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  1. Advances in high-throughput sequencing technologies have reduced the cost of genotyping dramatically and led to genomic prediction being widely used in animal and plant breeding, and increasingly in human gene...

    Authors: Lilin Yin, Haohao Zhang, Xiang Zhou, Xiaohui Yuan, Shuhong Zhao, Xinyun Li and Xiaolei Liu

    Citation: Genome Biology 2020 21:146

    Content type: Method

    Published on:

  2. At least 50% of patients with suspected Mendelian disorders remain undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding variants that are not captured by WES contribute to this fr...

    Authors: Sateesh Maddirevula, Hiroyuki Kuwahara, Nour Ewida, Hanan E. Shamseldin, Nisha Patel, Fatema Alzahrani, Tarfa AlSheddi, Eman AlObeid, Mona Alenazi, Hessa S. Alsaif, Maha Alqahtani, Maha AlAli, Hatoon Al Ali, Rana Helaby, Niema Ibrahim, Firdous Abdulwahab…

    Citation: Genome Biology 2020 21:145

    Content type: Research

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  3. Stable gene repression is essential for normal growth and development. Polycomb repressive complexes 1 and 2 (PRC1&2) are involved in this process by establishing monoubiquitination of histone 2A (H2Aub1) and ...

    Authors: Lejon E. M. Kralemann, Shujing Liu, Minerva S. Trejo-Arellano, Rafael Muñoz-Viana, Claudia Köhler and Lars Hennig

    Citation: Genome Biology 2020 21:144

    Content type: Research

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  4. Maize ears and tassels are two separate types of inflorescence which are initiated by similar developmental processes but gradually develop distinct architectures. However, coordinated trans and cis regulation of...

    Authors: Yonghao Sun, Liang Dong, Ying Zhang, Da Lin, Weize Xu, Changxiong Ke, Linqian Han, Lulu Deng, Guoliang Li, David Jackson, Xingwang Li and Fang Yang

    Citation: Genome Biology 2020 21:143

    Content type: Research

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  5. Repeat-induced point (RIP) mutation in Neurospora crassa degrades transposable elements by targeting repeats with C→T mutations. Whether RIP affects core genomic sequence in important ways is unknown.

    Authors: Long Wang, Yingying Sun, Xiaoguang Sun, Luyao Yu, Lan Xue, Zhen He, Ju Huang, Dacheng Tian, Laurence D. Hurst and Sihai Yang

    Citation: Genome Biology 2020 21:142

    Content type: Research

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  6. We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deamina...

    Authors: Chao Li, Yuan Zong, Shuai Jin, Haocheng Zhu, Dexing Lin, Shengnan Li, Jin-Long Qiu, Yanpeng Wang and Caixia Gao

    Citation: Genome Biology 2020 21:141

    Content type: Method

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  7. The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFN-stimulated genes. Comprehensive catalogs of IFN-stimulate...

    Authors: Craig H. Kerr, Michael A. Skinnider, Daniel D. T. Andrews, Angel M. Madero, Queenie W. T. Chan, R. Greg Stacey, Nikolay Stoynov, Eric Jan and Leonard J. Foster

    Citation: Genome Biology 2020 21:140

    Content type: Research

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  8. Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted inCLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of da...

    Authors: Fan Chen and Sündüz Keleş

    Citation: Genome Biology 2020 21:139

    Content type: Method

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  9. Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely rema...

    Authors: Sharadha Sakthikumar, Ananya Roy, Lulu Haseeb, Mats E. Pettersson, Elisabeth Sundström, Voichita D. Marinescu, Kerstin Lindblad-Toh and Karin Forsberg-Nilsson

    Citation: Genome Biology 2020 21:127

    Content type: Research

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  10. Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been...

    Authors: Nicolai Karcher, Edoardo Pasolli, Francesco Asnicar, Kun D. Huang, Adrian Tett, Serena Manara, Federica Armanini, Debbie Bain, Sylvia H. Duncan, Petra Louis, Moreno Zolfo, Paolo Manghi, Mireia Valles-Colomer, Roberta Raffaetà, Omar Rota-Stabelli, Maria Carmen Collado…

    Citation: Genome Biology 2020 21:138

    Content type: Research

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  11. CRISPR-based genome perturbation provides a new avenue to conveniently change DNA sequences, transcription, and epigenetic modifications in genetic screens. However, it remains challenging to assay the complex...

    Authors: Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Yingzheng Liu, Zhenxing Yu, Yinyao Qi, Zhike Lu and Lijia Ma

    Citation: Genome Biology 2020 21:136

    Content type: Method

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  12. To investigate the epigenetic and transcriptional mechanisms of coronary artery disease (CAD) risk, as well as the functional regulation of chromatin structure and function, we create a catalog of genetic vari...

    Authors: Quanyi Zhao, Michael Dacre, Trieu Nguyen, Milos Pjanic, Boxiang Liu, Dharini Iyer, Paul Cheng, Robert Wirka, Juyong Brian Kim, Hunter B. Fraser and Thomas Quertermous

    Citation: Genome Biology 2020 21:135

    Content type: Research

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  13. An amendment to this paper has been published and can be accessed via the original article.

    Authors: Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos and Jane A. Skok

    Citation: Genome Biology 2020 21:133

    Content type: Author Correction

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    The original article was published in Genome Biology 2020 21:108

  14. The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyc...

    Authors: Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Čabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh…

    Citation: Genome Biology 2020 21:132

    Content type: Research

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  15. Many microbial agents have been implicated as contributors to cancer genesis and development, and the search to identify and characterize new cancer-related organisms is ongoing. Modern developments in methodo...

    Authors: Sumeed Syed Manzoor, Annemiek Doedens and Michael B. Burns

    Citation: Genome Biology 2020 21:131

    Content type: Review

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  16. Single-cell RNA sequencing has been widely adopted to estimate the cellular composition of heterogeneous tissues and obtain transcriptional profiles of individual cells. Multiple approaches for optimal sample ...

    Authors: Elena Denisenko, Belinda B. Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, Olivier Clément, Rebecca K. Simmons, Ryan Lister and Alistair R. R. Forrest

    Citation: Genome Biology 2020 21:130

    Content type: Research

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  17. Thousands of experiments and studies use the human reference genome as a resource each year. This single reference genome, GRCh38, is a mosaic created from a small number of individuals, representing a very sm...

    Authors: Alaina Shumate, Aleksey V. Zimin, Rachel M. Sherman, Daniela Puiu, Justin M. Wagner, Nathan D. Olson, Mihaela Pertea, Marc L. Salit, Justin M. Zook and Steven L. Salzberg

    Citation: Genome Biology 2020 21:129

    Content type: Research

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  18. Ribosomal profiling has revealed the translation of thousands of sequences outside annotated protein-coding genes, including small open reading frames of less than 100 codons, and the translational regulation ...

    Authors: Pedro Patraquim, Muhammad Ali Shahzad Mumtaz, José Ignacio Pueyo, Julie Louise Aspden and Juan-Pablo Couso

    Citation: Genome Biology 2020 21:128

    Content type: Research

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  19. To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate r...

    Authors: Liqing Tian, Yongjin Li, Michael N. Edmonson, Xin Zhou, Scott Newman, Clay McLeod, Andrew Thrasher, Yu Liu, Bo Tang, Michael C. Rusch, John Easton, Jing Ma, Eric Davis, Austyn Trull, J. Robert Michael, Karol Szlachta…

    Citation: Genome Biology 2020 21:126

    Content type: Method

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  20. Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200-nucle...

    Authors: Magali Hennion, Jean-Michel Arbona, Laurent Lacroix, Corinne Cruaud, Bertrand Theulot, Benoît Le Tallec, Florence Proux, Xia Wu, Elizaveta Novikova, Stefan Engelen, Arnaud Lemainque, Benjamin Audit and Olivier Hyrien

    Citation: Genome Biology 2020 21:125

    Content type: Method

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  21. African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microb...

    Authors: Meagan A. Rubel, Arwa Abbas, Louis J. Taylor, Andrew Connell, Ceylan Tanes, Kyle Bittinger, Valantine N. Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman and Sarah A. Tishkoff

    Citation: Genome Biology 2020 21:122

    Content type: Research

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  22. Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics. We use two independent assemblies and an optical map-based merging pipeline to produce a maize...

    Authors: Jianing Liu, Arun S. Seetharam, Kapeel Chougule, Shujun Ou, Kyle W. Swentowsky, Jonathan I. Gent, Victor Llaca, Margaret R. Woodhouse, Nancy Manchanda, Gernot G. Presting, David A. Kudrna, Magdy Alabady, Candice N. Hirsch, Kevin A. Fengler, Doreen Ware, Todd P. Michael…

    Citation: Genome Biology 2020 21:121

    Content type: Short Report

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  23. Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structu...

    Authors: Boyang Shi, Jinsong Zhang, Jian Heng, Jing Gong, Ting Zhang, Pan Li, Bao-Fa Sun, Ying Yang, Ning Zhang, Yong-Liang Zhao, Hai-Lin Wang, Feng Liu, Qiangfeng Cliff Zhang and Yun-Gui Yang

    Citation: Genome Biology 2020 21:120

    Content type: Research

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  24. Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isofor...

    Authors: Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy R. B. Newman, Shunichi Kosugi, Lauren M. McIntyre, Victoria Moreno-Manzano and Ana Conesa

    Citation: Genome Biology 2020 21:119

    Content type: Software

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  25. A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a g...

    Authors: Isaac Kremsky and Victor G. Corces

    Citation: Genome Biology 2020 21:118

    Content type: Research

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  26. Non-canonical residues, caps, crosslinks, and nicks are important to many functions of DNAs, RNAs, proteins, and complexes. However, we do not fully understand how networks of such non-canonical macromolecules...

    Authors: Paul F. Lang, Yassmine Chebaro, Xiaoyue Zheng, John A. P. Sekar, Bilal Shaikh, Darren A. Natale and Jonathan R. Karr

    Citation: Genome Biology 2020 21:117

    Content type: Method

    Published on:

  27. The development of sequencing technologies has promoted the survey of genome-wide chromatin accessibility at single-cell resolution. However, comprehensive analysis of single-cell epigenomic profiles remains a...

    Authors: Bin Li, Young Li, Kun Li, Lianbang Zhu, Qiaoni Yu, Pengfei Cai, Jingwen Fang, Wen Zhang, Pengcheng Du, Chen Jiang, Jun Lin and Kun Qu

    Citation: Genome Biology 2020 21:116

    Content type: Method

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  28. Positional weight matrix (PWM) is a de facto standard model to describe transcription factor (TF) DNA binding specificities. PWMs inferred from in vivo or in vitro data are stored in many databases and used in...

    Authors: Giovanna Ambrosini, Ilya Vorontsov, Dmitry Penzar, Romain Groux, Oriol Fornes, Daria D. Nikolaeva, Benoit Ballester, Jan Grau, Ivo Grosse, Vsevolod Makeev, Ivan Kulakovskiy and Philipp Bucher

    Citation: Genome Biology 2020 21:114

    Content type: Research

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  29. Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample ...

    Authors: Ramon Massoni-Badosa, Giovanni Iacono, Catia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodriguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elias Campo, Antonio Julià, José Ignacio Martín-Subero and Holger Heyn

    Citation: Genome Biology 2020 21:112

    Content type: Short Report

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  30. Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computati...

    Authors: Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni and Oliver Stegle

    Citation: Genome Biology 2020 21:111

    Content type: Method

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  31. Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, the molecular mechanisms underlying the role of PML-RARα in leukemogenesis ...

    Authors: Ping Wang, Zhonghui Tang, Byoungkoo Lee, Jacqueline Jufen Zhu, Liuyang Cai, Przemyslaw Szalaj, Simon Zhongyuan Tian, Meizhen Zheng, Dariusz Plewczynski, Xiaoan Ruan, Edison T. Liu, Chia-Lin Wei and Yijun Ruan

    Citation: Genome Biology 2020 21:110

    Content type: Research

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  32. Unsupervised compression algorithms applied to gene expression data extract latent or hidden signals representing technical and biological sources of variation. However, these algorithms require a user to sele...

    Authors: Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein and Casey S. Greene

    Citation: Genome Biology 2020 21:109

    Content type: Research

    Published on:

  33. Ubiquitously expressed CTCF is involved in numerous cellular functions, such as organizing chromatin into TAD structures. In contrast, its paralog, CTCFL, is normally only present in the testis. However, it is...

    Authors: Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphege P. Nora, Sana B. Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos and Jane A. Skok

    Citation: Genome Biology 2020 21:108

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2020 21:133

  34. Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions betwee...

    Authors: Andrew J. Gentles, Angela Bik-Yu Hui, Weiguo Feng, Armon Azizi, Ramesh V. Nair, Gina Bouchard, David A. Knowles, Alice Yu, Youngtae Jeong, Alborz Bejnood, Erna Forgó, Sushama Varma, Yue Xu, Amanda Kuong, Viswam S. Nair, Rob West…

    Citation: Genome Biology 2020 21:107

    Content type: Research

    Published on:

  35. RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacteri...

    Authors: Oguzhan Begik, Morghan C. Lucas, Huanle Liu, Jose Miguel Ramirez, John S. Mattick and Eva Maria Novoa

    Citation: Genome Biology 2020 21:97

    Content type: Research

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  36. Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool to dissect cell-specific effects of drug treatment in complex tissues. This application requires high levels of precision, robustness, and quantit...

    Authors: Brenda Marquina-Sanchez, Nikolaus Fortelny, Matthias Farlik, Andhira Vieira, Patrick Collombat, Christoph Bock and Stefan Kubicek

    Citation: Genome Biology 2020 21:106

    Content type: Research

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  37. Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major fa...

    Authors: Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Severine Domenichini, Natalia Y. Rodriguez Granados, Soonkap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza-Mianza, Caroline Juery, Etienne Paux, Graham Moore…

    Citation: Genome Biology 2020 21:104

    Content type: Research

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  38. There is an increasing demand for accurate and fast metagenome classifiers that can not only identify bacteria, but all members of a microbial community. We used a recently developed concept in read mapping to...

    Authors: Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell and Edward C. Holmes

    Citation: Genome Biology 2020 21:103

    Content type: Software

    Published on:

  39. The REPIC (RNA EPItranscriptome Collection) database records about 10 million peaks called from publicly available m6A-seq and MeRIP-seq data using our unified pipeline. These data were collected from 672 samples...

    Authors: Shun Liu, Allen Zhu, Chuan He and Mengjie Chen

    Citation: Genome Biology 2020 21:100

    Content type: Database

    Published on:

  40. Influenza is a severe respiratory illness that continually threatens global health. It has been widely known that gut microbiota modulates the host response to protect against influenza infection, but mechanis...

    Authors: Qiang Zhang, Jin Hu, Jia-Wu Feng, Xiao-Tong Hu, Ting Wang, Wen-Xiao Gong, Kun Huang, Yi-Xiong Guo, Zhong Zou, Xian Lin, Run Zhou, Yu-Qi Yuan, An-Ding Zhang, Hong Wei, Gang Cao, Chen Liu…

    Citation: Genome Biology 2020 21:99

    Content type: Research

    Published on: