PXD059887

PXD059887 is an original dataset announced via ProteomeXchange.

Title	Marti_et_al_Prediction of metabolic dynamics through deep learning and high-throughput multiomics data
Description	Synthetic biology’s remarkable potential to tackle important societal problems is held back by our inability to predictably engineer biological systems. Here, we collected one of the largest public multiomics synthetic biology datasets generated to date, and used it to train machine learning algorithms that are able to predict product and metabolic dynamics with great accuracy, starting to approach the predictive capabilities found in physics and chemistry. These predictions were provided for a non-model yeast, Pichia kudriavzevii, displaying carbon fluxes very different from model yeasts, and already engineered to produce large amounts of malonic acid, a desirable biomanufacturing target. Recommendations for genetic interventions obtained from this model improved final production, and illustrated existing limitations in leveraging predictive models of metabolism. This work shows the key role that machine learning can potentially play to significantly reduce the development time of novel synthetic biology products, paving the way for a timely replacement of the thousands of petrochemicals used in the modern economy, to create a working circular bioeconomy that can help mitigate climate change.
HostingRepository	PanoramaPublic
AnnounceDate	2026-02-10
AnnouncementXML	Submission_2026-02-10_18:40:40.546.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Chris Petzold
SpeciesList	scientific name: Pichia kudriavzevii; NCBI TaxID: 4909;
ModificationList	Deamidated; Carbamidomethyl
Instrument	6460 Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-16 10:36:00	ID requested
⏵ 1	2026-02-10 18:40:41	announced

no publication

submitter keyword: Metabolic engineering, biomanufacturing, machine learning, AI/ML, multiomics

Chris Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
lab head
Chris Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

Panorama Public dataset URI