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Related Concept Videos

Categories and Inductive Inferences10:08

Categories and Inductive Inferences

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Source: Laboratories of Nicholaus Noles and Judith Danovitch—University of Louisville
It might be possible for the human brain to keep track of each individual person, place, or thing encountered, but that would be a very inefficient use of time and cognitive resources. Instead, humans develop categories. Categories are mental representations of real things that can be used for a variety of purposes. For example, individuals can use the perceptual features of animals to place them into a...
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HIV tropism can be inferred from the V3 region of the viral envelope. V3 is PCR amplified in triplicate using nested RT-PCR, sequenced, and interpreted using bioinformatic software. Samples with with 1 or more sequence(s) with low g2P scores are classified as non-R5...
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Methylation at CpG dinucleotides is a chemical modification of DNA hypothesized to play important roles in regulating gene expression. In particular, the methylation of clusters of methylation sites, called “CpG islands”, near promoters and other gene regulatory elements may contribute to the stable silencing of genes, for example, during epigenetic processes such as genomic imprinting and X-chromosome inactivation. At the same time, aberrant CpG methylation has been shown to be...
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Enhanced Reduced Representation Bisulfite Sequencing is a method for the preparation of sequencing libraries for DNA methylation analysis based on restriction enzyme digestion combined with cytosine bisulfite conversion. This protocol requires 50 ng of starting material and yields base pair resolution data at GC-rich genomic...
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This experimental protocol demonstrates the use of virtual prism adaptation therapy (VPAT) in healthy adults and the association between VPAT and functional near infrared spectroscopy to determine the effect of VPAT on cortical activation. Results suggest that VPAT may be feasible and could induce similar behavioral adaptation as conventional prism adaptation...
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Related Experiment Video

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How Children Categorize Objects and Make Inductive Inferences
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PRISM: methylation pattern-based, reference-free inference of subclonal makeup.

Dohoon Lee1, Sangseon Lee2, Sun Kim1,2,3

  • 1Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.

Bioinformatics (Oxford, England)
|September 13, 2019
PubMed
Summary
This summary is machine-generated.

PRISM is a new tool that analyzes DNA methylation patterns to identify cancer subclones. This method reveals tumor evolutionary history from an epigenetic perspective, aiding in cancer research.

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Related Experiment Videos

Last Updated: Jan 19, 2026

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Area of Science:

  • Computational biology
  • Epigenetics
  • Cancer genomics

Background:

  • Characterizing cancer subclones is vital for cancer treatment.
  • Existing bioinformatics tools primarily use mutations and copy number variations.
  • DNA methylation reprogramming is significant in myeloid malignancies, but tools to analyze subclonally reprogrammed methylation are lacking.

Purpose of the Study:

  • To develop a bioinformatics tool, PRISM, for inferring tumor subclone composition using DNA methylation patterns.
  • To address the gap in analyzing subclonally reprogrammed methylation for tumor subpopulation identification.

Main Methods:

  • PRISM utilizes DNA methylation patterns from reduced representation bisulfite sequencing.
  • It employs a hidden Markov model for in silico correction of methylation patterns.
  • A beta-binomial mixture model and expectation-maximization algorithm are used to infer subclone composition.

Main Results:

  • PRISM successfully infers the composition of epigenetically distinct tumor subclones.
  • The tool corrects erroneous methylation patterns for accurate analysis.
  • Application to acute myeloid leukemia (AML) samples demonstrated PRISM's ability to reveal epigenetic evolutionary history.

Conclusions:

  • PRISM offers a novel approach to cancer subclone characterization using DNA methylation.
  • The tool can infer tumor evolutionary trajectories from an epigenetic standpoint.
  • PRISM provides insights into the epigenetic heterogeneity of tumors, particularly in myeloid malignancies.