Python scripts - OmicsDI

Show results for

Unknown (213)
Proteomics (114)
Transcriptomics (71)
Genomics (41)
Metabolomics (6)
Models (4)
Other (2)

Organisms

Allexis (114)
Arabidopsis thaliana (114)
Mus musculus (25)
Homo sapiens (21)
Arabidopsis thaliana (8)
Drosophila melanogaster (5)
Bifidobacterium longum (3)
Tetranychus urticae (3)
Schizosaccharomyces pombe (2)
Caenorhabditis elegans (2)
Canis lupus familiaris (2)
Saccharomyces cerevisiae (2)
Danio rerio (2)
Arabidopsis (1)
Apilactobacillus kunkeei (1)
Prochlorococcus marinus str. NATL2A (1)
Alternaria brassicicola (1)
Brassica oleracea (1)
Lactobacillus johnsonii (1)
Melon necrotic spot virus (1)
Staphylococcus aureus subsp. aureus NCTC 8325 (1)
Youcai mosaic virus (1)
Caulobacter vibrioides (1)
Cucumis melo (1)
Oryza sativa (1)
Bacillus subtilis (1)
Staphylococcus aureus (1)
Pseudomonas aeruginosa (1)
Escherichia coli str. K-12 substr. MG1655 (1)
synthetic construct (1)

Organisms

Mus musculus (7)
Homo sapiens (3)
Streptomyces venezuelae (1)
Neurospora crassa (1)
rice paddy metagenome (1)
Caenorhabditis elegans (1)
Saccharomyces cerevisiae (1)
synthetic construct (1)

Repository

pride (114)
biostudies-arrayexpress (89)
ENA (21)
MetaboLights (6)
geo (4)
BioModels (2)
FAIRDOMHub (2)

Tissue

Cell culture (16)
Blood plasma (4)
Amniotic fluid (3)
Blood platelet (3)
Epithelial cell (3)
Eye (3)
Platelet (3)
Bone marrow (2)
Brain (2)
Heart (2)
Inner ear (2)
Lens (2)
Liver (2)
Permanent cell line cell (2)
Promastigote (2)
Skeletal muscle (2)
Utricle (2)
Vestibular hair cell (2)
Abdominal aorta (1)
Amnion (1)
Aortic smooth muscle cell (1)
Aortic valve (1)
B cell (1)
Blood (1)
Blood cell (1)
Breast cancer cell line (1)
Breast epithelium (1)
HEK-293 cell (1)
HeLa cell (1)
IGROV-1 cell (1)

Disease

Cardiovascular system disease (3)
Acute leukemia (2)
Breast cancer (2)
Glaucoma (2)
Lung cancer (2)
Abdominal aortic aneurysm (1)
Acute myeloid leukemia (1)
Charcot-Marie-Tooth disease (1)
Chronic myeloid leukemia (1)
Cutaneous malignant melanoma 1 (1)
Duchenne muscular dystrophy (1)
Exfoliation syndrome (1)
Leishmaniasis (1)
Leishmaniasis (1)
Limbic encephalitis (1)
Malignant neoplasm of ovary (1)
Metabolic dysfunction-associated steatotic liver disease (1)
Myotonic dystrophy type 1 (1)
Obesity (1)
Osteoarthritis (1)
Osteosarcoma (1)
Pancreatic cancer (1)
Pancreatic ductal adenocarcinoma (1)
Parkinson's disease (1)
Sickle cell anemia (1)
Spinal muscular atrophy (1)
Temporal lobe epilepsy (1)
Zika fever (1)

Technology Type

Mass Spectrometry (114)
Shotgun proteomics (60)
Bottom-up proteomics (31)
Chemical cross-linking coupled with mass spectrometry proteomics (10)
Data-dependent acquisition (10)
Affinity purification coupled with mass spectrometry proteomics (7)
Data-independent acquisition (7)
SWATH MS (4)
Mass spectrometry assay (3)
Mass spectrometry (3)
DiaPASEF (3)
HDMSE (3)
SRM/MRM (2)
Affinity proteomics (1)
Gel-based experiment (1)
Top-down proteomics (1)

Instrument Platform

NextSeq 500 (5)
Illumina HiSeq 2500 (4)
Retsch MM400 (2)
NextSeq 550 (2)
Illumina HiSeq 2000 (2)
Computer Workstation (1)
UMI small RNA library preparation kit (BGI) (1)
Handheld homogenizer, centrifuge (1)
Incubator at 35 °C, centrifuge (1)
AB SOLiD 4 System (1)
DNBSEQ-G400 (1)
Illumina NovaSeq 6000 (1)
Illumina HiSeq 3000 (1)
Direct infusion MS - negative (1)
Gas Chromatography MS - (1)
Liquid Chromatography MS - Positive (LC-MS (Positive)) (1)
Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)
Liquid Chromatography MS - positive - reverse phase (1)

Publication Date

2026 (22)
2015 (22)
2025 (20)
2021 (19)
2023 (19)
2022 (17)
2014 (14)
2024 (13)
2016 (12)
2013 (11)
2018 (10)
2012 (9)
2019 (7)
2020 (7)
2010 (6)
2011 (4)
2009 (3)
2017 (2)

UNIPROT ID/AC

Q940Y5 (1)
Q9S7Z8 (1)
Q9LTS3 (1)
O04291 (1)
Q9SB04 (1)
P49678 (1)
Q9SSC9 (1)
Q9SL42 (1)
Q96247 (1)

CHEBI ID

CHEBI:76233 (2)
CHEBI:28044 (2)
CHEBI:16196 (2)
CHEBI:23530 (1)
CHEBI:144719 (1)
CHEBI:144718 (1)
CHEBI:7851 (1)
CHEBI:84565 (1)
CHEBI:138017 (1)
CHEBI:134218 (1)
CHEBI:136276 (1)
CHEBI:207185 (1)
CHEBI:226124 (1)
CHEBI:233168 (1)
CHEBI:175610 (1)
CHEBI:43561 (1)
CHEBI:232564 (1)
CHEBI:138460 (1)
CHEBI:187471 (1)
CHEBI:136982 (1)
CHEBI:5819 (1)
CHEBI:34615 (1)
CHEBI:141348 (1)
CHEBI:166484 (1)
CHEBI:167524 (1)
CHEBI:83253 (1)
CHEBI:38813 (1)
CHEBI:5194 (1)
CHEBI:82228 (1)
CHEBI:39171 (1)

Metabolite Name

ST 27:0;O5 (1)
ST 26:4;O2;Gly (1)
ST 26:3;O2;Gly (1)
ST 26:2;O2 (1)
ST 26:1;O2 (1)
ST 26:0;O5 (1)
ST 24:5;O3 (1)
ST 24:1;O4;Tau (1)
ST 24:1;O3 (1)
ST 21:4;O2 (1)
ST 21:1;O3 (1)
ST 20:1;O2;S (1)
ST 19:2;O (1)
ST 19:0 (1)
ST 18:1;O2;S (1)
SPB 20:3;O (1)
SPB 20:2;O (1)
SPB 18:3;O (1)
SM 40:5;O2 (1)
SHexCer 40:5;O2 (1)
SHexCer 40:4;O3 (1)
SHexCer 40:4;O2 (1)
SHexCer 40:3;O3 (1)
SHexCer 40:2;O2 (1)
SHexCer 38:5;O3 (1)
SHexCer 38:4;O3 (1)
SHexCer 38:4;O2 (1)
SHexCer 38:3;O3 (1)
SHexCer 38:2;O3 (1)
SHexCer 36:4;O3 (1)

First Public Date

2025 (4)
2024 (4)
2021 (3)
2019 (3)
2023 (2)
2022 (2)
2016 (2)
2014 (1)

Modelling Approach

Ordinary differential equation model (1)
Constraint-based model (1)

Lab affiliation

ETH Zurich, Institute of Molecular Systems Biology (3)
Washington University in St. Louis (3)
Division of Maternal Fetal Medicine Department of Obstetrics and Gynecology Oregon Health & Science University 3181 SW Sam Jackson Park Road, Mail Code L-458, Portland, OR, 97239, USA (2)
Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, United Kingdom (2)
Mass Spectrometry Facility, Max Perutz Labs, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria (2)
Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany (2)
AG Functional Proteomics, University Hospital Jena (1)
Abiel Roche-Lima, MSc., PhD. Assistant Professor Director, Integrated Informatics Services core IIS-RCMI University of Puerto Rico Medical Science Campus RCMI Program PO Box 365067 San Juan, PR. 00936-5067 Phone: +1 787 758-2525 x 2194 (1)
Assistant Professor, Department of Chemistry Assistant Professor, Thomas C. Jenkins Department of Biophysics (by courtesy) (1)
Associate Professor Magnetic Resonance Mass Spectrometry Perth, Western Australia, Australia (1)
BRIC, University of Copenhagen, Denmark. (1)
Bio21 Institute, University of Melbourne (1)
Biology Department University of Wisconsin-La Crosse 1725 State St. La Crosse, WI 54601 USA (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands and Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands (1)
Bionanoscience Department, TU Delft, Netherlands (1)
Biotech Research and Innovation Centre (BRIC) University of Copenhagen Ole Maaløes Vej 5 2200 Copenhagen N Denmark (1)
Brigham and Women's Hospital (1)
Cell Biology and Physiology, Washington University in St. Louis, United States (1)
Center for Bio/Molecular Science & Engineering (Code 6900), US Naval Research Laboratory, Washington DC, USA (1)
Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA (1)
Centre for Proteomic Research, Biological Sciences, University of Southampton (1)
Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany (1)
Children's Medical Research Institute, Faculty of Medicine and Health, Westmead, NSW, Australia (1)
Deparment of Chemistry, Syracuse University (1)
Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria (1)
Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands (1)
Department of Analytical Biochemistry, University of Groningen (1)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (1)
Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA ( lab head ) (1)
Department of Biomedical Engineering, Schulich School of Engineering, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada. Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 1N4, Canada. Snyder Institute for Chronic Diseases, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada. (1)