Biology - OmicsDI

OmicsDI

Browse
Submit Data
Databases
API
Help

715843 Results

Show all Save search Copy query

Show results for

Unknown (642415)
Genomics (49053)
Transcriptomics (11710)
Proteomics (10105)
Models (1217)
Metabolomics (550)
Other (454)
Methylation profiling (161)
Multiomics (80)
Genomic (77)
Clinical (38)

Organisms

Homo sapiens (6639)
Mus musculus (3323)
Arabidopsis thaliana (553)
Saccharomyces cerevisiae (408)
Rattus norvegicus (304)
Escherichia coli (135)
Canis lupus familiaris (42)
Schizosaccharomyces pombe (41)
cellular organisms (39)
Mammalia (32)
Xenopus laevis (32)
Trypanosoma brucei (18)
Bacillus subtilis (17)
Viridiplantae (13)
Neurospora crassa (13)
Halobacterium salinarum (9)
Cryptococcus neoformans (9)
Arabidopsis (8)
Murinae (8)
Rattus (7)
Eukaryota (5)
Clavispora lusitaniae (5)
Methanosarcina barkeri (4)
Leishmania (4)
Saccharomyces cerevisiae S288C (4)
Chordata (4)
Mus (4)
Yarrowia lipolytica (3)
Drosophila (3)
Sporobolomyces roseus (2)

Organisms

Homo sapiens (11260)
Mus musculus (9531)
Arabidopsis thaliana (1465)
Drosophila melanogaster (1046)
Saccharomyces cerevisiae (877)
Caenorhabditis elegans (617)
Danio rerio (565)
Rattus norvegicus (456)
Yucca gloriosa (377)
Camelina sativa (327)
Escherichia coli (204)
Oryza sativa (183)
Sus scrofa (156)
Gallus gallus (153)
Schizosaccharomyces pombe (152)
Zea mays (120)
Bos taurus (119)
Escherichia coli str. K-12 substr. MG1655 (93)
Plasmodium falciparum (91)
Glycine max (90)
Candida albicans (90)
Macaca mulatta (84)
Solanum lycopersicum (79)
Xenopus laevis (77)
Xenopus tropicalis (74)
Halobacterium salinarum NRC-1 (72)
soil metagenome (65)
Bombyx mori (61)
synthetic construct (55)
Bacillus subtilis (54)

Repository

ENA (46936)
pride (8749)
biostudies-arrayexpress (8152)
geo (5830)
BioModels (1114)
MassIVE (609)
MetaboLights (409)
EGA (406)
iProX (298)
PeptideAtlas (175)
jPOST (139)
GNPS (136)
FAIRDOMHub (88)
dbGaP (77)
LINCS (61)
PanoramaPublic (54)
GPMDB (53)
PAXDB (48)
EVA (34)
Cell Collective (8)
PMR (7)
MetabolomicsWorkbench (5)
ExpressionAtlas (3)
NODE (1)

Tissue

Digestive System (95)
Others (37)
Blood (4)
Brain (2)
Forebrain and midbrain (1)
Temporal lobe (1)
Diencephalon (1)
Diencephalon and midbrain (1)
Forebrain fragment (1)
Medulla oblongata (1)
Choroid plexus (1)
Pituitary and diencephalon (1)
Forebrain (1)
Basal ganglion (1)
Hindbrain (1)
Spinal cord (1)
Telencephalon (1)
Pons (1)
Brain fragment (1)
Midbrain (1)
Hindbrain fragment (1)
Hindbrain without cerebellum (1)
Stomach (1)
Cerebral cortex (1)
Hippocampus (1)
Cerebellum (1)
Liver (1)
Eye (1)
Female Reproductive System (1)
Ovary (1)

Disease

Alzheimer's disease (43)
Non-small cell lung carcinoma (32)
Parkinson's disease (27)
Multiple myeloma (22)
Influenza (22)
Normal (19)
Diabetes mellitus (6)
Crohn's disease (4)
Cancer (4)
Leishmaniasis (3)
Neurodegenerative disease (3)
Rheumatoid arthritis (2)
Osteoarthritis (2)
Ovarian disease (2)
Polycythemia due to hypoxia (2)
Sclerosing cholangitis (1)
Ulcerative colitis (1)
Acute pancreatitis (1)
Swine influenza (1)
Tauopathy (1)
Cerebral degeneration (1)
Retinal degeneration (1)
Huntington's disease (1)
Ocular albinism (1)
Retinal disease (1)
Retinal detachment (1)
Cartilage disease (1)
Cataract (1)
Asthma (1)
Cholesterol ester storage disease (1)

Technology Type

Illumina (35)
Illumina HiSeq 2500 (ILLUMINA) (21)
Illumina HiSeq 2000 (13)
Illumina HiSeq 2500 (4)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2500 (ILLUMINA) (2)
Illumina MiSeq (2)
Illumina HiSeq 2000, ILLUMINA (2)
ION_TORRENT, Ion Torrent PGM (1)
Illumina CytoSNP, Illumina HumanOmni2.5, ILLUMINA, Illumina 450k, Illumina HiSeq 2000 (1)
Human Cardio Metabochip (1)
ABI_SOLID, Illumina HiSeq 2000, Illumina 450K, AB 5500xl Genetic Analyzer, AB 5500 Genetic Analyzer, ILLUMINA (1)
ILLUMINA, NextSeq 500 (1)
Illumina, unknown (1)
Illumina HiSeq 2500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina_450K, Illumina_HumanHT-12_V4, ILLUMINA, Illumina HiSeq 2000 (1)
Illumina HiSeq 3000 (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
Illumina HiSeq 2000, Illumina HiSeq 2500 (ILLUMINA), ILLUMINA, Illumina HiSeq 2500 (1)
ILLUMINA, Illumina HiSeq 2000, Illumina HiSeq 2500 (ILLUMINA) (1)
Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 2000, Illumina HiSeq 2500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500, Illumina HiSeq 2000 (1)
Illumina_450K (1)
Illumina HiSeq 2000, NextSeq 500, ILLUMINA (1)
ILLUMINA, Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Illumina MiSeq (1)
ILLUMINA, Illumina HiSeq 2000 (1)
ABI_SOLID, Illumina Genome Analyzer IIx, Affymetrix_GenomeWide_SNP6.34 (1)
AB SOLiD System 3.0 (1)
Affymetrix_SNP6_raw, Illumina HT 12, Agilent ncRNA 60k (1)

Instrument Platform

Illumina NovaSeq 6000 (174)
Illumina HiSeq 2500 (120)
NextSeq 500 (108)
Illumina HiSeq 2000 (96)
Illumina HiSeq 4000 (65)
NextSeq 2000 (27)
NextSeq 550 (24)
Illumina MiSeq (19)
Illumina NovaSeq X (17)
Illumina Genome Analyzer II (11)
Variable Atmosphere Incubator (9)
Affymetrix GeneChip Scanner 3000 7G (7)
Spectronic Helios Alpha UV-Vis spectrophotometer (7)
Bioanalyser (7)
N/A (7)
NanoDrop (6)
Illumina HiSeq 3000 (6)
Axon GenePix 4000B scanning hardware (5)
NA (5)
DNBSEQ-G400 (5)
Illumina HiSeq 1000 (5)
BGISEQ-500 (5)
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, (4)
10X Genomics reagent kit (4)
Ultracentrifuge (4)
Axon- GenePix4000B (4)
Illumina HiSeq 1500 (4)
PromethION (3)
10X Chromium Controller (3)
GeneQuant (3)

Publication Date

2025 (2280)
2024 (2196)
2022 (1761)
2023 (1666)
2013 (1598)
2021 (1564)
2015 (1526)
2026 (1469)
2020 (1380)
2010 (1352)
2014 (1284)
2016 (1096)
2019 (1095)
2011 (1081)
2012 (1078)
2018 (823)
2017 (739)
2008 (500)
2009 (442)
2005 (306)
2007 (224)
2006 (113)
2004 (59)
2003 (15)
2002 (9)

UNIPROT ID/AC

P04075 (204)
P14618 (70)
P05062 (69)
P09972 (69)
P00338 (69)
P07195 (69)
P30613 (69)
P06744 (69)
P00390 (67)
P37268 (67)
Q99714 (67)
P09417 (67)
Q01959 (67)
Q9UHI5 (67)
Q9NS82 (67)
O95477 (67)
Q9BYZ2 (67)
P05091 (67)
P17174 (67)
P07864 (67)
P36969 (67)
P21399 (67)
Q01581 (67)
Q9BQG2 (66)
B3KXN9 (66)
Q53HM1 (66)
Q86SK9 (66)
E9KL42 (66)
Q3I5F7 (66)
P33897 (66)

ENSEMBL ID

ENSG00000165661 (4)
ENSG00000176654 (4)
ENSG00000204531 (4)
ENSG00000141510 (3)
ENSG00000135679 (3)
ENSG00000148200 (2)
ENSG00000165556 (2)
ENSG00000141448 (2)
ENSMUST00000021413 (2)
ENSMUST00000019997 (2)
ENST00000261769 (1)
ENST00000227507 (1)
ENST00000242261 (1)
ENST00000263341 (1)
ENSG00000151468 (1)
ENSG00000158828 (1)
ENSG00000154277 (1)
ENSG00000151552 (1)
ENSG00000116288 (1)
ENSG00000116688 (1)
ENSG00000142319 (1)
ENSG00000149295 (1)
ENSG00000213585 (1)
ENSG00000115317 (1)
ENSG00000093010 (1)
ENSG00000126602 (1)
ENSG00000180176 (1)
ENSG00000198074 (1)
ENSG00000111275 (1)
ENSG00000145335 (1)

CHEBI ID

CHEBI:15428 (308)
CHEBI:16761 (277)
CHEBI:17754 (273)
CHEBI:17895 (263)
CHEBI:17295 (258)
CHEBI:17268 (253)
CHEBI:16828 (250)
CHEBI:17191 (249)
CHEBI:15603 (249)
CHEBI:15971 (246)
CHEBI:17203 (246)
CHEBI:16977 (245)
CHEBI:17115 (242)
CHEBI:16680 (240)
CHEBI:16643 (237)
CHEBI:17196 (231)
CHEBI:17411 (224)
CHEBI:16349 (213)
CHEBI:15343 (212)
CHEBI:16526 (211)
CHEBI:18021 (204)
CHEBI:15379 (202)
CHEBI:29033 (196)
CHEBI:16240 (193)
CHEBI:15377 (192)
CHEBI:29034 (191)
CHEBI:15414 (191)
CHEBI:27931 (190)
CHEBI:17561 (188)
CHEBI:16189 (187)

Metabolite Name

Creatine (62)
Hypoxanthine (60)
Taurine (59)
Adenine (57)
L-Phenylalanine (55)
Adenosine (53)
Choline (52)
Creatinine (52)
Inosine (51)
L-Tyrosine (50)
Citric acid (49)
Xanthine (49)
Glycine (48)
L-Tryptophan (48)
Uridine (47)
L-Histidine (46)
Guanosine (45)
L-Glutamine (44)
Uracil (43)
Cytidine (43)
Glycine (42)
Isoleucine (40)
Valine (39)
Betaine (39)
L-Threonine (39)
Cytosine (39)
Glucose (39)
L-Valine (39)
Leucine (38)
Ornithine (38)

First Public Date

2014 (6934)
2025 (4875)
2024 (4446)
2019 (3739)
2023 (3671)
2026 (3358)
2021 (3271)
2020 (3254)
2022 (3171)
2017 (2427)
2018 (2403)
2013 (2163)
2015 (1788)
2016 (1379)
2012 (31)
2011 (15)
2010 (11)

Modelling Approach

Ordinary differential equation model (542)
Constraint-based model (158)
Other (34)
Logical model (20)
Boolean model (7)
Computational model (6)
Mathematical model (6)
Differential equation model (6)
Metabolic network (5)
Petri net (4)
Delayed differential equation model (4)
Physiologically based pharmacokinetic model (3)
Cellular potts model (3)
Partial differential equation model (3)
Machine learning (2)
Agent-based model (2)
Markov model (1)
Multi-value logic model (1)
Biochemical network (1)
Differential algebraic equation model (1)
Population model (1)

Study status

Recruiting (16)
Completed (11)
Not provided (4)
Active, not recruiting (3)
Terminated (2)
Not yet recruiting (2)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (126)
Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States (60)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (31)
Institute of Molecular Biology (IMB) (28)
ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland (25)
European Molecular Biology Laboratory (22)
Institute for Systems Biology (20)
Institute of Molecular Biology (IMB), Mainz, Germany (20)
Department of Biology, University of Fribourg Chemin du Musée 10, 1700 Fribourg, Switzerland T +41 26 300 8631 (19)
Department of Chemistry & Chemical Biology, Northeastern University (18)
ETH Zurich, Institute of Molecular Systems Biology (16)
Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland (16)
Department of Chemistry and Chemical Biology, Harvard University (15)
Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada (14)
Max-Planck-Institute for Biology of Ageing Department of Mitochondrial Proteostasis Joseph-Stelzmann-Str. 9b 50931 Cologne (14)
Department of Molecular Biology, Princeton University, USA (13)
General and molecular microbiology, Institute for chemistry and biology of the marine environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany (13)
Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium (13)
Institute of Molecular Systems Biology, ETH Zurich (13)
Systems Biology Ireland, University College Dublin (13)
Department of Cell Biology, Harvard Medical School (12)
IMB, Ackermannweg 4, 55128 Mainz (12)
University of Oxford (12)
Department of Biochemistry and Molecular Biology, University of Georgia, Athens (GA), USA. (11)
Department of Molecular Biology and Genetics, Aarhus University, Denmark (11)
Department of Molecular Biology, Princeton University (11)
Division of Cell Matrix Biology & Regenerative Medicine (L5) / Division of Cell Matrix Biology & Regenerative Medicine, University of Manchester (11)
Molecular Biosciences and the Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX USA (11)
National Key Laboratory of Medical Molecular Biology & Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (11)
Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology (11)

Keyword

Liquid biopsy (2)
Bevacizumab (2)
Cetuximab (2)
Genetic profiling (1)
Immunohistochemistry, (1)
Monoclonal antibodies, (1)
Predictive model, (1)
Antiangiogenic agents, (1)
Medical imaging (1)
Light Exercise (1)
Throid Cancer (1)
Patients with metastatic colorectal cancer who did not receive (1)
Systemic treatment for their metastatic disease (1)
Colorectal cancer with liver metastases (1)
Metastatic or unresectable locally advanced malignancies. (1)
Genomic alterations. (1)
Biological crizotinib targets (ALK, MET, ROS1, RON, AXL). (1)
Pancreatic tumor (1)
Esophageal tumor (1)
Thymus tumor (1)
Thyroid Tumor (1)
Thyroid Nodule (1)
Lung Tumor (1)
Supportive Care (1)
Exhaustive genetic and immunological analyses (1)
Targeted therapies (1)
Immunological tumor microenvironment (1)
Tumor microenvironment heterogeneity (1)
Tumor resection (1)
Lymphocytic density (1)

IsPrivate

False (1114)

Model Flag

Non Kinetic (375)
Sbml Extended (2)

Submitter Keywords

FROG (43)
Not Peer Reviewed (27)
Machine Learning Model (22)
Immuno-oncology (15)
Ersilia (4)
FAIR-AIML (4)
TransQST (4)
Manuscript Accepted (3)
Oncology (2)
COVID-19 (2)

Classification

bacteria (1043)
fungi (287)
protozoa (259)
helminths (64)
viruses (64)

Modification

Not available (40)
15.994915 (28)
57.021464 (25)
2x(15)N labeled L-lysine (22)
4x(15)N labeled L-arginine (22)
N6 (17)
4-tetrahydrothiazine-3-carboxylic acid (15)
N6-dimethyl-L-lysine (10)
4 (7)
42.010565 (6)
+3amu) (5)
79.966331 (4)
4x(2)H labeled dimethylated residue (3)
6x(2)H labeled dimethylated L-arginine (3)
-17.026549 (2)
0.984016 (2)
10.008269 (2)
144.102062 (2)
45.987721 (2)
4x(2)H labeled dimethylated L-lysine (2)
8.014199 (2)
1.99407 (1)
15.977156 (1)
227.126991 (1)
27.994915 (1)
3.98814 (1)
31.989829 (1)
58.005479 (1)
9.030194 (1)
Heavy form - site K (1)

Study type

Transcription profiling by array (4504)
RNA-seq of coding RNA (1258)
ChIP-seq (515)
ChIP-chip by tiling array (336)
RNA-seq of non coding RNA (277)
Unknown experiment type (240)
Comparative genomic hybridization by array (196)
Other (162)
Methylation profiling by array (96)
RNA-seq of coding RNA from single cells (89)
Transcription profiling by tiling array (64)
DNA-seq (44)
RNA-seq of total RNA (39)
Methylation profiling by high throughput sequencing (32)
Genotyping by array (29)
Transcription profiling by SAGE (27)
ChIP-chip by array (25)
Transcription profiling by RT-PCR (25)
Proteomic profiling by array (18)
High-throughput sequencing (14)
MicroRNA profiling by array (14)
Cell line - High-throughput sequencing (13)
Bisulfite-seq (13)
RNAi profiling by array (10)
MicroRNA profiling by high throughput sequencing (10)
Animal - High-throughput sequencing (8)
Plant - High-throughput sequencing (7)
ScATAC-seq (7)
Single nucleus RNA sequencing (7)
ATAC-seq (6)

Release Date

2022 (58037)
2021 (56172)
2025 (55328)
2023 (54322)
2024 (47678)
2020 (47352)
2019 (40403)
2018 (36933)
2017 (33856)
2016 (32891)
2015 (31415)
2014 (28244)
2013 (21182)
2012 (19382)
2011 (16598)
2010 (14503)
2009 (11680)
2008 (9954)
2007 (7131)
2026 (7046)
2006 (5381)
2005 (3799)
2004 (2523)
2003 (2033)
2002 (1641)
2001 (1404)
2000 (1260)
1999 (1004)
1998 (911)
1997 (364)

Location

United States (8)
France (8)
China (5)
Italy (2)
United Kingdom (2)
Austria (2)
Syria (1)
Hong Kong (1)
Taiwan (1)
New Zealand (1)
South Korea (1)
Poland (1)
Germany (1)
Israel (1)
Spain (1)

Previous page
1 / 71585
You're on page 1
page 2
page 3
page 4
page 5
page ...
page 71585
Next page

Sort by:

Relevance

Page size

Growth control of the eukaryote cell: a systems biology study in yeast

Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each function...

2012-04-19 | MTBLS8 | MetaboLights

The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis

Drastic alteration in macronutrients causes large changes in gene expression in the photosynthetic unicellular alga Chlamydomonas reinhardtii. Preliminary data suggested that cells follow a biphasic response to this change hinging on the initiation of lipid accumulation, and we hypothesized that ...

2015-06-29 | MTBLS208 | MetaboLights

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning a...

2018-07-31 | MTBLS492 | MetaboLights

Comprehensive systems biology analysis of a seven-month cigarette smoke inhalation study in C57BL/6 mice

Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of smoke derived from a prototype modified risk tobacco product (pMRTP) as compare...

2015-11-19 | MTBLS143 | MetaboLights

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

Phenomic and multiomic characterisation of microsatellite-stable colorectal cancer reveals novel biology and targets of vulnerability

Integrating data from approximately 2,000 tumour samples, corresponding to ~4,500 platform-specific multiomic sample profiles, and 195,246 single cells/nuclei from diverse in-house and publicly available datasets, single-to-integrated multiomic and clinical phenome data fusion analysis uncovers t...

2026-09-15 | MTBLS15127 | MetaboLights

Understanding the response to endurance exercise using a systems biology approach: combining blood metabolomics, transcriptomics and miRNome in horses

Not available

ORGANISM(S): Equus caballus

ST000503 | MetabolomicsWorkbench

Multi-layer omics dataset for cross-species translational systems biology

Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and ...

ORGANISM(S): Rattus norvegicus

2014-06-10 | E-MTAB-2091 | biostudies-arrayexpress

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

Studies on the production of fungal polyketides in Aspergillus nidulans using systems biology tools

Using genetic engineering tools available for the model organism Aspergillus nidulans, we constructed two recombinant strains; one expressing the model polyketide Penicillium griseofulvum 6-methylsalicylic acid (6-MSA) polyketide synthase gene, and one expressing the 6-MSA gene and overexpressing th...

ORGANISM(S): Emericella nidulans

2009-02-27 | E-GEOD-12859 | biostudies-arrayexpress