systems structural biology

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Unknown (8377)
Transcriptomics (396)
Proteomics (243)
Genomics (143)
Metabolomics (31)
Models (17)
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Genomic (1)
Other (1)

Organisms

Homo sapiens (148)
Mus musculus (82)
Arabidopsis thaliana (16)
Saccharomyces cerevisiae (14)
Danio rerio (10)
Rattus norvegicus (8)
Drosophila melanogaster (8)
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Hordeum vulgare (6)
Escherichia coli (6)
Streptomyces coelicolor (5)
Medicago truncatula (4)
Oryza sativa Japonica Group (4)
Gallus gallus (4)
Escherichia coli str. K-12 substr. MG1655 (4)
Arabidopsis (3)
Haemophilus influenzae R2866 (3)
Oryza sativa Indica Group (3)
Bos taurus (3)
Bifidobacterium breve UCC2003 (2)
Aspergillus niger (2)
Zymomonas mobilis (2)
Gossypium hirsutum (2)
Populus trichocarpa x Populus deltoides (2)
Toxoplasma gondii (2)
Brassica napus (2)
Daphnia magna (2)
Zea mays (2)
Solenopsis invicta (2)
Nicotiana tabacum (1)

Organisms

Mus musculus (24)
Homo sapiens (22)
Caenorhabditis elegans (4)
Arabidopsis thaliana (4)
Saccharomyces cerevisiae (4)
Escherichia coli K-12 (3)
Saccharolobus solfataricus P2 (2)
Saccharolobus islandicus REY15A (2)
Pimephales promelas (2)
Micropterus salmoides (2)
Streptomyces coelicolor A3(2) (2)
Bacillus subtilis (2)
Escherichia coli (2)
Sporomusa sp. KB1 (1)
Saccharolobus islandicus LAL14/1 (1)
Spirodela polyrhiza (1)
Thermoplasma acidophilum DSM 1728 (1)
Aplysia californica (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Trypanosoma brucei (1)
Borreliella burgdorferi (1)
Xylella fastidiosa (1)
Medicago truncatula (1)
Drosophila melanogaster (1)
Candida albicans (1)
Zea mays (1)
Zea mays subsp. mays (1)
Bacillus subtilis subsp. subtilis str. 168 (1)
Staphylococcus aureus (1)
Rattus norvegicus (1)

Repository

biostudies-arrayexpress (399)
pride (202)
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MassIVE (26)
geo (20)
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PeptideAtlas (1)

Tissue

Cell culture (20)
Early embryonic cell (12)
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Heart (5)
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Liver (2)
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Stem cell (2)
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Arterial system endothelium (1)
Bacterial protein (1)
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Jump-In-T-REx HEK293 cell (1)
T cell (1)

Disease

Normal (4)
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Disease free (2)
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Acute leukemia (1)
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Huntington Disease (1)
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Lymphoma (1)
Malaria (1)
Obesity (1)
Plasmodium falciparum malaria (1)
Prostate adenocarcinoma (1)
Schizophrenia (1)
Severe acute respiratory syndrome (1)
Trypanosomiasis (1)
Type 2 diabetes mellitus (1)

Technology Type

Mass Spectrometry (202)
Chemical cross-linking coupled with mass spectrometry proteomics (63)
Shotgun proteomics (59)
Mass spectrometry (23)
Bottom-up proteomics (19)
Data-dependent acquisition (16)
Data-independent acquisition (16)
SWATH MS (16)
Affinity purification coupled with mass spectrometry proteomics (15)
Top-down proteomics (13)
SRM/MRM (6)
Mass spectrometry assay (5)
Gel-based experiment (5)
NMR spectroscopy (3)
HDMSE (3)
MSE (2)
AB SOLiD System 3.0 (1)
RNA mass spectrometry (1)

Instrument Platform

Illumina NovaSeq 6000 (22)
Illumina HiSeq 2500 (13)
Illumina HiSeq 2000 (9)
Illumina HiSeq 4000 (8)
NextSeq 500 (7)
Single cells were captured using the 10x Genomics Chromium Controller. (2)
ScanArray 5000 [PerkinElmer] (2)
Chemostat (2)
NextSeq 2000 (2)
Illumina MiSeq (2)
Agilent TapeStation (1)
NanoDrop 2000 Spectrophotometer, Agilent 2100 Bioanalyzer (1)
Sequel II (1)
Element AVITI (1)
Chromium Single Cell 3’ Reagent kits v2 (1)
BD FACSMelody (1)
10x Genomics Chromium (1)
Agilent 2100 Bioanalyzer, Applied Biosystems 7900HT Sequence Detection System, Illumina TruSeq Small RNA Sample Preparation Kit (1)
RNeasy mini Kit, Ribo-Zero Human/Mouse/Rat kit (1)
Leica CX3050S cryostat (1)
Hamamatsu NanoZoomer S60 (1)
PacBio RS II (1)
Ultracentrifuge (1)
Agilent 2100 Bioanalyzer (1)
Spectronic Helios Alpha UV-Vis spectrophotometer (1)
Illumina Genome Analyzer IIx (1)
Axon- GenePix4000B (1)
418 [Affymetrix] (1)
Illumina NovaSeq X (1)
None (1)

Publication Date

2013 (64)
2025 (59)
2015 (59)
2024 (50)
2010 (50)
2023 (44)
2022 (38)
2014 (37)
2011 (37)
2012 (36)
2020 (34)
2021 (32)
2026 (29)
2009 (25)
2019 (24)
2018 (20)
2016 (19)
2017 (16)
2008 (14)
2007 (7)
2005 (6)
2006 (5)
2004 (1)

UNIPROT ID/AC

Q93WK5 (3)
Q8L500 (3)
Q9LKL2 (3)
O81713 (3)
Q8IZH2 (1)
Q96RS0 (1)
P62306 (1)
P62304 (1)
P62308 (1)
P62318 (1)
P62314 (1)
P14678 (1)
P62316 (1)
O14744 (1)
P52297 (1)
Q14974 (1)
P52292 (1)
Q16637 (1)
P43487 (1)
Q92973 (1)
Q9H814 (1)
O95149 (1)
O14980 (1)
P52298 (1)
Q09161 (1)
P08621 (1)
P09012 (1)
P09234 (1)
Q180S4 (1)
Q189W2 (1)

ENSEMBL ID

ENSMUSG00000027651 (1)
ENSMUSG00000072849 (1)
ENSMUSP00000141097 (1)

CHEBI ID

CHEBI:33699 (3)
CHEBI:15422 (2)
CHEBI:74035 (1)
CHEBI:84596 (1)
CHEBI:64301 (1)
CHEBI:37565 (1)
CHEBI:34146 (1)
CHEBI:15558 (1)
CHEBI:15632 (1)
CHEBI:28728 (1)
CHEBI:15627 (1)
CHEBI:58189 (1)
CHEBI:58601 (1)
CHEBI:57634 (1)
CHEBI:17969 (1)
CHEBI:15554 (1)
CHEBI:15551 (1)
CHEBI:28209 (1)
CHEBI:15646 (1)
CHEBI:15647 (1)
CHEBI:15651 (1)
CHEBI:15843 (1)
CHEBI:15628 (1)
CHEBI:15626 (1)
CHEBI:43474 (1)
CHEBI:24636 (1)
CHEBI:15379 (1)
CHEBI:28013 (1)
CHEBI:14314 (1)
CHEBI:18367 (1)

Metabolite Name

Arginine (12)
Tyrosine (12)
Choline (12)
Citrate (12)
Proline (11)
Lysine (11)
Hypoxanthine (11)
Citrulline (11)
Adenine (11)
Histidine (11)
Phenylalanine (11)
Threonine (11)
Glucose (11)
Glutamine (11)
Succinate (11)
Alanine (11)
Adenosine (11)
Spermidine (11)
Phytosphingosine (10)
2'-deoxyadenosine (10)
N-methylproline (10)
Trimethylamine N-oxide (10)
Stachydrine (10)
Sphinganine (10)
Ribitol (10)
Pyridoxamine (10)
N-acetylhistidine (10)
Alpha-tocopherol (10)
5-oxoproline (10)
Uridine (10)

First Public Date

2014 (26)
2023 (18)
2024 (11)
2025 (10)
2022 (9)
2026 (8)
2017 (8)
2019 (6)
2020 (4)
2018 (4)
2015 (4)
2013 (4)
2016 (3)

Modelling Approach

Ordinary differential equation model (8)
Petri net (2)
Metabolic network (1)
Constraint-based model (1)

Lab affiliation

ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland (16)
ETH Zurich, Institute of Molecular Systems Biology (14)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland (11)
Institute of Molecular Systems Biology, ETH Zurich (9)
Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland Faculty of Science, University of Zurich, Zurich, Switzerland (7)
Institute for Systems Biology (5)
IMSB, ETH Zurich (4)
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium (3)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland. (3)
Department of Plant Systems Biology, University of Hohenheim, 70599 Stuttgart, Germany (2)
ETH Zurich, Institute of Molecular Biology and Biophysics, Zurich, Switzerland (2)
Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany (2)
Institute For Systems Biology (2)
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland (2)
Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, United Kingdom (2)
Leibniz Institute for Virology (LIV), Germany; Centre for Structural Systems Biology (CSSB), Germany; University of Siegen, Germany; Deutsches Elektronen-Synchrotron (DESY), Germany; European XFEL GmbH, Germany. (2)
Peking University (2)
Research Unit in Biology of Microorganisms (URBM), Namur Research Institute for life Sciences (Narilis), University of Namur, Namur, Belgium (2)
School of Integrative Plant Science Plant Biology Section, Cornell University (2)
University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany (2)
University of Cologne, Germany (2)
1: Department of Molecular Biology, Division of Chemistry andBioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria 2: Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria (1)
1Brunason Center for Translational Vision Research, Department of Ophthalmology and Visual Sciences, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA, 92697, USA; 2Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA; 3Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, 92697, USA (1)
Associate professor, department of Biology. University of Rochester,NY, USA University of Rochester Mass Spectrometry Resource Laboratory, NY, USA (lab head) (1)
Berlin Institute for Medical System Biology @ Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association Hannoversche Str. 28, 10115 Berlin Germanyt (1)
BioOrganique Mass Spectrometry Lab (LSMBO), Institut Pluridisciplinaire hubert Curien (IPHC) UMR7178, CNRS, University of Strasbourg (1)
Biochemistry & Molecular Biology Cumming School of Medicine University of Calgary, Canada (1)
Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA (1)
Biomedical Research Institute of Lleida Dr. Pifarré Foundation (IRBLLEIDA) - +Pec Proteomics Research Group (+PPRG) - Neuroscience Area – University Hospital Arnau de Vilanova (HUAV), 80 Av. Rovira Roure, 25198, Lleida, Spain Department of Medical Basic Sciences, University of Lleida (UdL), +Pec Proteomics Research Group (+PPRG), 25198, Lleida, Spain (1)
CSSB Centre for Structural Systems Biology c/o Deutsches Elektronen-Synchrotron DESY Notkestraße 85, Building 15 D-22607 Hamburg (1)

IsPrivate

False (17)

Model Flag

Non Kinetic (7)

Classification

bacteria (8)
fungi (1)
protozoa (1)

Modification

2x(15)N labeled L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
4x(15)N labeled L-arginine (1)
4x(2)H labeled dimethylated residue (1)
Not available (1)

Study type

Transcription profiling by array (204)
RNA-seq of coding RNA (92)
Comparative genomic hybridization by array (15)
ChIP-seq (13)
RNA-seq of coding RNA from single cells (12)
RNA-seq of non coding RNA (10)
Other (9)
Unknown experiment type (7)
Transcription profiling by tiling array (6)
High-throughput sequencing (4)
RNA-seq of total RNA (4)
DNA-seq (3)
Human - Single-cell sequencing (2)
Genotyping by array (2)
Bisulfite-seq (2)
Methylation profiling by high throughput sequencing (2)
Transcription profiling by SAGE (1)
ChIP-chip by tiling array (1)
Human - High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Proteomic profiling by mass spectrometer (1)
ChIP-chip by array (1)
CLIP-seq (1)
ATAC-seq (1)
MicroRNA profiling by array (1)

Release Date

2025 (812)
2022 (721)
2021 (700)
2023 (687)
2024 (628)
2020 (608)
2015 (480)
2019 (472)
2016 (465)
2017 (458)
2018 (445)
2014 (441)
2013 (372)
2012 (335)
2011 (279)
2010 (242)
2009 (153)
2008 (132)
2026 (120)
2007 (78)
2006 (56)
2005 (26)
2004 (20)
2003 (13)
2002 (13)
2001 (6)
2000 (6)
1998 (3)
1999 (2)

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Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/wi...

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health

In order to explore opportunities for personalized and predictive health care, we collected serial clinical measurements, health surveys and multiomics profiles (genomics, proteomics, autoantibodies, metabolomics and gut microbiome) from 96 individuals. The participants underwent data-driven heal...

2021-09-02 | MTBLS2187 | MetaboLights

Illuminating the dark space of neutral glycosphingolipidome by selective enrichment and profiling at multi-structural levels

Glycosphingolipids (GSLs) are essential components of cell membranes, particularly enriched in the nervous system. Altered molecular distributions of GSLs are increasingly associated with human diseases, emphasizing the significance of lipidomic profiling. Traditional GSL analysis methods are ham...

2024-06-25 | MTBLS10400 | MetaboLights

Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses

Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular m...

ORGANISM(S): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

2013-09-04 | E-GEOD-21165 | biostudies-arrayexpress

Systems biology of the structural proteome.

Not available

S-EPMC4787049 | biostudies-literature

Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach.

Not available

S-EPMC2435525 | biostudies-literature

Chemical Systems Biology Reveals Mechanisms of Dissociated Glucocorticoid Receptor Signaling

PRJNA628707 | ENA

The structural biology of CRISPR-Cas systems.

Not available