Integrating multi-layered biological priors to improve genomic prediction accuracy in beef cattle by Zhida Zhao, Qunhao Niu, Jiayuan Wu, Tianyi Wu, Xueyuan Xie, Zezhao Wang, Lupei Zhang, Huijiang Gao, Xue Gao, Lingyang Xu, Bo Zhu, Junya Li

“…Abstract Background Integrating multi-layered information can enhance the accuracy of genomic prediction for complex traits. However, the improvement and application of effective strategies for genomic prediction (GP) using multi-omics data remains challenging. …”
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Dissecting the genetic architecture of sunflower disc diameter using genome‐wide association study by Yavuz Delen, Ravi V. Mural, Semra Palali‐Delen, Gen Xu, James C. Schnable, Ismail Dweikat, Jinliang Yang

“…Using these SNPs and the disc diameter phenotype, we conducted a genome‐wide association study (GWAS) employing two statistical approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU). …”
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The complete chloroplast genome of Viola vaginata (Violaceae), an endemic species of the snowy region in Japan by Yayoi Takahashi, Masato Fujiwara, Masaaki Ozeki, Masayuki U. Saito, Takaya Iwasaki

Subjects: “…Chloroplast genome…”
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First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale by Ivan Tsers, Ekaterina Marenina, Azat Meshcherov, Olga Petrova, Olga Gogoleva, Alexander Tkachenko, Natalia Gogoleva, Yuri Gogolev, Evgenii Potapenko, Olga Muraeva, Mira Ponomareva, Viktor Korzun, Vladimir Gorshkov

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The complete mitochondrial genome and phylogenetic analyses of Cathartes melambrotus (Wetmore 1964) (Aves: Cathartidae) by Robert Driver, Renee Li

“…The complete mitochondrial genome of C. melambrotus was reported in this study. …”
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Chromosome-level genome assembly and annotation of the gynogenetic large-scale loach (Paramisgurnus dabryanus) by Lei Zhang, Wanting Zhang, Yingyin Cheng, Yutong Fang, Xin Guan, Ao Gong, Yanxin Jiang, You Duan, Lei Huang, Waqar Younas, Yaping Wang, Mijuan Shi, Xiao-Qin Xia

“…However, the lack of a high-quality reference genome has hindered further research. In this study, we performed PacBio HiFi and Hi-C sequencing on a female (ZW) specimen and assembled the first high-quality chromosome-level genome of the large-scale loach. …”
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Genome-Wide Identification and Characterization of the LRR-RLK Gene Family in Two Vernicia Species by Huiping Zhu, Yangdong Wang, Hengfu Yin, Ming Gao, Qiyan Zhang, Yicun Chen

“…International Journal of Genomics…”
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Identification of the clinical and genetic characteristics of gliomas with gene fusions by integrated genomic and transcriptomic analysis by Guo-zhong Yi, Hua-yang Zhang, Tian-shi Que, Shan-qiang Qu, Zhi-yong Li, Song-tao Qi, Wen-yan Feng, Guang-long Huang

“…This study identified detectable oncogene fusions in glioma patients through an integrated analysis of genomic and transcriptomic data, which encompassed whole exon sequencing and next-generation RNA sequencing. …”
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De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses by Donglai Xiao, Lu Ma, Chi Yang, Zhenghe Ying, Xiaoling Jiang, Yan-quan Lin

“…As a conclusion, the genome content of S. latifolia sheds light on its genetic basis of the reported medicinal properties and could also be used as a reference genome for comparative studies on fungi.…”
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Combining genomics and epidemiology to investigate a zoonotic outbreak of rabies in Romblon Province, Philippines by Mirava Yuson, Criselda T. Bautista, Eleanor M. Rees, Carlijn Bogaardt, Van Denn D. Cruz, Rowan Durrant, Anna Formstone, Daria L. Manalo, Duane R. Manzanilla, Mikolaj Kundergorski, Leilanie Nacion, Hannaniah Aloyon, Jude Karlo Bolivar, Jeromir Bondoc, Christina Cobbold, Efraim Panganiban, Shynie Vee. M. Telmo, Jobin Maestro, Mary Elizabeth G. Miranda, Nai Rui Chng, Kirstyn Brunker, Katie Hampson

“…Using Integrated Bite Case Management (IBCM) and whole genome sequencing (WGS), we enhanced rabies surveillance to detect an outbreak in a formerly rabies-free island province in the Philippines. …”
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Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker by Mariana Papalia, Rocio Stucchi, Valeria Alexander, Liliana Clara, Mariángeles Visus, Gabriel Gutkind, Marcela Radice

“…Objective: To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants. …”
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CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics by Young-Kyu Park, Tae-Wook Kang, Su-Jin Baek, Kwon-Il Kim, Seon-Young Kim, Doheon Lee, Yong Sung Kim

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Importance of integrating epidemiological and genomic surveillance of seasonal influenza viruses to monitor global circulation by Zhiyuan Chen, Hongjie Yu

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Human-genome single nucleotide polymorphisms affecting transcription factor binding and their role in pathogenesis by E. V. Antontseva, A. O. Degtyareva, E. E. Korbolina, I. S. Damarov, T. I. Merkulova

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Trajectory inference from single-cell genomics data with a process time model. by Meichen Fang, Gennady Gorin, Lior Pachter

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Genome-Wide and Gene-Specific Epigenomic Platforms for Hepatocellular Carcinoma Biomarker Development Trials by Christina Michailidi, Ethan Soudry, Mariana Brait, Leonel Maldonado, Andrew Jaffe, Carmen Ili-Gangas, Priscilla Brebi-Mieville, Jimena Perez, Myoung Sook Kim, Xiaoli Zhong, Quiang Yang, Blanca Valle, Stephen J. Meltzer, Michael Torbenson, Manel Esteller, David Sidransky, Rafael Guerrero-Preston

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Pre-T cell receptor-α immunodeficiency detected exclusively using whole genome sequencing by Daniele Merico, Nigel Sharfe, Harjit Dadi, Bhooma Thiruvahindrapuram, Jill de Rijke, Zakia Dahi, Mehdi Zarrei, Abdulrahman Al Ghamdi, Azhar Al Shaqaq, Linda Vong, Stephen W. Scherer, Chaim M. Roifman

“…npj Genomic Medicine…”
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A Chromosome-level genome assembly of the alpine medicinal plant Bergenia purpurascens (Saxifragaceae) by Xue-Die Liu, Alex D. Twyford, Peter M. Hollingsworth, Ya-Huang Luo, Sheng-Ping Ming, Bo-Yun Yang, Lian-Ming Gao, Shao-Lin Tan

“…Repeat sequences accounted for 56.72% of the genome. The reference genome of B. purpurascens serves as a valuable resource for studying bergenin biosynthesis, and understanding adaptation of plants to alpine environments.…”
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Comparative Genome Characterization of a Petroleum-Degrading Bacillus subtilis Strain DM2 by Shi-Weng Li, Meng-Yuan Liu, Rui-Qi Yang

“…International Journal of Genomics…”
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A high-quality chromosome-scale genome assembly of the Cherokee rose (Rosa laevigata) by Yi Wang, Huijun Yan, Xianqin Qiu, Hao Zhang, Yonghong Zhang, Hongying Jian

“…Repeat annotation revealed 659,558 (285.6 Mb) repeat elements, accounting for 57.8% of the genome. The chromosome-scale genome provides valuable information to facilitate comparative genomic analysis of rose family and will accelerate genome-guided breeding and germplasm improvement of both R. laevigata itself and modern roses.…”
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