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Repository

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biostudies-arrayexpress (679)
geo (578)
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pride (302)
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HIV (1)
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Mass Spectrometry (302)
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SWATH MS (14)
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SRM/MRM (4)
Top-down proteomics (4)
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ILLUMINA, Illumina HiSeq 2500 (2)
Affinity proteomics (2)
MSE (2)
Combined on identical nucleotide universal identifier, Illumina HumanWG-6 version 3 or Illumina HumanHT-12 expression bead chip (1)
ABI_SOLID, AB 5500xl Genetic Analyzer, AB SOLiD 4 System (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
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Illumina Genome Analyzer IIx (1)
SomaScan affinity proteomics (1)
Metaproteomics (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina HiSeq 2500 (31)
Illumina HiSeq 2000 (18)
NextSeq 500 (13)
Illumina NovaSeq 6000 (11)
Illumina HiSeq 4000 (7)
NextSeq 550 (5)
Illumina Genome Analyzer IIx (3)
Agilent Scanner G2505B (2)
Illumina NovaSeq X (2)
NextSeq 2000 (2)
High-performance computing workstation (1)
Protocol computer workstation running R statistical software (1)
Thermal cycler (PCR); Covaris ME220 focused ultrasonicator; magnetic separation rack; Agilent TapeStation system (D5000 and D1000 ScreenTape assays); Qubit fluorometer or equivalent; microcentrifuge. (1)
JANUS® G3 MDT automated liquid handling workstation (PerkinElmer); thermal cycler or incubator (42 °C); Zymo DNA Clean & Concentrator columns; AMPure XP magnetic bead purification system; magnetic separation rack. (1)
Multichannel pipettes or automated liquid handler; 384-well tissue culture plates; Class II biological safety cabinet; CO₂ incubator (37 °C, 5% CO₂). (1)
See Description (1)
See Desciption (1)
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MoFlo XDP (Beckman Coulter) or a FACSAria II (Becton Dickinson) (1)
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BD FACS JAZZ (1)
Agilent High resolution C scanner (1)
Maxwell 16 Instrument (1)
BD FACSARIA III (1)

Publication Date

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2013 (96)
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2016 (85)
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2010 (70)
2018 (66)
2005 (64)
2011 (64)
2017 (56)
2009 (50)
2008 (42)
2007 (12)
2006 (7)

UNIPROT ID/AC

Q00764 (16)
P31688 (16)
P33401 (16)
P37012 (16)
P32861 (16)
P04049 (6)
Q02750 (6)
P04637 (6)
P28482 (5)
P62993 (5)
P24941 (4)
P38936 (4)
Q12189 (4)
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P23254 (4)
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P53319 (4)
P38720 (4)
P23900 (4)
P11412 (4)
P62136 (4)
P24864 (4)
P60568 (4)
P45983 (4)
Q13315 (4)
Q16539 (4)
Q9R0T8 (3)
P11802 (3)
Q01094 (3)

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:15422 (51)
CHEBI:18021 (51)
CHEBI:17754 (51)
CHEBI:15361 (49)
CHEBI:16761 (47)
CHEBI:16236 (44)
CHEBI:16551 (44)
CHEBI:15343 (43)
CHEBI:16027 (43)
CHEBI:4167 (40)
CHEBI:16908 (37)
CHEBI:15846 (37)
CHEBI:30031 (36)
CHEBI:17794 (32)
CHEBI:16001 (32)
CHEBI:16108 (32)
CHEBI:17835 (31)
CHEBI:30089 (30)
CHEBI:17665 (30)
CHEBI:46398 (29)
CHEBI:15978 (28)
CHEBI:17154 (28)
CHEBI:29052 (27)
CHEBI:16828 (25)
CHEBI:16084 (24)
CHEBI:28013 (24)
CHEBI:16526 (24)
CHEBI:15379 (23)
CHEBI:28602 (23)
CHEBI:16077 (22)

Metabolite Name

Creatine (10)
Taurine (10)
Isoleucine (9)
Glutamine (9)
Creatinine (9)
Leucine (8)
Methionine (8)
Proline (8)
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Phenylalanine (7)
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Adenine (7)
Tryptophan (6)
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Taurine (6)
Proline (6)
Alanine (6)
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Choline (6)
Xanthine (6)
Inosine (6)
Sucrose (6)
2-oxindole-3-acetic acid|5-methoxyindole-2-carboxylic acid|5-hydroxyindole-3-acetic acid (5)
Tuberonic acid (5)
Tuberonic acid methyl ester (5)
Jasmonic acid methyl ester (5)
3-oxo-2-(2-(Z)-pentenyl)-cyclopentane-1-octanoic acid (5)
Cucurbic acid|9,10-dihydrojasmonic acid (5)
Cis/trans-12-oxo-phytodienoic acid (5)

First Public Date

2026 (158)
2024 (151)
2025 (137)
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2022 (97)
2021 (89)
2020 (80)
2019 (62)
2018 (58)
2014 (51)
2017 (29)
2016 (22)
2015 (22)
2013 (8)
2012 (1)

Modelling Approach

Ordinary differential equation model (264)
Constraint-based model (34)
Logical model (7)
Mathematical model (5)
Other (5)
Petri net (3)
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Multi-value logic model (1)
Finite element spatial model (1)
Computational model (1)
Protein-protein interaction network (1)
Delayed differential equation model (1)
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Population model (1)
Metabolic network (1)

Study status

Not provided (1)
Not yet recruiting (1)
Recruiting (1)
Completed (1)

Lab affiliation

Ruhr University Bochum, Germany (10)
Professor at Department of Pharmacy, Drug Delivery, Uppsala University (4)
King's College London (4)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (3)
ETH Zurich, Institute of Molecular Systems Biology (3)
University of Greifswald, Institute for Microbiology, Department for Microbial Proteomics (3)
Daglig leder, PROMEC Institutt for klinisk og molekylær medisin lars.hagen@ntnu.no 73598508 72573342 Laboratoriesenteret, 231.04.008, Øya, Erling Skjalgssons gate 1 (3)
Chair of Proteomics and Bioanalytics, Technische Universität München, Germany (3)
University of Edinburgh (3)
Division of Cell Signalling and Immunology, University of Dundee, Dundee, UK. (2)
Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France (2)
Cancer Research UK Cambridge Institute University of Cambridge Li Ka Shing Centre Cambridge CB2 0RE United Kingdom (2)
Ruhr-Universität Bochum LS Biochemie der Pflanzen Universitätsstraße 150 44780 Bochum (2)
Ruhr-University Bochum, Germany (2)
Lab Head, UQ Diamantina Institute,The University of Queensland (2)
General Manager of PROMEC Department of Clinical and Molecular Medicine +4773598508 +4772573342 Laboratoriesenteret, 231.04.008, Øya, Erling Skjalgssons gate 1 Norway (2)
Mossakowski Medical Research Institute, Polish Academy of Sciences (2)
Breast Cancer Now The Institute of Cancer Research (2)
Biochemistry & Molecular Biology Cumming School of Medicine University of Calgary, Canada (2)
Genome Biology Unit and Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany (2)
Dept of Experimental Medical Science, Wallenberg Neuroscience Center, Lund University, Sweden (2)
Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway (2)
IRCCS Istituto G Gaslini (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)
Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh (1)
SULFAGING group, Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., DORTMUND, GERMANy (1)
MRC Centre for Drug Safety Science, Department of Pharmacology & Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK. (1)
1. School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia 2. Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan (1)
Ahmet Hoke M.D., Ph.D. FRCPC Professor, Neurology and Neuroscience Director, Neuromuscular Division Director, Merkin Peripheral Neuropathy and Nerve Regeneration Center Editor-in-Chief, Experimental Neurology Johns Hopkins School of Medicine 855 N. Wolfe St., Rangos 248 Baltimore, MD, 21205 USA (1)
Department of Ecogenomics and Systems Biology, Division Molecular Systems Biology, University of Vienna, Austria (1)

IsPrivate

False (348)

Model Flag

Non Kinetic (21)
Non Miriam (2)
Sbml Extended (1)

Submitter Keywords

Immuno-oncology (17)
Manuscript Accepted (3)
FROG (3)
Not Peer Reviewed (3)
Ersilia (1)
FAIR-AIML (1)
Machine Learning Model (1)
TransQST (1)
COVID-19 (1)

Classification

bacteria (20)
fungi (2)
protozoa (2)
helminths (1)
viruses (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (2)
Not available (2)
15.994915 (1)
N6 (1)
4-tetrahydrothiazine-3-carboxylic acid (1)

Study type

Transcription profiling by array (341)
ChIP-seq (110)
RNA-seq of coding RNA (91)
ChIP-chip by tiling array (19)
Methylation profiling by array (18)
ChIP-chip by array (11)
Comparative genomic hybridization by array (11)
Methylation profiling by high throughput sequencing (11)
RNA-seq of coding RNA from single cells (10)
Unknown experiment type (8)
Other (8)
RNA-seq of total RNA (7)
Animal - High-throughput sequencing (5)
RNA-seq of non coding RNA (5)
Transcription profiling by SAGE (4)
Observational (4)
Transcription profiling by tiling array (3)
Cell line - High-throughput sequencing (2)
Genotyping by array (2)
DNA-seq (2)
RAN-seq of total RNA from single cells (1)
Baseline (1)
One-color microarray (1)
Plant - High-throughput sequencing (1)
Cell line - One-color microarray (1)
RNAi profiling by array (1)
MicroRNA profiling by high throughput sequencing (1)
ATAC-seq (1)
RIP-seq (1)
MicroRNA profiling by array (1)

Release Date

2022 (3758)
2023 (3223)
2021 (3216)
2025 (3079)
2024 (2598)
2020 (2549)
2019 (2132)
2018 (1716)
2017 (1409)
2016 (1268)
2015 (1037)
2014 (765)
2013 (579)
2026 (435)
2012 (423)
2011 (353)
2010 (288)
2009 (213)
2008 (161)
2006 (117)
2007 (99)
2005 (75)
2004 (41)
2002 (19)
2003 (18)
2001 (7)
2000 (5)
1999 (2)
1998 (1)

Location

United Kingdom (2)
Germany (1)
France (1)

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Microbial community-scale metabolic modelling predicts personalized short-chain fatty acid production profiles in the human gut

Microbially derived short-chain fatty acids (SCFAs) in the human gut are tightly coupled to host metabolism, immune regulation and integrity of the intestinal epithelium. However, the production of SCFAs can vary widely between individuals consuming the same diet, with lower levels often associated ...

2026-05-26 | MTBLS2308 | MetaboLights

Genome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa

Background: Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics...

2018-02-28 | MTBLS630 | MetaboLights

A primer on multiscale modelling of infectious disease systems.

Not available

S-EPMC6326222 | biostudies-literature

Effect of internationally imported cases on internal spread of COVID-19: a mathematical modelling study.

Not available

S-EPMC7801817 | biostudies-literature

Mathematical modelling of vaccination rollout and NPIs lifting on COVID-19 transmission with VOC: a case study in Toronto, Canada.

Not available

S-EPMC9283818 | biostudies-literature

One-line-fits-all: a knockdown strategy for rapid, generic and versatile modelling of muscular dystrophies in 3D-tissue-engineered-skeletal-muscle

Humanized 3D-tissue-engineered-skeletal-muscles (3D-TESMs) offer advanced disease modelling, but their application often require isogenic controls and involves laborious and time consuming methodology. Here, by combining 3D-TESM and shRNA approaches, we developed a “one-line-fits-all” disease modell...

ORGANISM(S): Homo sapiens (Human)

2024-02-26 | PXD042227 | Pride