Cytokinin Oxidase (CKX) Family Members in ‘duli’ (<i>Pyrus betulifolia Bunge</i>): Genome-Wide Identification and Tissue Expression Profile Under Abiotic Stress by Weimin Wang, Ting Xie, Jiaojiao He, Kuozhen Nie, Zijuan He, Yuxing Zhang, Yingli Li

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Corrigendum: Development of a 50K SNP array for whole-genome analysis and its application in the genetic localization of eggplant (Solanum melongena L.) fruit shape by Chuying Yu, Qihong Yang, Weiliu Li, Yaqin Jiang, Guiyun Gan, Liangyu Cai, Xinchun Li, Zhiqiang Li, Wenjia Li, Min Zou, Yang Yang, Yikui Wang

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Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism by Annamalai Muthiah, Susanna R. Keller, Jae K. Lee

“…International Journal of Genomics…”
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MOLECULAR MARKERS IN GENETIC STUDIES AND BREEDING by E. K. Khlestkina

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Antibiotic susceptibility and molecular characterization based on whole-genome sequencing of Staphylococcus aureus causing invasive infection in children and women living in Southwest China during 2018–2023 by Li Liu, Ziyi Yan, Fumei He, Jie Chen, Linghan Kuang, Xingxin Liu, Yali Cui, Xia Wang, Chenglin Miao, Hong Li, Yongmei Jiang

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Human_SNP_TATAdb: a database of SNPs that statistically significantly change the affinity of the TATA-binding protein to human gene promoters: genome-wide analysis and use cases by S. V. Filonov, N. L. Podkolodnyy, O. A. Podkolodnaya, N. N. Tverdokhleb, P. M. Ponomarenko, D. A. Rasskazov, A. G. Bogomolov, M. P. Ponomarenko

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Whole Genome Identification and Integrated Analysis of Long Non-Coding RNAs Responding ABA-Mediated Drought Stress in <i>Panax ginseng</i> C.A. Meyer by Peng Chen, Cheng Chang, Lingyao Kong

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Saprotrophic Wood Decay Ability and Plant Cell Wall Degrading Enzyme System of the White Rot Fungus <i>Crucibulum laeve</i>: Secretome, Metabolome and Genome Investigations by Alexander V. Shabaev, Olga S. Savinova, Konstantin V. Moiseenko, Olga A. Glazunova, Tatyana V. Fedorova

“…Multiple copies of the family AA1_1, AA3_2, AA7 and LPMOs CAZyme genes, as well as eight genes encoding proteins of the YvrE superfamily (COG3386), which includes sugar lactone lactonases, were predicted in the <i>C. laeve</i> genome. According to metabolic pathway analysis, the litter saprotroph <i>C. laeve</i> can catabolize D-gluconic and D-galacturonic acids, and possibly other aldonic acids, which seems to confer certain ecological advantages.…”
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Collection of SARS-CoV-2 Virus from the Air of a Clinic within a University Student Health Care Center and Analyses of the Viral Genomic Sequence by John A. Lednicky, Sripriya N. Shankar, Maha A. Elbadry, Julia C. Gibson, Md. Mahbubul Alam, Caroline J. Stephenson, Arantzazu Eiguren-Fernandez, J. Glenn Morris, Carla N. Mavian, Marco Salemi, James R. Clugston, Chang-Yu Wu

“…Abstract The progression of COVID-19 worldwide can be tracked by identifying mutations within the genomic sequence of SARS-CoV-2 that occur as a function of time. …”
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Highly Variable Genomic Landscape of Endogenous Retroviruses in the C57BL/6J Inbred Strain, Depending on Individual Mouse, Gender, Organ Type, and Organ Location by Kang-Hoon Lee, Debora Lim, David Greenhalgh, Kiho Cho

“…International Journal of Genomics…”
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Production and characterization of nervous necrosis virus vaccine antigens in wild type and CRISPR/Cas9 genome edited Nicotiana benthamiana and edible crop lettuce Lactuca sativa by Iva Andrasevic, Hang Su, Espen Rimstad, Jihong Liu Clarke

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Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia by Andriansjah Rukmana, Cynthia Gozali, Linda Erlina

“…All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein–Jensen medium culture and then sequenced. …”
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Genome-wide identification and expression analysis of bHLH gene family revealed their potential roles in abiotic stress response, anthocyanin biosynthesis and trichome formation in Glycyrrhiza uralensis by Guohua Ding, Yanping Shi, Kerui Xie, Hongbin Li, Guanghui Xiao

“…Despite this, the comprehensive characteristics of licorice bHLH gene family are not well-documented.ResultsIn this study, a detailed and thorough genome-wide identification and expression analysis of Glycyrrhiza uralensis bHLH gene family was carried out, resulting in the identification of 139 licorice bHLH members. …”
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Characterization of the genomic landscape of canine diffuse large B-cell lymphoma reveals recurrent H3K27M mutations linked to progression-free survival by Anna Darlene van der Heiden, Raphaela Pensch, Sophie Agger, Heather L. Gardner, William Hendricks, Victoria Zismann, Shukmei Wong, Natalia Briones, Bryce Turner, Karin Forsberg-Nilsson, Cheryl London, Kerstin Lindblad-Toh, Maja Louise Arendt

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COVID-19 Whole-Genome Resequencing with Redundant Tiling PCR and Subtract-Based Amplicon Normalization Successfully Characterized SARS-CoV-2 Variants in Clinical Specimens by Tatsuki Sugi, Mizanur Rahman, Rummana Rahim, Abu Hasan, Naoko Kawai, Kyoko Hayashida, Junya Yamagishi

“…With an increasing number of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) sequences gathered worldwide, we recognize that deletion mutants and nucleotide substitutions that may affect whole-genome sequencing are accumulating. Here, we propose an additional strategy for tiling PCR for whole-genome resequencing, which can make the pipeline robust for mutations at the primer annealing site by a redundant amplicon scheme. …”
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Genome-wide identification and expression analysis of CBF/DREB1 gene family in Medicago sativa L. and functional verification of MsCBF9 affecting flowering time by Jing Cui, Yajing Li, Hao Liu, Xu Jiang, Lili Zhang, Hongbo Dai, Xue Wang, Fei He, Mingna Li, Junmei Kang

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Complete Genome Sequence of Photobacterium damselae Subsp. damselae Strain SSPD1601 Isolated from Deep-Sea Cage-Cultured Sebastes schlegelii with Septic Skin Ulcer by Yongxiang Yu, Zheng Zhang, Yingeng Wang, Meijie Liao, Xiaojun Rong, Bin Li, Kai Wang, Jing Chen, Hao Zhang

“…International Journal of Genomics…”
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Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland by Anna Tumeo, Francesca McDonagh, Aneta Kovarova, Kate Ryan, Christina Clarke, Georgios Miliotis

“…Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). …”
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A Review of the Psyllid Genus <i>Epipsylla</i> (Hemiptera, Psyllidae) from the Chinese Mainland with Phylogenetic Considerations and the Description of a New Species by Zhixin He, Daniel Burckhardt, Xinyu Luo, Rongzhen Xu, Wanzhi Cai, Fan Song

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Endometrial Receptivity–Lessons from “Omics” by Louie Ye, Evdokia Dimitriadis

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