Search Results - "van Dam, Jesse C. J."

SyNDI: synchronous network data integration framework by Lindfors, Erno, van Dam, Jesse C J, Lam, Carolyn Ming Chi, Zondervan, Niels A, Martins Dos Santos, Vitor A P, Suarez-Diez, Maria

“…Systems biology takes a holistic approach by handling biomolecules and their interactions as big systems. Network based approach has emerged as a natural way…”
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Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling by Pham, Nhung, van Heck, Ruben G A, van Dam, Jesse C J, Schaap, Peter J, Saccenti, Edoardo, Suarez-Diez, Maria

“…Genome-scale metabolic models (GEMs) are manually curated repositories describing the metabolic capabilities of an organism. GEMs have been successfully used…”
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NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis by Poncheewin, Wasin, Hermes, Gerben D A, van Dam, Jesse C J, Koehorst, Jasper J, Smidt, Hauke, Schaap, Peter J

“…NG-Tax 2.0 is a semantic framework for FAIR high-throughput analysis and classification of marker gene amplicon sequences including bacterial and archaeal 16S…”
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SALARECON connects the Atlantic salmon genome to growth and feed efficiency by Zakhartsev, Maksim, Rotnes, Filip, Gulla, Marie, Øyås, Ove, van Dam, Jesse C J, Suarez-Diez, Maria, Grammes, Fabian, Hafþórsson, Róbert Anton, van Helvoirt, Wout, Koehorst, Jasper J, Schaap, Peter J, Jin, Yang, Mydland, Liv Torunn, Gjuvsland, Arne B, Sandve, Simen R, Martins Dos Santos, Vitor A P, Vik, Jon Olav

“…Atlantic salmon (Salmo salar) is the most valuable farmed fish globally and there is much interest in optimizing its genetics and rearing conditions for growth…”
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Regulation of Three Virulence Strategies of Mycobacterium tuberculosis: A Success Story by Zondervan, Niels A, van Dam, Jesse C J, Schaap, Peter J, Martins Dos Santos, Vitor A P, Suarez-Diez, Maria

“…Tuberculosis remains one of the deadliest diseases. Emergence of drug-resistant and multidrug-resistant strains makes treating tuberculosis increasingly…”
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The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation by van Dam, Jesse C. J., Koehorst, Jasper J., Vik, Jon Olav, Martins dos Santos, Vitor A. P., Schaap, Peter J., Suarez-Diez, Maria

“…The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain a coherent RDF graph the chosen…”
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Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis by van Dam, Jesse C J, Schaap, Peter J, Martins dos Santos, Vitor A P, Suárez-Diez, María

“…Different methods have been developed to infer regulatory networks from heterogeneous omics datasets and to construct co-expression networks. Each algorithm…”
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SAPP: functional genome annotation and analysis through a semantic framework using FAIR principles by Koehorst, Jasper J, van Dam, Jesse C J, Saccenti, Edoardo, Martins dos Santos, Vitor A P, Suarez-Diez, Maria, Schaap, Peter J

“…Abstract Summary To unlock the full potential of genome data and to enhance data interoperability and reusability of genome annotations we have developed SAPP,…”
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Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data by Koehorst, Jasper J., van Dam, Jesse C. J., van Heck, Ruben G. A., Saccenti, Edoardo, dos Santos, Vitor A. P. Martins, Suarez-Diez, Maria, Schaap, Peter J.

“…Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and…”
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The Empusa code generator: bridging the gap between the intended and the actual content of RDF resources by van Dam, Jesse C. J, Koehorst, Jasper J, Schaap, Peter J, Suarez-Diez, Maria

“…The RDF data model facilitates integration of diverse data available in structured and semi-structured formats. To obtain an RDF graph with a low amount of…”
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Semantic Systems Biology of Prokaryotes: Heterogeneous Data Integration To Understand Bacterial Metabolism by van Dam, Jesse J. C

“…The goal of this thesis is to improve the prediction of genotype to phenotypeassociations with a focus on metabolic phenotypes of prokaryotes. This goal…”
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RDF2Graph a tool to recover, understand and validate the ontology of an RDF resource by van Dam, Jesse Cj, Koehorst, Jasper J, Schaap, Peter J, Martins Dos Santos, Vitor Ap, Suarez-Diez, Maria

“…Semantic web technologies have a tremendous potential for the integration of heterogeneous data sets. Therefore, an increasing number of widely used biological…”
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