Protocol to Identify Unknown Flanking DNA Using Partially Overlapping Primer-based PCR for Genome Walking by Mengya Jia, Dongqin Ding, Xiaohua Liu, Haixing Li

“…Genome walking is a popular molecular technique for accessing unknown flanking DNAs, which has been widely used in biology-related fields. …”
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Genome-wide association study of myofiber type composition traits in a yellow-feather broiler population by Chengyu Fan, Yanju Shan, Ming Zhang, Yunjie Tu, Gaige Ji, Xiaojun Ju, Jingting Shu, Yifan Liu

Subjects: “…Genome-wide association study…”
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Genome-Wide Identification of Genes Probably Relevant to the Uniqueness of Tea Plant (Camellia sinensis) and Its Cultivars by Yan Wei, Wang Jing, Zhou Youxiang, Zhao Mingming, Gong Yan, Ding Hua, Peng Lijun, Hu Dingjin

“…International Journal of Genomics…”
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Copy Number Variation of UGT 2B Genes in Indian Families Using Whole Genome Scans by Avinash M. Veerappa, Prakash Padakannaya, Nallur B. Ramachandra

“…We investigated the presence of CNVs in UGT2B genes in 31 members from eight Indian families using Affymetrix Genome-Wide Human SNP Array 6.0 chip. Results. Our data revealed >50% of the study members carried CNVs in UGT2B genes, of which 76% showed deletion polymorphism. …”
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Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant <i>Escherichia coli</i> Isolated in Kazakhstan by Pavel G. Alexyuk, Andrey P. Bogoyavlenskiy, Yergali S. Moldakhanov, Kuralay S. Akanova, Adolat N. Manakbayeva, Timur Kerimov, Vladimir E. Berezin, Madina S. Alexyuk

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Blood Genomics Identifies Three Subtypes of Systemic Lupus Erythematosus: “IFN-High,” “NE-High,” and “Mixed” by Mintian Cui, Taotao Li, Xinwei Yan, Chao Wang, Qi Shen, Hongbiao Ren, Liangshuang Li, Ruijie Zhang

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Mitochondrial genome insights into the phylogenetics and biogeographic evolution of snow trout (Cyprinidae, Schizothorax) in the Tien Shan Mountains by Akbarjon Rozimov, Yufan Wang, Min Wang, Ming Zou, Jobir Sobirov, Erkin Karimov, Bakhtiyor Kholmatov, Jörg Freyhof, Sirojiddin Namozov, Chongnv Wang, Xinxin Li, Baocheng Guo

“…These genomes range from 16,584 to 16,592 bp in length and include 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs, and a control region. …”
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Parallel algorithm for sensitive sequence recognition from long-read genome data with high error rate by Cheng ZHONG, Hui SUN

“…To solve the problem that existing algorithms were difficult to effectively identify sensitive sequences in genomic data for long-read with high error rate, a recognition algorithm using hybrid CPU and GPU parallel computing, called CGPU-F3SR, was proposed.Firstly, the long-read in genomic data were partitioned into multiple short-read, and the Bloom filtering mechanism was used to avoid repeated calculation of the short-read.Secondly, the k-mer coding strategy was used to extract in parallel the error information of all short-read, the recognition accuracy was promoted by improving the sequence similarity calculation model.Finally, CPU and GPU were used to coordinate and parallel to accelerate the calculation of short-read similarity to improve recognition efficiency.As a result, both two types of sensitive sequences including short tandem repeats and disease related sequences could be identified efficiently and accurately from genome data for long-read with high error rate.The experimental results of recognizing sensitive sequences from genomic data for long-read with length 100～400 kbp each show that, compared with existing parallel algorithm, the average recognition accuracy and precision rate of proposed CPU/GPU parallel algorithm CGPU-F3SR are increased by 7.77% and 43.07% respectively, its average false positive rate is reduced by 7.41%, and its average recognition throughput is increased by 2.44 times.…”
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Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae) by Ru Wang, Yongjian Luo, Zheng Lan, Daoshou Qiu

“…While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. …”
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Three-dimensional linkage analysis with digital PCR for genome integrity and identity of recombinant adeno-associated virus by Tam Duong, Michele Firmo, Chien-Ting Li, Bingnan Gu, Peng Wang

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Novel Genomic Aberrations in Testicular Germ Cell Tumors by Array-CGH, and Associated Gene Expression Changes by Rolf I. Skotheim, Reija Autio, Guro E. Lind, Sigrid M. Kraggerud, Peter W. Andrews, Outi Monni, Olli Kallioniemi, Ragnhild A. Lothe

“…Conclusion: This first genome-wide integrated array-CGH and gene expression profiling of TGCT provides novel insights into the genome biology underlying testicular tumorigenesis.…”
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Whole-genome sequencing reveals transmission pattern and drug resistance of Mycobacterium tuberculosis intra- or inter-hosts by Feng Ding, Wanfei Liu, Chi Wu, Chi Wu, Wensi Zhang, Shuyan Chen, Shuyan Chen, Wenjie Lai, Wenjie Lai, Jiayao Qu, Jiayao Qu, Qiang Lin, Shuihua Lu, Jiuxin Qu, Jiuxin Qu

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Taming wild genomes: perspectives on mechanisms governing differential introgression in exotic rice germplasm and their applications in breeding by Avinash Shrestha, Christian J. Stephens, Rosalyn B. Angeles-Shim

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Genomic Analysis of a Serotype 5 Streptococcus pneumoniae Outbreak in British Columbia, Canada, 2005–2009 by Ruth R. Miller, Morgan G. I. Langille, Vincent Montoya, Anamaria Crisan, Aleksandra Stefanovic, Irene Martin, Linda Hoang, David M. Patrick, Marc Romney, Gregory Tyrrell, Steven J. M. Jones, Fiona S. L. Brinkman, Patrick Tang

“…Two isolates representing the beginning and end of the outbreak were whole-genome sequenced. The sequences were analyzed for single nucleotide variants (SNVs) and putative genomic islands. …”
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A genomic analysis of twinning rate and its relationship with other reproductive traits in Holstein-Friesian cattle by Brian W. Kirkpatrick, Donagh P. Berry

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Evaluating Genomic Selection in beef cattle: Insights from computer simulations using real SNP data by Lino César Ramírez Ayala, Jordi Leno-Colorado, Laura M. Zingaretti, Elies Ramón Gurrea, Yuliaxis Ramayo-Caldas, Miguel Pérez-Enciso

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Genome Analysis of Pass2 a Semi-Automated Database of Protein Alignments Organised as Structural Superfamilies by Anirban Bhaduri, V. Mallika, R. Sowdhamini

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Defective homologous recombination and genomic instability predict increased responsiveness to carbon ion radiotherapy in pancreatic cancer by Brock J. Sishc, Janapriya Saha, Elizabeth M. Alves, Lianghao Ding, Huiming Lu, Shih-Ya Wang, Katy L. Swancutt, James H. Nicholson, Angelica Facoetti, Arnold Pompos, Mario Ciocca, Todd A. Aguilera, Michael D. Story, Anthony J. Davis

“…Increased radiosensitivity was linked to impaired DNA double-strand break (DSB) repair, particularly in cell lines with deficiencies in the homologous recombination (HR) repair pathway and/or elevated genomic instability from replication stress. Furthermore, pretreatment with the HR inhibitor B02 significantly enhanced CIRT sensitivity in a radioresistant PDAC cell line when irradiated in the spread-out Bragg peak but not at the entry position of the beam. …”
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Sequencing whole genomes of the West Javanese population in Indonesia reveals novel variants and improves imputation accuracy by Edwin Ardiansyah, Anca-Lelia Riza, Sofiati Dian, Sofiati Dian, Ahmad Rizal Ganiem, Ahmad Rizal Ganiem, Bachti Alisjahbana, Bachti Alisjahbana, Todia P. Setiabudiawan, Arjan van Laarhoven, Reinout van Crevel, Vinod Kumar, Vinod Kumar

Subjects: “…whole genome sequencing…”
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Complete chloroplast genome of eight Phaius (Orchidaceae) species from China: comparative analysis and phylogenetic relationship by Kaifeng Tao, Lu Tang, Yan Luo, Lu Li

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