ArticleBioData mining2013
Unraveling genomic variation from next generation sequencing data.
Article in BioData mining, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Pharmacogenomics-Based Detection of Variants Involved in Pain, Anti-inflammatory and Immunomodulating Agents Pathways by Whole Exome Sequencing and DeepIranian journal of medical sciences · 2025Article
- BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.Microbiome · 2023Article
- Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery.Cells · 2023Review
- Correlation between CRISPR Loci Diversity in Three Enterobacterial Taxa.International journal of molecular sciences · 2022Article
- Revolutionized virome research using systems microbiology approaches.Experimental biology and medicine (Maywood, N.J.) · 2022Review
- Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern.BMC plant biology · 2022Article
- Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants.American journal of human genetics · 2021Article
- Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing.Biology · 2020Review
- Protocols for the Analysis of microRNA Expression, Biogenesis, and Function in Immune Cells.Current protocols in immunology · 2019Article
- Bipartite graphs in systems biology and medicine: a survey of methods and applications.GigaScience · 2018Review
- Genome-wide comparative analysis of four Indian Drosophila species.Molecular genetics and genomics : MGG · 2017Article
- Comparative genomics of Tunisian Leishmania major isolates causing human cutaneous leishmaniasis with contrasting clinical severity.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2017Article
- Impact of germline and somatic missense variations on drug binding sites.The pharmacogenomics journal · 2017Article
- Article
- Article
- A review of genome-wide association studies for multiple sclerosis: classical and hypothesis-driven approaches.Human genetics · 2015Review
- Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.Bioinformatics and biology insights · 2015Review
- Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.GigaScience · 2015Review
- Best practices for evaluating single nucleotide variant calling methods for microbial genomics.Frontiers in genetics · 2015Review
- Whole genome sequencing in pharmacogenomics.Frontiers in pharmacology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elucidating the content of a DNA sequence is critical to deeper understand and decode the genetic information for any biological system. As next generation sequencing (NGS) techniques have become cheaper and more advanced in throughput over time, great innovations and breakthrough conclusions have been generated in various biological areas. Few of these areas, which get shaped by the new technological advances, involve evolution of species, microbial mapping, population genetics, genome-wide association studies (GWAs), comparative genomics, variant analysis, gene expression, gene regulation, epigenetics and personalized medicine. While NGS techniques stand as key players in modern biological research, the analysis and the interpretation of the vast amount of data that gets produced is a not an easy or a trivial task and still remains a great challenge in the field of bioinformatics. Therefore, efficient tools to cope with information overload, tackle the high complexity and provide meaningful visualizations to make the knowledge extraction easier are essential. In this article, we briefly refer to the sequencing methodologies and the available equipment to serve these analyses and we describe the data formats of the files which get produced by them. We conclude with a thorough review of tools developed to efficiently store, analyze and visualize such data with emphasis in structural variation analysis and comparative genomics. We finally comment on their functionality, strengths and weaknesses and we discuss how future applications could further develop in this field.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.