Computational modelling

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Models (104)
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synthetic construct (2)
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Technology Type

Mass Spectrometry (29)
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Data-independent acquisition (2)
ABI_SOLID, AB 5500xl Genetic Analyzer, AB SOLiD 4 System (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
Affymetrix SNP 6.0, Illumina HT 12, Aperio image - H&E stained tissue_section (1)
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Instrument Platform

Illumina HiSeq 2500 (6)
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Illumina HiSeq 2000 (2)
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Liquid Chromatography MS - positive - hilic (2)
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Illumina Genome Analyzer II (1)
NA (1)
NextSeq 2000 (1)
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Q Exactive (1)
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Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)

Publication Date

2024 (56)
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2005 (26)
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2017 (12)
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2020 (8)
2013 (8)
2016 (6)
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2018 (3)
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2009 (3)
2014 (2)
2011 (2)
2007 (1)

UNIPROT ID/AC

Q00764 (13)
P31688 (13)
P33401 (13)
P37012 (13)
P32861 (13)
P01583 (2)
P45452 (2)
P02458 (2)
P07522 (2)
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ENSEMBL ID

ENSG00000149968 (2)
ENSG00000100234 (1)
ENSG00000102265 (1)
ENSG00000184557 (1)
ENSG00000137745 (1)
ENSG00000196611 (1)
ENSG00000177606 (1)
ENSG00000170345 (1)
ENSG00000158859 (1)
ENSG00000168036 (1)
ENSG00000033327 (1)
ENSG00000100985 (1)
ENSG00000102908 (1)
ENSG00000118260 (1)
ENSG00000163739 (1)
ENSG00000120659 (1)
ENSDARG00000063559 (1)
ENSDARG00000090714 (1)
ENSDARG00000051873 (1)
ENSDARG00000061100 (1)
ENSDARG00000035506 (1)
ENSDARG00000024112 (1)
ENSDARG00000057714 (1)
ENSDARG00000010347 (1)
ENSDARG00000059411 (1)
ENSDARG00000036809 (1)
ENSDARG00000035565 (1)
ENSDARG00000029952 (1)
ENSDARG00000045414 (1)
ENSDARG00000020270 (1)

CHEBI ID

CHEBI:16908 (22)
CHEBI:15422 (21)
CHEBI:15846 (21)
CHEBI:16761 (21)
CHEBI:16027 (21)
CHEBI:18021 (21)
CHEBI:15361 (21)
CHEBI:4167 (20)
CHEBI:16551 (20)
CHEBI:15343 (20)
CHEBI:30031 (20)
CHEBI:17754 (20)
CHEBI:16001 (20)
CHEBI:17794 (20)
CHEBI:17835 (20)
CHEBI:16108 (20)
CHEBI:29052 (20)
CHEBI:17665 (20)
CHEBI:16084 (20)
CHEBI:16236 (20)
CHEBI:28013 (19)
CHEBI:28602 (19)
CHEBI:15978 (16)
CHEBI:16077 (15)
CHEBI:46398 (14)
CHEBI:17659 (14)
CHEBI:18066 (14)
CHEBI:18283 (13)
CHEBI:30089 (13)
CHEBI:28087 (7)

Metabolite Name

Phenethylamine (3)
Betaine (3)
Thymine (3)
Spermine (3)
Ornithine (3)
Estrone (3)
Glutathione (3)
Arginine (3)
Tyrosine (3)
Phenylalanine (3)
Adenine (3)
Creatinine (3)
Creatine (3)
Tryptophan (3)
Valin (2)
Threonin (2)
Cycloleucylprolyl (2)
Climbazole (2)
Caffeine-D9 (2)
AFMU (2)
Indole-3-carbaldehyde (2)
Imidazoleacetic Acid (2)
N-Acetyl-DL-serine (2)
Oxybenzone (2)
Anatabine (2)
Melatonine (2)
3-Phenyllactic acid (2)
Kojic Acid (2)
Enilconazole (2)
Prolinamide (2)

First Public Date

2023 (14)
2021 (14)
2024 (11)
2025 (9)
2026 (8)
2017 (5)
2020 (4)
2015 (4)
2019 (3)
2014 (3)
2013 (3)
2022 (1)
2018 (1)
2016 (1)

Modelling Approach

Ordinary differential equation model (76)
Constraint-based model (10)
Logical model (6)
Computational model (1)
Mathematical model (1)
Protein-protein interaction network (1)
Delayed differential equation model (1)

Lab affiliation

Professor at Department of Pharmacy, Drug Delivery, Uppsala University (4)
Genome Biology Unit and Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany (2)
Biomedical Center, Chromatin Proteomics Group, Department of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Strasse 9, 82152 Planegg-Martinsried, Germany. (1)
Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, United States of America (1)
Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London (1)
Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green, Dublin 2, Ireland. Centre for Systems Medicine, Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St Stephen’s Green, Dublin 2, Ireland. (1)
Departmento de Ciencias Básicas Biomédicas, Facultad de Ciencias de la Salud, Universidad de Talca, Talca, Región del Maule, Chile (1)
Full Professor for Analytical Chemistry Institute of Chemical Technologies and Analytics TU Wien Getreidemarkt 9/E164 A-1060 Vienna Austria (1)
Full Professor of Systems Biology and Director of Computational Modelling Systems Biology Ireland, University College Dublin, Dublin, Ireland. Conway Institute of Biomolecular & Biomedical Research,University College Dublin, Dublin, Ireland. School of Medicine and Medical Science, University College Dublin, Dublin, Ireland. Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA (1)
German Institute of Human Nutrition Potsdam-Rehbrucke, Nuthetal, Germany, Deutsches Herzzentrum der Charite - Medical Heart Center of Charite and German Heart Institute Berlin, Institute of Computer-assisted Cardiovascular Medicine, Berlin, Germany (1)
IST (Institute of Science and Technology) Austria, Klosterneuburg, Lower Austria, Austria (1)
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague (1)
Lab for Metabolic Signaling, Department of Pediatrics, University of Groningen, University Medical Center Groningen (UMCG), 9713 AV Groningen, The Netherlands and School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26111 Oldenburg, Germany (1)
Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute, Fiocruz, Paraná, Brazil (1)
SULFAGING group, Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., DORTMUND, GERMANy (1)
School of Biochemistry, Faculty of Life Sciences, University of Bristol (1)
School of Biosciences University of Sheffield Western Bank Sheffield S10 2TN United Kingdom (1)
School of Life and Enviromental Sciences, Charles Perkins Centre, The University of Sydney (1)
School of Medical Sciences, Faculty of Medicine and Healthy, University of Sydney, Sydney, Australia. (1)
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK (1)
University College Dublin, School of Medicine, Systems Biology Ireland Belfield Dublin 4 (1)
University of Dundee (1)
University of Liverpool (1)
University of Liverpool, Institute of Life Course and Medical Sciences, University of Liverpool, United Kingdom (1)
Dr. J.C. Wolters Principal investigator University Medical Center Groningen Laboratory of Pediatrics Visiting address: Antonius Deusinglaan 1 (ERIBA 6th floor), 9713 AV Groningen, The Netherlands Mail address: P.O.Box 196, 9700 AD Groningen, The Netherlands HPC XB23/Room 3226.0657 Phone: +31 (0) 50 3636276 www.labpediatricsrug.nl (1)

IsPrivate

False (100)

Model Flag

Non Kinetic (3)

Submitter Keywords

FROG (2)
Ersilia (1)
FAIR-AIML (1)
Machine Learning Model (1)
Manuscript Accepted (1)
Immuno-oncology (1)

Classification

bacteria (4)

Modification

4-tetrahydrothiazine-3-carboxylic acid (1)
N6 (1)
Not available (1)

Study type

Transcription profiling by array (17)
RNA-seq of coding RNA (7)
ChIP-seq (4)
RNA-seq of total RNA (4)
RNA-seq of coding RNA from single cells (2)

Release Date

2021 (392)
2022 (389)
2023 (353)
2025 (331)
2024 (310)
2020 (282)
2019 (237)
2017 (174)
2018 (165)
2016 (159)
2015 (135)
2014 (94)
2013 (84)
2010 (55)
2026 (53)
2012 (48)
2011 (46)
2009 (34)
2006 (25)
2008 (23)
2007 (16)
2005 (9)
2004 (4)
2003 (2)
2001 (1)

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Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna

Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the...

MTBLS2273 | MetaboLights

Computational Modelling of Myocardial Metabolism in Patients with Advanced Heart Failure

Although perturbations of myocardial metabolism and energy depletion are fundamental characteristics of heart failure (HF) pathophysiology, interindividual variability in bioenergetic phenotypes and their clinical implications remain poorly understood. Here, we used large-scale proteomics data from ...

ORGANISM(S): Homo sapiens (Human)

2025-06-10 | PXD053721 | Pride