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  1. One challenge facing omics association studies is the loss of statistical power when adjusting for confounders and multiple testing. The traditional statistical procedure involves fitting a confounder-adjusted...

    Authors: Sangyoon Yi, Xianyang Zhang, Lu Yang, Jinyan Huang, Yuanhang Liu, Chen Wang, Daniel J. Schaid and Jun Chen
    Citation: Genome Biology 2021 22:208
  2. Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication st...

    Authors: Yongzheng Li, Boxin Xue, Mengling Zhang, Liwei Zhang, Yingping Hou, Yizhi Qin, Haizhen Long, Qian Peter Su, Yao Wang, Xiaodong Guan, Yanyan Jin, Yuan Cao, Guohong Li and Yujie Sun
    Citation: Genome Biology 2021 22:206
  3. Authors: Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud-Nissen, James K. Biedler, Flavia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna-Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie…
    Citation: Genome Biology 2021 22:205

    The original article was published in Genome Biology 2020 21:215

  4. The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, provi...

    Authors: Lingzhan Xue, Yu Gao, Meiying Wu, Tian Tian, Haiping Fan, Yongji Huang, Zhen Huang, Dapeng Li and Luohao Xu
    Citation: Genome Biology 2021 22:203
  5. GRIDSS2 is the first structural variant caller to explicitly report single breakends—breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic re...

    Authors: Daniel L. Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclan, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley and Anthony T. Papenfuss
    Citation: Genome Biology 2021 22:202
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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

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

  24. 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
  25. 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

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

  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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

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

  37. 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
  38. 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
  39. 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
  40. 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

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

  41. 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
  42. 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
  43. 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
  44. 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
  45. 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

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