Search Results - "Kutmon, Martina"

WikiPathways: connecting communities by Martens, Marvin, Ammar, Ammar, Riutta, Anders, Waagmeester, Andra, Slenter, Denise N, Hanspers, Kristina, A. Miller, Ryan, Digles, Daniela, Lopes, Elisson N, Ehrhart, Friederike, Dupuis, Lauren J, Winckers, Laurent A, Coort, Susan L, Willighagen, Egon L, Evelo, Chris T, Pico, Alexander R, Kutmon, Martina

“…Abstract WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the…”
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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research by Slenter, Denise N, Kutmon, Martina, Hanspers, Kristina, Riutta, Anders, Windsor, Jacob, Nunes, Nuno, Mélius, Jonathan, Cirillo, Elisa, Coort, Susan L, Digles, Daniela, Ehrhart, Friederike, Giesbertz, Pieter, Kalafati, Marianthi, Martens, Marvin, Miller, Ryan, Nishida, Kozo, Rieswijk, Linda, Waagmeester, Andra, Eijssen, Lars M T, Evelo, Chris T, Pico, Alexander R, Willighagen, Egon L

“…Abstract WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine…”
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WikiPathways: capturing the full diversity of pathway knowledge by Kutmon, Martina, Riutta, Anders, Nunes, Nuno, Hanspers, Kristina, Willighagen, Egon L, Bohler, Anwesha, Mélius, Jonathan, Waagmeester, Andra, Sinha, Sravanthi R, Miller, Ryan, Coort, Susan L, Cirillo, Elisa, Smeets, Bart, Evelo, Chris T, Pico, Alexander R

“…WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data…”
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PathVisio 3: an extendable pathway analysis toolbox by Kutmon, Martina, van Iersel, Martijn P, Bohler, Anwesha, Kelder, Thomas, Nunes, Nuno, Pico, Alexander R, Evelo, Chris T

“…PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe…”
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WikiPathways 2024: next generation pathway database by Agrawal, Ayushi, Balcı, Hasan, Hanspers, Kristina, Coort, Susan L, Martens, Marvin, Slenter, Denise N, Ehrhart, Friederike, Digles, Daniela, Waagmeester, Andra, Wassink, Isabel, Abbassi-Daloii, Tooba, Lopes, Elisson N, Iyer, Aishwarya, Acosta, Javier Millán, Willighagen, Lars G, Nishida, Kozo, Riutta, Anders, Basaric, Helena, Evelo, Chris T, Willighagen, Egon L, Kutmon, Martina, Pico, Alexander R

“…Abstract WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of…”
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CyTargetLinker app update: A flexible solution for network extension in Cytoscape [version 2; peer review: 2 approved] by Kutmon, Martina, Ehrhart, Friederike, Willighagen, Egon L, Evelo, Chris T, Coort, Susan L

“…Here, we present an update of the open-source CyTargetLinker app for Cytoscape ( http://apps.cytoscape.org/apps/cytargetlinker) that introduces new automation…”
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Comparison of metabolic states using genome-scale metabolic models by Sarathy, Chaitra, Breuer, Marian, Kutmon, Martina, Adriaens, Michiel E, Evelo, Chris T, Arts, Ilja C W

“…Genome-scale metabolic models (GEMs) are comprehensive knowledge bases of cellular metabolism and serve as mathematical tools for studying biological…”
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CyTargetLinker: a cytoscape app to integrate regulatory interactions in network analysis by Kutmon, Martina, Kelder, Thomas, Mandaviya, Pooja, Evelo, Chris T A, Coort, Susan L

“…The high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the…”
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Exploring pathway interactions to detect molecular mechanisms of disease: 22q11.2 deletion syndrome by Shin, Woosub, Kutmon, Martina, Mina, Eleni, van Amelsvoort, Therese, Evelo, Chris T, Ehrhart, Friederike

“…22q11.2 Deletion Syndrome (22q11DS) is a genetic disorder characterized by the deletion of adjacent genes at a location specified as q11.2 of chromosome 22,…”
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Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients by Pham, Nhung, Hu, Finterly, Evelo, Chris T., Kutmon, Martina

“…The ACE2 receptors essential for SARS-CoV-2 infections are expressed not only in the lung but also in many other tissues in the human body. To better…”
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From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results by Cirillo, Elisa, Kutmon, Martina, Gonzalez Hernandez, Manuel, Hooimeijer, Tom, Adriaens, Michiel E, Eijssen, Lars M T, Parnell, Laurence D, Coort, Susan L, Evelo, Chris T

“…Genome-wide association studies (GWAS) have become a common method for discovery of gene-disease relationships, in particular for complex diseases like Type 2…”
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Understanding signaling and metabolic paths using semantified and harmonized information about biological interactions by Miller, Ryan A, Kutmon, Martina, Bohler, Anwesha, Waagmeester, Andra, Evelo, Chris T, Willighagen, Egon L

“…To grasp the complexity of biological processes, the biological knowledge is often translated into schematic diagrams of, for example, signalling and metabolic…”
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A novel insight into neurological disorders through HDAC6 protein–protein interactions by Bahram Sangani, Nasim, Koetsier, Jarno, Mélius, Jonathan, Kutmon, Martina, Ehrhart, Friederike, Evelo, Chris T., Curfs, Leopold M. G., Reutelingsperger, Chris P., Eijssen, Lars M. T.

“…Due to its involvement in physiological and pathological processes, histone deacetylase 6 (HDAC6) is considered a promising pharmaceutical target for several…”
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Allele-specific expression analysis for complex genetic phenotypes applied to a unique dilated cardiomyopathy cohort by van Beek, Daan, Verdonschot, Job, Derks, Kasper, Brunner, Han, de Kok, Theo M., Arts, Ilja C. W., Heymans, Stephane, Kutmon, Martina, Adriaens, Michiel

“…Allele-specific expression (ASE) analysis detects the relative abundance of alleles at heterozygous loci as a proxy for cis -regulatory variation, which…”
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A resource to explore the discovery of rare diseases and their causative genes by Ehrhart, Friederike, Willighagen, Egon L., Kutmon, Martina, van Hoften, Max, Curfs, Leopold M. G., Evelo, Chris T.

“…Here, we describe a dataset with information about monogenic, rare diseases with a known genetic background, supplemented with manually extracted provenance…”
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Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts by Winckers, Laurent A., Evelo, Chris T., Willighagen, Egon L., Kutmon, Martina

“…Some engineered nanomaterials incite toxicological effects, but the underlying molecular processes are understudied. The varied physicochemical properties…”
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Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways by Siddiqa, Amnah, Cirillo, Elisa, Tareen, Samar H.K., Ali, Amjad, Kutmon, Martina, Eijssen, Lars M.T., Ahmad, Jamil, Evelo, Chris T., Coort, Susan L.

“…ANGPTL8 (Angiopoietin-like protein 8) is a newly identified hormone emerging as a novel drug target for treatment of diabetes mellitus and dyslipidemia due to…”
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Author Correction: A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses by Waagmeester, Andra, Willighagen, Egon L, Su, Andrew I, Kutmon, Martina, Gayo, Jose Emilio Labra, Fernández-Ãlvarez, Daniel, Groom, Quentin, Schaap, Peter J, Verhagen, Lisa M, Koehorst, Jasper J

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A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses by Waagmeester, Andra, Willighagen, Egon L, Su, Andrew I, Kutmon, Martina, Gayo, Jose Emilio Labra, Fernández-Álvarez, Daniel, Groom, Quentin, Schaap, Peter J, Verhagen, Lisa M, Koehorst, Jasper J

“…Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may…”
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Ten simple rules for creating reusable pathway models for computational analysis and visualization by Hanspers, Kristina, Kutmon, Martina, Coort, Susan L, Digles, Daniela, Dupuis, Lauren J, Ehrhart, Friederike, Hu, Finterly, Lopes, Elisson N, Martens, Marvin, Pham, Nhung, Shin, Woosub, Slenter, Denise N, Waagmeester, Andra, Willighagen, Egon L, Winckers, Laurent A, Evelo, Chris T, Pico, Alexander R

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