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Genetic sequence database
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Although large-scale, next-generation sequencing (NGS) studies of cancers hold promise for enabling precision oncology, challenges remain in integrating NGS with clinically validated biomarkers. To overcome such challenges, we utilized the Database of Evidence for Precision Oncology (DEPO) to link druggability to genomic, transcriptomic, and proteomic biomarkers.
20p
vibransone
28-03-2024
3
2
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Here, we present the Northeast Asian Reference Database (NARD), including whole-genome sequencing data of 1779 individuals from Korea, Mongolia, Japan, China, and Hong Kong. NARD provides the genetic diversity of Korean (n = 850) and Mongolian (n = 384) ancestries that were not present in the 1000 Genomes Project Phase 3 (1KGP3).
10p
vibransone
28-03-2024
2
2
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In this study, we sequenced the chloroplast gene region (matK) to identify the genetic characteristics of T. chantrieri and their phylogenetic inference in the genus Tacca in Ba Vi National Park (Ba Vi NP). This study contributes to developing a DNA barcode database as a foundation for conservation, evolution, and biological systems.
11p
viblackwidow
07-04-2023
11
3
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The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses.
17p
vinarcissa
21-03-2023
5
1
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The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway.
10p
vinarcissa
21-03-2023
2
1
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Biodiversity assessment approaches based on molecular biology techniques such as metabarcoding, RAD-seq, or SnaPshot sequencing are increasingly applied in assessing marine and aquatic ecosystems. Here we present a new reference database for fsh meta-barcoding based on mitochondrial genes.
12p
vinarcissa
21-03-2023
3
1
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Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data.
4p
vihagrid
30-01-2023
8
3
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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
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This study aimed to identify potential biomarkers, by means of bioinformatics, affecting the occurrence and development of septic shock. Methods: Download GSE131761 septic shock data set from NCBI geo database, including 33 control samples and 81 septic shock samples. GSE131761 and sequencing data were used to identify and analyze differentially expressed genes in septic shock patients and normal subjects.
13p
vihagrid
30-01-2023
8
3
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Here we release a new version of EchinoDB, EchinoDB v2.0 (https://echinodb.uncc.edu). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.
16p
vihagrid
30-01-2023
9
3
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An important application of modern genomics is diagnosing genetic disorders. We use the largest publicly available exome sequence database to show that this key clinical service can currently be performed much more effectively in individuals of European genetic ancestry.
3p
viaristotle
29-01-2022
6
0
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The study included 114 postmenopausal osteoporosis patients. BMD was measured in the lumbar spine and the femoral neck. Genetic analysis was performed using Sanger sequencing. Genotypes data for 263 female European population group were obtained from the 1000Genomes database.
7p
lazzaro
30-12-2021
8
0
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Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breeding. In the model plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR content has become possible now because several Nicotiana genomes have been sequenced. We conducted a genomewide SSR characterization and marker development across seven Nicotiana genomes.
12p
vibeauty
23-10-2021
8
1
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Euplotes, a ciliated protozoan, is a useful unicellular model organism. Studies on Euplotes have provided excellent insights into various basic biological principles. We have recently sequenced the macronuclear genome of the common freshwater species Euplotes octocarinatus to provide novel insights into Euplotes genetics and molecular biology.
6p
vibeauty
23-10-2021
9
1
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Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far.
13p
vitzuyu2711
29-09-2021
14
1
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Research purpose: Determine the composition, structure of mitochondrial genome, compare the difference in sequence, identify specific genetic characteristics of the six indigenous pig breeds, thereby contributing to the database to identification and conservation.
27p
extraenglish
24-05-2021
17
4
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Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines.
13p
vijichea2711
28-05-2021
7
1
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Breast cancer is one of the leading causes of cancer-related deaths in women, and there is a demand in developing an Asian-based genetic profiling database for breast cancer in improving the treatment response.
14p
vianrose2711
27-04-2021
6
1
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Collecting complete data of mitochondrial genome of 6 indigenous pig breeds in Vietnam (I, Mong Cai, Muong Lay, Huong, Muong Khuong and Ha Lang pigs) and deposited on the Genebank; determine the composition, structure of mitochondrial genome, compare the difference in sequence, identify specific genetic characteristics of the six indigenous pig breeds, thereby contributing to the database to identification and conservation.
27p
capheviahe26
25-01-2021
13
3
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Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence.
12p
vikentucky2711
24-11-2020
7
1
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