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Št. zadetkov: 18
Graph thresholding algorithm benchmarking dataset
Carissa Bleker
Raziskovalni podatki
Oznake: biological data analysis;graph theoretical algorithms;thresholding algorithms;gene co-expression;
Assortment of correlation graphs for testing graph thresholding algorithms.
Leto: 2024 Vir: Nacionalni inštitut za biologijo (NIB)
Integration of gene expression data with causal networks
Mihael Rajh, Tomaž Curk, Carissa Bleker
Magistrsko delo
Oznake: bioinformatics;casual reasoning;gene expression;computer science;master's thesis;
With the increased availability of large gene expression datasets comes an increased need for informed methods of data analysis. One class of recent methods involves the use of causal biological networks, which depict causal relationships between molecular events inside the cell. These networks offe ...
Leto: 2023 Vir: Fakulteta za računalništvo in informatiko (UL FRI)
Comparison of methods for gene regulatory network inference
Anže Drmaž, Rok Blagus, Carissa Bleker
Magistrsko delo
Oznake: methods for inference of gene regulatory networks;simulated test networks;transcription factors;target genes;gene expression;
The main goal of our work was to systematically evaluate and compare different methods for gene regulatory network (GRN) inference. GRN inference is a challenging task due to the high dimensionality of gene expression data and the complex regulatory interactions between transcription factors (TFs) a ...
Leto: 2026 Vir: Fakulteta za elektrotehniko (UL FE)
Orthologue translation pipeline - from SKM to crop and crop wild relatives
Maja Zagorščak, Carissa Bleker, Mojca Juteršek
Programska oprema
Oznake:
Translation pipeline from SKM to crop and crop wild relatives
Leto: 2026 Vir: Nacionalni inštitut za biologijo (NIB)
Explainable graph neural networks for link prediction in plant molecular interaction networks
Klara Šuštar, Tomaž Curk, Carissa Bleker, Jan Zrimec
Magistrsko delo
Oznake: graph neural networks;link prediction;molecular interaction networks;Arabidopsis thaliana;batch effect correction;variational autoencoder;scArches;explainable artificial intelligence;CKN;
Plant molecular biology leans on curated interaction networks such as the Comprehensive Knowledge Network (CKN) of Arabidopsis thaliana, yet it is rarely tested whether building such a network into a learning system helps at all, and if so, where. This thesis integrates CKN with public expression da ...
Leto: 2026 Vir: Fakulteta za računalništvo in informatiko (UL FRI)
Integration of multi-omics data and deep phenotyping
Maja Zagorščak, Andrej Blejec, Carissa Bleker, Jan Zrimec
Programska oprema
Oznake: feature selection;network analysis;omics;omics data integration;phenotyping;proteomics data analysis;statistical analysis;
Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato
Leto: 2025 Vir: Nacionalni inštitut za biologijo (NIB)
Predstavitev programskih orodij Python in R
Maja Zagorščak, Carissa Bleker, Jan Zrimec, Marko Petek, Anže Županič
Video in druga učna gradiva
Oznake: podatki;ravnanje s podatki;ravnanje z raziskovalnimi podatki;raziskovalni podatki;odprta znanost;programska orodja;Python;R;
Predstavitev programskih orodij Python in R
Leto: 2024 Vir: Nacionalni inštitut za biologijo (NIB)
Evidence-based unification of potato gene models with the UniTato collaborative genome browser
Maja Zagorščak, Jan Zrimec, Carissa Bleker, Nadja Francesca Nolte, Mojca Juteršek, Živa Ramšak, Kristina Gruden, Marko Petek
Izvirni znanstveni članek
Oznake: bioinformatska analiza;anotacije genskih modelov;pregledovalnik genoma krompirja;model krompirjevega genoma;bioinformatics analysis;plant genome annotation;gene model annotations;Phureja group;GFF files;poTato genome model;UniTato;
Potato (Solanum tuberosum) is the most popular tuber crop and a model organism. A variety of gene models for potato exist, and despite frequent updates, they are not unified. This hinders the comparison of gene models across versions, limits the ability to reuse experimental data without significant ...
Leto: 2024 Vir: Nacionalni inštitut za biologijo (NIB)
Orodja za delo z delotoki
Marko Vidak, Bojan Kverh, Polonca Ferk, Branimir Leskošek, Maja Zagorščak, Nadja Francesca Nolte, Carissa Bleker, Marko Petek, Anže Županič
Druge monografije in druga zaključena dela
Oznake: odprti podatki;odprta znanost;delo z delotoki;projekt Spoznaj;okolje Galaxy;raziskovalni podatki;uporabljanje podatkov;
Orodja za delo z delotoki
Leto: 2024 Vir: Digitalni repozitorij raziskovalnih organizacij Slovenije
Evaluating plant growth–defense trade-offs by modelingthe interaction between primary and secondary metabolism
Jan Zrimec, Sandra Correo, Maja Zagorščak, Marko Petek, Carissa Bleker, Katja Stare, Christian Schuy, Sophia Sonnewald, Kristina Gruden, Zoran Nikoloski
Izvirni znanstveni članek
Oznake: sistemska biologija;metabolno modeliranje;obramba rastlin;sekundarni metabolizem;systems biology;constraint-based metabolic modeling;growth-defence trade-offs;secondary metabolism;
Understanding the molecular mechanisms behind plant response to stress can enhancebreeding strategies and help us design crop varieties with improved stress tolerance,yield, and quality. To investigate resource redistribution from growth- to defense-relatedprocesses in an essential tuber crop, potat ...
Leto: 2025 Vir: Nacionalni inštitut za biologijo (NIB)
Št. zadetkov: 18
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