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Unknown (55671)
Genomics (1707)
Transcriptomics (482)
Proteomics (325)
Metabolomics (76)
Models (48)
Genomic (16)
Other (4)
Clinical (2)
Methylation profiling (1)
Multiomics (1)

Organisms

Homo sapiens (331)
Mus musculus (146)
Danio rerio (27)
Oryza sativa Japonica Group (17)
Arabidopsis thaliana (16)
Rattus norvegicus (15)
Drosophila melanogaster (13)
Gallus gallus (10)
Saccharomyces cerevisiae (9)
Fagus sylvatica (8)
Sus scrofa (6)
Caenorhabditis elegans (5)
Pinus pinaster (3)
Populus trichocarpa x Populus deltoides (3)
Zea mays (3)
Candida albicans (3)
Schizosaccharomyces pombe (3)
Oryza sativa (3)
Raphidocelis subcapitata (2)
Talaromyces marneffei (2)
Eugenia uniflora (2)
Theobroma cacao (2)
Chlorocebus sabaeus (2)
Xenopus laevis (2)
Apis mellifera (2)
Oryctolagus cuniculus (2)
Saccharomyces cerevisiae S288C (1)
Clostridioides difficile (1)
Macaca fascicularis (1)
Eukaryota (1)

Organisms

Homo sapiens (513)
Mus musculus (447)
Rattus norvegicus (33)
Drosophila melanogaster (24)
Schizosaccharomyces pombe (19)
Arabidopsis thaliana (17)
Escherichia coli (13)
Danio rerio (12)
Saccharomyces cerevisiae (11)
Pasteurella multocida subsp. multocida (9)
Sus scrofa (9)
Fagus sylvatica (8)
Solanum lycopersicum (8)
Canis lupus familiaris (7)
Gallus gallus (7)
Macaca mulatta (6)
Streptococcus agalactiae (6)
Stevia rebaudiana (5)
Brassica napus (5)
Pasteurella multocida (5)
Oryza sativa (5)
Oryza sativa Japonica Group (5)
Perilla frutescens (4)
Brachypodium distachyon (4)
Callithrix jacchus (4)
Triticum aestivum (4)
Novosphingobium sp. HR1a (3)
Zygosaccharomyces sp. (3)
Copidosoma floridanum (3)
Ranitomeya imitator (3)

Repository

ENA (1581)
biostudies-arrayexpress (467)
pride (159)
EGA (98)
MetaboLights (76)
MassIVE (68)
BioModels (48)
geo (46)
iProX (42)
PeptideAtlas (32)
dbGaP (16)
jPOST (9)
PAXDB (7)
EVA (4)
PanoramaPublic (4)
GPMDB (2)

Tissue

Cell culture (50)
Others (31)
Permanent cell line cell (16)
Blood plasma (8)
Brain (7)
Kidney (5)
Epithelial cell (4)
Blood serum (3)
Cerebrospinal fluid (3)
Embryonic stem cell (3)
Fibroblast (3)
Leaf (3)
Neural cell (3)
B cell (2)
Bone (2)
Early embryonic cell (2)
Endothelial cell of umbilical vein (2)
Fungal cell (2)
Liver (2)
Lung (2)
Macrophage (2)
Pancreatic ductal cell (2)
Placenta (2)
Primary cell (2)
Skeletal muscle fiber (2)
Stem cell (2)
Platelet (1)
B-lymphocyte (1)
HeLa cell (1)
JURKAT cell (1)

Disease

Schizophrenia (4)
Breast cancer (3)
Disease free (3)
Melanoma (3)
Amyotrophic lateral sclerosis (2)
Not Available (2)
Brain glioblastoma multiforme (2)
Lymphoma (2)
Pancreatic cancer (2)
Paranoid schizophrenia (2)
Zika virus congenital syndrome (2)
Parkinson's disease (1)
Neuroendocrine tumor (1)
Serous Cystadenocarcinoma (1)
HIV-1 seropositive (1)
Chondroblastoma (1)
Kaposi's sarcoma (1)
Dystrophic (1)
Mock infected (1)
Represent tolerant CD4+ T cells that have not been activated (1)
Colorectal cancer (1)
Colon carcinoma (1)
Chicken Anaemia Virus infected (1)
Intracranial aneurysm and subarachnoid haemorrhage (1)
Glioblastoma (1)
Neoplastic Syndromes, Hereditary (1)
Neoplasms (1)
Brain cancer (1)
COVID-19 (1)
Cardiovascular system disease (1)

Technology Type

Mass Spectrometry (159)
Shotgun proteomics (80)
Mass spectrometry (60)
Bottom-up proteomics (39)
Data-dependent acquisition (21)
Affinity purification coupled with mass spectrometry proteomics (17)
Mass spectrometry assay (13)
HDMSE (13)
MSE (8)
Chemical cross-linking coupled with mass spectrometry proteomics (6)
Gel-based experiment (5)
SRM/MRM (5)
NMR spectroscopy (4)
All-ion fragmentation (4)
Top-down proteomics (4)
Illumina HiSeq 2500, ILLUMINA (2)
Illumina HiSeq 2500 (2)
Illumina HiSeq 2000 (2)
Illumina MiSeq (2)
Data-independent acquisition (2)
SWATH MS (2)
Human Cardio Metabochip (1)
ILLUMINA, NextSeq 500 (1)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 3000 (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
AB SOLiD System 3.0 (1)
Mass spectrometry imaging (1)

Instrument Platform

Illumina NovaSeq 6000 (57)
NextSeq 500 (19)
Illumina HiSeq 4000 (16)
NextSeq 2000 (15)
Illumina HiSeq 2500 (15)
Illumina NovaSeq X (9)
Illumina HiSeq 2000 (6)
Agilent High resolution C scanner (4)
NextSeq 550 (4)
NA (3)
BGISEQ-500 (3)
Single-Cell Extraction: For enzymatic digestion, pronase (Septomyces argeus, 1 mg/mL) was applied for 25 minutes at room temperature for P0 to P8 datasets. Cells were dissociated and triturated into a single-cell suspension in ACSF supplemented with 1% fetal calf serum (FCS) and DNase (1 µL/10 mL). Trituration was performed using three glass Pasteur pipettes of decreasing diameters. For P30 datasets, enzymatic digestion and cell dissociation were carried out using the Worthington Papain Dissociation System, following the manufacturer’s instructions. Single-Nuclei Extraction: For nuclei isolation, the Hibernate™-E Medium was removed, and 500 µL of chilled 0.1X NP40 Lysis Buffer was added. Tissue was homogenized using a Pellet Pestle (15 strokes) and incubated on ice for 5 minutes. The suspension was pipette-mixed 10 times using a wide-bore pipette tip and incubated for an additional 10 minutes on ice. Following lysis, 500 µL of chilled wash buffer was added, and the mixture was pipette-mixed 5 times using a regular-bore pipette tip. The suspension was filtered through a 30 µm cell strainer into a 50 mL tube to remove debris. The filtered suspension was transferred to a 1.5 mL tube and centrifuged at 950 × g for 10 minutes at 4°C. The supernatant was carefully removed, and the nuclei pellet was retained for downstream analysis. (2)
ScanArray 5000 [PerkinElmer] (2)
DNBSEQ-T7 (2)
Illumina MiSeq (2)
Illumina HiSeq 3000 (2)
TruSeq Stranded Total RNA kit (Illumina) (1)
NanoDrop 2000 Spectrophotometer, Agilent 2100 Bioanalyzer (1)
Lab Bench (1)
Microsyringe for intraperitoneal injection (1)
Computational server/cluster, Software: R (v4.3.x), Seurat package (v5.1.0) (1)
Biological safety cabinet, Centrifuge, Cell strainer, Automated cell counter/Hemocytometer (1)
Surgical dissection tools (1)
Chromium Next GEM Chip G (1)
10X v3 (1)
Thermal cycler, Magnetic stand / beads, Pipettes and tips, Microcentrifuge tubes, Plate shaker (1)
Centrifuge, Pipettes and tips, Agilent 2100 Bioanalyzer, NanoDrop spectrophotometer, Vortex mixer (1)
Liquid nitrogen, -80°C freezer, Surgical tools (scalpels, forceps), Sample tubes / cryovials (1)
BD Rhapsody system (1)
Computer (1)

Publication Date

2025 (133)
2024 (98)
2026 (73)
2013 (70)
2010 (53)
2012 (44)
2011 (43)
2023 (42)
2021 (41)
2014 (37)
2022 (35)
2016 (35)
2020 (30)
2017 (30)
2015 (29)
2008 (29)
2019 (28)
2018 (28)
2009 (22)
2005 (15)
2007 (14)
2006 (6)

UNIPROT ID/AC

Q01650 (1)
A0A516GHF6 (1)
A0A516GI62 (1)
A0A1S8KLP3 (1)
A0A516GIL8 (1)
A0A516GHA2 (1)
A0A516GK59 (1)
A0A328KB23 (1)
A0A516GHF8 (1)
A0A516GHZ8 (1)
A0A328KG15 (1)
A0A516GHD7 (1)
A0A516GIH9 (1)
A0A516GKD6 (1)
A0A1S8KPN1 (1)
A0A516GHM9 (1)
A0A1S8KP79 (1)
A0A1S8KP82 (1)
A0A516GK60 (1)
A0A516GI34 (1)
A0A1S8KPH4 (1)
A0A516GGF9 (1)
A0A516GLA9 (1)
A0A328KU01 (1)
A0A328KB09 (1)
A0A1S8KP34 (1)
A0A516GKS7 (1)
A0A328KFV5 (1)
A0A1S8KPI3 (1)
A0A328KNH5 (1)

ENSEMBL ID

ENSG00000170477 (29)
ENSG00000229353 (1)

CHEBI ID

CHEBI:27897 (20)
CHEBI:16680 (13)
CHEBI:16027 (12)
CHEBI:16977 (10)
CHEBI:30754 (3)
CHEBI:15763 (3)
CHEBI:15372 (3)
CHEBI:18304 (3)
CHEBI:16810 (3)
CHEBI:28938 (3)
CHEBI:29985 (3)
CHEBI:16240 (3)
CHEBI:15377 (3)
CHEBI:18361 (3)
CHEBI:15740 (3)
CHEBI:15379 (3)
CHEBI:15351 (3)
CHEBI:15346 (3)
CHEBI:15414 (3)
CHEBI:17111 (3)
CHEBI:18009 (3)
CHEBI:15422 (3)
CHEBI:16474 (3)
CHEBI:16526 (3)
CHEBI:9408 (2)
CHEBI:45901 (2)
CHEBI:26854 (2)
CHEBI:3672 (2)
CHEBI:5725 (2)
CHEBI:12492 (2)

Metabolite Name

Uridine (14)
Taurine (13)
Citric acid (13)
Adenine (13)
Xanthine (13)
Uric acid (12)
Hypoxanthine (12)
L-Tryptophan (11)
Inosine (11)
Succinic acid (10)
Shikimic acid (10)
L-Histidine (10)
L-Tyrosine (10)
Xanthosine (9)
Deoxycholic acid (9)
Adenosine (9)
L-Glutamine (9)
Hexadecanedioic acid (9)
Adipic acid (9)
L-Phenylalanine (9)
L-Norleucine (8)
Gluconic acid (8)
Benzoic acid (8)
L-Asparagine (8)
L-Threonine (8)
12-Hydroxydodecanoic acid (8)
Arachidonic acid (8)
Salicylic acid (8)
Linoleic acid (8)
Azelaic acid (8)

First Public Date

2014 (281)
2023 (155)
2022 (126)
2019 (120)
2025 (116)
2024 (115)
2020 (112)
2021 (105)
2026 (104)
2018 (85)
2017 (83)
2013 (73)
2015 (62)
2016 (42)
2012 (1)
2010 (1)

Modelling Approach

Constraint-based model (32)
Ordinary differential equation model (11)
Machine learning (1)
Computational model (1)
Delayed differential equation model (1)

Study status

Active, not recruiting (2)

Lab affiliation

Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil (5)
Liverpool John Moores University (5)
Beavis Informatics Ltd. (4)
Biochemistry and molecular biology department, Universidade Federal de Goias, Brazil (4)
Federal University of Goias (3)
UHN (3)
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 (2)
Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. (2)
Department of Computing and Control Engineering, University of Chemistry and Technology in Prague, Technická 5, 166 28 Praha 6, Czech Republic (2)
Department of Mathematics and Computer Science, University of Antwerp, Belgium (2)
Dept. of Biochemistry, Laboratory of Neuroproteomic, Biology Institute, Brazil (2)
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK (2)
Lab of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil. (2)
Leiden University Medical Center (2)
1. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; 2. Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; 3. Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; 4. Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany; (1)
1. Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; 2. Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; 3. Quantitative Biology Center (QBiC), University of Tübingen, Germany; 4. Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; 5. Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany (1)
1Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States (1)
Academy Professor, Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Turku, Finland (1)
Applied Bioinformatics, Department for Computer Science, University of Tuebingen, Sand 14, 72076 Tuebingen,Germany (1)
Assistant Professor of Biological Sciences Augusta University C2014 Science Hall 2500 Walton Way, Augusta-GA (1)
Biomedical Center Munich Molecular Biology Großhaderner Strasse 9 82152 Planegg-Martinsried (1)
Biomedical Informatics, The Ohio State University, United States (1)
Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany; Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Germany; Quantitative Biology Center (QBiC), University of Tübingen, Germany; Institute for Translational Bioinformatics, University Hospital Tübingen, Germany; Institute for Bioinformatics and Medical Informatics, University of Tübingen, Germany; (1)
Biotech Research & Innovation Center (BRIC), University of Copenhagen, Denmark (1)
CNIC (1)
CNRS, IBMC, FRC1589, Proteomics Core Facility (1)
Canada Research Chair in Proteomics and Systems Biology, Faculty of Dentistry, Department of Oral Biological and Medical Sciences, University of British Columbia (1)
CeMM Principal Investigator (1)
Cell Biology and Physiology, Washington University in St. Louis (1)
Center for Epigenetics Van Andel Research Institute Grand Rapics, Michigan 49503, USA (1)

Keyword

Health Behaviors (1)
Oncology Providers (1)
EHR (1)
Informatics (1)
Survivor (1)
Lynch syndrome (1)
Hereditary breast and ovarian cancer (1)

IsPrivate

False (48)

Model Flag

Non Kinetic (2)
Non Miriam (1)

Submitter Keywords

FROG (11)
Not Peer Reviewed (8)
Ersilia (2)
FAIR-AIML (2)
Machine Learning Model (2)
TransQST (1)
COVID-19 (1)

Classification

bacteria (56)
viruses (4)

Modification

Not available (5)
4x(2)H labeled dimethylated residue (1)

Study type

Transcription profiling by array (243)
RNA-seq of coding RNA (122)
RNA-seq of total RNA (14)
RNA-seq of coding RNA from single cells (9)
RNA-seq of non coding RNA (9)
Unknown experiment type (7)
Bisulfite-seq (6)
ChIP-seq (6)
DNA-seq (6)
Methylation profiling by array (5)
Comparative genomic hybridization by array (4)
Other (4)
Proteomic profiling by array (4)
Animal - One-color microarray (3)
ChIP-chip by array (3)
MicroRNA profiling by high throughput sequencing (3)
Methylation profiling by high throughput sequencing (3)
Transcription profiling by SAGE (2)
Transcription profiling by tiling array (2)
RNAi profiling by array (2)
ATAC-seq (2)
Interventional (2)
ChIP-chip by tiling array (1)
Animal - High-throughput sequencing (1)
Genotyping by array (1)
Spatial transcriptomics by high-throughput sequencing (1)
Exome sequencing (1)
Ribo-seq (1)
MicroRNA profiling by array (1)
Genotyping by high throughput sequencing (1)

Release Date

2022 (6613)
2025 (6400)
2021 (6236)
2023 (6112)
2024 (5505)
2020 (4648)
2019 (3723)
2018 (3106)
2017 (2499)
2016 (2084)
2015 (1896)
2014 (1677)
2013 (1095)
2012 (942)
2026 (902)
2011 (800)
2010 (586)
2009 (399)
2008 (290)
2007 (204)
2006 (128)
2005 (100)
2004 (62)
2003 (59)
2002 (28)
2001 (23)
2000 (13)
1999 (3)
1998 (2)
1997 (2)

Location

United States (2)

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The Global Health Informatics landscape and JAMIA.

Not available

S-EPMC10018257 | biostudies-literature

Early experiences with combined fellowship training in clinical informatics.

Not available

S-EPMC7647293 | biostudies-literature

Development of a core competency framework for clinical informatics.

Not available

S-EPMC8286765 | biostudies-literature

Domains, tasks, and knowledge for health informatics practice: results of a practice analysis.

Not available

S-EPMC7647284 | biostudies-literature

The emerging role of clinical informatics fellows in service learning during the COVID-19 pandemic.

Not available

S-EPMC7717323 | biostudies-literature

Veterinary informatics: forging the future between veterinary medicine, human medicine, and One Health initiatives-a joint paper by the Association for Veterinary Informatics (AVI) and the CTSA One Health Alliance (COHA).

Not available

S-EPMC7382640 | biostudies-literature

Vanderbilt Clinical Informatics Center Education Strategy: To Infinity and Beyond!

Not available

S-EPMC11864845 | biostudies-literature

Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge.

Not available

S-EPMC4583778 | biostudies-literature

Clinical informatics solutions in COVID-19 pandemic: Scoping literature review.

Not available

S-EPMC8949656 | biostudies-literature

Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies for Glycopeptide Analysis

Mass spectrometry-based glycoproteomics studies now routinely report thousands of intact glycopeptides. Diverse informatics solutions aiding the challenging glycopeptide identification process have recently appeared, but their strengths and weaknesses have not been established leaving a critical kno...

ORGANISM(S): Homo sapiens (Human)

2021-11-03 | PXD024101 | Pride

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OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

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58332 Results

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