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  1. Gene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function in vivo. However, because different gene disruption strategies use different mechanisms to...

    Authors: Vishnu Hosur, Benjamin E. Low, Daniel Li, Grace A. Stafford, Vivek Kohar, Leonard D. Shultz and Michael V. Wiles

    Citation: Genome Biology 2020 21:168

    Content type: Research

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  2. High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largel...

    Authors: Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W.K. Ho, Richard P. Harvey and Kitty K. Lo

    Citation: Genome Biology 2020 21:167

    Content type: Method

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  3. Gene fusions have been studied extensively, as frequent drivers of tumorigenesis as well as potential therapeutic targets. In many well-known cases, breakpoints occur at two intragenic positions, leading to in...

    Authors: Jae Won Yun, Lixing Yang, Hye-Young Park, Chang-Woo Lee, Hongui Cha, Hyun-Tae Shin, Ka-Won Noh, Yoon-La Choi, Woong-Yang Park and Peter J. Park

    Citation: Genome Biology 2020 21:166

    Content type: Research

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  4. The functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA reveal...

    Authors: Rajiv K. Parvathaneni, Edoardo Bertolini, Md Shamimuzzaman, Daniel L. Vera, Pei-Yau Lung, Brian R. Rice, Jinfeng Zhang, Patrick J. Brown, Alexander E. Lipka, Hank W. Bass and Andrea L. Eveland

    Citation: Genome Biology 2020 21:165

    Content type: Research

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  5. Genomes computationally inferred from large metagenomic data sets are often incomplete and may be missing functionally important content and strain variation. We introduce an information retrieval system for l...

    Authors: C. Titus Brown, Dominik Moritz, Michael P. O’Brien, Felix Reidl, Taylor Reiter and Blair D. Sullivan

    Citation: Genome Biology 2020 21:164

    Content type: Method

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  6. Gene expression is a key determinant of cellular response. Natural variation in gene expression bridges genetic variation to phenotypic alteration. Identification of the regulatory variants controlling the gen...

    Authors: Shengxue Liu, Cuiping Li, Hongwei Wang, Shuhui Wang, Shiping Yang, Xiaohu Liu, Jianbing Yan, Bailin Li, Mary Beatty, Gina Zastrow-Hayes, Shuhui Song and Feng Qin

    Citation: Genome Biology 2020 21:163

    Content type: Research

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  7. Investigating genome evolution in response to therapy is difficult in human tissue samples. To address this challenge, we develop an unbiased whole-genome plasma DNA sequencing approach that concurrently measu...

    Authors: Naveen Ramesh, Emi Sei, Pei Ching Tsai, Shanshan Bai, Yuehui Zhao, Patricia Troncoso, Paul G. Corn, Christopher Logothetis, Amado J. Zurita and Nicholas E. Navin

    Citation: Genome Biology 2020 21:162

    Content type: Research

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  8. Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, an...

    Authors: Ruiwen Fan, Zhongru Gu, Xuanmin Guang, Juan Carlos Marín, Valeria Varas, Benito A. González, Jane C. Wheeler, Yafei Hu, Erli Li, Xiaohui Sun, Xukui Yang, Chi Zhang, Wenjun Gao, Junping He, Kasper Munch, Russel Corbett-Detig…

    Citation: Genome Biology 2020 21:159

    Content type: Research

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  9. The relationship between transcription and the 3D chromatin structure is debated. Multiple studies have shown that transcription affects global Cohesin binding and 3D genome structures. However, several other ...

    Authors: Yongpeng Jiang, Jie Huang, Kehuan Lun, Boyuan Li, Haonan Zheng, Yuanjun Li, Rong Zhou, Wenjia Duan, Chenlu Wang, Yuanqing Feng, Hong Yao, Cheng Li and Xiong Ji

    Citation: Genome Biology 2020 21:158

    Content type: Research

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  10. Haematopoietic stem cells (HSCs) first arise during development in the aorta-gonad-mesonephros (AGM) region of the embryo from a population of haemogenic endothelial cells which undergo endothelial-to-haematop...

    Authors: Giovanni Canu, Emmanouil Athanasiadis, Rodrigo A. Grandy, Jose Garcia-Bernardo, Paulina M. Strzelecka, Ludovic Vallier, Daniel Ortmann and Ana Cvejic

    Citation: Genome Biology 2020 21:157

    Content type: Research

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  11. The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methyla...

    Authors: C. Anthony Scott, Jack D. Duryea, Harry MacKay, Maria S. Baker, Eleonora Laritsky, Chathura J. Gunasekara, Cristian Coarfa and Robert A. Waterland

    Citation: Genome Biology 2020 21:156

    Content type: Research

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  12. Mapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). The advantages of this approach, and the mechanisms underlying ASM in norm...

    Authors: Catherine Do, Emmanuel L. P. Dumont, Martha Salas, Angelica Castano, Huthayfa Mujahed, Leonel Maldonado, Arunjot Singh, Sonia C. DaSilva-Arnold, Govind Bhagat, Soren Lehman, Angela M. Christiano, Subha Madhavan, Peter L. Nagy, Peter H. R. Green, Rena Feinman, Cornelia Trimble…

    Citation: Genome Biology 2020 21:153

    Content type: Research

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  13. Malignant transformation and progression of cancer are driven by the co-evolution of cancer cells and their dysregulated tumor microenvironment (TME). Recent studies on immunotherapy demonstrate the efficacy i...

    Authors: Jian Chen, Yun Tan, Fenghuan Sun, Likun Hou, Chi Zhang, Tao Ge, Huansha Yu, Chunxiao Wu, Yuming Zhu, Liang Duan, Liang Wu, Nan Song, Liping Zhang, Wei Zhang, Di Wang, Chang Chen…

    Citation: Genome Biology 2020 21:152

    Content type: Research

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  14. Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to ident...

    Authors: Anupama Jha, Joseph K. Aicher, Matthew R. Gazzara, Deependra Singh and Yoseph Barash

    Citation: Genome Biology 2020 21:149

    Content type: Method

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  15. Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of ...

    Authors: Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho and Romain Koszul

    Citation: Genome Biology 2020 21:148

    Content type: Software

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  16. 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

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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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

    Published on:

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

  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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

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  42. 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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