mdh.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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
Graph Centrality Based Prediction of Cancer Genes
Mälardalen University, School of Education, Culture and Communication, Educational Sciences and Mathematics. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden. (MAM)
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
Mälardalen University, School of Education, Culture and Communication, Educational Sciences and Mathematics. (MAM)ORCID iD: 0000-0002-1624-5147
Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden.
Show others and affiliations
2016 (English)In: Engineering Mathematics II: Algebraic, Stochastic and Analysis Structures for Networks, Data Classification and Optimization / [ed] Sergei Silvestrov; Milica Rancic, Springer, 2016, 275-311 p.Chapter in book (Refereed)
Abstract [en]

Current cancer therapies including surgery, radiotherapy and chemotherapy are often plagued by high failure rates. Designing more targeted and personalized treatment strategies requires a detailed understanding of druggable tumor drivergenes. As a consequence, the detection of cancer driver genes has evolved to a critical scientific field integrating both high-through put experimental screens as well as computational and statistical strategies. Among such approaches, network based prediction tools have recently been accentuated and received major focus due to their potential to model various aspects of the role of cancer genes in a biological system. In this chapter, we focus on how graph centralities obtained from biological networks have been used to predict cancer genes. Specifically, we start by discussing the current problems in cancer therapy and the reasoning behind using network based cancer gene prediction, followed by an outline of biological networks, their generation and properties. Finally, we review major concepts, recent results as well as future challenges regarding the use of graph centralities in cancer gene prediction.

Place, publisher, year, edition, pages
Springer, 2016. 275-311 p.
Series
Springer Proceedings in Mathematics and Statistics, ISSN 2194-1009 ; 179
Keyword [en]
graph, graph centrality, biological networks, cancer therapies, cancer driver genes, biological system
National Category
Computational Mathematics Bioinformatics (Computational Biology) Bioinformatics and Systems Biology Genetics Medical and Health Sciences
Research subject
Mathematics/Applied Mathematics
Identifiers
URN: urn:nbn:se:mdh:diva-33381DOI: 10.1007/978-3-319-42105-6Scopus ID: 2-s2.0-85012877104ISBN: 978-3-319-42104-9 (print)ISBN: 978-3-319-42105-6 (print)OAI: oai:DiVA.org:mdh-33381DiVA: diva2:1034024
Available from: 2016-10-11 Created: 2016-10-11 Last updated: 2017-09-28Bibliographically approved
In thesis
1. PageRank in Evolving Networks and Applications of Graphs in Natural Language Processing and Biology
Open this publication in new window or tab >>PageRank in Evolving Networks and Applications of Graphs in Natural Language Processing and Biology
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

This thesis is dedicated to the use of graph based methods applied to ranking problems on the Web-graph and applications in natural language processing and biology.

Chapter 2-4 of this thesis is about PageRank and its use in the ranking of home pages on the Internet for use in search engines. PageRank is based on the assumption that a web page should be high ranked if it is linked to by many other pages and/or by other important pages. This is modelled as the stationary distribution of a random walk on the Web-graph.

Due to the large size and quick growth of the Internet it is important to be able to calculate this ranking very efficiently. One of the main topics of this thesis is how this can be made more efficiently, mainly by considering specific types of subgraphs and how PageRank can be calculated or updated for those type of graph structures. In particular we will consider the graph partitioned into strongly connected components and how this partitioning can be utilized.

Chapter 5-7 is dedicated to graph based methods and their application to problems in Natural language processing. Specifically given a collection of texts (corpus) we will compare different clustering methods applied to Pharmacovigilance terms (5), graph based models for the identification of semantic relations between biomedical words (6) and modifications of CValue for the annotation of terms in a corpus.

In Chapter 8-9 we look at biological networks and the application of graph centrality measures for the identification of cancer genes. Specifically in (8) we give a review over different centrality measures and their application to finding cancer genes in biological networks and in (9) we look at how well the centrality of vertices in the true network is preserved in networks generated from experimental data.

Place, publisher, year, edition, pages
Västerås: Mälardalen University, 2016
Series
Mälardalen University Press Dissertations, ISSN 1651-4238 ; 217
National Category
Mathematics
Research subject
Mathematics/Applied Mathematics
Identifiers
urn:nbn:se:mdh:diva-33459 (URN)978-91-7485-298-1 (ISBN)
Public defence
2016-12-08, Kappa, Mälardalens högskola, Västerås, 13:15 (English)
Opponent
Supervisors
Available from: 2016-10-24 Created: 2016-10-24 Last updated: 2016-11-23Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textScopushttp://www.springer.com/gp/book/9783319421049

Search in DiVA

By author/editor
Engström, ChristopherSilvestrov, Sergei
By organisation
Educational Sciences and Mathematics
Computational MathematicsBioinformatics (Computational Biology)Bioinformatics and Systems BiologyGeneticsMedical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
isbn
urn-nbn

Altmetric score

doi
isbn
urn-nbn
Total: 424 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • 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