Papin Jason A JA

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Models (4)
Metabolomics (2)
Transcriptomics (1)

Organisms

Homo sapiens (1)

Repository

BioModels (3)
MetaboLights (2)
biostudies-arrayexpress (1)
Cell Collective (1)

Technology Type

NMR spectroscopy (1)
Mass spectrometry (1)

Instrument Platform

Bruker (1)
Liquid Chromatography MS - negative - reverse phase (1)
Liquid Chromatography MS - positive - reverse phase (1)

Publication Date

2015 (3)
2009 (1)
2021 (1)
2019 (1)

CHEBI ID

CHEBI:26271 (2)
CHEBI:26986 (2)
CHEBI:16811 (2)
CHEBI:16708 (2)
CHEBI:27266 (2)
CHEBI:17750 (2)
CHEBI:25094 (2)
CHEBI:16040 (2)
CHEBI:27248 (2)
CHEBI:17568 (2)
CHEBI:16695 (2)
CHEBI:15741 (2)
CHEBI:78320 (2)
CHEBI:15940 (2)
CHEBI:16027 (2)
CHEBI:17154 (2)
CHEBI:16335 (2)
CHEBI:27897 (2)
CHEBI:15354 (2)
CHEBI:17368 (2)
CHEBI:170071 (1)
CHEBI:170070 (1)
CHEBI:170061 (1)
CHEBI:172382 (1)
CHEBI:172381 (1)
CHEBI:170058 (1)
CHEBI:170054 (1)
CHEBI:170051 (1)
CHEBI:170047 (1)
CHEBI:170046 (1)

Metabolite Name

Octadecanoicacid (1)
Perfluoroctanoic acid (PFOA) (1)
Hexadecanoicacid (1)
Xylenesulfonate (1)
2-Hydroxy glutaric acid (1)
Benazol P (1)
(1R,3R,4S,5R)-3,4-bis({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy})-1,5-dihydroxycyclohexane-1-carboxylic acid (1)
2-({2-[4-(4-Fluorophenyl)piperazino]-2-oxoethyl}sulfanyl)acetic acid (1)
3-Desoxy-3,4-methylenedioxy pyrovalerone (1)
(+/-)-threo-Methylnaphthidate (1)
6-(2-chloroanilino)-4-oxo-2-(4-pyridyl)-3,4-dihydro-2H-1,3-thiazine-5-carbonitrile (1)
2-(4-Methoxybenzylidene)quinuclidin-3-one (1)
1-(Benzylamino)-3-(3,4-dimethylphenoxy)propan-2-ol (1)
2-Hydroxy-4'-(2-hydroxyethoxy)-2-methylpropiophenone (1)
4-(2-hydroxyphenyl)-8,9-dimethyl-2,3-dihydro-1H-1,5-benzodiazepin-2-one (1)
1-(1,3,3-Trimethyl-2,3-dihydro-1H-indol-2-yliden)acetone (1)
5-(2-Thienyl)nicotinic acid (1)
N-(4-Hydroxypentyl)-3-carboxyindole metabolite (1)
N1-(5-oxo-5,6,7,8-tetrahydronaphthalen-2-yl)acetamide (1)
3-Indolebutyricacid (1)
1,3,4,10-Tetrahydro-9(2H)-acridinone (1)
6-hydroxy-4-methyl-2-phenyl-2,3-dihydropyridazin-3-one (1)
2-oxo-1,2-dihydroquinoline-4-carboxylate (1)
NP-003319 (1)
2-(Methylamino)-2,3-dihydro-1H-benzo[de]isoquinoline-1,3-dione (1)
2-Hydroxy-2-methylbutyronitrile (1)
Norepinephrine(Noradrenaline) (1)
Acetylarginine (1)
N-Methylcaprolactam (1)
3-Hydroxy-5-(hydroxymethyl)-2-methylisonicotinaldehyde oxime (1)

IsPrivate

False (3)

Model Flag

Non Kinetic (3)

Modelling Approach

Constraint-based model (3)

Study type

Transcription profiling by array (1)

Release Date

2009 (1)

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Inferring metabolic mechanisms of interaction within a defined gut microbiota

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform ...

2019-10-29 | MTBLS705 | MetaboLights

Untargeted metabolomics reveals species-specific metabolite production and shared nutrient consumption by Pseudomonas aeruginosa and Staphylococcus aureus

While bacterial metabolism is known to impact antibiotic efficacy and virulence, the metabolic capacities of individual microbes in cystic fibrosis lung infections are difficult to disentangle from sputum samples. Here, we show that untargeted metabolomic profiling of supernatants of multiple str...

2021-05-26 | MTBLS2105 | MetaboLights

Transcriptional profiling of a novel pro-angiogenic small molecule phthalimide neovascular factor 1 (PNF1)

We generated the transcriptional regulatory footprint of phthalimide neovascular factor 1 (PNF1)—a novel synthetic small molecule that exhibits significant in vitro endothelial potency and significant in vivo microvascular network expansion—by performing comparative microarray analysis on PNF1-stimu...

ORGANISM(S): Homo sapiens

2009-07-17 | E-GEOD-17119 | biostudies-arrayexpress

Chavali2008 - Genome-scale metabolic network of Leishmania major (iAC560)

Chavali2008 - Genome-scale metabolic network of Leishmania major (iAC560) This model is described in the article: Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Chavali AK, Whittemore JD, Eddy JA, Williams KT, Papin JA. Mol. Syst. Biol. 2...

2015-07-30 | MODEL1507180059 | BioModels

Oberhardt2008 - Genome-scale metabolic network of Pseudomonas aeruginosa (iMO1056)

Oberhardt2008 - Genome-scale metabolic network of Pseudomonas aeruginosa (iMO1056) This model is described in the article: Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. Oberhardt MA, Puchałka J, Fryer KE, Martins dos Santo...

2015-07-30 | MODEL1507180020 | BioModels

Puchalka2008 - Genome-scale metabolic network of Pseudomonas putida (iJP815)

Puchalka2008 - Genome-scale metabolic network of Pseudomonas putida (iJP815) This model is described in the article: Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. Puchałka J, Oberhardt MA,...

2015-07-30 | MODEL1507180044 | BioModels

Metabolic Interactions in the Gut Microbiome

We present a novel methodology to construct a Boolean dynamic model from time series metagenomic information and integrate this modeling with genome-scale metabolic network reconstructions to identify metabolic underpinnings for microbial interactions. We apply this in the context of a critical heal...

5731 | Cell Collective

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