Best Andrew A - OmicsDI

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Transcriptomics (142)
Unknown (57)
Genomics (35)
Proteomics (20)
Metabolomics (7)
Models (2)
Other (2)
Genomic (1)

Organisms

Homo sapiens (90)
Mus musculus (51)
Drosophila melanogaster (5)
Caenorhabditis elegans (4)
Sorghum bicolor (3)
Streptococcus pneumoniae (3)
Callithrix jacchus (2)
synthetic construct (2)
Oryctolagus cuniculus (2)
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Danio rerio (2)
Arabidopsis thaliana (2)
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Brassica rapa subsp. pekinensis (1)
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Populus maximowiczii x Populus nigra (1)
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Nicotiana benthamiana (1)
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Oncorhynchus mykiss (1)
Ovis aries (1)
Bos taurus (1)
Macaca fascicularis (1)
Rattus norvegicus (1)

Organisms

Notamacropus eugenii (2)

Repository

biostudies-arrayexpress (157)
EGA (15)
pride (15)
MetaboLights (7)
ENA (5)
MassIVE (3)
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Tissue

Cell culture (4)
Blood (1)
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Disease

Not Available (2)
Vitamin B12 deficiency (1)
Schizophrenia (1)
Colon cancer metastasis (1)
Normal (1)
Acute leukemia (1)
Alzheimer's disease (1)

Technology Type

Mass Spectrometry (15)
Bottom-up proteomics (11)
Mass spectrometry (6)
Shotgun proteomics (3)
ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2000, Ion Torrent PGM (1)
Illumina HiSeq 2500 (1)
Illumina HumanExome-12v1_A-GenCall, zCall, GenoSNP, - Illuminus (1)
NMR spectroscopy (1)
Affinity purification coupled with mass spectrometry proteomics (1)
Mass spectrometry imaging (1)
Top-down proteomics (1)

Instrument Platform

Illumina HiSeq 4000 (5)
GenePix Professional 4200A [Axon Instruments] (3)
Illumina HiSeq 2500 (3)
Illumina NovaSeq 6000 (3)
NextSeq 500 (3)
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Instrument (2)
ShARC (1)
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N/A (1)
LTQ Orbitrap (1)
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Q Exactive (1)
Autoflex speed smartbeam (1)
Liquid Chromatography MS - alternating - hilic (1)
Liquid Chromatography MS - negative - hilic (1)
Liquid Chromatography MS - negative - reverse phase (1)
Liquid Chromatography MS - positive - hilic (1)
Nuclear Magnetic Resonance (NMR) - (1)
QExactive Plus (1)

Publication Date

2015 (33)
2016 (22)
2010 (22)
2013 (17)
2014 (16)
2012 (14)
2011 (8)
2025 (7)
2024 (6)
2021 (6)
2009 (6)
2008 (6)
2007 (5)
2023 (3)
2019 (3)
2017 (3)
2026 (2)
2018 (2)
2005 (2)
2022 (1)

CHEBI ID

CHEBI:16449 (3)
CHEBI:18237 (3)
CHEBI:26271 (3)
CHEBI:30769 (3)
CHEBI:15422 (2)
CHEBI:15713 (2)
CHEBI:15996 (2)
CHEBI:16027 (2)
CHEBI:16695 (2)
CHEBI:16737 (2)
CHEBI:16742 (2)
CHEBI:16761 (2)
CHEBI:17202 (2)
CHEBI:18186 (2)
CHEBI:25017 (2)
CHEBI:25094 (2)
CHEBI:27266 (2)
CHEBI:27570 (2)
CHEBI:28044 (2)
CHEBI:28300 (2)
CHEBI:29016 (2)
CHEBI:78320 (2)
CHEBI:1148 (1)
CHEBI:135063 (1)
CHEBI:14314 (1)
CHEBI:14336 (1)
CHEBI:15351 (1)
CHEBI:15354 (1)
CHEBI:15366 (1)
CHEBI:15414 (1)

Metabolite Name

Arginine (2)
Creatinine (2)
Histidine (2)
Lysine (2)
Phenylalanine (2)
Proline (2)
Tyrosine (2)
Tyrosine (2)
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate (1)
2-hydroxybutyrate (1)
2-hydroxyglutarate (m+0) (1)
2-hydroxyglutarate (m+1) (1)
2-hydroxyglutarate (m+2) (1)
2-hydroxyglutarate (m+3) (1)
2-hydroxyglutarate (m+4) (1)
2-hydroxyglutarate (m+5) (1)
2-hydroxyisovalerate (1)
2-hydroxyvalerate (1)
2-oxoglutarate (m+0) (1)
2-oxoglutarate (m+1) (1)
2-oxoglutarate (m+2) (1)
2-oxoglutarate (m+3) (1)
2-oxoglutarate (m+4) (1)
2-oxoglutarate (m+5) (1)
3-hydroxybutyrate (1)
3-hydroxymethylglutarate (m+0) (1)
3-hydroxymethylglutarate (m+1) (1)
3-hydroxymethylglutarate (m+2) (1)
3-hydroxymethylglutarate (m+3) (1)
3-phosphoserine (m+0) (1)

IsPrivate

False (1)

Submitter Keywords

FAIR-AIML (1)
Machine Learning Model (1)

First Public Date

2025 (2)
2022 (2)
2021 (1)

Modelling Approach

Computational model (1)

Study type

Transcription profiling by array (81)
RNA-seq of coding RNA (25)
ChIP-seq (14)
Methylation profiling by array (7)
Other (6)
Unknown experiment type (5)
RNA-seq of coding RNA from single cells (4)
Transcription profiling by RT-PCR (2)
RNA-seq of total RNA (2)
RNA-seq of non coding RNA (2)
Transcription profiling by SAGE (1)
Cell line - Methylation microarray (1)
MNase-seq (1)
Whole chromosome random sequencing (1)
Genotyping by array (1)
Bisulfite-seq (1)
Comparative genomic hybridization by array (1)
ATAC-seq (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2015 (23)
2016 (22)
2010 (22)
2014 (18)
2013 (18)
2012 (15)
2025 (12)
2021 (12)
2024 (11)
2011 (10)
2022 (8)
2023 (6)
2009 (6)
2008 (6)
2019 (5)
2007 (5)
2020 (5)
2018 (3)
2017 (3)
2026 (2)
2005 (2)

Lab affiliation

Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada (10)
Boston University (1)
Fondazione Pisana per la Scienza, Pisa, Italy (1)
Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia (1)
PolyLC Inc., 9151 Rumsey Road, ste. 175, Columbia, MD 21045 USA (1)
University of Michigan, Department of Pathology (1)

Tags

xref:PubMed:33911273 (2)
xref:EuropePMC:PMC8732746 (1)

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Diagnostic utility of clinicodemographic, biochemical and metabolite variables to identify viable pregnancies in a symptomatic cohort during early gestation.

Study question: Can a novel machine learning pipeline create predictive models that identify a composite biomarker to differentiate live normally sited pregnancies (LNSP) from non-viable pregnancies in women presenting with pain and/or bleeding in early gestation?

Summary answer: Serum met...

2025-08-14 | MTBLS6219 | MetaboLights

Anion-Exchange Chromatography of Tryptic and Phosphopeptides: WAX vs. SAX and AEX vs. ERLIC

At a pH > 5, phosphopeptides have two negative charges per residue and are well-retained in anion-exchange chromatography. However, the peptides with one or two phosphate groups are not separated from the peptides with multiple Asp or Glu residues, which interfere with the identification of phosph...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2017-03-29 | MSV000080774 | MassIVE

Chemotherapy Modulation by a Cancer-Associated Microbiota Metabolite (Targeted metabolomics - 2methylisocitrate)

Understanding how the microbiota produces regulatory metabolites is of significance for cancer and cancer therapy. Using a host-microbe-drug-nutrient 4-way screening approach, we evaluated the role of nutrition at the molecular level in the context of 5-fluorouracil toxicity. Notably, our screens...

2025-09-16 | MTBLS9994 | MetaboLights

Panorama of ancient metazoan macromolecular complexes: Xenopus laevis

By combining extensive biochemical fractionation with quantitative mass spectrometry, we directly examined the composition of soluble multiprotein complexes among diverse animal models. The project has been jointly supervised by Andrew Emili and Edward M. Marcotte. Project website: http://metazoa.me...

ORGANISM(S): Xenopus laevis (African clawed frog)

2015-06-22 | PXD002326 | Pride