To Matthew M - OmicsDI

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Transcriptomics (637)
Genomics (490)
Proteomics (369)
Unknown (328)
Metabolomics (49)
Models (41)
Genomic (7)
Multiomics (4)
Other (1)

Organisms

Homo sapiens (736)
Mus musculus (206)
Drosophila melanogaster (89)
Arabidopsis thaliana (38)
Saccharomyces cerevisiae (26)
Rattus norvegicus (23)
Escherichia coli (16)
Streptomyces venezuelae (12)
Danio rerio (11)
Bos taurus (8)
Macaca mulatta (5)
Xenopus laevis (5)
Glycine max (5)
synthetic construct (4)
Oryza sativa (4)
Oncorhynchus mykiss (4)
Thalassiosira pseudonana CCMP1335 (3)
Aspergillus niger (3)
Salmo salar (3)
Vibrio cholerae (3)
Escherichia coli str. K-12 substr. MG1655 (3)
Candida albicans (3)
Sus scrofa (3)
Eukaryota (2)
Neurospora crassa (2)
Clostridium botulinum (2)
Arabidopsis (1)
Mammalia (1)
Neisseria gonorrhoeae (1)
Schizosaccharomyces pombe (1)

Organisms

Homo sapiens (2)
Mus musculus (1)

Repository

biostudies-arrayexpress (799)
EGA (326)
pride (200)
MassIVE (130)
BioModels (37)
MetaboLights (33)
GNPS (16)
PanoramaPublic (13)
PeptideAtlas (10)
dbGaP (7)
jPOST (7)
PAXDB (5)
ENA (4)
Cell Collective (2)
FAIRDOMHub (2)
iProX (2)
EVA (1)
geo (1)
GPMDB (1)

Tissue

Cell culture (25)
Permanent cell line cell (11)
Epithelial cell (9)
Bone (8)
Fibroblast (8)
Kidney (8)
Photosynthetic cell (8)
Brain (7)
HeLa cell (7)
Lung (6)
Dental plaque (5)
Liver (5)
Blood plasma (4)
Skin (4)
Blood (3)
Heart (3)
Leaf (3)
Whole body (3)
Others (2)
Antler (2)
B cell (2)
Blood serum (2)
Breast (2)
Breast cancer cell (2)
Cell suspension culture (2)
Colon (2)
Dental pulp (2)
Early embryonic cell (2)
Female Reproductive System (1)
Ovary (1)

Disease

Disease free (22)
Breast cancer (5)
Cervix carcinoma (4)
Normal (3)
Herpes simplex (3)
Neurodegenerative disease (2)
Melanoma (2)
Acute leukemia (2)
Cardiovascular system disease (2)
Colon cancer (2)
Osteosarcoma (2)
Parkinson's disease (2)
Plasmodium falciparum malaria (2)
Renal fibrosis (2)
Hyperparathyroidism (1)
Hypoparathyroidism (1)
Inherited blood coagulation disease (1)
Extra-adrenal sympathetic paraganglioma (1)
Psoriasis vulgaris (1)
Whitehart (1)
Kaposi's sarcoma (1)
AIDS-KS, HIV+, nodular (late) stage (1)
Colon carcinoma (1)
Breast carcinoma (invasive ductal) (1)
Not Available (1)
High Grade Ovarian Serous Adenocarcinoma (1)
Acute myeloid leukemia (1)
Bone osteosarcoma (1)
Cervical cancer (1)
Cockayne syndrome (1)

Technology Type

Mass Spectrometry (200)
Shotgun proteomics (123)
Bottom-up proteomics (37)
Mass spectrometry (29)
Affinity purification coupled with mass spectrometry proteomics (22)
Illumina HiSeq 2000 (14)
Illumina 15K (8)
Mass spectrometry assay (4)
Illumina Genome Analyzer II, Illumina HiSeq 2000 (2)
Illumina HiSeq 2500 (2)
AB 5500 Genetic Analyzer (1)
AB SOLiD 4 System, Illumina HiSeq 2500, Illumina HiSeq 2000, AB SOLiD System 3.0 (1)
Affymetrix 6.0 (1)
Affymetrix 6.0, Illumina_670k - Illuminus, Illumina 1.2M (1)
COMPLETE_GENOMICS, Complete Genomics (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina 1.2M, Affymetrix 6.0 (1)
Illumina 1.2M, Affymetrix 6.0, Affymetrix 6.0 - CHIAMO (1)
Illumina 2.5M, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer II (1)
Illumina Genome Analyzer IIx, Illumina HiSeq 2000 (1)
Illumina HiSeq 2000, Affymetrics_SNP_6.0-, Illumina Genome Analyzer IIx (1)
Illumina HiSeq 2000, Illumina HumanOmni5-Quad and exome sequencing, ILLUMINA (1)
Illumina HiSeq 2500, ILLUMINA (1)
Illumina HiSeq 2500, Illumina MiSeq, NextSeq 500, Illumina HiSeq 2000 (1)
Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip (1)
Illumina MiSeq (1)
Illumina Omni 2.5, Illiumina Omni 2.5 (1)
Illumina_670k - Illuminus, Affymetrix 6.0, Illumina 1.2M (1)
NMR spectroscopy (1)

Instrument Platform

Illumina HiSeq 2000 (14)
Illumina HiSeq 2500 (13)
Illumina NovaSeq 6000 (11)
Illumina HiSeq 4000 (10)
Illumina MiSeq (4)
NextSeq 500 (4)
IScan (3)
Illumina NovaSeq X (3)
Bio-Rad CFX96 Real-time System (2)
3M Sodium Acetate, 100% Ethanol (2)
Promega PCR Master Mix. Bio-Rad Thermal Cycler (2)
Qiagen DNeasy (2)
AB 3730 Genetic Analyzer (2)
Illumina Genome Analyzer II (2)
NextSeq 2000 (2)
FACSAria III (BD Sciences) (1)
Illumina Hybridisation Oven (1)
HPC (1)
Nikon Eclipse Ti2 with brightfield and fluorescence capacity (TRITC) (1)
Leica Biosystems Cryostat (1)
Thermal cycler; magnetic separation rack; Qubit Fluorometer; Agilent TapeStation 4200 (1)
Microcentrifuge; magnetic separation rack; Qubit Flu/spectrophotometer; Agilent TapeStation 4200 (1)
Incubator shaker; spectrophotometer; Cmag measurement system; flow cytometer (1)
Element AVITI (1)
CL2 lab (1)
Punch biopsy - fibroblasts; commercial stock - HEKa (1)
BD LSRFortessa (1)
MACS Whole Skin Dissociation Kit (1)
10x Genomics Chromium (1)
Infors-HT Labfors chemostat (1)

Publication Date

2013 (155)
2014 (106)
2015 (99)
2011 (82)
2010 (81)
2012 (76)
2016 (73)
2022 (54)
2024 (52)
2018 (50)
2019 (48)
2021 (46)
2025 (45)
2023 (44)
2026 (38)
2020 (38)
2008 (37)
2009 (35)
2017 (34)
2007 (27)
2006 (9)
2005 (8)
2004 (4)

UNIPROT ID/AC

P12259 (5)
P00451 (4)
P00734 (4)
P00740 (4)
P00742 (4)
P01008 (4)
P08709 (4)
P10646 (4)
P13726 (4)
O81713 (2)
P04070 (2)
Q9LKL2 (2)
O00300 (1)
O14788 (1)
O15528 (1)
P00488 (1)
P00747 (1)
P00748 (1)
P01137 (1)
P01270 (1)
P02671 (1)
P02675 (1)
P02679 (1)
P03951 (1)
P03952 (1)
P04695 (1)
P05160 (1)
P07204 (1)
P07225 (1)
P10415 (1)

ENSEMBL ID

ENSG00000170477 (3)
ENSG00000147251 (2)
ENSG00000204131 (2)
ENSG00000229353 (2)
ENSG00000247315 (2)

CHEBI ID

CHEBI:17823 (2)
CHEBI:29108 (2)
CHEBI:33699 (2)
CHEBI:10033 (1)
CHEBI:10698 (1)
CHEBI:10983 (1)
CHEBI:10986 (1)
CHEBI:109895 (1)
CHEBI:111762 (1)
CHEBI:1148 (1)
CHEBI:1156 (1)
CHEBI:11805 (1)
CHEBI:11851 (1)
CHEBI:1189 (1)
CHEBI:11892 (1)
CHEBI:11951 (1)
CHEBI:12427 (1)
CHEBI:12876 (1)
CHEBI:128769 (1)
CHEBI:12936 (1)
CHEBI:12947 (1)
CHEBI:1296 (1)
CHEBI:12962 (1)
CHEBI:13115 (1)
CHEBI:13534 (1)
CHEBI:13705 (1)
CHEBI:144365 (1)
CHEBI:1463 (1)
CHEBI:14649 (1)
CHEBI:15035 (1)

Metabolite Name

Adenosine (10)
3-phosphoglycerate (8)
2-hydroxyglutarate (7)
Adenine (7)
Beta-alanine (7)
Guanine (7)
3-methyl-2-oxobutyrate (6)
Arginine (6)
Carnitine (6)
Choline (6)
Glycine (6)
Guanosine (6)
Isoleucine (6)
Leucine (6)
Malate (6)
Ornithine (6)
Pyridoxine (6)
1-methylnicotinamide (5)
2-aminoadipate (5)
3-ureidopropionate (5)
AMP (5)
CDP-choline (5)
CMP (5)
Coenzyme A (5)
FAD (5)
N-acetylglutamate (5)
N-acetylmethionine (5)
N-acetylphenylalanine (5)
N6-acetyllysine (5)
NAD+ (5)

First Public Date

2022 (1)
2021 (1)
2014 (1)
2013 (1)

Modelling Approach

Ordinary differential equation model (12)
Constraint-based model (6)
Mathematical model (2)
Computational model (1)
Deep learning (1)
Metabolic network (1)

Lab affiliation

BioArCh, University of York, UK (7)
Baylor College of Medicine (6)
Pacific Northwest National Laboratory (5)
BioArCh, University of York, United Kingdom (4)
Assistant Professor Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition Department of Pharmacology and Cancer Biology Duke University Medical Center (3)
Manchester Institute of Biotechnology, School of Biological Sciences, Manchester Academic Health Sciences Centre, The University of Manchester, Princess Street, Manchester, M1 7DN, UK (3)
Pacific Northwest National Laboratory, USA (3)
Centre for Blood Research, Department of Oral Biological and Medical Sciences, University of British Columbia, Vancouver, BC, Canada (2)
Department of Chemistry Center for Gastrointestinal Biology and Disease Integrated Program for Biological and Genome Sciences University of North Carolina at Chapel Hill (2)
Department of Genome Sciences, University of Washington, Seattle, USA (2)
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA (2)
Department of Molecular Biology, Princeton University (2)
Dept. of Biochemistry and Molecular Genetics, University of Colorado-Denver: Anschutz Medical Campus, Aurora, CO (2)
Francis Crick Institute 1 Midland Road London NW1 1AT (2)
Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA Department of Medicine – Renal Division, Brigham and Women’s Hospital, Boston, MA (2)
Marine Chemistry and Geochemistry Woods Hole Oceanographic Institution (2)
Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution (2)
Robarts Research Institute, Department of Biochemistry,Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7 (2)
School of Life Sciences, Faculty of Science, University of Technology Sydney. (2)
School of Life Sciences, University of Technology Sydney (2)
Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK (2)
The Globe Institute, University of Copenhagen (2)
University of Edinburgh (2)
University of Washington Department of Chemistry (2)
Westerdijk Fungal Biodiversity Institute (2)
, Dana-Farber Cancer Institute, Harvard Medical School 360 Longwood Avenue Longwood Center, LC4117 Boston, MA 02215 (1)
1. Tuberculosis Research Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia 2. The University of Sydney, Discipline of Infectious Diseases & Immunology and Sydney Institute for Infectious Diseases, Camperdown, NSW 2050, Australia (1)
1.Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA 2.Department of Microbiology, Harvard Medical School, Boston, MA, USA 3.Howard Hughes Medical Institute, Boston, MA, USA (1)
1.School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong 3216, Australia 2.Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, 3168 Melbourne, Australia 3.Department of Molecular and Translational Science, Monash University, 3168 Melbourne, Australia (1)
1Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA (1)

IsPrivate

False (37)

Model Flag

Non Kinetic (5)

Submitter Keywords

FROG (3)
Ersilia (2)
Machine Learning Model (2)
FAIR-AIML (1)

Modification

4-tetrahydrothiazine-3-carboxylic acid (2)
2x(15)N labeled L-lysine (1)
4x(2)H labeled dimethylated residue (1)
N6 (1)
N6-dimethyl-L-lysine (1)

Study type

Transcription profiling by array (374)
ChIP-seq (129)
RNA-seq of coding RNA (82)
Methylation profiling by array (37)
Comparative genomic hybridization by array (26)
Other (19)
RNA-seq of non coding RNA (19)
Methylation profiling by high throughput sequencing (17)
DNA-seq (12)
ChIP-chip by tiling array (11)
Unknown experiment type (8)
High-throughput sequencing (8)
Genotyping by array (8)
Transcription profiling by tiling array (6)
ChIP-chip by array (6)
RNA-seq of coding RNA from single cells (6)
ATAC-seq (5)
RNA-seq of total RNA (4)
Capture-C (3)
One-color microarray (2)
Proteomic profiling by array (2)
Genotyping by high throughput sequencing (2)
Cell line - Methylation microarray (1)
MNase-seq (1)
RNA-seq of non coding RNA from single cells (1)
Human - High-throughput sequencing (1)
Cell line - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Trajectory (1)
RNAi profiling by array (1)

Release Date

2013 (161)
2014 (109)
2015 (95)
2011 (86)
2010 (81)
2012 (80)
2016 (62)
2021 (49)
2020 (47)
2022 (43)
2008 (39)
2009 (37)
2024 (36)
2025 (34)
2017 (33)
2018 (31)
2023 (28)
2007 (28)
2019 (19)
2026 (16)
2006 (7)
2004 (4)
2005 (2)

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Optimised LC-MS Metabolomic Profiling Reveals Emergent Changes to Monocyte Metabolism in Response to Lipopolysaccharide

Immunometabolism examines the links between immune cell function and metabolism. Dysregulation of immune cell metabolism is now an established feature of innate immune cell activation. Advances in liquid chromatography mass spectrometry (LC-MS) technologies have allowed discovery of unique insights ...

2025-11-17 | MTBLS6730 | MetaboLights

Cumulative (Dis)Advantage and the Matthew Effect in Life-Course Analysis.

Not available

S-EPMC4659671 | biostudies-literature

The Matthew effect in science funding.

Not available

S-EPMC5948972 | biostudies-literature

PKM2 methylation by CARM1 activates aerobic glycolysis to promote tumorigenesis

Metabolic reprogramming is a hallmark of cancer. Herein we discover that the key glycolytic enzyme pyruvate kinase M2 isoform (PKM2), but not the related isoform PKM1, is methylated by co-activator-associated arginine methyltransferase 1 (CARM1). PKM2 methylation reversibly shifts the balance of met...

2021-07-30 | MTBLS533 | MetaboLights

Matthew-Wood syndrome is caused by truncating mutations in the retinol-binding protein receptor gene STRA6.

Not available

S-EPMC1867105 | biostudies-literature

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

A shotgun metabolomics approach to characterize the dissolved organic matter pool in the Samail Ophiolite aquifer

The process of serpentinization has been implicated in supporting life on both early Earth and other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on modern Earth, characterizing microbial act...

2023-03-02 | MTBLS6081 | MetaboLights

Treatment success for patients with tuberculosis receiving care in areas severely affected by Hurricane Matthew - Haiti, 2016.

Not available

S-EPMC7968710 | biostudies-literature

Differences in county-level cardiovascular disease mortality rates due to damage caused by hurricane Matthew and the moderating effect of social capital: a natural experiment.

Not available

S-EPMC9830798 | biostudies-literature

The use of metabolomics to monitor simultaneous changes in metabolic variables following supramaximal low volume high intensity exercise

High intensity exercise (HIE) stimulates greater physiological remodeling when compared to workload matched low-moderate intensity exercise. This study utilized an untargeted metabolomics approach to examine the metabolic perturbations that occur following two workload matched supramaximal low volum...

2015-06-15 | MTBLS191 | MetaboLights

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