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190 results on '"Verhoeven, Aswin"'

1. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging

Author

Singh, Shalini, Giron, Leila B., Shaikh, Maliha W., Shankaran, Shivanjali, Engen, Phillip A., Bogin, Zlata R., Bambi, Simona A., Goldman, Aaron R., Azevedo, Joao L. L. C., Orgaz, Lorena, de Pedro, Nuria, González, Patricia, Giera, Martin, Verhoeven, Aswin, Sánchez-López, Elena, Pandrea, Ivona, Kannan, Toshitha, Tanes, Ceylan E., Bittinger, Kyle, Landay, Alan L., Corley, Michael J., Keshavarzian, Ali, and Abdel-Mohsen, Mohamed

Published
2024
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9. Ethnic Disparities in Lipid Metabolism and Clinical Outcomes between Dutch South Asians and Dutch White Caucasians with Type 2 Diabetes Mellitus

Author

Yuan, Lushun, primary, Verhoeven, Aswin, additional, Blomberg, Niek, additional, van Eyk, Huub J., additional, Bizino, Maurice B., additional, Rensen, Patrick C. N., additional, Jazet, Ingrid M., additional, Lamb, Hildo J., additional, Rabelink, Ton J., additional, Giera, Martin, additional, and van den Berg, Bernard M., additional

Published
2024
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11. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV

Author

Singh, Shalini, primary, Giron, Leila B., additional, Shaikh, Maliha W., additional, Shankaran, Shivanjali, additional, Engen, Phillip A., additional, Bogin, Zlata R., additional, Bambi, Simona A., additional, Goldman, Aaron R., additional, Azevedo, Joao L. L. C., additional, Orgaz, Lorena, additional, de Pedro, Nuria, additional, González, Patricia, additional, Giera, Martin, additional, Verhoeven, Aswin, additional, Sánchez-López, Elena, additional, Pandrea, Ivona Vasile, additional, Kannan, Toshitha, additional, Tanes, Ceylan E., additional, Bittinger, Kyle, additional, Landay, Alan L., additional, Corley, Michael J., additional, Keshavarzian, Ali, additional, and Abdel-Mohsen, Mohamed, additional

Published
2023
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13. Circulating metabolites and general cognitive ability and dementia: Evidence from 11 cohort studies

Author

van der Lee, Sven J., Teunissen, Charlotte E., Pool, René, Shipley, Martin J., Teumer, Alexander, Chouraki, Vincent, Melo van Lent, Debora, Tynkkynen, Juho, Fischer, Krista, Hernesniemi, Jussi, Haller, Toomas, Singh-Manoux, Archana, Verhoeven, Aswin, Willemsen, Gonneke, de Leeuw, Francisca A., Wagner, Holger, van Dongen, Jenny, Hertel, Johannes, Budde, Kathrin, Willems van Dijk, Ko, Weinhold, Leonie, Ikram, M. Arfan, Pietzner, Maik, Perola, Markus, Wagner, Michael, Friedrich, Nele, Slagboom, P. Eline, Scheltens, Philip, Yang, Qiong, Gertzen, Robert E., Egert, Sarah, Li, Shuo, Hankemeier, Thomas, van Beijsterveldt, Catharina E.M., Vasan, Ramachandran S., Maier, Wolfgang, Peeters, Carel F.W., Jörgen Grabe, Hans, Ramirez, Alfredo, Seshadri, Sudha, Metspalu, Andres, Kivimäki, Mika, Salomaa, Veikko, Demirkan, Ayşe, Boomsma, Dorret I., van der Flier, Wiesje M., Amin, Najaf, and van Duijn, Cornelia M.

Published
2018
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14. Altered high‐density lipoprotein composition is associated with risk for complications in type 2 diabetes mellitus in South Asian descendants: A cross‐sectional, case‐control study on lipoprotein subclass profiling

Author

Yuan, Lushun, primary, Li‐Gao, Ruifang, additional, Verhoeven, Aswin, additional, van Eyk, Huub J., additional, Bizino, Maurice B., additional, Rensen, Patrick C. N., additional, Giera, Martin, additional, Jazet, Ingrid M., additional, Lamb, Hildo J., additional, Rabelink, Ton J., additional, and van den Berg, Bernard M., additional

Published
2023
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16. A metabolic profile of all-cause mortality risk identified in an observational study of 44,168 individuals

Author

Deelen, Joris, Kettunen, Johannes, Fischer, Krista, van der Spek, Ashley, Trompet, Stella, Kastenmüller, Gabi, Boyd, Andy, Zierer, Jonas, van den Akker, Erik B., Ala-Korpela, Mika, Amin, Najaf, Demirkan, Ayse, Ghanbari, Mohsen, van Heemst, Diana, Ikram, M. Arfan, van Klinken, Jan Bert, Mooijaart, Simon P., Peters, Annette, Salomaa, Veikko, Sattar, Naveed, Spector, Tim D., Tiemeier, Henning, Verhoeven, Aswin, Waldenberger, Melanie, Würtz, Peter, Davey Smith, George, Metspalu, Andres, Perola, Markus, Menni, Cristina, Geleijnse, Johanna M., Drenos, Fotios, Beekman, Marian, Jukema, J. Wouter, van Duijn, Cornelia M., and Slagboom, P. Eline

Published
2019
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17. Altered HDL composition is associated with risk for complications in type 2 diabetes mellitus in South Asian descendants: a cross-sectional, case-control study on lipoprotein subclass profiling

Author

Yuan, Lushun, primary, Li-Gao, Ruifang, additional, Verhoeven, Aswin, additional, Eyk, Huub J. van, additional, Bizino, Maurice B., additional, Rensen, Patrick C.N., additional, Giera, Martin, additional, Jazet, Ingrid M., additional, Lamb, Hildo J., additional, Rabelink, Ton J., additional, and Berg, Bernard M., additional

Published
2022
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18. Urinary Metabolic Profiling in Volunteers Undergoing Malaria Challenge in Gabon

Author

Betouke Ongwe, Madeleine Eunice, primary, Kohler, Isabelle, additional, Manurung, Mikhael D., additional, Verhoeven, Aswin, additional, Derks, Rico, additional, Janse, Jacqueline J., additional, Mouwenda, Yoanne D., additional, Kremsner, Peter G., additional, Adegnika, Ayola A., additional, Lell, Bertrand, additional, Everts, Bart, additional, Mayboroda, Oleg A., additional, and Yazdanbakhsh, Maria, additional

Published
2022
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22. Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study

Author

Ducarmon, Quinten R, primary, Zwittink, Romy D, additional, Willems, Roel P J, additional, Verhoeven, Aswin, additional, Nooij, Sam, additional, van der Klis, Fiona R M, additional, Franz, Eelco, additional, Kool, Jolanda, additional, Giera, Martin, additional, Vandenbroucke-Grauls, Christina M J E, additional, Fuentes, Susana, additional, and Kuijper, Ed J, additional

Published
2022
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24. Comprehensive (apo)lipoprotein profiling in patients with genetic hypertriglyceridemia using LC-MS and NMR spectroscopy:Lipoprotein profiling in genetic HTG

Author

Straat, Maaike E., Martinez-Tellez, Borja, Nahon, Kimberly J., Janssen, Laura G.M., Verhoeven, Aswin, van der Zee, Leonie, Mulder, Monique T., Kooijman, Sander, Boon, Mariëtte R., van Lennep, Jeanine E.Roeters, Cobbaert, Christa M., Giera, Martin, Rensen, Patrick C.N., Straat, Maaike E., Martinez-Tellez, Borja, Nahon, Kimberly J., Janssen, Laura G.M., Verhoeven, Aswin, van der Zee, Leonie, Mulder, Monique T., Kooijman, Sander, Boon, Mariëtte R., van Lennep, Jeanine E.Roeters, Cobbaert, Christa M., Giera, Martin, and Rensen, Patrick C.N.

Abstract

Background: Mutations in genes encoding lipoprotein lipase (LPL) or its regulators can cause severe hypertriglyceridemia (HTG). Thus far, the effect of genetic HTG on the lipid profile has been mainly determined via conventional techniques. Objective: To show detailed differences in the (apo)lipoprotein profile of patients with genetic HTG by combining LC-MS and NMR techniques. Methods: Fasted serum from 7 patients with genetic HTG and 10 normolipidemic controls was used to measure the concentration of a spectrum of apolipoproteins by LC-MS, and to estimate the concentration and size of lipoprotein subclasses and class-specific lipid composition using NMR spectroscopy. Results: Patients with genetic HTG compared to normolipidemic controls had higher levels of apoB48 (fold change [FC] 11.3, P<0.001), apoC-I (FC 1.5, P<0.001), apoC-II (FC 4.3, P=0.007), apoC-III (FC 3.4, P<0.001), and apoE (FC 4.3, P<0.001), without altered apoB100. In addition, patients with genetic HTG had higher concentrations of TG-rich lipoproteins (i.e., chylomicrons and very low-density lipoproteins [VLDL]; FC 3.0, P<0.001), but lower LDL (FC 0.4, P=0.001), of which medium and small-sized LDL particles appeared even absent. While the correlation coefficient between NMR and enzymatic analysis in normolipidemic controls was high, it was considerably reduced in patients with genetic HTG. Conclusion: The lipoprotein profile of patients with genetic HTG is predominated with large lipoproteins (i.e., chylomicrons, VLDL), explaining high levels of apoC-I, apoC-II, apoC-III and apoE, whereas small atherogenic LDL particles are absent. The presence of chylomicrons in patients with HTG weakens the accuracy of the NMR-based model as it was designed for normolipidemic fasted individuals.

Published
2022

25. Genetics and Not Shared Environment Explains Familial Resemblance in Adult Metabolomics Data

Author

Pool, Rene, Hagenbeek, Fiona A., Hendriks, Anne M., van Dongen, Jenny, Willemsen, Gonneke, de Geus, Eco, van Dijk, Ko Willems, Verhoeven, Aswin, Suchiman, H. Eka, Beekman, Marian, Slagboom, P. Eline, Harms, Amy C., Hankemeier, Thomas, Boomsma, Dorret, I, Beekman, M., Suchiman, H. E. D., Amin, N., Beulens, J. W., van der Bom, J. A., Bomer, N., Demirkan, A., van Hilten, J. A., Meessen, J. M. T. A., Pool, R., Moed, M. H., Fu, J., Onderwater, G. L. J., Rutters, F., So-Osman, C., van der Flier, W. M., van der Heijden, A. A. W. A., van der Spek, A., Asselbergs, F. W., Boersma, E., Elders, P. M., Geleijnse, J. M., Ikram, M. A., Kloppenburg, M., Meulenbelt, I, Mooijaart, S. P., Nelissen, R. G. H. H., Netea, M. G., Penninx, B. W. J. H., Stehouwer, C. D. A., Teunissen, C. E., Terwindt, G. M., 't Hart, L. M., van den Maagdenberg, A. M. J. M., van der Harst, P., van der Horst, I. C. C., van der Kallen, C. J. H., van Greevenbroek, M. M. J., van Spil, W. E., Wijmenga, C., Zwinderman, A. H., Zhernikova, A., Jukema, J. W., Wolf, J. J. H. Barkey, Cats, D., Mei, H., Slofstra, M., Swertz, M., van den Akker, E. B., Deelen, J., Reinders, M. J. T., Boomsma, D., I, van Duijn, C. M., Slagboom, P. E., Interne Geneeskunde, MUMC+: MA Interne Geneeskunde (3), MUMC+: MA Med Staf Artsass Interne Geneeskunde (9), MUMC+: MA Endocrinologie (9), MUMC+: MA Maag Darm Lever (9), MUMC+: MA Hematologie (9), MUMC+: MA Medische Oncologie (9), MUMC+: MA Nefrologie (9), MUMC+: MA Reumatologie (9), RS: Carim - V01 Vascular complications of diabetes and metabolic syndrome, Groningen Institute for Gastro Intestinal Genetics and Immunology (3GI), Molecular Neuroscience and Ageing Research (MOLAR), Cardiovascular Centre (CVC), Critical care, Anesthesiology, Peri-operative and Emergency medicine (CAPE), Center for Liver, Digestive and Metabolic Diseases (CLDM), Medical Microbiology and Infection Prevention, Graduate School, Tytgat Institute for Liver and Intestinal Research, AGEM - Amsterdam Gastroenterology Endocrinology Metabolism, Obstetrics and Gynaecology, Cardiology, Public and occupational health, Gastroenterology and Hepatology, Paediatric Endocrinology, Biological Psychology, APH - Health Behaviors & Chronic Diseases, APH - Personalized Medicine, APH - Mental Health, APH - Methodology, Epidemiology and Data Science, Obstetrics and gynaecology, ACS - Diabetes & metabolism, ACS - Heart failure & arrhythmias, Anatomy and neurosciences, Anesthesiology, General practice, Internal medicine, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, Laboratory Medicine, Amsterdam Neuroscience - Neurodegeneration, Amsterdam Neuroscience - Neuroinfection & -inflammation, Amsterdam Reproduction & Development (AR&D), AMS - Musculoskeletal Health, AMS - Tissue Function & Regeneration, Rheumatology, Gastroenterology and hepatology, APH - Aging & Later Life, and APH - Digital Health

Subjects
Male, Netherlands Twin Register (NTR), 0301 basic medicine, Shared environment, Metabolite, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Genome-wide association study, heritability, METABOLITES, Keywords: Classical twin design, chemistry.chemical_compound, 0302 clinical medicine, metabolite classes, Twins, Dizygotic, EPIDEMIOLOGY, Classical twin design, Genetics (clinical), Genetics, HERITABILITY, shared environment, Obstetrics and Gynecology, Phenotype, Quartile, Metabolome, Female, Adult, Dizygotic twin, POWER, TWIN, Environment, Biology, enrichment analysis, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Metabolomics, AGE, Diseases in Twins, Humans, Family, GENOME-WIDE ASSOCIATION, Classical twin design [Keywords], Twins, Monozygotic, PROFILES, Heritability, Diet, Metabolomics data, 030104 developmental biology, chemistry, Pediatrics, Perinatology and Child Health, Gene-Environment Interaction, 030217 neurology & neurosurgery
Abstract

Metabolites are small molecules involved in cellular metabolism where they act as reaction substrates or products. The term ‘metabolomics’ refers to the comprehensive study of these molecules. The concentrations of metabolites in biological tissues are under genetic control, but this is limited by environmental factors such as diet. In adult mono- and dizygotic twin pairs, we estimated the contribution of genetic and shared environmental influences on metabolite levels by structural equation modeling and tested whether the familial resemblance for metabolite levels is mainly explained by genetic or by environmental factors that are shared by family members. Metabolites were measured across three platforms: two based on proton nuclear magnetic resonance techniques and one employing mass spectrometry. These three platforms comprised 237 single metabolic traits of several chemical classes. For the three platforms, metabolites were assessed in 1407, 1037 and 1116 twin pairs, respectively. We carried out power calculations to establish what percentage of shared environmental variance could be detected given these sample sizes. Our study did not find evidence for a systematic contribution of shared environment, defined as the influence of growing up together in the same household, on metabolites assessed in adulthood. Significant heritability was observed for nearly all 237 metabolites; significant contribution of the shared environment was limited to 6 metabolites. The top quartile of the heritability distribution was populated by 5 of the 11 investigated chemical classes. In this quartile, metabolites of the class lipoprotein were significantly overrepresented, whereas metabolites of classes glycerophospholipids and glycerolipids were significantly underrepresented.

Published
2020

26. Perspectives on automated composition of workflows in the life sciences:[version 1; peer review: 2 approved]

Author

Lamprecht, Anna-Lena, Palmblad, Magnus, Ison, Jon, Schwämmle, Veit, Manir, Mohammad Sadnan Al, Altintas, Ilkay, Amor, Ammar Ben Hadj, Capella-Gutierrez, Salvador, Charonyktakis, Paulos, Crusoe, Michael R., Gil, Yolanda, Goble, Carole, Griffin, Timothy J., Groth, Paul, Ienasescu, Hans, Jagtap, Pratik, Kalaš, Matúš, Kasalica, Vedran, Khanteymoori, Alireza, Kuhn, Tobias, Mei, Hailiang, Ménager, Hervé, Möller, Steffen, Robert, Vincent, Soiland-Reyes, Stian, Stevens, Robert, Szaniszlo, Szoke, Verberne, Suzan, Verhoeven, Aswin, and Wolstencroft, Katherine

Subjects
life sciences, semantic domain modelling, computational pipelines, workflow benchmarking, scientific workflows, bioinformatics, automated workflow composition
Abstract

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus.This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years.A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future

Published
2021

27. Perspectives on automated composition of workflows in the life sciences

Author

Lamprecht, Anna-Lena, primary, Palmblad, Magnus, additional, Ison, Jon, additional, Schwämmle, Veit, additional, Al Manir, Mohammad Sadnan, additional, Altintas, Ilkay, additional, Baker, Christopher J. O., additional, Ben Hadj Amor, Ammar, additional, Capella-Gutierrez, Salvador, additional, Charonyktakis, Paulos, additional, Crusoe, Michael R., additional, Gil, Yolanda, additional, Goble, Carole, additional, Griffin, Timothy J., additional, Groth, Paul, additional, Ienasescu, Hans, additional, Jagtap, Pratik, additional, Kalaš, Matúš, additional, Kasalica, Vedran, additional, Khanteymoori, Alireza, additional, Kuhn, Tobias, additional, Mei, Hailiang, additional, Ménager, Hervé, additional, Möller, Steffen, additional, Richardson, Robin A., additional, Robert, Vincent, additional, Soiland-Reyes, Stian, additional, Stevens, Robert, additional, Szaniszlo, Szoke, additional, Verberne, Suzan, additional, Verhoeven, Aswin, additional, and Wolstencroft, Katherine, additional

Published
2021
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28. Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved]

Author

Lamprecht, Anna-Lena, Palmblad, Magnus, Ison, Jon, Schwämmle, Veit, Al Manir, Mohammad Sadnan, Altintas, Ilkay, Baker, Christopher J. O., Ben Hadj Amor, Ammar, Capella-Gutierrez, Salvador, Charonyktakis, Paulos, Crusoe, Michael R., Gil, Yolanda, Goble, Carole, Griffin, Timothy J., Groth, Paul, Ienasescu, Hans, Jagtap, Pratik, Kalaš, Matúš, Kasalica, Vedran, Khanteymoori, Alireza, Kuhn, Tobias, Mei, Hailiang, Ménager, Hervé, Möller, Steffen, Richardson, Robin A., Robert, Vincent, Soiland-Reyes, Stian, Stevens, Robert, Szaniszlo, Szoke, Verberne, Suzan, Verhoeven, Aswin, and Wolstencroft, Katherine

Subjects
Knowledge-based systems: 425 [VDP], Science, Beregningsvitenskap, Medicine, Life Science, Computational Science, Livsvitenskap, Kunnskapsbaserte systemer: 425 [VDP]
Abstract

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future. publishedVersion

Published
2021

29. Perspectives on automated composition of workflows in the life sciences

Author

Lamprecht, Anna-Lena, Palmblad, Magnus, Ison, Jon, Schwämmle, Veit, Al Manir, Mohammad Sadnan, Altintas, Ilkay, Baker, Christopher J O, Ben Hadj Amor, Ammar, Capella-Gutierrez, Salvador, Charonyktakis, Paulos, Crusoe, Michael R, Gil, Yolanda, Goble, Carole, Griffin, Timothy J, Groth, Paul, Ienasescu, Hans, Jagtap, Pratik, Kalaš, Matúš, Kasalica, Vedran, Khanteymoori, Alireza, Kuhn, Tobias, Mei, Hailiang, Ménager, Hervé, Möller, Steffen, Richardson, Robin A, Robert, Vincent, Soiland-Reyes, Stian, Stevens, Robert, Szaniszlo, Szoke, Verberne, Suzan, Verhoeven, Aswin, Wolstencroft, Katherine, Lamprecht, Anna-Lena, Palmblad, Magnus, Ison, Jon, Schwämmle, Veit, Al Manir, Mohammad Sadnan, Altintas, Ilkay, Baker, Christopher J O, Ben Hadj Amor, Ammar, Capella-Gutierrez, Salvador, Charonyktakis, Paulos, Crusoe, Michael R, Gil, Yolanda, Goble, Carole, Griffin, Timothy J, Groth, Paul, Ienasescu, Hans, Jagtap, Pratik, Kalaš, Matúš, Kasalica, Vedran, Khanteymoori, Alireza, Kuhn, Tobias, Mei, Hailiang, Ménager, Hervé, Möller, Steffen, Richardson, Robin A, Robert, Vincent, Soiland-Reyes, Stian, Stevens, Robert, Szaniszlo, Szoke, Verberne, Suzan, Verhoeven, Aswin, and Wolstencroft, Katherine

Abstract

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic pro

Published
2021

30. Author Correction: Heritability estimates for 361 blood metabolites across 40 genome-wide association studies (Nature Communications, (2020), 11, 1, (39), 10.1038/s41467-019-13770-6)

Author

Hagenbeek, Fiona A., Pool, René, van Dongen, Jenny, Draisma, H. M., Jan Hottenga, Jouke, Willemsen, Gonneke, Abdellaoui, Abdel, Fedko, Iryna O., den Braber, Anouk, Visser, Pieter Jelle, de Geus, Eco J.C.N., Willems van Dijk, Ko, Verhoeven, Aswin, Suchiman, H. Eka, Beekman, Marian, Slagboom, P. Eline, van Duijn, Cornelia M., Barkey Wolf, J. J.H., Cats, D., Amin, N., Beulens, J. W., van der Bom, J. A., Bomer, N., Demirkan, A., van Hilten, J. A., Meessen, J. M.T.A., Moed, M. H., Fu, J., Onderwater, G. L.J., Rutters, F., So-Osman, C., van der Flier, W. M., van der Heijden, A. A.W.A., van der Spek, A., Asselbergs, F. W., Boersma, E., Elders, P. M., Geleijnse, J. M., Ikram, M. A., Kloppenburg, M., Meulenbelt, I., Mooijaart, S. P., Nelissen, R. G.H.H., Netea, M. G., Penninx, B. W.J.H., Stehouwer, C. D.A., Teunissen, C. E., Terwindt, G. M., ‘t Hart, L. M., van den Maagdenberg, A. M.J.M., van der Harst, P., van der Horst, I. C.C., van der Kallen, C. J.H., van Greevenbroek, M. M.J., van Spil, W. E., Wijmenga, C., Zwinderman, A. H., Zhernikova, A., Jukema, J. W., Mei, H., Slofstra, M., Swertz, M., van den Akker, E. B., Deelen, J., Reinders, M. J.T., Harms, Amy C., Hankemeier, Thomas, Bartels, Meike, Nivard, Michel G., Boomsma, Dorret I., Neurology, APH - Health Behaviors & Chronic Diseases, ACS - Heart failure & arrhythmias, Epidemiology and Data Science, General practice, APH - Methodology, APH - Mental Health, Psychiatry, Clinical chemistry, APH - Aging & Later Life, APH - Personalized Medicine, APH - Digital Health, and ACS - Diabetes & metabolism

Abstract

The original version of the Supplementary Information associated with this Article included an incorrect Supplementary Data 1 file, in which additional delimiters were included in the first column for a number of rows, resulting in column shifts for some of these rows. The HTML has been updated to include a corrected version of Supplementary Data 1; the original incorrect version of Supplementary Data 1 can be found as Supplementary Information associated with this Correction. In addition, the original version of this Article contained an error in the author affiliations. An affiliation of Abdel Abdellaoui with Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands was inadvertently omitted. This has now been corrected in both the PDF and HTML versions of the Article.

Published
2020

31. Change in Urinary Myoinositol/Citrate Ratio Associates with Progressive Loss of Renal Function in ADPKD Patients.

Author

Dekker, Shosha E.I., Verhoeven, Aswin, Frey, Daria, Soonawala, Darius, Peters, Dorien J.M., Mayboroda, Oleg A., and de Fijter, Johan W.

Subjects
POLYCYSTIC kidney disease, INOSITOL, KIDNEY physiology, CLINICAL decision support systems
Abstract

Introduction: In autosomal dominant polycystic kidney disease (ADPKD) patients, predicting renal disease progression is important to make a prognosis and to support the clinical decision whether to initiate renoprotective therapy. Conventional markers all have their limitations. Metabolic profiling is a promising strategy for risk stratification. We determined the prognostic performance to identify patients with a fast progressive disease course and evaluated time-dependent changes in urinary metabolites. Methods: Targeted, quantitative metabolomics analysis (1H NMR-spectroscopy) was performed on spot urinary samples at two time points, baseline (n = 324, 61% female; mean age 45 years, SD 11; median eGFR 61 mL/min/1.73 m2, IQR 42–88; mean years of creatinine follow-up 3.7, SD 1.3) and a sample obtained after 3 years of follow-up (n = 112). Patients were stratified by their eGFR slope into fast and slow progressors based on an annualized change of > −3.0 or ≤ −3.0 mL/min/1.73 m2/year, respectively. Fifty-five urinary metabolites and ratios were quantified, and the significant ones were selected. Logistic regression was used to determine prognostic performance in identifying those with a fast progressive course using baseline urine samples. Repeated-measures ANOVA was used to analyze whether changes in urinary metabolites over a 3-year follow-up period differed between fast and slow progressors. Results: In a single urinary sample, the prognostic performance of urinary metabolites was comparable to that of a model including height-adjusted total kidney volume (htTKV, AUC = 0.67). Combined with htTKV, the predictive value of the metabolite model increased (AUC = 0.75). Longitudinal analyses showed an increase in the myoinositol/citrate ratio (p < 0.001) in fast progressors, while no significant change was found in those with slow progression, which is in-line with an overall increase in the myoinositol/citrate ratio as GFR declines. Conclusion: A metabolic profile, measured at a single time point, showed at least equivalent prognostic performance to an imaging-based risk marker in ADPKD. Changes in urinary metabolites over a 3-year follow-up period were associated with a fast progressive disease course. [ABSTRACT FROM AUTHOR]

Published
2022
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32. Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition

Author

Colombo, Alessio Vittorio, primary, Sadler, Rebecca Katie, additional, Llovera, Gemma, additional, Singh, Vikramjeet, additional, Roth, Stefan, additional, Heindl, Steffanie, additional, Sebastian Monasor, Laura, additional, Verhoeven, Aswin, additional, Peters, Finn, additional, Parhizkar, Samira, additional, Kamp, Frits, additional, Gomez de Aguero, Mercedes, additional, MacPherson, Andrew J, additional, Winkler, Edith, additional, Herms, Jochen, additional, Benakis, Corinne, additional, Dichgans, Martin, additional, Steiner, Harald, additional, Giera, Martin, additional, Haass, Christian, additional, Tahirovic, Sabina, additional, and Liesz, Arthur, additional

Published
2021
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34. Author response: Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition

Author

Colombo, Alessio Vittorio, primary, Sadler, Rebecca Katie, additional, Llovera, Gemma, additional, Singh, Vikramjeet, additional, Roth, Stefan, additional, Heindl, Steffanie, additional, Sebastian Monasor, Laura, additional, Verhoeven, Aswin, additional, Peters, Finn, additional, Parhizkar, Samira, additional, Kamp, Frits, additional, Gomez de Aguero, Mercedes, additional, MacPherson, Andrew J, additional, Winkler, Edith, additional, Herms, Jochen, additional, Benakis, Corinne, additional, Dichgans, Martin, additional, Steiner, Harald, additional, Giera, Martin, additional, Haass, Christian, additional, Tahirovic, Sabina, additional, and Liesz, Arthur, additional

Published
2021
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35. Heritability estimates for 361 blood metabolites across 40 genome-wide association studies

Author

Hagenbeek, Fiona A., Pool, René, van Dongen, Jenny, Draisma, Harmen H.M., Hottenga, Jouke Jan, Willemsen, Gonneke, Abdellaoui, Abdel, Fedko, Iryna O., den Braber, Anouk, Visser, Pieter Jelle, de Geus, Eco J.C.N., Willems van Dijk, Ko, Verhoeven, Aswin, Suchiman, H.E., Beekman, Marian, Slagboom, Eline P., van Duijn, Cornelia M., Barkey Wolf, J.J.H., Cats, D., Amin, N., Beulens, J.W., van der Bom, J.A., Bomer, N., Demirkan, A., van Hilten, J.A., Meessen, J.M.T.A., Moed, M.H., Fu, J., Onderwater, G.L.J., Rutters, F., So-Osman, C., van der Flier, W.M., van der Heijden, A.A.W.A., van der Spek, A., Asselbergs, F.W., Boersma, E., Elders, P.M., Geleijnse, J.M., Ikram, M.A., Kloppenburg, M., Meulenbelt, I., Mooijaart, S.P., Nelissen, R.G.H.H., Netea, M.G., Penninx, B.W.J.H., Stehouwer, C.D.A., Teunissen, C.E., Terwindt, G.M., Jukema, J.W., Reinders, M.J.T., Hagenbeek, Fiona A., Pool, René, van Dongen, Jenny, Draisma, Harmen H.M., Hottenga, Jouke Jan, Willemsen, Gonneke, Abdellaoui, Abdel, Fedko, Iryna O., den Braber, Anouk, Visser, Pieter Jelle, de Geus, Eco J.C.N., Willems van Dijk, Ko, Verhoeven, Aswin, Suchiman, H.E., Beekman, Marian, Slagboom, Eline P., van Duijn, Cornelia M., Barkey Wolf, J.J.H., Cats, D., Amin, N., Beulens, J.W., van der Bom, J.A., Bomer, N., Demirkan, A., van Hilten, J.A., Meessen, J.M.T.A., Moed, M.H., Fu, J., Onderwater, G.L.J., Rutters, F., So-Osman, C., van der Flier, W.M., van der Heijden, A.A.W.A., van der Spek, A., Asselbergs, F.W., Boersma, E., Elders, P.M., Geleijnse, J.M., Ikram, M.A., Kloppenburg, M., Meulenbelt, I., Mooijaart, S.P., Nelissen, R.G.H.H., Netea, M.G., Penninx, B.W.J.H., Stehouwer, C.D.A., Teunissen, C.E., Terwindt, G.M., Jukema, J.W., and Reinders, M.J.T.

Abstract

Metabolomics examines the small molecules involved in cellular metabolism. Approximately 50% of total phenotypic differences in metabolite levels is due to genetic variance, but heritability estimates differ across metabolite classes. We perform a review of all genome-wide association and (exome-) sequencing studies published between November 2008 and October 2018, and identify >800 class-specific metabolite loci associated with metabolite levels. In a twin-family cohort (N = 5117), these metabolite loci are leveraged to simultaneously estimate total heritability (h2 total), and the proportion of heritability captured by known metabolite loci (h2 Metabolite-hits) for 309 lipids and 52 organic acids. Our study reveals significant differences in h2 Metabolite-hits among different classes of lipids and organic acids. Furthermore, phosphatidylcholines with a high degree of unsaturation have higher h2 Metabolite-hits estimates than phosphatidylcholines with low degrees of unsaturation. This study highlights the importance of common genetic variants for metabolite levels, and elucidates the genetic architecture of metabolite classes.

Published
2020

36. Determination of internuclear distances in uniformly labeled molecules by rotational-resonance solid-state NMR

Author

Williamson, Philip T.F., Verhoeven, Aswin, Ernst, Matthias, and Meier, Beat H.

Subjects
Chemical reactions -- Research, Nuclear magnetic resonance -- Usage, Chemistry
Abstract

Rotational-resonance magic-angle spinning NMR experiments are frequently used to measure dipolar couplings and to determine internuclear distances. The analysis introduced here describes a many-spin system as a pair of active spins and a set of passive spins.

Published
2003

37. Disruptions of Anaerobic Gut Bacteria Are Associated with Stroke and Post-stroke Infection: a Prospective Case–Control Study

Author

Haak, Bastiaan W., primary, Westendorp, Willeke F., additional, van Engelen, Tjitske S. R., additional, Brands, Xanthe, additional, Brouwer, Matthijs C., additional, Vermeij, Jan-Dirk, additional, Hugenholtz, Floor, additional, Verhoeven, Aswin, additional, Derks, Rico J., additional, Giera, Martin, additional, Nederkoorn, Paul J., additional, de Vos, Willem M., additional, van de Beek, Diederik, additional, and Wiersinga, W. Joost, additional

Published
2020
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39. Microbiota-derived short chain fatty acids promote Aβ plaque deposition

Author

Colombo, Alessio Vittorio, primary, Sadler, Rebecca K., additional, Llovera, Gemma, additional, Singh, Vikramjeet, additional, Roth, Stefan, additional, Heindl, Steffanie, additional, Monasor, Laura Sebastian, additional, Verhoeven, Aswin, additional, Peters, Finn, additional, Parhizkar, Samira, additional, Kamp, Frits, additional, de Agüero, Mercedes Gomez, additional, Macpherson, Andrew J., additional, Winkler, Edith, additional, Herms, Jochen, additional, Benakis, Corinne, additional, Dichgans, Martin, additional, Steiner, Harald, additional, Giera, Martin, additional, Haass, Christian, additional, Tahirovic, Sabina, additional, and Liesz, Arthur, additional

Published
2020
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42. A metabolomic profile is associated with the risk of incident coronary heart disease

Author

Vaarhorst, Anika A.M., Verhoeven, Aswin, Weller, Claudia M., Böhringer, Stefan, Göraler, Sibel, Meissner, Axel, Deelder, André M., Henneman, Peter, Gorgels, Anton P.M., van den Brandt, Piet A., Schouten, Leo J., van Greevenbroek, Marleen M., Merry, Audrey H.H., Verschuren, Monique W.M., van den Maagdenberg, Arn M.J.M., van Dijk, Ko Willems, Isaacs, Aaron, Boomsma, Dorret, Oostra, Ben A., van Duijn, Cornelia M., Jukema, Wouter J., Boer, Jolanda M.A., Feskens, Edith, Heijmans, Bastiaan T., and Slagboom, Eline P.

Published
2014
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45. Genome-wide association study of plasma triglycerides, phospholipids and relation to cardio-metabolic risk factors

Author

Demirkan, Ayşe, primary, Pool, Rene, additional, Deelen, Joris, additional, Beekman, Marian, additional, Liu, Jun, additional, Harms, Amy C., additional, Vaarhorst, Anika, additional, Hagenbeek, Fiona A, additional, Willemsen, Gonneke, additional, Verhoeven, Aswin, additional, Amin, Najaf, additional, van Dijk, Ko Willems, additional, Hankemeier, Thomas, additional, Boomsma, Dorret I., additional, Slagboom, Eline, additional, and van Duijn, Cornelia M., additional

Published
2019
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47. Urinary metabolites associate with the rate of kidney function decline in patients with autosomal dominant polycystic kidney disease.

Author

Dekker, Shosha E. I., Verhoeven, Aswin, Soonawala, Darius, Peters, Dorien J. M., de Fijter, Johan W., and Mayboroda, Oleg A.

Subjects
*POLYCYSTIC kidney disease, *THIOUREA, *GLOMERULAR filtration rate, *CITRATES, *CALCULI
Abstract

Background: The variable course of autosomal dominant polycystic kidney disease (ADPKD), and the advent of renoprotective treatment require early risk stratification. We applied urinary metabolomics to explore differences associated with estimated glomerular filtration rate (eGFR; CKD-EPI equation) and future eGFR decline. Methods: Targeted, quantitative metabolic profiling (1H NMR-spectroscopy) was performed on baseline spot urine samples obtained from 501 patients with ADPKD. The discovery cohort consisted of 338 patients (56% female, median values for age 46 [IQR 38 to 52] years, eGFR 62 [IQR 45 to 85] ml/min/1.73m2, follow-up time 2.5 [range 1 to 3] years, and annual eGFR slope –3.3 [IQR –5.3 to –1.3] ml/min/1.73m2/year). An independent cohort (n = 163) was used for validation. Multivariate modelling and linear regression were used to analyze the associations between urinary metabolites and eGFR, and eGFR decline over time. Results: Twenty-nine known urinary metabolites were quantified from the spectra using a semi-automatic quantification routine. The model optimization routine resulted in four metabolites that most strongly associated with actual eGFR in the discovery cohort (F = 128.9, P = 7×10−54, R2 = 0.724). A model using the ratio of two other metabolites, urinary alanine/citrate, showed the best association with future annual change in eGFR (F = 51.07, P = 7.26×10−12, R2 = 0.150). This association remained significant after adjustment for clinical risk markers including height-adjusted total kidney volume (htTKV). Results were confirmed in the validation cohort. Conclusions: Quantitative NMR profiling identified urinary metabolic markers that associated with actual eGFR and future rate of eGFR decline. The urinary alanine/citrate ratio showed additional value beyond conventional risk markers. [ABSTRACT FROM AUTHOR]

Published
2020
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48. Proteomic identification of Axc, a novel beta-lactamase with carbapenemase activity in a meropenem-resistant clinical isolate of Achromobacter xylosoxidans

Author

Fleurbaaij, Frank, primary, Henneman, Alex A., additional, Corver, Jeroen, additional, Knetsch, Cornelis W., additional, Smits, Wiep Klaas, additional, Nauta, Sjoerd T., additional, Giera, Martin, additional, Dragan, Irina, additional, Kumar, Nitin, additional, Lawley, Trevor D., additional, Verhoeven, Aswin, additional, van Leeuwen, Hans C., additional, Kuijper, Ed J., additional, and Hensbergen, Paul J., additional

Published
2017
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