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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Related Experiment Video

Updated: Jul 24, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
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HiCognition: a visual exploration and hypothesis testing tool for 3D genomics.

Christoph C H Langer1, Michael Mitter1, Roman R Stocsits2

  • 1Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.

Genome Biology
|July 5, 2023
PubMed
Summary

HiCognition integrates 3D genome structure with 1D genomics data for pattern discovery. This machine learning tool reveals insights into genome structure-function relationships.

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Last Updated: Jul 24, 2025

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome browsers offer limited visualization of genomic regions and lack statistical analysis capabilities.
  • Understanding the interplay between 3D chromosome conformation and 1D genomic profiles is crucial for deciphering genome function.

Purpose of the Study:

  • To introduce HiCognition, a novel tool for visual exploration and machine learning analysis of genomic data.
  • To enable the detection of patterns and associations between 3D chromosome conformation and diverse 1D genomics profiles.
  • To facilitate the investigation of how molecular components influence genome structure and function.

Main Methods:

  • Development of a new genomic region set concept for data organization.
  • Implementation of a flexible user interface for visual exploration.
  • Integration of machine learning algorithms for pattern detection and association analysis.

Main Results:

  • HiCognition successfully visualizes and analyzes multiple genomics datasets, overcoming limitations of traditional genome browsers.
  • The tool facilitates the identification of patterns and associations between 3D chromosome conformation and 1D genomics profiles.
  • Demonstrated the utility of HiCognition in revealing the contribution of transcription factors and cohesion subunits to chromosome conformation.

Conclusions:

  • HiCognition provides a powerful platform for exploring complex genomic data, integrating 3D structure with 1D profiles.
  • The tool's machine learning capabilities enhance the discovery of meaningful biological insights from genomic datasets.
  • HiCognition advances our understanding of the intricate relationship between genome architecture and cellular function.