Fiona - OmicsDI

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Unknown (673)
Transcriptomics (125)
Genomics (71)
Proteomics (34)
Models (11)
Metabolomics (10)
Genomic (1)
Other (1)
Multiomics (1)

Organisms

Homo sapiens (74)
Mus musculus (58)
Aerococcus urinae NBRC 15544 = CCUG 36881 (27)
Allexis (27)
Beta vulgaris subsp. vulgaris (27)
Canis lupus familiaris (27)
Carya cathayensis (27)
Clostridioides difficile 630 (27)
Cyanophora paradoxa (27)
Ensifer adhaerens (27)
Enterococcus faecalis (27)
Globicatella sanguinis (27)
Histomonas meleagridis (27)
Human immunodeficiency virus 1 (27)
Leishmania major strain Friedlin (27)
Listeria monocytogenes (27)
Lotus japonicus (27)
Danio rerio (9)
Trypanosoma brucei (6)
Drosophila melanogaster (6)
Strongyloides ratti (3)
Gallus gallus (3)
Rattus norvegicus (3)
Arabidopsis thaliana (2)
Salmonella enterica (1)
Brassica rapa (1)
Streptomyces coelicolor (1)
Bos taurus (1)
Triticum aestivum (1)
Saccharomyces cerevisiae (1)

Organisms

Mus musculus (4)
Homo sapiens (3)
Medicago truncatula (1)
Mycobacterium tuberculosis (1)

Repository

biostudies-arrayexpress (134)
ENA (33)
EGA (31)
pride (27)
BioModels (8)
MetaboLights (8)
MassIVE (5)
FAIRDOMHub (3)
GNPS (2)
dbGaP (1)
geo (1)
GPMDB (1)
jPOST (1)
PeptideAtlas (1)

Tissue

Blood plasma (5)
Cell culture (5)
Small intestine (4)
Stomach (4)
Colon (3)
Duodenum (3)
Jejunum (3)
Epithelial cell (2)
Ileum (2)
Rectum (2)
Brain (1)
Blood serum (1)
Bone marrow (1)
Colon ascendens (1)
Colon sigmoideum (1)
Fibroblast (1)
GIP cell (1)
Gastrointestinal tract (1)
Islet of Langerhans (1)
Lymphoblast (1)
Pancreas (1)
Pancreatic alpha cell (1)
Pancreatic delta cell (1)
Pancreatic islet (1)
Pancreatic islet beta cell (1)
Pluripotent stem cell (1)
Root nodule (1)
T cell (1)
Type M enteroendocrine cell (1)
Whole body (1)

Disease

Type 2 diabetes mellitus (4)
Porphyria NOS (2)
Lung cancer (2)
Hign immune pressure (1)
Short day torpor (1)
Melanoma (1)
Normal (1)
Not Available (1)
Chronic myeloid leukemia (1)
Colorectal carcinoma (1)
Disease free (1)
Endometriosis (1)
Lymphoma (1)
Obesity (1)
Pancreatic endocrine carcinoma (1)
Parkinson's disease (1)
Postgastrectomy syndrome (1)
Prostate adenocarcinoma (1)
Squamous cell carcinoma (1)

Technology Type

Mass Spectrometry (27)
Top-down proteomics (12)
Mass spectrometry (8)
Shotgun proteomics (7)
Bottom-up proteomics (6)
Affinity purification coupled with mass spectrometry proteomics (3)
ISelect Beadchip (1)
Illumina 1.2M, Affymetrix 6.0, Affymetrix 6.0 - CHIAMO (1)
Illumina HiSeq 2500 (1)
Data-dependent acquisition (1)
DiaPASEF (1)
SRM/MRM (1)
SWATH MS (1)

Instrument Platform

Illumina HiSeq 4000 (9)
Illumina NovaSeq 6000 (6)
Illumina HiSeq 2000 (5)
Q Exactive (4)
Axon- GenePix4000B (3)
Illumina HiSeq 2500 (3)
Bio-Rad CFX96 Real-time System (2)
Orbitrap Fusion (2)
Nikon Eclipse Ti2 with brightfield and fluorescence capacity (TRITC) (1)
Leica Biosystems Cryostat (1)
BD LSRFortessa (1)
MACS Whole Skin Dissociation Kit (1)
Ilumina HiScan H166 (1)
IScan (Illumina) (1)
Illumina iScan (1)
GenePix 4000A [Axon Instruments] (1)
Scanning hardware (1)
NA (1)
NextSeq 550 (1)
Illumina HiSeq 3000 (1)
NextSeq 500 (1)
Q Exactive Plus (1)
Instrument (1)
LTQ Velos (1)
QExactive (Thermo Scientific) (1)
Agilent 5975C GC/MSD (1)
Agilent 6520 series quadrupole time-of-flight mass spectrometer (QTOF MS) (1)
Exactive (Thermo Scientific) (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - negative - hilic (1)

Publication Date

2014 (19)
2012 (17)
2024 (15)
2025 (12)
2015 (12)
2010 (11)
2017 (10)
2021 (10)
2008 (10)
2007 (10)
2016 (9)
2019 (8)
2018 (8)
2023 (7)
2022 (6)
2020 (6)
2013 (5)
2011 (5)
2009 (4)
2005 (3)
2006 (2)
2026 (1)

UNIPROT ID/AC

Q9GRG6 (5)
A0A024R8H9 (1)
A0A024RAN2 (1)
A0A024RC46 (1)
A0A087WT59 (1)
A0A087WTX5 (1)
A0A087WXI0 (1)
A0A087WYL9 (1)
A0A087WZE9 (1)
A0A087X130 (1)
A0A087X1S3 (1)
A0A087X1V9 (1)
A0A0A0MR66 (1)
A0A0A0MS51 (1)
A0A0A0MSA7 (1)
A0A0C4DG89 (1)
A0AVT1 (1)
A0FGR8 (1)
A0FGR8-2 (1)
A0FGR8-6 (1)
A0M8Q6 (1)
A0MZ66 (1)
A1L020 (1)
A1X283 (1)
A2BFH1 (1)
A2NB46 (1)
A2NUT2 (1)
A2RRP1 (1)
A3KN83 (1)
A4D110 (1)

ENSEMBL ID

ENSG00000170477 (1)
ENSG00000247315 (1)

CHEBI ID

CHEBI:15422 (9)
CHEBI:16908 (9)
CHEBI:4170 (8)
CHEBI:16027 (8)
CHEBI:17794 (8)
CHEBI:16761 (8)
CHEBI:18009 (7)
CHEBI:14336 (6)
CHEBI:40595 (6)
CHEBI:28874 (6)
CHEBI:13389 (6)
CHEBI:57642 (6)
CHEBI:15379 (6)
CHEBI:17754 (6)
CHEBI:17138 (6)
CHEBI:15361 (6)
CHEBI:16526 (6)
CHEBI:18021 (6)
CHEBI:17234 (6)
CHEBI:35490 (5)
CHEBI:17842 (5)
CHEBI:58273 (5)
CHEBI:58121 (5)
CHEBI:48928 (5)
CHEBI:16474 (5)
CHEBI:16708 (4)
CHEBI:33942 (2)
CHEBI:28757 (2)
CHEBI:33842 (1)
CHEBI:57622 (1)

Metabolite Name

Uracil (3)
Carnosine (3)
L-Proline (3)
L-Threonine (3)
Nicotinamide (3)
Adenosine (3)
L-Tryptophan (3)
Adenine (3)
N-(octanoyl)-L-homoserine (2)
Di-n-Undecylamine (2)
L-proline amide (2)
LL-2,6-Diaminoheptanedioate (2)
O-Butanoylcarnitine (2)
NG,NG-Dimethyl-L-arginine (2)
Gentioflavine (2)
N2-(D-1-Carboxyethyl)-L-arginine (2)
Guanidinoacetate (2)
Imidazole-4-acetate (2)
(1-Ribosylimidazole)-4-acetate (2)
N-Acetyl-L-histidine (2)
Picolinamide (2)
Thiamin (2)
Sn-glycero-3-Phosphocholine (2)
L-Glutamate 5-semialdehyde (2)
N6-Methyl-L-lysine (2)
Choline phosphate (2)
(R)-Lactate (2)
1-Oleoylglycerophosphocholine (2)
Phosphodimethylethanolamine (2)
Myo-inositol (2)

First Public Date

2024 (10)
2023 (8)
2025 (6)
2026 (3)
2014 (3)
2021 (1)
2020 (1)
2018 (1)

Modelling Approach

Ordinary differential equation model (6)
Logical model (2)

Lab affiliation

Calico Life Sciences (3)
Metabolic Research Laboratories, University of Cambridge (3)
Institute of Metabolic Science, University of Cambridge (2)
Wellcome Trust MRC Institute of Metabolic Science (2)
1The Ritchie Centre, Hudson Institute of Medical Research.Shanti Gurung1(shanti.gurung@hudson.org.au) Jacqueline Piskopos1(jpis0002@student.monash.edu) Joel Steele2 (joel.steele@monash.edu) Ralf Schittenhelm2 (ralf.schittenhelm@monash.edu) Anup Shah2 (anup.shah@monash.edu) Fiona Cousins1 (fiona.cousins@hudson.org.au) Thomas Tapmeier1,3 (thomas.tapmeier@monash.edu) Caroline E. Gargett1,3 (caroline.gargett@hudson.org.au) (1)
Biology department, Maynooth University, Republic of Ireland (1)
Calico Labs, United States (1)
Calico Life Sciences LLC (1)
Calico Life Sciences, CA, USA (1)
Department of Molecular and Clinical Cancer Medicine University of Liverpool United Kingdom (1)
Dept. for Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tubingen, Germany (1)
Discovery Biology, AstraZeneca Pharmaceuticals (1)
Flinders Centre for Innovation in Cancer, Flinders University, Level 3, Flinders Centre for Innovation in Cancer Building, Flinders Drive, Bedford Park 5042, Australia. (1)
Fujian Agriculture and Forestry University (1)
Institute of Metabolic Research, MRC Metabolic Research Laboratories, Cambridge University (1)
McGill University Department of Biology and Bieler School of Environment (1)
Medical Research Laboratories, University of Cambridge (1)
Metabolic Research Laboratories, Cambridge University (1)
Proteome Dynamics Lab, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (1)
Wellcome Trust, MRC Institute of Metabolic Science, Cambridge University (1)
Wellcome Trust, MRC Institute of Metabolic Science, University of Cambridge. (1)

IsPrivate

False (8)

Model Flag

Non Kinetic (2)

Classification

bacteria (1)

Study type

Transcription profiling by array (83)
RNA-seq of coding RNA (11)
Methylation profiling by array (6)
ChIP-seq (5)
Unknown experiment type (3)
ChIP-chip by tiling array (3)
MicroRNA profiling by array (3)
RNA-seq of total RNA (3)
Human - High-throughput sequencing (2)
ChIP-chip by array (2)
RNA-seq of coding RNA from single cells (2)
Methylation profiling by high throughput sequencing (2)
Animal - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Genotyping by array (1)
Spatial transcriptomics by high-throughput sequencing (1)
RNA-seq of non coding RNA (1)

Release Date

2022 (113)
2023 (96)
2024 (87)
2021 (81)
2025 (80)
2020 (68)
2018 (43)
2019 (39)
2016 (30)
2017 (28)
2015 (23)
2014 (22)
2026 (20)
2012 (16)
2010 (15)
2007 (11)
2008 (10)
2011 (5)
2009 (5)
2013 (4)
2006 (4)
2005 (3)
2003 (1)
2002 (1)
1999 (1)

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FIONA on Caenorhabditis elegans.

Not available

S-EPMC2814247 | biostudies-literature

Fiona: a parallel and automatic strategy for read error correction.

Not available

S-EPMC4147893 | biostudies-literature

Investigating the use of finerenone in children with chronic kidney disease and proteinuria: design of the FIONA and open-label extension studies.

Not available

S-EPMC10956186 | biostudies-literature

Plasma and kidney proteome profiling combined with laser capture microdissection reveal large increases in immunoglobulins with age

One of the main hallmarks of aging is aging-associated inflammation, also known as inflammaging. In this study, by comparing young and old mice using LC-MS profiling, we show that immunoglobulins are the proteins that are most increased with age in plasma. This observation appears to have been previ...

ORGANISM(S): Mus musculus (Mouse)

2024-07-03 | PXD051031 | Pride

Revisiting the Hayflick Limit: Insights from an Integrated Analysis of Changing Transcripts, Proteins, Metabolites and Chromatin.

Replicative senescence (RS) as a model has become the central focus of research into cellular aging in vitro. Despite decades of study, this process through which cells cease dividing is not fully understood in culture, and even much less so in vivo during development and with aging. Here, we revisi...

ORGANISM(S): Homo sapiens (Human)

2022-04-04 | PXD028799 | Pride

Hayflick limit Proteomics

Effect of a 6-Week Structured Exercise Intervention on TNF-α During the Chronic Recovery Phase of a Burn Injury Compared to Regular Daily Activities: A Pilot Randomised Cross-Over Trial.

Not available

S-EPMC12921761 | biostudies-literature

Fiona Bradley

Not available

S-EPMC1125619 | biostudies-literature

Fiona Melville Bennett

Not available

S-EPMC1122665 | biostudies-literature

Feasibility of conducting a randomized controlled trial to explore the muscular influence of post-operative intravenous iron treatment for anaemia after major abdominal surgery.

Not available

S-EPMC12286669 | biostudies-literature

An epitranscriptomic mechanism regulating chlorophyll biosynthesis in Arabidopsis

Light modulates expression of nuclear-encoded chloroplast proteins to promote chlorophyll biosynthesis and photosynthesis in plants. Photoregulatory mechanisms regulating transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how photoresponsiv...

ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress)

2024-01-26 | PXD040660 | Pride

Fiona Light Chlorophyll M6a

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