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  1. Naïve and primed pluripotent stem cells (PSCs) represent two different pluripotent states. Primed PSCs following in vitro culture exhibit lower developmental potency as evidenced by failure in germline chimera...

    Authors: Haifeng Fu, Weiyu Zhang, Niannian Li, Jiao Yang, Xiaoying Ye, Chenglei Tian, Xinyi Lu and Lin Liu

    Citation: Genome Biology 2021 22:201

    Content type: Research

    Published on:

  2. Recent studies highlight the role of metabolites in immune diseases, but it remains unknown how much of this effect is driven by genetic and non-genetic host factors.

    Authors: Xiaojing Chu, Martin Jaeger, Joep Beumer, Olivier B. Bakker, Raul Aguirre-Gamboa, Marije Oosting, Sanne P. Smeekens, Simone Moorlag, Vera P. Mourits, Valerie A. C. M. Koeken, Charlotte de Bree, Trees Jansen, Ian T. Mathews, Khoi Dao, Mahan Najhawan, Jeramie D. Watrous…

    Citation: Genome Biology 2021 22:198

    Content type: Research

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  3. Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we ...

    Authors: Melania Barile, Ivan Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C. Marioni, Carolina Guibentif and Berthold Göttgens

    Citation: Genome Biology 2021 22:197

    Content type: Research

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  4. In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strateg...

    Authors: Samuel M. Nicholls, Radoslaw Poplawski, Matthew J. Bull, Anthony Underwood, Michael Chapman, Khalil Abu-Dahab, Ben Taylor, Rachel M. Colquhoun, Will P. M. Rowe, Ben Jackson, Verity Hill, Áine O’Toole, Sara Rey, Joel Southgate, Roberto Amato, Rich Livett…

    Citation: Genome Biology 2021 22:196

    Content type: Editorial

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  5. There is no effective way to detect structure variations (SVs) and extra-chromosomal circular DNAs (ecDNAs) at single-cell whole-genome level. Here, we develop a novel third-generation sequencing platform-base...

    Authors: Xiaoying Fan, Cheng Yang, Wen Li, Xiuzhen Bai, Xin Zhou, Haoling Xie, Lu Wen and Fuchou Tang

    Citation: Genome Biology 2021 22:195

    Content type: Method

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  6. Biological aging estimators derived from DNA methylation data are heritable and correlate with morbidity and mortality. Consequently, identification of genetic and environmental contributors to the variation i...

    Authors: Daniel L. McCartney, Josine L. Min, Rebecca C. Richmond, Ake T. Lu, Maria K. Sobczyk, Gail Davies, Linda Broer, Xiuqing Guo, Ayoung Jeong, Jeesun Jung, Silva Kasela, Seyma Katrinli, Pei-Lun Kuo, Pamela R. Matias-Garcia, Pashupati P. Mishra, Marianne Nygaard…

    Citation: Genome Biology 2021 22:194

    Content type: Research

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  7. Transposable elements are increasingly recognized as a source of cis-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into...

    Authors: Julius Judd, Hayley Sanderson and Cédric Feschotte

    Citation: Genome Biology 2021 22:193

    Content type: Research

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  8. Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficien...

    Authors: Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Benedikt Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchis, Martin Vingron, Marina Chekulaeva…

    Citation: Genome Biology 2021 22:191

    Content type: Research

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  9. Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic...

    Authors: Laura Schulz, Manuel Torres-Diz, Mariela Cortés-López, Katharina E. Hayer, Mukta Asnani, Sarah K. Tasian, Yoseph Barash, Elena Sotillo, Kathi Zarnack, Julian König and Andrei Thomas-Tikhonenko

    Citation: Genome Biology 2021 22:190

    Content type: Short Report

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  10. N6-methyladenosine (m6A) is the most common RNA modification in eukaryotes and has been implicated as a novel epigenetic marker that is involved in various biological processes. The pattern and functional dissect...

    Authors: Kun Zhang, Xinjian Zhuang, Zhuozhuo Dong, Kai Xu, Xijun Chen, Fang Liu and Zhen He

    Citation: Genome Biology 2021 22:189

    Content type: Research

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  11. Single-cell RNA sequencing (scRNA-seq) has enabled the unbiased, high-throughput quantification of gene expression specific to cell types and states. With the cost of scRNA-seq decreasing and techniques for sa...

    Authors: Anna S. E. Cuomo, Giordano Alvari, Christina B. Azodi, Davis J. McCarthy and Marc Jan Bonder

    Citation: Genome Biology 2021 22:188

    Content type: Research

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  12. Drought threatens the food supply of the world population. Dissecting the dynamic responses of plants to drought will be beneficial for breeding drought-tolerant crops, as the genetic controls of these respons...

    Authors: Xi Wu, Hui Feng, Di Wu, Shijuan Yan, Pei Zhang, Wenbin Wang, Jun Zhang, Junli Ye, Guoxin Dai, Yuan Fan, Weikun Li, Baoxing Song, Zedong Geng, Wanli Yang, Guoxin Chen, Feng Qin…

    Citation: Genome Biology 2021 22:185

    Content type: Research

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  13. The human microbiome plays an important role in cancer. Accumulating evidence indicates that commensal microbiome-derived DNA may be represented in minute quantities in the cell-free DNA of human blood and cou...

    Authors: Enrique Zozaya-Valdés, Stephen Q. Wong, Jeanette Raleigh, Athena Hatzimihalis, Sarah Ftouni, Anthony T. Papenfuss, Shahneen Sandhu, Mark A. Dawson and Sarah-Jane Dawson

    Citation: Genome Biology 2021 22:187

    Content type: Research

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  14. TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (...

    Authors: Atsushi Onodera, Edahí González-Avalos, Chan-Wang Jerry Lio, Romain O. Georges, Alfonso Bellacosa, Toshinori Nakayama and Anjana Rao

    Citation: Genome Biology 2021 22:186

    Content type: Research

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  15. Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method f...

    Authors: Jiaqiang Zhu, Shiquan Sun and Xiang Zhou

    Citation: Genome Biology 2021 22:184

    Content type: Method

    Published on:

  16. Genetic variation in response to the environment, that is, genotype-by-environment interaction (GxE), is fundamental in the biology of complex traits and diseases. However, existing methods are computationally...

    Authors: Jisu Shin and Sang Hong Lee

    Citation: Genome Biology 2021 22:183

    Content type: Method

    Published on:

  17. Long-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq. We present LIQA to quantify isofo...

    Authors: Yu Hu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li and Kai Wang

    Citation: Genome Biology 2021 22:182

    Content type: Method

    Published on:

  18. Authors: Nisha Padmanabhan, Huang Kie Kyon, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-Ok Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Ong Xuewen, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee…

    Citation: Genome Biology 2021 22:181

    Content type: Author Correction

    Published on:

    The original article was published in Genome Biology 2021 22:167

  19. Canonical nonsense-mediated decay (NMD) is an important splicing-dependent process for mRNA surveillance in mammals. However, processed pseudogenes are not able to trigger NMD due to their lack of introns. It ...

    Authors: Liqiang Tan, Weisheng Cheng, Fang Liu, Dan Ohtan Wang, Linwei Wu, Nan Cao and Jinkai Wang

    Citation: Genome Biology 2021 22:180

    Content type: Research

    Published on:

  20. Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived...

    Authors: Zhi-Qiang Chen, Yanjun Zan, Pascal Milesi, Linghua Zhou, Jun Chen, Lili Li, BinBin Cui, Shihui Niu, Johan Westin, Bo Karlsson, Maria Rosario García-Gil, Martin Lascoux and Harry X. Wu

    Citation: Genome Biology 2021 22:179

    Content type: Research

    Published on:

    The Publisher Correction to this article has been published in Genome Biology 2021 22:210

  21. Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects an...

    Authors: Askarbek Orakov, Anthony Fullam, Luis Pedro Coelho, Supriya Khedkar, Damian Szklarczyk, Daniel R. Mende, Thomas S. B. Schmidt and Peer Bork

    Citation: Genome Biology 2021 22:178

    Content type: Method

    Published on:

  22. Early DNA replication occurs within actively transcribed chromatin compartments in mammalian cells, raising the immediate question of how early DNA replication coordinates with transcription to avoid collision...

    Authors: Yang Liu, Chen Ai, Tingting Gan, Jinchun Wu, Yongpeng Jiang, Xuhao Liu, Rusen Lu, Ning Gao, Qing Li, Xiong Ji and Jiazhi Hu

    Citation: Genome Biology 2021 22:176

    Content type: Research

    Published on:

  23. The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and...

    Authors: Guifang Lin, Cheng He, Jun Zheng, Dal-Hoe Koo, Ha Le, Huakun Zheng, Tej Man Tamang, Jinguang Lin, Yan Liu, Mingxia Zhao, Yangfan Hao, Frank McFraland, Bo Wang, Yang Qin, Haibao Tang, Donald R. McCarty…

    Citation: Genome Biology 2021 22:175

    Content type: Research

    Published on:

  24. The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated molecules, thereby facilitating the counting of distinct molecules from se...

    Authors: Johan Gustafsson, Jonathan Robinson, Jens Nielsen and Lior Pachter

    Citation: Genome Biology 2021 22:174

    Content type: Method

    Published on:

  25. Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still unde...

    Authors: Mayra Furlan-Magaril, Masami Ando-Kuri, Rodrigo G. Arzate-Mejía, Jörg Morf, Jonathan Cairns, Abraham Román-Figueroa, Luis Tenorio-Hernández, A. César Poot-Hernández, Simon Andrews, Csilla Várnai, Boo Virk, Steven W. Wingett and Peter Fraser

    Citation: Genome Biology 2021 22:162

    Content type: Research

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  26. Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studi...

    Authors: Étienne Fafard-Couture, Danny Bergeron, Sonia Couture, Sherif Abou-Elela and Michelle S. Scott

    Citation: Genome Biology 2021 22:172

    Content type: Research

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  27. Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required ...

    Authors: Claudia Vivori, Panagiotis Papasaikas, Ralph Stadhouders, Bruno Di Stefano, Anna Ribó Rubio, Clara Berenguer Balaguer, Serena Generoso, Anna Mallol, José Luis Sardina, Bernhard Payer, Thomas Graf and Juan Valcárcel

    Citation: Genome Biology 2021 22:171

    Content type: Research

    Published on:

  28. Prime editors, novel genome-editing tools consisting of a CRISPR-Cas9 nickase and an engineered reverse transcriptase, can induce targeted mutagenesis. Nevertheless, much effort is required to optimize and imp...

    Authors: Soo-Ji Park, Tae Yeong Jeong, Seung Kyun Shin, Da Eun Yoon, Soo-Yeon Lim, Sol Pin Kim, Jungmin Choi, Hyunji Lee, Jeong-Im Hong, Jinhee Ahn, Je Kyung Seong and Kyoungmi Kim

    Citation: Genome Biology 2021 22:170

    Content type: Short Report

    Published on:

  29. Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays to allow diagnosis and prevention of transmission. Reverse transcription-polymerase chain reaction (RT-PCR) provi...

    Authors: Scott Sherrill-Mix, Young Hwang, Aoife M. Roche, Abigail Glascock, Susan R. Weiss, Yize Li, Leila Haddad, Peter Deraska, Caitlin Monahan, Andrew Kromer, Jevon Graham-Wooten, Louis J. Taylor, Benjamin S. Abella, Arupa Ganguly, Ronald G. Collman, Gregory D. Van Duyne…

    Citation: Genome Biology 2021 22:169

    Content type: Research

    Published on:

  30. Epigenetic mark such as DNA methylation plays pivotal roles in regulating ripening of both climacteric and non-climacteric fruits. However, it remains unclear whether mRNA m6A methylation, which has been shown to...

    Authors: Leilei Zhou, Renkun Tang, Xiaojing Li, Shiping Tian, Bingbing Li and Guozheng Qin

    Citation: Genome Biology 2021 22:168

    Content type: Research

    Published on:

  31. CIMP (CpG island methylator phenotype) is an epigenetic molecular subtype, observed in multiple malignancies and associated with the epigenetic silencing of tumor suppressors. Currently, for most cancers inclu...

    Authors: Nisha Padmanabhan, Huang Kie Kyon, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-Ok Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Ong Xuewen, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee…

    Citation: Genome Biology 2021 22:167

    Content type: Research

    Published on:

    The Author Correction to this article has been published in Genome Biology 2021 22:181

  32. Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid spec...

    Authors: Xu Cai, Lichun Chang, Tingting Zhang, Haixu Chen, Lei Zhang, Runmao Lin, Jianli Liang, Jian Wu, Michael Freeling and Xiaowu Wang

    Citation: Genome Biology 2021 22:166

    Content type: Research

    Published on:

  33. Advancing RNA structural probing techniques with next-generation sequencing has generated demands for complementary computational tools to robustly extract RNA structural information amidst sampling noise and ...

    Authors: Paolo Marangio, Ka Ying Toby Law, Guido Sanguinetti and Sander Granneman

    Citation: Genome Biology 2021 22:165

    Content type: Method

    Published on:

  34. High-throughput chromosome conformation capture assays, such as Hi-C, have shown that the genome is organized into organizational units such as topologically associating domains (TADs), which can impact gene r...

    Authors: Da-Inn Lee and Sushmita Roy

    Citation: Genome Biology 2021 22:164

    Content type: Method

    Published on:

  35. A pressing challenge in single-cell transcriptomics is to benchmark experimental protocols and computational methods. A solution is to use computational simulators, but existing simulators cannot simultaneousl...

    Authors: Tianyi Sun, Dongyuan Song, Wei Vivian Li and Jingyi Jessica Li

    Citation: Genome Biology 2021 22:163

    Content type: Method

    Published on:

    The Publisher Correction to this article has been published in Genome Biology 2021 22:177

  36. Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence ali...

    Authors: Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan and Ryan M. Layer

    Citation: Genome Biology 2021 22:161

    Content type: Method

    Published on:

  37. Elevated temperatures can cause physiological, biochemical, and molecular responses in plants that can greatly affect their growth and development. Mutations are the most fundamental force driving biological e...

    Authors: Zhaogeng Lu, Jiawen Cui, Li Wang, Nianjun Teng, Shoudong Zhang, Hon-Ming Lam, Yingfang Zhu, Siwei Xiao, Wensi Ke, Jinxing Lin, Chenwu Xu and Biao Jin

    Citation: Genome Biology 2021 22:160

    Content type: Research

    Published on:

  38. Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome. However, few studies have examined the role of SVs in high-altitude adaptation and little...

    Authors: Cheng Quan, Yuanfeng Li, Xinyi Liu, Yahui Wang, Jie Ping, Yiming Lu and Gangqiao Zhou

    Citation: Genome Biology 2021 22:159

    Content type: Research

    Published on:

  39. treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or le...

    Authors: Ruizhu Huang, Charlotte Soneson, Pierre-Luc Germain, Thomas S.B. Schmidt, Christian Von Mering and Mark D. Robinson

    Citation: Genome Biology 2021 22:157

    Content type: Method

    Published on:

  40. Lung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development. However, the ...

    Authors: Chongze Yuan, Haojie Chen, Shiqi Tu, Hsin-Yi Huang, Yunjian Pan, Xiuqi Gui, Muyu Kuang, Xuxia Shen, Qiang Zheng, Yang Zhang, Chao Cheng, Hui Hong, Xiaoting Tao, Yizhou Peng, Xingxin Yao, Feilong Meng…

    Citation: Genome Biology 2021 22:156

    Content type: Research

    Published on:

  41. Nascent RNA profiling is growing in popularity; however, there is no standard analysis pipeline to uniformly process the data and assess quality. Here, we introduce PEPPRO, a comprehensive, scalable workflow f...

    Authors: Jason P. Smith, Arun B. Dutta, Kizhakke Mattada Sathyan, Michael J. Guertin and Nathan C. Sheffield

    Citation: Genome Biology 2021 22:155

    Content type: Software

    Published on:

  42. The majority of pancreatic ductal adenocarcinomas (PDAC) are diagnosed at the metastatic stage, and standard therapies have limited activity with a dismal 5-year survival rate of only 8%. The liver and lung ar...

    Authors: Won Jin Ho, Rossin Erbe, Ludmila Danilova, Zaw Phyo, Emma Bigelow, Genevieve Stein-O’Brien, Dwayne L. Thomas II, Soren Charmsaz, Nicole Gross, Skylar Woolman, Kayla Cruz, Rebecca M. Munday, Neeha Zaidi, Todd D. Armstrong, Marcelo B. Sztein, Mark Yarchoan…

    Citation: Genome Biology 2021 22:154

    Content type: Research

    Published on:

  43. Most research articles presenting new data analysis methods claim that “the new method performs better than existing methods,” but the veracity of such statements is questionable. Our manuscript discusses and ...

    Authors: Stefan Buchka, Alexander Hapfelmeier, Paul P. Gardner, Rory Wilson and Anne-Laure Boulesteix

    Citation: Genome Biology 2021 22:152

    Content type: Short Report

    Published on:

  44. Androgen receptor (AR) is critical to the initiation, growth, and progression of prostate cancer. Once activated, the AR binds to cis-regulatory enhancer elements on DNA that drive gene expression. Yet, there ...

    Authors: Chia-Chi Flora Huang, Shreyas Lingadahalli, Tunc Morova, Dogancan Ozturan, Eugene Hu, Ivan Pak Lok Yu, Simon Linder, Marlous Hoogstraat, Suzan Stelloo, Funda Sar, Henk van der Poel, Umut Berkay Altintas, Mohammadali Saffarzadeh, Stephane Le Bihan, Brian McConeghy, Bengul Gokbayrak…

    Citation: Genome Biology 2021 22:149

    Content type: Research

    Published on:

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