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  1. Despite having been extensively studied, it remains largely unclear why humans bear a particularly high risk of cancer. The antagonistic pleiotropy hypothesis predicts that primate-specific genes (PSGs) tend t...

    Authors: Chenyu Ma, Chunyan Li, Huijing Ma, Daqi Yu, Yufei Zhang, Dan Zhang, Tianhan Su, Jianmin Wu, Xiaoyue Wang, Li Zhang, Chun-Long Chen and Yong E. Zhang
    Citation: Genome Biology 2022 23:251
  2. DNA N6-methyldeoxyadenosine (6mA) is rarely present in mammalian cells and its nuclear role remains elusive.

    Authors: Kai-Wen Hsu, Joseph Chieh-Yu Lai, Jeng-Shou Chang, Pei-Hua Peng, Ching-Hui Huang, Der-Yen Lee, Yu-Cheng Tsai, Chi-Jung Chung, Han Chang, Chao-Hsiang Chang, Ji-Lin Chen, See-Tong Pang, Ziyang Hao, Xiao-Long Cui, Chuan He and Kou-Juey Wu
    Citation: Genome Biology 2022 23:249
  3. We present SIEVE, a statistical method for the joint inference of somatic variants and cell phylogeny under the finite-sites assumption from single-cell DNA sequencing. SIEVE leverages raw read counts for all ...

    Authors: Senbai Kang, Nico Borgsmüller, Monica Valecha, Jack Kuipers, Joao M. Alves, Sonia Prado-López, Débora Chantada, Niko Beerenwinkel, David Posada and Ewa Szczurek
    Citation: Genome Biology 2022 23:248
  4. DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capa...

    Authors: Roberto Rossini, Vipin Kumar, Anthony Mathelier, Torbjørn Rognes and Jonas Paulsen
    Citation: Genome Biology 2022 23:247
  5. Mammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear.

    Authors: Yongpeng Jiang, Jie Huang, Kai Tian, Xiao Yi, Haonan Zheng, Yi Zhu, Tiannan Guo and Xiong Ji
    Citation: Genome Biology 2022 23:246
  6. Heat-imposed crop failure is often attributed to reduced thermotolerance of floral tissues; however, the underlying mechanism remains unknown. Here, we demonstrate that m6A RNA methylation increases in Arabidopsi...

    Authors: Ling Wang, Haiyan Zhuang, Wenwen Fan, Xia Zhang, Haihong Dong, Hongxing Yang and Jungnam Cho
    Citation: Genome Biology 2022 23:244
  7. Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genom...

    Authors: Marina Brasó-Vives, Ferdinand Marlétaz, Amina Echchiki, Federica Mantica, Rafael D. Acemel, José L. Gómez-Skarmeta, Diego A. Hartasánchez, Lorlane Le Targa, Pierre Pontarotti, Juan J. Tena, Ignacio Maeso, Hector Escriva, Manuel Irimia and Marc Robinson-Rechavi
    Citation: Genome Biology 2022 23:243
  8. Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. ...

    Authors: Tom L. Kaufmann, Marina Petkovic, Thomas B. K. Watkins, Emma C. Colliver, Sofya Laskina, Nisha Thapa, Darlan C. Minussi, Nicholas Navin, Charles Swanton, Peter Van Loo, Kerstin Haase, Maxime Tarabichi and Roland F. Schwarz
    Citation: Genome Biology 2022 23:241
  9. There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but relia...

    Authors: Julianne K. David, Sean K. Maden, Mary A. Wood, Reid F. Thompson and Abhinav Nellore
    Citation: Genome Biology 2022 23:240
  10. The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been ad...

    Authors: Chunlin Xiao, Zhong Chen, Wanqiu Chen, Cory Padilla, Michael Colgan, Wenjun Wu, Li-Tai Fang, Tiantian Liu, Yibin Yang, Valerie Schneider, Charles Wang and Wenming Xiao
    Citation: Genome Biology 2022 23:237
  11. Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that ...

    Authors: Jasmijn A. Baaijens, Alessandro Zulli, Isabel M. Ott, Ioanna Nika, Mart J. van der Lugt, Mary E. Petrone, Tara Alpert, Joseph R. Fauver, Chaney C. Kalinich, Chantal B. F. Vogels, Mallery I. Breban, Claire Duvallet, Kyle A. McElroy, Newsha Ghaeli, Maxim Imakaev, Malaika F. Mckenzie-Bennett…
    Citation: Genome Biology 2022 23:236
  12. Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patte...

    Authors: Zhikai Liang, Zachary A. Myers, Dominic Petrella, Julia Engelhorn, Thomas Hartwig and Nathan M. Springer
    Citation: Genome Biology 2022 23:234
  13. Regulation of gene expression plays an essential role in controlling the phenotypes of plants. Brassica napus (B. napus) is an important source for the vegetable oil in the world, and the seed oil content is an i...

    Authors: Zengdong Tan, Yan Peng, Yao Xiong, Feng Xiong, Yuting Zhang, Ning Guo, Zhuo Tu, Zhanxiang Zong, Xiaokun Wu, Jiang Ye, Chunjiao Xia, Tao Zhu, Yinmeng Liu, Hongxiang Lou, Dongxu Liu, Shaoping Lu…
    Citation: Genome Biology 2022 23:233
  14. Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, moun...

    Authors: Jianqi She, Minghao Du, Zhanzhan Xu, Yueqi Jin, Yu Li, Daoning Zhang, Changyu Tao, Jian Chen, Jiadong Wang and Ence Yang
    Citation: Genome Biology 2022 23:231
  15. Overweight and obesity are defined by an anomalous or excessive fat accumulation that may compromise health. To find single-nucleotide polymorphisms (SNPs) influencing metabolic phenotypes associated with the ...

    Authors: Lara P. Fernández, Nerea Deleyto-Seldas, Gonzalo Colmenarejo, Alba Sanz, Sonia Wagner, Ana Belén Plata-Gómez, Mónica Gómez-Patiño, Susana Molina, Isabel Espinosa-Salinas, Elena Aguilar-Aguilar, Sagrario Ortega, Osvaldo Graña-Castro, Viviana Loria-Kohen, Pablo J. Fernández-Marcos, Alejo Efeyan and Ana Ramírez de Molina
    Citation: Genome Biology 2022 23:230
  16. Single-cell DNA methylation profiling currently suffers from excessive noise and/or limited cellular throughput. We developed scTAM-seq, a targeted bisulfite-free method for profiling up to 650 CpGs in up to 1...

    Authors: Agostina Bianchi, Michael Scherer, Roser Zaurin, Kimberly Quililan, Lars Velten and Renée Beekman
    Citation: Genome Biology 2022 23:229
  17. CRISPR tools can generate knockout and knock-in animal models easily, but the models can contain off-target genomic lesions or random insertions of donor DNAs. Simpler methods to identify off-target lesions an...

    Authors: Masayuki Tanaka, Keiko Yokoyama, Hideki Hayashi, Sanae Isaki, Kanae Kitatani, Ting Wang, Hisako Kawata, Hideyuki Matsuzawa, Channabasavaiah B. Gurumurthy, Hiromi Miura and Masato Ohtsuka
    Citation: Genome Biology 2022 23:228
  18. Comprehensive characterisation of genome engineering technologies is relevant for their development and safe use in human gene therapy. Short-read based methods can overlook insertion events in repetitive regi...

    Authors: Dimitrije Ivančić, Júlia Mir-Pedrol, Jessica Jaraba-Wallace, Núria Rafel, Avencia Sanchez-Mejias and Marc Güell
    Citation: Genome Biology 2022 23:227
  19. RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance...

    Authors: Elisabeth Meyer, Kaitlin Chaung, Roozbeh Dehghannasiri and Julia Salzman
    Citation: Genome Biology 2022 23:226
  20. DNA methylation (DNAm)-based predictors hold great promise to serve as clinical tools for health interventions and disease management. While these algorithms often have high prediction accuracy, the consistenc...

    Authors: Anil P. S. Ori, Ake T. Lu, Steve Horvath and Roel A. Ophoff
    Citation: Genome Biology 2022 23:225
  21. A major driver of cancer chromosomal instability is replication stress, the slowing or stalling of DNA replication. How replication stress and genomic instability are connected is not known. Aphidicolin-induce...

    Authors: Nadeem Shaikh, Alice Mazzagatti, Simone De Angelis, Sarah C. Johnson, Bjorn Bakker, Diana C. J. Spierings, René Wardenaar, Eleni Maniati, Jun Wang, Michael A. Boemo, Floris Foijer and Sarah E. McClelland
    Citation: Genome Biology 2022 23:223
  22. The rapid accumulation of single-cell RNA sequencing (scRNA-seq) data presents unique opportunities to decode the genetically mediated cell-type specificity in complex diseases. Here, we develop a new method, ...

    Authors: Peilin Jia, Ruifeng Hu, Fangfang Yan, Yulin Dai and Zhongming Zhao
    Citation: Genome Biology 2022 23:220
  23. In this study, we propose iDNA-ABF, a multi-scale deep biological language learning model that enables the interpretable prediction of DNA methylations based on genomic sequences only. Benchmarking comparisons...

    Authors: Junru Jin, Yingying Yu, Ruheng Wang, Xin Zeng, Chao Pang, Yi Jiang, Zhongshen Li, Yutong Dai, Ran Su, Quan Zou, Kenta Nakai and Leyi Wei
    Citation: Genome Biology 2022 23:219
  24. The early embryonic divisions of many organisms, including fish, flies, and frogs, are characterized by a very rapid S-phase caused by high rates of replication initiation. In somatic cells, S-phase is much lo...

    Authors: Miguel M. Santos, Mark C. Johnson, Lukáš Fiedler and Philip Zegerman
    Citation: Genome Biology 2022 23:217
  25. DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigeneti...

    Authors: Jonathan Higham, Lyndsay Kerr, Qian Zhang, Rosie M. Walker, Sarah E. Harris, David M. Howard, Emma L. Hawkins, Anca-Larisa Sandu, J. Douglas Steele, Gordon D. Waiter, Alison D. Murray, Kathryn L. Evans, Andrew M. McIntosh, Peter M. Visscher, Ian J. Deary, Simon R. Cox…
    Citation: Genome Biology 2022 23:216
  26. Earth’s environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isola...

    Authors: Jon G. Sanders, Weiwei Yan, Deus Mjungu, Elizabeth V. Lonsdorf, John A. Hart, Crickette M. Sanz, David B. Morgan, Martine Peeters, Beatrice H. Hahn and Andrew H. Moeller
    Citation: Genome Biology 2022 23:212
  27. We present two methods for enhancing the efficiency of mitochondrial DNA (mtDNA) editing in mice with DddA-derived cytosine base editors (DdCBEs). First, we fused DdCBEs to a nuclear export signal (DdCBE-NES) ...

    Authors: Seonghyun Lee, Hyunji Lee, Gayoung Baek, Eunji Namgung, Joo Min Park, Sanghun Kim, Seongho Hong and Jin-Soo Kim
    Citation: Genome Biology 2022 23:211
  28. Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for nor...

    Authors: Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier and Curtis Huttenhower
    Citation: Genome Biology 2022 23:208
  29. Histone lactylation has been recently described as a novel histone post-translational modification linking cellular metabolism to epigenetic regulation.

    Authors: Eva Galle, Chee-Wai Wong, Adhideb Ghosh, Thibaut Desgeorges, Kate Melrose, Laura C. Hinte, Daniel Castellano-Castillo, Magdalena Engl, Joao Agostinho de Sousa, Francisco Javier Ruiz-Ojeda, Katrien De Bock, Jonatan R. Ruiz and Ferdinand von Meyenn
    Citation: Genome Biology 2022 23:207
  30. During normal zygotic division, two haploid parental genomes replicate, unite and segregate into two biparental diploid blastomeres.

    Authors: Tine De Coster, Heleen Masset, Olga Tšuiko, Maaike Catteeuw, Yan Zhao, Nicolas Dierckxsens, Ainhoa Larreategui Aparicio, Eftychia Dimitriadou, Sophie Debrock, Karen Peeraer, Marta de Ruijter-Villani, Katrien Smits, Ann Van Soom and Joris Robert Vermeesch
    Citation: Genome Biology 2022 23:201
  31. False duplications in genome assemblies lead to false biological conclusions. We quantified false duplications in popularly used previous genome assemblies for platypus, zebra finch, and Anna’s Hummingbird, an...

    Authors: Byung June Ko, Chul Lee, Juwan Kim, Arang Rhie, Dong Ahn Yoo, Kerstin Howe, Jonathan Wood, Seoae Cho, Samara Brown, Giulio Formenti, Erich D. Jarvis and Heebal Kim
    Citation: Genome Biology 2022 23:205
  32. Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as com...

    Authors: Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M. Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V. Mello, Seoae Cho…
    Citation: Genome Biology 2022 23:204
  33. The laboratory mouse was domesticated from the wild house mouse. Understanding the genetics underlying domestication in laboratory mice, especially in the widely used classical inbred mice, is vital for studie...

    Authors: Ming Liu, Caixia Yu, Zhichao Zhang, Mingjing Song, Xiuping Sun, Jaroslav Piálek, Jens Jacob, Jiqi Lu, Lin Cong, Hongmao Zhang, Yong Wang, Guoliang Li, Zhiyong Feng, Zhenglin Du, Meng Wang, Xinru Wan…
    Citation: Genome Biology 2022 23:203
  34. Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic l...

    Authors: Stephen J. Clark, Ricard Argelaguet, Tim Lohoff, Felix Krueger, Deborah Drage, Berthold Göttgens, John C. Marioni, Jennifer Nichols and Wolf Reik
    Citation: Genome Biology 2022 23:202

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