DNA sequencing data
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We provide the first country record of Opisthotropis durandi Teynié, Lottier, David, Nguyen & Vogel, 2014 from Vietnam based on a single snake specimen from Dien Bien Province. The species previously was only known from the Lao People’s Democratic Republic (Laos). DNA sequence data of a male specimen from Vietnam match those of a specimen of O. durandi from Phongsali province, Laos, and the newly collected individual from Vietnam also corresponds to O. durandi in terms of diagnostic morphological features, except for a slightly higher ventral number (185 versus 177−181).
7p dianmotminh02 03-05-2024 5 1 Download
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The present study aims to identify Neofusicoccum isolates collected from lotus with symptoms of dieback, blight, and wilted leaves. Species were identified based on their morphology and comparison of the DNA sequence data for ITS rDNA and β-tubulin (tub-2). The taxonomy and phylogenetic relationships of pathogen isolates were investigated, and their pathogenic abilities were determined.
17p viritesh 02-04-2024 5 1 Download
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In this study, we characterised the evolutionary pattern of metastatic CRC (mCRC) by analysing bulk and single-cell exome sequencing data of primary and metastatic tumours from 7 CRC patients with liver metastases. Here, 7 CRC patients were analysed by bulk whole-exome sequencing (WES); 4 of these were also analysed using single-cell sequencing.
14p vibransone 28-03-2024 6 2 Download
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The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities.
21p viellison 28-03-2024 3 2 Download
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Variation in cell composition can dramatically impact analyses in bulk tissue samples. A commonly employed approach to mitigate this issue is to adjust statistical models using estimates of cell abundance derived directly from omics data.
14p vicwell 29-02-2024 3 1 Download
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Ebook "Pattern recognition in bioinformatics: 5th IAPR international conference, PRIB 2010 Nijmegen, The Netherlands, September 22-24, 2010 proceedings" has two main objectives: the creation and maintenance of biological databases and the analysis of life sciences data in order to unravel the mysteries of biological function. Computer science methods such as pattern recognition, machine learning, and data mining have a great deal to offer the field of bioinformatics.
458p tachieuhoa 28-01-2024 4 2 Download
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The study using molecular data from three DNA regions (matK, rbcL, and trnH-psbA) supported the monophyly of Melodinus. The M. cochinchinensis from Vietnam and China are closely related. There are some genetic variations in the sequences of Melodinus cochinchinensis from Belgium versus Asiatic M. cochinchinensis, as well as the phylogenetic position of the species, suggesting the possibility of misidentification of M. cochinchinensis from Belgium.
7p giangnhanly 02-10-2023 8 3 Download
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Advances in next generation sequencing allow us to do DNA sequencing rapidly at a relatively low cost. Multiple bioinformatics methods have been developed to identify genomic variants from whole genome or whole exome sequencing data. The development of better variant calling methodologies is limited by the difficulty of assessing the accuracy and completeness of a new method.
7p vicaptainmarvel 21-04-2023 5 2 Download
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In a previous study, a gene GL0694641 coding for endoglucanase containing 3 domains GH5- CBM72-CBM72 was exploited from metagenomic DNA data of bacteria in Vietnamese goats’ rumen. The gene (eg5) encoding the mature enzyme (without signal peptide coding sequence) was optimized codons, artificially synthesized, and inserted into the pET22b(+) vector at NcoI and XhoI to generate expression vector pET22-eg5 for expression of the gene in Eschrichia coli.
11p vicaptainmarvel 21-04-2023 5 2 Download
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Investigating population continuity with ancient DNA under a spatially explicit simulation framework
Recent advances in sequencing technologies have allowed for the retrieval of ancient DNA data (aDNA) from skeletal remains, providing direct genetic snapshots from diverse periods of human prehistory.
13p vinarcissa 21-03-2023 6 1 Download
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Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. Here, we analyzed genomic data collected from 136 Korean Native cattle, known as Hanwoo, using advanced statistical methods.
13p vinarcissa 21-03-2023 7 1 Download
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Double minute chromosomes are circular fragments of DNA whose presence is associated with the onset of certain cancers. Double minutes are lethal, as they are highly amplified and typically contain oncogenes. Locating double minutes can supplement the process of cancer diagnosis, and it can help to identify therapeutic targets.
7p vinarcissa 21-03-2023 3 1 Download
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Cellobiohydrolase (EC 3.2.1.91) is one of the important enzymes involved in cellulose hydrolysis. In this study, the gene sequences encoding cellobiohydrolase were extracted from the metagenome DNA data of microorganisms surrounding white-rot fungi in Cuc Phuong National Park based on the KEGG database. 73 ORFs encoding cellobiohydrolase were obtained, of which 15 ORFs contained complete genes, 6 ORFs with functional regions.
8p vineville 08-02-2023 5 1 Download
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Genome-wide association studies performed on triglycerides (TGs) have not accounted for epigenetic mechanisms that may partially explain trait heritability. Parent-of-origin (POO) effect association analyses using an agnostic approach or a candidate approach were performed for pretreatment TG levels, posttreatment TG levels, and pre-and posttreatment TG-level differences in the real GAW20 family data set.
5p vihagrid 30-01-2023 6 3 Download
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The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used.
14p vihagrid 30-01-2023 8 3 Download
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Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer–promoter links. We show that current enhancer–promoter inference methods produce a high rate of false positive links. We introduce FOCS, a new inference method, and by benchmarking against ChIAPET, HiChIP, and eQTL data show that it results in lower false discovery rates and at the same time higher inference power.
14p vimichaelfaraday 25-03-2022 13 1 Download
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Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease. However, Hi-C experiments are costly to perform and involve multiple complex experimental steps; thus, accurate methods for measuring the quality and reproducibility of Hi-C data are essential to determine whether the output should be used further in a study.
19p vigalileogalilei 27-02-2022 11 1 Download
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Accurate variant calling and genotyping represent major limiting factors for downstream applications of single-cell genomics. Here, we report Conbase for the identification of somatic mutations in single-cell DNA sequencing data.
18p vigalileogalilei 27-02-2022 9 1 Download
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Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association.
12p vigalileogalilei 27-02-2022 12 1 Download
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Despite the tremendous growth of the DNA sequencing data in the last decade, our understanding of the human genome is still in its infancy. To understand the implications of genetic variants in the light of population genetics and molecular evolution.
16p vielonmusk 30-01-2022 13 0 Download