAS applies the establis...

    Authors: Yuhua Zhang, Corbin Quick, Ketian Yu, Alvaro Barbeira, Francesca Luca, Roger Pique-Regi, Hae Kyung Im and Xiaoquan Wen

    Citation: Genome Biology 2020 21:232

    Content type: Method

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  37. GetOrganelle is a state-of-the-art toolkit to accurately assemble organelle genomes from whole genome sequencing data. It recruits organelle-associated reads using a modified “baiting and iterative mapping” ap...

    Authors: Jian-Jun Jin, Wen-Bin Yu, Jun-Bo Yang, Yu Song, Claude W. dePamphilis, Ting-Shuang Yi and De-Zhu Li

    Citation: Genome Biology 2020 21:241

    Content type: Software

    Published on: