Computational biology

OmicsDI

Browse
Submit Data
Databases
API
Help

62476 Results

Show all Save search Copy query

Show results for

Unknown (57268)
Genomics (3172)
Transcriptomics (932)
Proteomics (511)
Models (451)
Metabolomics (80)
Multiomics (25)
Other (20)
Genomic (10)
Methylation profiling (6)
Clinical (2)

Organisms

Homo sapiens (682)
Mus musculus (230)
Saccharomyces cerevisiae (58)
Rattus norvegicus (35)
Arabidopsis thaliana (34)
Escherichia coli (19)
cellular organisms (10)
Canis lupus familiaris (4)
Xenopus laevis (4)
Aspergillus niger (4)
Neurospora crassa (3)
Arabidopsis (3)
Chordata (3)
Mammalia (3)
Cryptococcus neoformans (2)
Clavispora lusitaniae (2)
Sporobolomyces roseus (2)
Aspergillus terreus (2)
Fusarium oxysporum (2)
Sclerotinia sclerotiorum (2)
Histoplasma capsulatum (2)
Nakaseomyces glabratus (2)
Chaetomium globosum (2)
Lodderomyces elongisporus (2)
Pyricularia grisea (2)
5306 (2)
Aspergillus clavatus (2)
Schizosaccharomyces japonicus (2)
Botrytis cinerea (2)
Aspergillus oryzae (2)

Organisms

Homo sapiens (1094)
Mus musculus (772)
Drosophila melanogaster (67)
Rattus norvegicus (52)
Saccharomyces cerevisiae (52)
Caenorhabditis elegans (38)
Danio rerio (32)
Arabidopsis thaliana (28)
Gallus gallus (18)
Halobacterium salinarum NRC-1 (12)
Macaca mulatta (12)
synthetic construct (12)
Sus scrofa (11)
Oryza sativa (10)
Lethrinus laticaudis (7)
Galeorhinus galeus (7)
Schizosaccharomyces pombe (7)
Solanum lycopersicum (6)
Schmidtea mediterranea (5)
Centropyge heraldi (4)
Centropyge colini (4)
Galeocerdo cuvier (4)
Choerodon rubescens (4)
Cristiceps australis (4)
Pristipomoides typus (4)
Heterodontus portusjacksoni (4)
Lethrinus nebulosus (4)
Lutjanus quinquelineatus (4)
Orectolobus wardi (4)
Lutjanus sebae (4)

Repository

ENA (3031)
biostudies-arrayexpress (851)
BioModels (444)
pride (340)
geo (144)
EGA (97)
MetaboLights (78)
MassIVE (70)
iProX (42)
PeptideAtlas (34)
LINCS (23)
jPOST (12)
dbGaP (10)
PAXDB (8)
Cell Collective (5)
PanoramaPublic (5)
EVA (4)
GPMDB (3)
GNPS (2)
FAIRDOMHub (1)
NODE (1)
PMR (1)

Tissue

Cell culture (70)
Others (31)
Epithelial cell (26)
Permanent cell line cell (17)
Brain (14)
B cell (12)
Blood (12)
Fibroblast (11)
Kidney (10)
Lung (10)
T cell (9)
Embryonic stem cell (8)
HeLa cell (8)
Liver (8)
Blood cell (7)
Primary cell (7)
Blood plasma (6)
Cell suspension culture (6)
Whole body (6)
Bone marrow (5)
Colon (5)
Leaf (5)
Leukocyte (5)
Macrophage (5)
Plant cell (5)
Blood serum (4)
Embryo (4)
Peripheral blood mononuclear cell (4)
Early embryonic cell (3)
Platelet (1)

Disease

Breast cancer (16)
Disease free (9)
Acute leukemia (8)
Cervix carcinoma (7)
Multiple myeloma (5)
Lymphoma (5)
Diabetes mellitus (4)
Non-small cell lung carcinoma (3)
Glioblastoma (3)
Not Available (3)
Ovarian disease (2)
Osteoarthritis (1)
Cartilage disease (1)
Bacterial infectious disease (1)
Cholesterol embolism (1)
Influenza (1)
Alzheimer's disease (1)
Cancer (1)
Heart disease (1)
Neuroendocrine tumor (1)
HIV-1 seropositive (1)
Chondroblastoma (1)
Kaposi's sarcoma (1)
Mock infected (1)
Colorectal cancer (1)
Colon carcinoma (1)
Mixoid liposarcoma (1)
Chicken Anaemia Virus infected (1)
Inflammatory Bowel Diseases (1)
Colorectal Neoplasms (1)

Technology Type

Mass Spectrometry (340)
Shotgun proteomics (177)
Mass spectrometry (60)
Bottom-up proteomics (60)
Affinity purification coupled with mass spectrometry proteomics (46)
Data-dependent acquisition (29)
Gel-based experiment (26)
Fluorescence intensity (23)
KINOMEscan (23)
Data-independent acquisition (23)
Chemical cross-linking coupled with mass spectrometry proteomics (19)
SWATH MS (16)
Mass spectrometry assay (13)
Top-down proteomics (10)
RNA mass spectrometry (7)
SRM/MRM (7)
NMR spectroscopy (5)
DiaPASEF (4)
Illumina HiSeq 2500 (2)
Illumina HiSeq 2000 (2)
Illumina MiSeq (2)
All-ion fragmentation (2)
Human Cardio Metabochip (1)
ILLUMINA, NextSeq 500 (1)
Illumina HiSeq 2500, ILLUMINA (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)

Instrument Platform

Illumina NovaSeq 6000 (56)
NextSeq 500 (20)
Illumina HiSeq 2500 (18)
NextSeq 2000 (16)
Illumina HiSeq 4000 (16)
Illumina NovaSeq X (9)
Illumina HiSeq 2000 (6)
Affymetrix GeneChip Scanner 3000 7G (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)
Agilent 2100 Bioanalyzer (2)
ScanArray 5000 [PerkinElmer] (2)
Illumina HiSeq 1000 (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)

Publication Date

2024 (230)
2025 (179)
2014 (149)
2005 (145)
2016 (142)
2015 (141)
2013 (137)
2026 (108)
2010 (107)
2023 (95)
2022 (86)
2021 (77)
2012 (72)
2011 (67)
2020 (50)
2019 (46)
2017 (42)
2008 (42)
2018 (38)
2009 (25)
2006 (24)
2007 (17)
2004 (1)

UNIPROT ID/AC

P04075 (101)
P14618 (69)
P05062 (69)
P09972 (69)
P00338 (69)
P07195 (69)
P30613 (69)
P06744 (69)
Q9BYZ2 (67)
P07864 (67)
Q9BQG2 (66)
B3KXN9 (66)
Q53HM1 (66)
Q86SK9 (66)
E9KL42 (66)
Q3I5F7 (66)
P33897 (66)
Q99884 (66)
A8MU28 (66)
P35219 (66)
Q5FC00 (66)
Q15274 (66)
Q9NX14 (66)
Q9Y345 (66)
Q86YT5 (66)
Q53H96 (66)
Q9NWU1 (66)
Q96C36 (66)
Q9NRX3 (66)
O75610 (66)

ENSEMBL ID

ENSG00000165661 (4)
ENSG00000176654 (4)
ENSG00000204531 (4)
ENSG00000148200 (2)
ENSG00000165556 (2)
ENSG00000141448 (2)
ENST00000261769 (1)
ENST00000227507 (1)
ENST00000242261 (1)
ENST00000263341 (1)
ENSG00000151468 (1)
ENST00000297494 (1)
ENSG00000100234 (1)
ENSG00000102265 (1)
ENSG00000184557 (1)
ENSG00000137745 (1)
ENSG00000196611 (1)
ENSG00000177606 (1)
ENSG00000170345 (1)
ENSG00000158859 (1)
ENSG00000149968 (1)
ENSMUSG00000031170 (1)
ENSMUSG00000010064 (1)
ENSMUSG00000024036 (1)
ENSMUSG00000020261 (1)
ENSMUSG00000031156 (1)
ENSMUSG00000037434 (1)
ENSMUSG00000025082 (1)
ENSMUSG00000070436 (1)
ENSMUSG00000037936 (1)

CHEBI ID

CHEBI:16480 (131)
CHEBI:27931 (123)
CHEBI:17411 (122)
CHEBI:29034 (118)
CHEBI:29033 (118)
CHEBI:27402 (113)
CHEBI:37671 (106)
CHEBI:15361 (103)
CHEBI:16761 (102)
CHEBI:17137 (100)
CHEBI:61540 (98)
CHEBI:17754 (98)
CHEBI:4167 (94)
CHEBI:15343 (94)
CHEBI:30031 (91)
CHEBI:30089 (89)
CHEBI:18021 (88)
CHEBI:17268 (85)
CHEBI:46398 (84)
CHEBI:17029 (82)
CHEBI:16551 (79)
CHEBI:29108 (79)
CHEBI:31013 (77)
CHEBI:18189 (76)
CHEBI:15377 (76)
CHEBI:16526 (76)
CHEBI:16236 (75)
CHEBI:52328 (74)
CHEBI:57642 (74)
CHEBI:18191 (74)

Metabolite Name

L-Phenylalanine (16)
Adenine (15)
L-Histidine (14)
Taurine (14)
Citric acid (14)
Xanthine (14)
Uridine (14)
L-Tyrosine (14)
L-Threonine (13)
L-Tryptophan (13)
Uric acid (13)
Hypoxanthine (13)
L-Glutamine (12)
L-Leucine (12)
Creatinine (11)
Creatine (11)
L-Valine (11)
D-Glucose (10)
Thymine (10)
Choline (10)
L-Serine (10)
L-Isoleucine (10)
Inosine (10)
Glutathione (9)
L-Proline (9)
Ornithine (9)
Benzoic acid (9)
L-Arginine (9)
L-Asparagine (9)
L-Glutamic acid (9)

First Public Date

2014 (441)
2024 (345)
2023 (264)
2021 (245)
2020 (228)
2025 (213)
2019 (212)
2026 (189)
2018 (188)
2022 (181)
2017 (158)
2013 (138)
2015 (126)
2016 (102)
2011 (1)

Modelling Approach

Ordinary differential equation model (158)
Constraint-based model (101)
Logical model (9)
Computational model (6)
Metabolic network (5)
Differential equation model (4)
Delayed differential equation model (3)
Other (3)
Cellular potts model (3)
Mathematical model (2)
Agent-based model (2)
Machine learning (1)
Biochemical network (1)
Boolean model (1)
Physiologically based pharmacokinetic model (1)

Study status

Recruiting (1)
Completed (1)

Lab affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States (5)
Computational and Experimental Biology Group NOVA MEDICAL SCHOOL / FACULDADE DE CIÊNCIAS MÉDICAS UNIVERSIDADE NOVA DE LISBOA Rua Câmara Pestana, 6-6A | 1150-082 Lisboa Portugal (4)
Department of Structural and Computational Biology, Max Perutz Labs, Campus Vienna Biocenter 5, 1030 Vienna, Austria (3)
1) Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA 2) Proteomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA 3) Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA (2)
CRUK - Beatson Institute for Cancer Research - Switchback Rd, Bearsden, Glasgow G61 1BD - United Kingdom (2)
Center of experimental therapeutics Department of oncology UNIL CHUV Ludwig Institute for Cancer Research Lausanne Centre de recherche Agora Rue du Bugnon 25A CH-1005 Lausanne (2)
Centre for Genomics and Computational Biology Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ Tel: +44 (0)20 7882 8266 (2)
Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London (2)
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center (2)
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 (2)
Department of Cell Biology, Harvard Medical School, Boston MA 02115 (2)
Department of Immunology, Interfaculty Institute for Cell Biology, Eberhard Karls University Tübingen (2)
Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Campus Vienna Biocenter 5, 1030 Vienna, Austria (2)
Director, Translational Proteomics Research Unit, IRCM Director, Biomarker Pipeline for Precision Medicine Strategic Initiative Full IRCM Research Professor Full Research Professor, Department of Biochemistry and Molecular Medicine (accreditation for the Molecular Biology Programs), Université de Montréal Holder of the Bell-Bombardier Chair of Excellence Person in charge of responsible conduct of research, IRCM (2)
Division of Nephrology, University Hospitals Namur | Place Louise Godin 15, B-5000 Namur, Belgium (2)
ETH Zurich Institute of Molecular Systems Biology (2)
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany (2)
Genome Biology Unit and Proteomics Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany (2)
Inserm U1016, Institut Cochin, 24 rue du Faubourg Saint-Jacques, 75014 PARIS, FRANCE. (2)
Instituto de Nanobiotecnologıa (NANOBIOTEC), UBA-CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina (2)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (2)
Molecular Biotechnology & Systems Biology, TU Kaiserslautern, Kaiserslautern, Germany (2)
Pedro R. Cutillas Professor of Cell Signalling & Proteomics Centre for Genomics and Computational Biology Barts Cancer Institute - a Cancer Research UK Centre of Excellence Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ (2)
Reader in Centre for Genomics and Computational Biology Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ Tel: +44 (0)20 7882 8266 | Fax: +44 (0)20 7882 3891 | Email: p.cutillas@qmul.ac.uk www.bci.qmul.ac.uk/research/centre-profiles/haemato-oncology.html https://www.bci.qmul.ac.uk/en/staff/item/pedro-cutillas (2)
Reader | Centre for Genomics and Computational Biology Barts Cancer Institute Queen Mary, University of London John Vane Science Centre, Charterhouse Square, London EC1M 6BQ Tel: +44 (0)20 7882 8266 (2)
The Jenner Institute Nuffield Department of Medicine University of Oxford (2)
*Dr. Arun Sharma Protein Biochemistry and Structural Biology Division National Institute of Malaria Research (ICMR) Department of Health Research, Ministry of Health and Family Welfare, Govt. of India Sector-8, Dwarka, New Delhi- 110077 (1)
1) CNRS - ITAV USR3505, 31106 Toulouse, France 2) Nova Medical School, CEDOC- Chronic Diseases, 1150-082, Lisboa, Portugal (1)
1) Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany 2) Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, Bayreuth, Germany (1)
1Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA 2Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA 3Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA (1)

Keyword

Metabonomics (1)
Systems biology (1)
Intelligent knife (1)
NMR (1)
Mass spectrometry (1)

IsPrivate

False (444)

Model Flag

Non Kinetic (207)
Sbml Extended (1)

Submitter Keywords

FROG (18)
Not Peer Reviewed (10)
Machine Learning Model (5)
Ersilia (3)
FAIR-AIML (3)
Immuno-oncology (2)
Manuscript Accepted (1)
COVID-19 (1)

Classification

bacteria (15)
protozoa (9)
fungi (5)
viruses (2)

Modification

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

Study type

Transcription profiling by array (434)
RNA-seq of coding RNA (200)
Unknown experiment type (48)
RNA-seq of non coding RNA (37)
ChIP-seq (14)
RNA-seq of total RNA (13)
Comparative genomic hybridization by array (12)
Methylation profiling by array (11)
Transcription profiling by tiling array (10)
Other (10)
RNA-seq of coding RNA from single cells (10)
DNA-seq (7)
ChIP-chip by tiling array (6)
Bisulfite-seq (6)
ChIP-chip by array (4)
Transcription profiling by SAGE (3)
MicroRNA profiling by high throughput sequencing (3)
MicroRNA profiling by array (3)
Methylation profiling by high throughput sequencing (3)
High-throughput sequencing (2)
Cell line - High-throughput sequencing (2)
RNAi profiling by array (2)
Transcription profiling by RT-PCR (2)
ATAC-seq (2)
MicroRNA profiling by high-throughput sequencing (1)
Human - High-throughput sequencing (1)
Animal - High-throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
Ribo-seq (1)
Genotyping by high throughput sequencing (1)

Release Date

2025 (5283)
2021 (5122)
2022 (5120)
2023 (4964)
2024 (4584)
2020 (4104)
2019 (3612)
2018 (3244)
2017 (3032)
2015 (3022)
2016 (3009)
2014 (2744)
2013 (2047)
2012 (1597)
2011 (1396)
2010 (1267)
2009 (951)
2008 (787)
2026 (692)
2007 (569)
2006 (422)
2005 (241)
2004 (112)
2003 (86)
2002 (42)
2001 (33)
2000 (17)
1998 (11)
1999 (7)
1997 (1)

Location

United States (1)
United Kingdom (1)

Previous page
1 / 6248
You're on page 1
page 2
page 3
page 4
page 5
page ...
page 6248
Next page

Sort by:

Relevance

Page size

Experimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna

Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the...

MTBLS2273 | MetaboLights

Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing

This SuperSeries is composed of the following subset Series: GSE14694: Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (reproducibility) GSE14695: Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (standards) Ref...

ORGANISM(S): Arabidopsis thaliana

2009-06-02 | E-GEOD-14696 | biostudies-arrayexpress

Computational analysis of genome-wide DNA-methylation during the differentiation of human embryonic stem cells along the endodermal lineage

The generation of genome-wide data derived from methylated DNA immunoprecipitation followed by sequencing (MeDIP-Seq) has become a major tool for epigenetic studies in health and disease. The computational analysis of such data, however, still falls short on accuracy, sensitivity and speed. We propo...

ORGANISM(S): Homo sapiens

2010-07-26 | E-GEOD-21715 | biostudies-arrayexpress

Catalyzing computational biology research at an academic institute through an interest network.

Not available

S-EPMC12422415 | biostudies-literature

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

Not available

S-EPMC5638210 | biostudies-literature

Correction: A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis.

Not available

S-EPMC4783073 | biostudies-literature

A field guide to cultivating computational biology.

Not available

S-EPMC8525744 | biostudies-literature

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

A new online computational biology curriculum.

Not available

S-EPMC4055417 | biostudies-literature

Computational systems chemical biology.

Not available

S-EPMC3547368 | biostudies-literature