Browsing NTNU Open by Author "Kuiper, Martin"
Now showing items 1-20 of 53
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Adaptation of a logical model that depicts psoriatic keratinocytes towards patient-specific psoriasis logical models
Aker, Eir (Master thesis, 2022)Det finnes mange subgrupper av psoriasis, noe som gjør det utfordrende for leger å evaluere alvorlighetsgraden til pasientene. Sykdommen deles inn i alvorlig, moderat og mildt forløp, og disse alvorlighetsgradene styrer ... -
Analysis of the Drug Target Combination space of the AGS cancer model CASCADE 1.0 and the generic cancer model CASCADE 2.0
Hassaan, Mahmoud (Master thesis, 2022)Logical models are a promising method to predict the drug combinations without testing the massive number of possible combinations experimentally. In this project we analyzed two logical models the AGS cancer model CASCADE ... -
Automation of Drug Target Profiling for Logical Modelling
Kristine Lippestad (Master thesis, 2023)Kreft er en heterogen sykdomsgruppe som utgjør en betydelig global helseutfordring. I dag legges det inn store ressurser for å oppnå kreftkontroll. Betydelig framgang innen kreftforskning har resultert i flere nye og lovende ... -
BioGateway: A Semantic Systems Biology Tool for the Life Sciences
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2009)Background: Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that ... -
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator
Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven (Journal article; Peer reviewed, 2021)Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to ... -
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination
Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David; Hermjakob, Henning; Korcsmaros, Tamas; Kuiper, Martin; Lægreid, Astrid; Lo Surdo, Prisca; Lovering, Ruth C.; Orchard, Sandra; Porras, Pablo; Thomas, Paul; Touré, Vasundra; Zobolas, John; Licata, Luana (Peer reviewed; Journal article, 2019)Motivation Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models ... -
Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles
Heck, Kathleen; Lindholm, Håvard Takle; Niederdorfer, Barbara; Tsirvouli, Eirini; Kuiper, Martin; Flobak, Åsmund; Lægreid, Astrid Renner; Thommesen, Liv (Journal article; Peer reviewed, 2023) -
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund; Thommesen, Liv; Team, Dream (Journal article; Peer reviewed, 2019)The effectiveness of most cancer targeted therapies is short-lived. Tumors often developresistance that might be overcome with drug combinations. However, the number of possiblecombinations is vast, necessitating data-driven ... -
Contributions of the EMERALD project to assessing and improving microarray data quality
Beisvag, Vidar; Kauffmann, Audrey; Malone, James; Foy, Carole; Salit, Marc; Schimmel, H; Bongcam-Rudloff, Eric; Landegren, Ulf; Parkinson, Helen; Huber, Wolfgang; Brazma, Alvis; Sandvik, Arne Kristian; Kuiper, Martin (Journal article; Peer reviewed, 2011)While minimum information about a microarray experiment (MIAME) standards have helped to increase the value of the microarray data deposited into public databases like ArrayExpress and Gene Expression Omnibus (GEO), limited ... -
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons
Chatterjee, Anamika; Swierstra, Tsjalling; Kuiper, Martin (Peer reviewed; Journal article, 2022)Current research of gene regulatory mechanisms is increasingly dependent on the availability of high-quality information from manually curated databases. Biocurators undertake the task of extracting knowledge claims from ... -
Determination of quality metabolites in different brands of salmon fillets
Sokolová, Tatiana (Master thesis, 2017)Fish offer a multitude of nutritional benefits and its world´s food supply has grown rapidly in the last years. The quality of fish is an important factor for the fish industry and consumers, this field is required to be ... -
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling
Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid (Peer reviewed; Journal article, 2015)Discovery of efficient anti-cancer drug combinations is a major challenge, since experimental testing of all possible combinations is clearly impossible. Recent efforts to computationally predict drug combination responses ... -
Dynamically Controlled DNA Tiles: Looking Beyond the Self-assembly of Static Two-dimensional DNA-based Computational Structures
Gautam, Vinay Kumar (Doctoral theses at NTNU;2017:58, Doctoral thesis, 2017)Algorithmic self-assembly of DNA tiles enables computation and construction of DNA structures at the nanoscale, where the assembly process is guided by specific DNA interactions between complementary sticky-ends of tiles. ... -
Effect of Calibration Data Subsetting on Boolean Model Calibration and Drug Synergy Predictions
Hettasch, Thea Johanna Aandstad (Master thesis, 2023)Kreft er et samlebegrep for en rekke sykdomstilstander som kjennetegnes av unormal og ukontrollert celledeling, og forårsakes av avvikende regulering av ulike cellulære signalveier knyttet til cellevekst og celledød. Med ... -
emba: R package for analysis and visualization of biomarkers in boolean model ensembles
Zobolas, John; Kuiper, Martin; Flobak, Åsmund (Journal article; Peer reviewed, 2020) -
Experimental-Computational Approaches to Identify Synergistic Effects of Anti-Cancer Drugs
Niederdorfer, Barbara (Doctoral theses at NTNU;2019:384, Doctoral thesis, 2019)Drug combinations are hoped to improve treatment response to anti-cancer drugs by targeting the cancers vulnerabilities at diverse trajectories. With a large number of approved agents of chemotherapeutic and targeted ... -
Exploring Different Software Workflows to Optimise Biomarker Inference for Boolean Model Calibration and Drug Synergy Predictions
Gjøvaag, Victoria Nilsen (Master thesis, 2023)Identifisering av presise biomarkør aktiviteter fra biologisk data er en utfordring i systembiologiske metoder som tar i bruk persontilpassede logiske modeller for individbasert kreftbehandling. Til tross for fremveksten ... -
Finding gene regulatory network candidates using the gene expression knowledge base
Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2014)Background: Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ?omics? data can ... -
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E; Verschoren, A; Van Leemput, K (Journal article; Peer reviewed, 2010)Background: Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file ... -
A foundation for reference models for drug combinations with an application to Loewe’s reference model
De Mulder, Wim; Kuiper, Martin (Peer reviewed; Journal article, 2020)Background Treating patients with combinations of drugs that have synergistic effects has become widespread practice in the clinic. Drugs work synergistically when the observed effect of a drug combination is larger ...