Blar i NTNU Open på forfatter "Kuiper, Martin"
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ONTO-ToolKit: enabling bio-ontology engineering via Galaxy
Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2010)Background: The biosciences increasingly face the challenge of integrating a wide variety of available data, information and knowledge in order to gain an understanding of biological systems. Data integration is supported by ... -
ontoWiz: Making Tasks of Reasoning Fast
Ekseth, Ole Kristian (Master thesis, 2013)Oppgaven består i å lage et verktøy for søk i biomedisinske ontologier. -
Prediction of Protein Function using semantic Fingerprints - Multivariate Data Classification by Artificial Neural Networks involving dimensional Reduction
Linse, Christoph (Master thesis, 2016)In many fields of today's scientific research the amount of knowledge is far smaller than the amount of accessible data and often too limited to make meaningful analyses and draw reasonable conclusions. Hence, statistical ... -
Scientific knowledge in the age of computation: Explicated, computable and manageable?
Efstathiou, Sophia; Nydal, Rune; Lægreid, Astrid; Kuiper, Martin (Journal article; Peer reviewed, 2019)With increasing publication and data production, scientific knowledge stands not simply as an achievement but also as a challenge. Scientific publications and data are increasingly treated as resources that need to be ... -
Signaling Pathway Modules: network organization elements for understanding cancer and designing therapies.
Tsirvouli, Eirini (Master thesis, 2019)Cancer is a heterogeneous, complex disease and one of the leading causes of death worldwide. The high heterogeneity between individuals, even those affected by the same cancer type, can lead to distinct molecular and ... -
Software implementations allowing new approaches toward data analysis, modeling and curation of biological knowledge for Systems Medicine
Zobolas, John (Doctoral theses at NTNU;2021:255, Doctoral thesis, 2021)Cancer is one of the leading causes of death globally. To combat cancer, scientists want to understand the mechanisms that drive this disease so that effective treatments can be developed. However, regulatory mechanisms ... -
Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile
Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David; Arnold, Andreas; Kuiper, Martin; Vazquez, Frank; Pooggin, M; Heinlein, M (Journal article; Peer reviewed, 2011)Tobamoviruses encode a silencing suppressor that binds small RNA (sRNA) duplexes in vitro and supposedly in vivo to counteract antiviral silencing. Here, we used sRNA deep-sequencing combined with transcriptome profiling ... -
Systems Medicine: From Modeling Systems Perturbations to Predicting Drug Synergies
Flobakk, Åsmund (Doctoral thesis at NTNU;2016:55, Doctoral thesis, 2016)Computational approaches to systems biology and systems medicine enable the study of systems properties that emerge from integrating knowledge about complex interactions, such as in the study of cancer cell phenotypes ... -
TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat
Acencio, Marcio Luis; Vázquez, Miguel; Chawla, Konika; Lægreid, Astrid Renner; Kuiper, Martin (Journal article; Peer reviewed, 2023)Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. ... -
The beginning and the end of gene expression
Skancke, Jørgen (Doctoral thesis at NTNU;2016:8, Doctoral thesis, 2016)Summary of thesis: Gene expression -- the synthesis of RNA and protein -- requires most of the cell's energy and is a highly regulated process at all its levels. In this thesis, regulation of gene expression has been ... -
The BioGateway Cytoscape Plugin - A graphical interface to BioGateway within Cytoscape
Holmås, Stian Borgen (Master thesis, 2017)The BioGateway Knowledge Base, a semantic Systems Biology knowledge resource built using Semantic Web technologies, combines large datasets into an integrated repository for querying and information retrieval. It relies ... -
The Cytoscape BioGateway App: explorative network building from an RDF store
Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2019)The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway Resource Description Framework triple store, which contains functional and interaction information for proteins ... -
The Gene Ontology Resource: 20 years and still GOing strong.
The Gene Ontology, Consortium; that, includes; Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; among, others (Journal article; Peer reviewed, 2019)The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and ... -
UniBioDicts: Unified access to biological dictionaries
Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven (Peer reviewed; Journal article, 2020)We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts ...