Martina Summer-Kutmon

Martina Summer-Kutmon

Network biologist, bioinformatician, systems biologist

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portfolio

publications

Published in , 1900

Inferring causal molecular networks: empirical assessment through a community-based effort

Published in Nature Methods, 2016

Recommended citation: , S. M. Hill, L. M. Heiser, T. Cokelaer, M. Unger, N. K. Nesser, D. E. Carlin, Y. Zhang, A. Sokolov, E. O. Paull, C. K. Wong, K. Graim, A. Bivol, H. Wang, F. Zhu, B. Afsari, L. V. Danilova, A. V. Favorov, W. S. Lee, D. Taylor, C. W. Hu, B. L. Long, D. P. Noren, A. J. Bisberg, G. B. Mills, J. W. Gray, M. Kellen, T. Norman, S. Friend, A. A. Qutub, E. J. Fertig, Y. Guan, M. Song, J. M. Stuart, P. T. Spellman, H. Koeppl, G. Stolovitzky, J. Saez-Rodriguez, S. Mukherjee. (2016). "Inferring causal molecular networks: empirical assessment through a community-based effort." Nature Methods.
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The systems biology format converter

Published in BMC Bioinformatics, 2016

Recommended citation: N. Rodriguez, J. Pettit, P. Dalle Pezze, L. Li, A. Henry, M. P. van Iersel, G. Jalowicki, M. Kutmon, K. N. Natarajan, D. Tolnay, M. I. Stefan, C. T. Evelo, N. Le Novère. (2016). "The systems biology format converter." BMC Bioinformatics.
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Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures

Published in Journal of Proteome Research, 2017

Recommended citation: A. M. Curran, C. Fogarty Draper, M. Scott-Boyer, A. Valsesia, H. M. Roche, M. F. Ryan, M. J. Gibney, M. Kutmon, C. T. Evelo, S. L. Coort, A. Astrup, W. H. Saris, L. Brennan, J. Kaput. (2017). "Sexual Dimorphism, Age, and Fat Mass Are Key Phenotypic Drivers of Proteomic Signatures." Journal of Proteome Research.
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WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

Published in Nucleic Acids Research, 2018

Recommended citation: D. N. Slenter, M. Kutmon, K. Hanspers, A. Riutta, J. Windsor, N. Nunes, J. Mélius, E. Cirillo, S. L. Coort, D. Digles, F. Ehrhart, P. Giesbertz, M. Kalafati, M. Martens, R. Miller, K. Nishida, L. Rieswijk, A. Waagmeester, L. M. T. Eijssen, C. T. Evelo, A. R. Pico, E. L. Willighagen. (2018). "WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research." Nucleic Acids Research.
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Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open‐angle glaucoma

Published in Acta Ophthalmologica, 2020

Recommended citation: I. Liesenborghs, L. M. T. Eijssen, M. Kutmon, T. G. M. F. Gorgels, C. T. Evelo, H. J. M. Beckers, C. A. B. Webers, J. S. A. G. Schouten. (2020). "Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open‐angle glaucoma." Acta Ophthalmologica.
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The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension

Published in Investigative Opthalmology & Visual Science, 2020

Recommended citation: I. Liesenborghs, L. M. T. Eijssen, M. Kutmon, T. G. M. F. Gorgels, C. T. Evelo, H. J. M. Beckers, C. A. B. Webers, J. S. A. G. Schouten. (2020). "The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension." Investigative Opthalmology & Visual Science.
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SBML Level 3: an extensible format for the exchange and reuse of biological models

Published in Molecular Systems Biology, 2020

Recommended citation: S. M. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, F. T. Bergmann, A. Finney, C. S. Gillespie, T. Helikar, S. Hoops, R. S. Malik‐Sheriff, S. L. Moodie, I. I. Moraru, C. J. Myers, A. Naldi, B. G. Olivier, S. Sahle, J. C. Schaff, L. P. Smith, M. J. Swat, D. Thieffry, L. Watanabe, D. J. Wilkinson, M. L. Blinov, K. Begley, J. R. Faeder, H. F. Gómez, T. M. Hamm, Y. Inagaki, W. Liebermeister, A. L. Lister, D. Lucio, E. Mjolsness, C. J. Proctor, K. Raman, N. Rodriguez, C. A. Shaffer, B. E. Shapiro, J. Stelling, N. Swainston, N. Tanimura, J. Wagner, M. Meier‐Schellersheim, H. M. Sauro, B. Palsson, H. Bolouri, H. Kitano, A. Funahashi, H. Hermjakob, J. C. Doyle, M. Hucka, , R. R. Adams, N. A. Allen, B. R. Angermann, M. Antoniotti, G. D. Bader, J. Červený, M. Courtot, C. D. Cox, P. Dalle Pezze, E. Demir, W. S. Denney, H. Dharuri, J. Dorier, D. Drasdo, A. Ebrahim, J. Eichner, J. Elf, L. Endler, C. T. Evelo, C. Flamm, R. M. Fleming, M. Fröhlich, M. Glont, E. Gonçalves, M. Golebiewski, H. Grabski, A. Gutteridge, D. Hachmeister, L. A. Harris, B. D. Heavner, R. Henkel, W. S. Hlavacek, B. Hu, D. R. Hyduke, H. de Jong, N. Juty, P. D. Karp, J. R. Karr, D. B. Kell, R. Keller, I. Kiselev, S. Klamt, E. Klipp, C. Knüpfer, F. Kolpakov, F. Krause, M. Kutmon, C. Laibe, C. Lawless, L. Li, L. M. Loew, R. Machne, Y. Matsuoka, P. Mendes, H. Mi, F. Mittag, P. T. Monteiro, K. N. Natarajan, P. M. Nielsen, T. Nguyen, A. Palmisano, J. Pettit, T. Pfau, R. D. Phair, T. Radivoyevitch, J. M. Rohwer, O. A. Ruebenacker, J. Saez‐Rodriguez, M. Scharm, H. Schmidt, F. Schreiber, M. Schubert, R. Schulte, S. C. Sealfon, K. Smallbone, S. Soliman, M. I. Stefan, D. P. Sullivan, K. Takahashi, B. Teusink, D. Tolnay, I. Vazirabad, A. von Kamp, U. Wittig, C. Wrzodek, F. Wrzodek, I. Xenarios, A. Zhukova, J. Zucker. (2020). "SBMLLevel 3: an extensible format for the exchange and reuse of biological models." Molecular Systems Biology.
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Integrative multiomics analysis of human atherosclerosis reveals a serum response factor‐driven network associated with intraplaque hemorrhage

Published in Clinical and Translational Medicine, 2021

Recommended citation: H. Jin, P. Goossens, P. Juhasz, W. Eijgelaar, M. Manca, J. M. H. Karel, E. Smirnov, C. J. J. M. Sikkink, B. M. E. Mees, O. Waring, K. van Kuijk, G. E. Fazzi, M. J. J. Gijbels, M. Kutmon, C. T. A. Evelo, U. Hedin, M. J. A. P. Daemen, J. C. Sluimer, L. Matic, E. A. L. Biessen. (2021). "Integrative multiomics analysis of human atherosclerosis reveals a serum response factor‐driven network associated with intraplaque hemorrhage." Clinical and Translational Medicine.
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WikiPathways: connecting communities

Published in Nucleic Acids Research, 2021

Recommended citation: M. Martens, A. Ammar, A. Riutta, A. Waagmeester, D. N. Slenter, K. Hanspers, R. A. Miller, D. Digles, E. N. Lopes, F. Ehrhart, L. J. Dupuis, L. A. Winckers, S. L. Coort, E. L. Willighagen, C. T. Evelo, A. R. Pico, M. Kutmon. (2021). "WikiPathways: connecting communities." Nucleic Acids Research.
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An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study

Published in Genes & Nutrition, 2021

Recommended citation: M. Kalafati, M. Kutmon, C. T. Evelo, C. J. H. van der Kallen, C. G. Schalkwijk, C. D. A. Stehouwer, B. I. O. S. Consortium, E. E. Blaak, M. M. J. van Greevenbroek, M. Adriaens. (2021). "An interferon-related signature characterizes the whole blood transcriptome profile of insulin-resistant individuals—the CODAM study." Genes & Nutrition.
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Ten simple rules for creating reusable pathway models for computational analysis and visualization

Published in PLOS Computational Biology, 2021

Recommended citation: K. Hanspers, M. Kutmon, S. L. Coort, D. Digles, L. J. Dupuis, F. Ehrhart, F. Hu, E. N. Lopes, M. Martens, N. Pham, W. Shin, D. N. Slenter, A. Waagmeester, E. L. Willighagen, L. A. Winckers, C. T. Evelo, A. R. Pico. (2021). "Ten simple rules for creating reusable pathway models for computational analysis and visualization." PLOS Computational Biology.
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Published in , 1900

Published in , 1900

Finding the “switch” in platelet activation: prediction of key mediators involved in reversal of platelet activation using a novel network biology approach

Published in Journal of Proteomics, 2022

Recommended citation: T. Lemmens, D. Coenen, F. Swieringa, I. Niessen, S. Coort, R. Koenen, M. Kutmon, J. Cosemans. (2022). "Finding the “switch” in platelet activation: prediction of key mediators involved in reversal of platelet activation using a novel network biology approach." Journal of Proteomics.
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A systematically derived overview of the non-ubiquitous pathways and genes that define the molecular and genetic signature of the healthy trabecular meshwork

Published in Genomics, 2022

Recommended citation: I. Liesenborghs, J. S. Schouten, M. Kutmon, T. G. Gorgels, C. T. Evelo, W. H. Hubens, H. J. Beckers, C. A. Webers, L. M. Eijssen. (2022). "A systematically derived overview of the non-ubiquitous pathways and genes that define the molecular and genetic signature of the healthy trabecular meshwork." Genomics.
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Systems Biology in ELIXIR: modelling in the spotlight

Published in F1000Research, 2022

Recommended citation: V. Martins dos Santos, M. Anton, B. Szomolay, M. Ostaszewski, I. Arts, R. Benfeitas, V. Dominguez Del Angel, P. Ferk, D. Fey, C. Goble, M. Golebiewski, K. Gruden, K. F. Heil, H. Hermjakob, P. Kahlem, M. I. Klapa, J. Koehorst, A. Kolodkin, M. Kutmon, B. Leskošek, S. Moretti, W. Müller, M. Pagni, T. Rezen, M. Rocha, D. Rozman, D. Šafránek, R. S. M. Sheriff, M. Suarez Diez, K. Van Steen, H. V. Westerhoff, U. Wittig, K. Wolstencroft, A. Zupanic, C. T. Evelo, J. M. Hancock. (2022). "Systems Biology in ELIXIR: modelling in the spotlight." F1000Research.
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Guiding the choice of informatics software and tools for lipidomics research applications

Published in Nature Methods, 2023

Recommended citation: Z. Ni, M. Wölk, G. Jukes, K. Mendivelso Espinosa, R. Ahrends, L. Aimo, J. Alvarez-Jarreta, S. Andrews, R. Andrews, A. Bridge, G. C. Clair, M. J. Conroy, E. Fahy, C. Gaud, L. Goracci, J. Hartler, N. Hoffmann, D. Kopczyinki, A. Korf, A. F. Lopez-Clavijo, A. Malik, J. M. Ackerman, M. R. Molenaar, C. O’Donovan, T. Pluskal, A. Shevchenko, D. Slenter, G. Siuzdak, M. Kutmon, H. Tsugawa, E. L. Willighagen, J. Xia, V. B. O’Donnell, M. Fedorova. (2023). "Guiding the choice of informatics software and tools for lipidomics research applications." Nature Methods.
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Human Monocytes Exposed to SARS-CoV-2 Display Features of Innate Immune Memory Producing High Levels of CXCL10 upon Restimulation

Published in Journal of Innate Immunity, 2023

Recommended citation: J. Cvetkovic, R. H. Jacobi, A. Miranda-Bedate, N. Pham, M. Kutmon, J. Groot, M. D. van de Garde, E. Pinelli. (2023). "Human Monocytes Exposed to SARS-CoV-2 Display Features of Innate Immune Memory Producing High Levels of CXCL10 upon Restimulation." Journal of Innate Immunity.
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Published in , 1900

WikiPathways 2024: next generation pathway database

Published in Nucleic Acids Research, 2024

Recommended citation: A. Agrawal, H. Balcı, K. Hanspers, S. L. Coort, M. Martens, D. N. Slenter, F. Ehrhart, D. Digles, A. Waagmeester, I. Wassink, T. Abbassi-Daloii, E. N. Lopes, A. Iyer, J. M. Acosta, L. G. Willighagen, K. Nishida, A. Riutta, H. Basaric, C. T. Evelo, E. L. Willighagen, M. Kutmon, A. R. Pico. (2024). "WikiPathways 2024: next generation pathway database." Nucleic Acids Research.
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Systems Biology in ELIXIR: modelling in the spotlight

Published in F1000Research, 2024

Recommended citation: V. Martins dos Santos, M. Anton, B. Szomolay, M. Ostaszewski, I. Arts, R. Benfeitas, V. Dominguez Del Angel, E. Domínguez-Romero, P. Ferk, D. Fey, C. Goble, M. Golebiewski, K. Gruden, K. F. Heil, H. Hermjakob, P. Kahlem, M. I. Klapa, J. Koehorst, A. Kolodkin, M. Kutmon, B. Leskošek, S. Moretti, W. Müller, M. Pagni, T. Rezen, M. Rocha, D. Rozman, D. Šafránek, W. T. Scott, R. S. M. Sheriff, M. Suarez Diez, K. Van Steen, H. V. Westerhoff, U. Wittig, K. Wolstencroft, A. Zupanic, C. T. Evelo, J. M. Hancock. (2024). "Systems Biology in ELIXIR: modelling in the spotlight." F1000Research.
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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Published in Frontiers in Immunology, 2024

Recommended citation: A. Niarakis, M. Ostaszewski, A. Mazein, I. Kuperstein, M. Kutmon, M. E. Gillespie, A. Funahashi, M. L. Acencio, A. Hemedan, M. Aichem, K. Klein, T. Czauderna, F. Burtscher, T. G. Yamada, Y. Hiki, N. F. Hiroi, F. Hu, N. Pham, F. Ehrhart, E. L. Willighagen, A. Valdeolivas, A. Dugourd, F. Messina, M. Esteban-Medina, M. Peña-Chilet, K. Rian, S. Soliman, S. S. Aghamiri, B. L. Puniya, A. Naldi, T. Helikar, V. Singh, M. F. Fernández, V. Bermudez, E. Tsirvouli, A. Montagud, V. Noël, M. Ponce-de-Leon, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, A. Luna, J. Piñero, L. I. Furlong, I. Balaur, A. Rougny, Y. Jarosz, R. W. Overall, R. Phair, L. Perfetto, L. Matthews, D. A. B. Rex, M. Orlic-Milacic, L. C. M. Gomez, B. De Meulder, J. M. Ravel, B. Jassal, V. Satagopam, G. Wu, M. Golebiewski, P. Gawron, L. Calzone, J. S. Beckmann, C. T. Evelo, P. D’Eustachio, F. Schreiber, J. Saez-Rodriguez, J. Dopazo, M. Kuiper, A. Valencia, O. Wolkenhauer, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider, . (2024). "Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches." Frontiers in Immunology.
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A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Published in , 2025

Recommended citation: A. Niarakis, M. Ostaszewski, A. Mazein, I. Kuperstein, M. Kutmon, M. E. Gillespie, A. Funahashi, M. L. Acencio, A. Hemedan, M. Aichem, K. Klein, T. Czauderna, F. Burtscher, T. G. Yamada, Y. Hiki, N. F. Hiroi, F. Hu, N. Pham, F. Ehrhart, E. L. Willighagen, A. Valdeolivas, A. Dugourd, F. Messina, M. Esteban-Medina, M. Peña-Chilet, K. Rian, S. Soliman, S. S. Aghamiri, B. L. Puniya, A. Naldi, T. Helikar, V. Singh, M. F. Fernández, V. Bermudez, E. Tsirvouli, A. Montagud, V. Noël, M. P. de Leon, D. Maier, A. Bauch, B. M. Gyori, J. A. Bachman, A. Luna, J. Pinero, L. I. Furlong, I. Balaur, A. Rougny, Y. Jarosz, R. W. Overall, R. Phair, L. Perfetto, L. Matthews, D. A. B. Rex, M. Orlic-Milacic, M. G. L. Cristobal, B. De Meulder, J. M. Ravel, B. Jassal, V. Satagopam, G. Wu, M. Golebiewski, P. Gawron, L. Calzone, J. S. Beckmann, C. T. Evelo, P. D’Eustachio, F. Schreiber, J. Saez-Rodriguez, J. Dopazo, M. Kuiper, A. Valencia, O. Wolkenhauer, H. Kitano, E. Barillot, C. Auffray, R. Balling, R. Schneider, . (2025). "A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms." .
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Glyoxalase-1 overexpression attenuates arterial wall stiffening in diabetic mice

Published in Cardiovascular Diabetology, 2025

Recommended citation: M. G. Pencheva, E. Berends, K. W. F. van der Laan, A. Giudici, P. Niessen, J. L. J. M. Scheijen, P. Vangrieken, P. Leenders, T. Delhaas, F. Caiment, M. Kutmon, F. M. Trujillo, K. Wouters, S. Foulquier, B. Spronck, K. D. Reesink, C. G. Schalkwijk. (2025). "Glyoxalase-1 overexpression attenuates arterial wall stiffening in diabetic mice." Cardiovascular Diabetology.
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talks

teaching

Teaching experience 1

Undergraduate course, University 1, Department, 2014

This is a description of a teaching experience. You can use markdown like any other post.

Teaching experience 2

Workshop, University 1, Department, 2015

This is a description of a teaching experience. You can use markdown like any other post.