Logo: to the web site of Uppsala University

uu.sePublications from Uppsala University
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
A benchmarking study of the Ising model fitted to single cell RNA-sequencing data for the estimation of differentiation potential
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
2023 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

Glioblastoma (GBM) is the most aggressive form of adult diffuse gliomas, and the most prevalent among malignant primary brain tumors. The prognosis is poor, with a median survival of 15 months and unavoidable tumor recurrence. It is believed that a small population of cells, called cancer stem cells (CSCs), reside within the tumor and are at least partly responsible for the tumor re-initiation. In this thesis, we evaluate a new computational measure, based on the Ising model from statistical physics, for identifying the most stemlike cells in a population by considering single cell RNA-sequencing data. We evaluate a range of different optimizations on the model, and conclude that the model is already optimized with respect to the considered refinements. We also compare it to two other computational stemness measures and conclude that the Ising model shows comparable performance. With further refinements, it will be a valuable computational measure for scoring the stemness of single cells, for simulating data from a population of cells, and for investigating the effect of a drug treatment or gene knockout. This will help the understanding of complex glioblastoma tumor tissue and will allow the exploration of possible treatments. 

Place, publisher, year, edition, pages
2023. , p. 50
Series
UPTEC X ; 23024
Keywords [en]
differentiation potential, Ising models, single cell RNA sequencing, cancer stem cells, glioblastoma, entropy
National Category
Other Basic Medicine
Identifiers
URN: urn:nbn:se:uu:diva-506302OAI: oai:DiVA.org:uu-506302DiVA, id: diva2:1775307
Educational program
Molecular Biotechnology Engineering Programme
Supervisors
Examiners
Available from: 2023-06-28 Created: 2023-06-26 Last updated: 2023-06-28Bibliographically approved

Open Access in DiVA

The full text will be freely available from 2026-06-25 10:00
Available from 2026-06-25 10:00

By organisation
Biology Education Centre
Other Basic Medicine

Search outside of DiVA

GoogleGoogle Scholar

urn-nbn

Altmetric score

urn-nbn
Total: 330 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf