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  1. 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
  2. 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
  3. 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
  4. 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
  5. Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little i...

    Authors: Deyan Wang, Yiling Li, Mengmeng Li, Wenlu Yang, Xinzhi Ma, Lei Zhang, Yubo Wang, Yanlin Feng, Yuanyuan Zhang, Ran Zhou, Brian J. Sanderson, Ken Keefover-Ring, Tongming Yin, Lawrence B. Smart, Stephen P. DiFazio, Jianquan Liu…
    Citation: Genome Biology 2022 23:200
  6. Genomic safe harbors are regions of the genome that can maintain transgene expression without disrupting the function of host cells. Genomic safe harbors play an increasingly important role in improving the ef...

    Authors: Dewan Shrestha, Aishee Bag, Ruiqiong Wu, Yeting Zhang, Xing Tang, Qian Qi, Jinchuan Xing and Yong Cheng
    Citation: Genome Biology 2022 23:199
  7. Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. Fo...

    Authors: Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, Anthony Beucher, Daniel J. M. Crouch, Javier Garcia-Hurtado, Ignasi Moran, Manuel Irimia, Rashmi B. Prasad, Anna L. Gloyn, Lorella Marselli, Mara Suleiman, Thierry Berney, Eelco J. P. de Koning, Julie Kerr-Conte, Francois Pattou…
    Citation: Genome Biology 2022 23:196
  8. Genome-wide association studies do not always replicate well across populations, limiting the generalizability of polygenic risk scores (PRS). Despite higher incidence and mortality rates of prostate cancer in...

    Authors: Michelle S. Kim, Daphne Naidoo, Ujani Hazra, Melanie H. Quiver, Wenlong C. Chen, Corinne N. Simonti, Paidamoyo Kachambwa, Maxine Harlemon, Ilir Agalliu, Shakuntala Baichoo, Pedro Fernandez, Ann W. Hsing, Mohamed Jalloh, Serigne M. Gueye, Lamine Niang, Halimatou Diop…
    Citation: Genome Biology 2022 23:194
  9. Cytoplasmic polyadenylation element-binding protein 4 (CPEB4) is known to associate with cytoplasmic polyadenylation elements (CPEs) located in the 3′ untranslated region (UTR) of specific mRNAs and assemble a...

    Authors: Fabian Poetz, Svetlana Lebedeva, Johanna Schott, Doris Lindner, Uwe Ohler and Georg Stoecklin
    Citation: Genome Biology 2022 23:193
  10. Vertebrate CPEB proteins bind mRNAs at cytoplasmic polyadenylation elements (CPEs) in their 3′ UTRs, leading to cytoplasmic changes in their poly(A) tail lengths; this can promote translational repression or a...

    Authors: Berta Duran-Arqué, Manuel Cañete, Chiara Lara Castellazzi, Anna Bartomeu, Anna Ferrer-Caelles, Oscar Reina, Adrià Caballé, Marina Gay, Gianluca Arauz-Garofalo, Eulalia Belloc and Raúl Mendez
    Citation: Genome Biology 2022 23:192
  11. Crosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins ...

    Authors: Klara Kuret, Aram Gustav Amalietti, D. Marc Jones, Charlotte Capitanchik and Jernej Ule
    Citation: Genome Biology 2022 23:191
  12. A major challenge in neurodegenerative diseases concerns identifying biological disease signatures that track with disease progression or respond to an intervention. Several clinical trials in Huntington disea...

    Authors: Andreas Neueder, Kerstin Kojer, Tanja Hering, Daniel J. Lavery, Jian Chen, Nathalie Birth, Jaqueline Hallitsch, Sonja Trautmann, Jennifer Parker, Michael Flower, Huma Sethi, Salman Haider, Jong-Min Lee, Sarah J. Tabrizi and Michael Orth
    Citation: Genome Biology 2022 23:189
  13. Garlic is an entirely sterile crop with important value as a vegetable, condiment, and medicine. However, the evolutionary history of garlic remains largely unknown.

    Authors: Ningyang Li, Xueyu Zhang, Xiudong Sun, Siyuan Zhu, Yi Cheng, Meng Liu, Song Gao, Jiangjiang Zhang, Yanzhou Wang, Xiai Yang, Jianrong Chen, Fu Li, Qiaoyun He, Zheng Zeng, Xiaoge Yuan, Zhiman Zhou…
    Citation: Genome Biology 2022 23:188
  14. The PRDM9-dependent histone methylation H3K4me3 and H3K36me3 function in assuring accurate homologous recombination at recombination hotspots in mammals. Beyond histone methylation, H3 lysine 9 acetylation (H3...

    Authors: Shenli Yuan, Tao Huang, Ziyou Bao, Shiyu Wang, Xinyue Wu, Jiang Liu, Hongbin Liu and Zi-Jiang Chen
    Citation: Genome Biology 2022 23:187
  15. Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator ...

    Authors: Tom van Schaik, Ning Qing Liu, Stefano G. Manzo, Daan Peric-Hupkes, Elzo de Wit and Bas van Steensel
    Citation: Genome Biology 2022 23:185
  16. Out of the thousands of metabolites in a given specimen, most metabolomics experiments measure only hundreds, with poor overlap across experimental platforms. Here, we describe Metabolite Imputation via Rank-T...

    Authors: Benjamin A. Freeman, Sophie Jaro, Tricia Park, Sam Keene, Wesley Tansey and Ed Reznik
    Citation: Genome Biology 2022 23:184
  17. Crop improvement through cross-population genomic prediction and genome editing requires identification of causal variants at high resolution, within fewer than hundreds of base pairs. Most genetic mapping stu...

    Authors: Guillaume P. Ramstein and Edward S. Buckler
    Citation: Genome Biology 2022 23:183
  18. With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the computational challenge of efficiently and accurately constructing multiple genome alignments at an unprecedented scale. ...

    Authors: Bryce Kille, Advait Balaji, Fritz J. Sedlazeck, Michael Nute and Todd J. Treangen
    Citation: Genome Biology 2022 23:182
  19. RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin confor...

    Authors: Camille Fonouni-Farde, Aurélie Christ, Thomas Blein, María Florencia Legascue, Lucía Ferrero, Michaël Moison, Leandro Lucero, Juan Sebastián Ramírez-Prado, David Latrasse, Daniel Gonzalez, Moussa Benhamed, Leandro Quadrana, Martin Crespi and Federico Ariel
    Citation: Genome Biology 2022 23:181
  20. Maize (Zea mays L.) is at the vanguard facing the upcoming breeding challenges. However, both a super pan-genome for the Zea genus and a comprehensive genetic variation map for maize breeding are still lacking.

    Authors: Songtao Gui, Wenjie Wei, Chenglin Jiang, Jingyun Luo, Lu Chen, Shenshen Wu, Wenqiang Li, Yuebin Wang, Shuyan Li, Ning Yang, Qing Li, Alisdair R. Fernie and Jianbing Yan
    Citation: Genome Biology 2022 23:178
  21. Dyskerin is a nuclear protein involved in H/ACA box snoRNA-guided uridine modification of RNA. In humans, its defective function is associated with cancer development and induces specific post-transcriptional ...

    Authors: Federico Zacchini, Giulia Venturi, Veronica De Sanctis, Roberto Bertorelli, Claudio Ceccarelli, Donatella Santini, Mario Taffurelli, Marianna Penzo, Davide Treré, Alberto Inga, Erik Dassi and Lorenzo Montanaro
    Citation: Genome Biology 2022 23:177
  22. Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limit...

    Authors: Yuelin Yao, Shuli Liu, Charley Xia, Yahui Gao, Zhangyuan Pan, Oriol Canela-Xandri, Ava Khamseh, Konrad Rawlik, Sheng Wang, Bingjie Li, Yi Zhang, Erola Pairo-Castineira, Kenton D’Mellow, Xiujin Li, Ze Yan, Cong-jun Li…
    Citation: Genome Biology 2022 23:176
  23. We present a novel unsupervised deep learning approach called BindVAE, based on Dirichlet variational autoencoders, for jointly decoding multiple TF binding signals from open chromatin regions. BindVAE can dis...

    Authors: Meghana Kshirsagar, Han Yuan, Juan Lavista Ferres and Christina Leslie
    Citation: Genome Biology 2022 23:174
  24. Simple translocations and complex rearrangements are formed through illegitimate ligations of double-strand breaks of fusion partners and lead to generation of oncogenic fusion genes that affect cellular funct...

    Authors: Zhihao Xing, Huirong Mai, Xiaorong Liu, Xiaoying Fu, Xingliang Zhang, Lichun Xie, Yunsheng Chen, Adam Shlien and Feiqiu Wen
    Citation: Genome Biology 2022 23:173
  25. Recombination maps are  important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West Afri...

    Authors: Gerald van Eeden, Caitlin Uren, Evlyn Pless, Mira Mastoras, Gian D. van der Spuy, Gerard Tromp, Brenna M. Henn and Marlo Möller
    Citation: Genome Biology 2022 23:172
  26. A fused method using a combination of multi-omics data enables a comprehensive study of complex biological processes and highlights the interrelationship of relevant biomolecules and their functions. Driven by...

    Authors: Dongjin Leng, Linyi Zheng, Yuqi Wen, Yunhao Zhang, Lianlian Wu, Jing Wang, Meihong Wang, Zhongnan Zhang, Song He and Xiaochen Bo
    Citation: Genome Biology 2022 23:171
  27. Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportion...

    Authors: Iliana Soto, Mary Couvillion, Katja G. Hansen, Erik McShane, J. Conor Moran, Antoni Barrientos and L. Stirling Churchman
    Citation: Genome Biology 2022 23:170
  28. Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and ...

    Authors: Zheng Li and Xiang Zhou
    Citation: Genome Biology 2022 23:168
  29. Plants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramm...

    Authors: Hardik Kundariya, Robersy Sanchez, Xiaodong Yang, Alenka Hafner and Sally A. Mackenzie
    Citation: Genome Biology 2022 23:167
  30. Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is es...

    Authors: M. Senthil Kumar, Eric V. Slud, Christine Hehnly, Lijun Zhang, James Broach, Rafael A. Irizarry, Steven J. Schiff and Joseph N. Paulson
    Citation: Genome Biology 2022 23:166
  31. Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determine...

    Authors: Si-Cheng Liu, Yi-Li Feng, Xiu-Na Sun, Ruo-Dan Chen, Qian Liu, Jing-Jing Xiao, Jin-Na Zhang, Zhi-Cheng Huang, Ji-Feng Xiang, Guo-Qiao Chen, Yi Yang, Chao Lou, Hao-Dan Li, Zhen Cai, Shi-Ming Xu, Hui Lin…
    Citation: Genome Biology 2022 23:165
  32. Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA met...

    Authors: Alex de Mendoza, Trung Viet Nguyen, Ethan Ford, Daniel Poppe, Sam Buckberry, Jahnvi Pflueger, Matthew R. Grimmer, Sabine Stolzenburg, Ozren Bogdanovic, Alicia Oshlack, Peggy J. Farnham, Pilar Blancafort and Ryan Lister
    Citation: Genome Biology 2022 23:163
  33. Two-dimensional high-throughput data have become increasingly common in functional genomics studies, which raises new challenges in data analysis. Here, we introduce a new statistic called Zeta, initially deve...

    Authors: Yajing Hao, Shuyang Zhang, Changwei Shao, Junhui Li, Guofeng Zhao, Dong-Er Zhang and Xiang-Dong Fu
    Citation: Genome Biology 2022 23:162
  34. Low efficiency has seriously restricted the application of prime editing (PE) systems in plants. In this study, we develop an enhanced plant prime editor 2 system, enpPE2, by stacking various optimization stra...

    Authors: Juan Li, Like Chen, Jing Liang, Rongfang Xu, Yingli Jiang, Yizhen Li, Jian Ding, Min Li, Ruiying Qin and Pengcheng Wei
    Citation: Genome Biology 2022 23:161
  35. The most stable structure of DNA is the canonical right-handed double helix termed B DNA. However, certain environments and sequence motifs favor alternative conformations, termed non-canonical secondary struc...

    Authors: Ilias Georgakopoulos-Soares, Candace S. Y. Chan, Nadav Ahituv and Martin Hemberg
    Citation: Genome Biology 2022 23:159

    The Author Correction to this article has been published in Genome Biology 2022 23:164

  36. The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for point-of-care real-time...

    Authors: Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Yuval Dor, Aviad Zick, Amir Eden, Iacopo Petrini, Silvestro G. Conticello and Benjamin P. Berman
    Citation: Genome Biology 2022 23:158
  37. Authors: Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jefrey A. Borgia, Dana M. Hayden, Sam G. Pappas, Henry R. Govekar, Audrey E. Kam, Jochen Reiser, Kiran Turaga, Milan Radovich, Yong Zang…
    Citation: Genome Biology 2022 23:156

    The original article was published in Genome Biology 2022 23:113

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