Search Results - "Evelo, Chris T"

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: 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 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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Ten simple rules to make your publication look better by Ehrhart, Friederike, Evelo, Chris T

“…Reviewers will spot how much care and attention was paid to the details of the report, and that will affect their expectations about the technical work behind…”
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The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching by Willighagen, Egon L., Mayfield, John W., Alvarsson, Jonathan, Berg, Arvid, Carlsson, Lars, Jeliazkova, Nina, Kuhn, Stefan, Pluskal, Tomáš, Rojas-Chertó, Miquel, Spjuth, Ola, Torrance, Gilleain, Evelo, Chris T., Guha, Rajarshi, Steinbeck, Christoph

“…Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts…”
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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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GO-Elite: a flexible solution for pathway and ontology over-representation by ZAMBON, Alexander C, GAJ, Stan, HO, Isaac, HANSPERS, Kristina, VRANIZAN, Karen, EVELO, Chris T, CONKLIN, Bruce R, PICO, Alexander R, SALOMONIS, Nathan

“…We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In…”
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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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A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants by Cirillo, Elisa, Parnell, Laurence D, Evelo, Chris T

“…Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide…”
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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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Rett syndrome - biological pathways leading from MECP2 to disorder phenotypes by Ehrhart, Friederike, Coort, Susan L M, Cirillo, Elisa, Smeets, Eric, Evelo, Chris T, Curfs, Leopold M G

“…Rett syndrome (RTT) is a rare disease but still one of the most abundant causes for intellectual disability in females. Typical symptoms are onset at month…”
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COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms by Ostaszewski, Marek, Mazein, Alexander, Gillespie, Marc E., Kuperstein, Inna, Niarakis, Anna, Hermjakob, Henning, Pico, Alexander R., Willighagen, Egon L., Evelo, Chris T., Hasenauer, Jan, Schreiber, Falk, Dräger, Andreas, Demir, Emek, Wolkenhauer, Olaf, Furlong, Laura I., Barillot, Emmanuel, Dopazo, Joaquin, Orta-Resendiz, Aurelio, Messina, Francesco, Valencia, Alfonso, Funahashi, Akira, Kitano, Hiroaki, Auffray, Charles, Balling, Rudi, Schneider, Reinhard

“…Researchers around the world join forces to reconstruct the molecular processes of the virus-host interactions aiming to combat the cause of the ongoing…”
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User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis.org by Eijssen, Lars M T, Jaillard, Magali, Adriaens, Michiel E, Gaj, Stan, de Groot, Philip J, Müller, Michael, Evelo, Chris T

“…Quality control (QC) is crucial for any scientific method producing data. Applying adequate QC introduces new challenges in the genomics field where large…”
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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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The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services by van Iersel, Martijn P, Pico, Alexander R, Kelder, Thomas, Gao, Jianjiong, Ho, Isaac, Hanspers, Kristina, Conklin, Bruce R, Evelo, Chris T

“…Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be…”
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