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Relevant bibliographies by topics / Genomics bioinformatics variant discovery sequence analysis

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Academic literature on the topic 'Genomics bioinformatics variant discovery sequence analysis'

Author: Grafiati

Published: 14 March 2023

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Journal articles on the topic "Genomics bioinformatics variant discovery sequence analysis"

1

Ahmed, Zeeshan, Eduard Gibert Renart, and Saman Zeeshan. "Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping." PeerJ 9 (July 26, 2021): e11724. http://dx.doi.org/10.7717/peerj.11724.

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Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics

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2

Wiggans, G. R., D. J. Null, J. B. Cole, and H. D. Norman. "256 GENOMIC EVALUATION OF FERTILITY TRAITS AND DISCOVERY OF HAPLOTYPES THAT AFFECT FERTILITY OF US DAIRY CATTLE." Reproduction, Fertility and Development 28, no. 2 (2016): 260. http://dx.doi.org/10.1071/rdv28n2ab256.

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Genomic evaluations of dairy cattle became official in the United States in January 2009 for Holsteins and Jerseys, and later for Brown Swiss, Ayrshires, and Guernseys. Up to 33 yield, fitness, calving, and conformation traits are evaluated, and the fertility traits included daughter pregnancy rate and heifer and cow conception rates. Additional fertility traits, such as age at first calving and days from calving to first insemination, also are being studied. Male fertility (sire conception rate) is evaluated phenotypically rather than through genomics. Over 1 million animals have genotypes in

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3

Smith, Frances, David Brawand, Laura Steedman, et al. "A Comprehensive Next Generation Sequencing Gene Panel Focused on Unexplained Anemia." Blood 126, no. 23 (2015): 946. http://dx.doi.org/10.1182/blood.v126.23.946.946.

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Abstract Congenital anemia is difficult to diagnose once common causes have been excluded; for example 80% cases of congenital non-spherocytic hemolytic anemia are undiagnosed once pyruvate kinase and G6PD deficiencies have been excluded using phenotypic analysis. We describe a next generation sequencing strategy, targeting 147 genes, to facilitate the diagnosis of these conditions. The coding regions, splice sites and 200 bp into the untranslated regions were examined in each gene. All clinically significant variants were confirmed by Sanger sequencing, including confirmation in any appropria

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4

Bao, Riyue, Lei Huang, Jorge Andrade, et al. "Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing." Cancer Informatics 13s2 (January 2014): CIN.S13779. http://dx.doi.org/10.4137/cin.s13779.

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The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, preprocessing

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5

Yang, Junmeng, Anna Liu, Isabella He, and Yongsheng Bai. "Bioinformatics Analysis Revealed Novel 3′UTR Variants Associated with Intellectual Disability." Genes 11, no. 9 (2020): 998. http://dx.doi.org/10.3390/genes11090998.

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MicroRNAs (or miRNAs) are short nucleotide sequences (~17–22 bp long) that play important roles in gene regulation through targeting genes in the 3′untranslated regions (UTRs). Variants located in genomic regions might have different biological consequences in changing gene expression. Exonic variants (e.g., coding variant and 3′UTR variant) are often causative of diseases due to their influence on gene product. Variants harbored in the 3′UTR region where miRNAs perform their targeting function could potentially alter the binding relationships for target pairs, which could relate to disease ca

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6

Tremblay, Olivier, Zachary Thow, and A. Rod Merrill. "Several New Putative Bacterial ADP-Ribosyltransferase Toxins Are Revealed from In Silico Data Mining, Including the Novel Toxin Vorin, Encoded by the Fire Blight Pathogen Erwinia amylovora." Toxins 12, no. 12 (2020): 792. http://dx.doi.org/10.3390/toxins12120792.

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Mono-ADP-ribosyltransferase (mART) toxins are secreted by several pathogenic bacteria that disrupt vital host cell processes in deadly diseases like cholera and whooping cough. In the last two decades, the discovery of mART toxins has helped uncover the mechanisms of disease employed by pathogens impacting agriculture, aquaculture, and human health. Due to the current abundance of mARTs in bacterial genomes, and an unprecedented availability of genomic sequence data, mART toxins are amenable to discovery using an in silico strategy involving a series of sequence pattern filters and structural

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7

Alsamman, Alsamman M., Shafik D. Ibrahim, and Aladdin Hamwieh. "KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping." Bioinformatics 35, no. 17 (2019): 3187–90. http://dx.doi.org/10.1093/bioinformatics/btz004.

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Abstract Motivation Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool. Results To convert classical QTL markers int

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8

BLAXTER, M., M. ASLETT, D. GUILIANO, J. DAUB, and THE FILARIAL GENOME PROJECT. "Parasitic helminth genomics." Parasitology 118, no. 7 (1999): 39–51. http://dx.doi.org/10.1017/s0031182099004060.

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The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple cDNA libraries represent

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9

Karabayev, Daniyar, Askhat Molkenov, Kaiyrgali Yerulanuly, et al. "re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files." PeerJ 9 (May 3, 2021): e11333. http://dx.doi.org/10.7717/peerj.11333.

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Background High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation of genomics data becomes essential during the analysis of sequencing data. Different standard data types and file formats have been developed to store and analyze sequence and genomics data. Variant Call Format (VCF) is the most widespread genomics file type and standard format containing genomic information and variants of sequenced samples. Results Existing tools for proces

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10

Knight, Samantha JL, Ruth Clifford, Pauline Robbe, et al. "The Identification of Further Minimal Regions of Overlap in Chronic Lymphocytic Leukemia Using High-Resolution SNP Arrays." Blood 124, no. 21 (2014): 3315. http://dx.doi.org/10.1182/blood.v124.21.3315.3315.

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Abstract Background:Historically, the identification of minimal deleted regions (MDRs) has been a useful approach for pinpointing genes involved in the pathogenesis of human malignancies and constitutional disorders. Microarray technology has offered increased capability for newly identifying or refining existing MDRs and minimal overlapping regions (MORs) in cancer. Despite this, in chronic lymphocytic leukemia (CLL), published MORs that pinpoint only a few candidate genes have been limited and with the advent of NGS, the utility of high resolution array work as a discovery tool has become un

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