Mattia Zampieri

The glutamine-aspartate metabolic tradeoff between fast growth and metabolic flexibility.

This study identifies a metabolic tradeoff between fast growth and flexibility in cancer cells and stem cells by analyzing glutamine and aspartate metabolism.

A perturbation atlas of mouse neural organoids resolves macroglial reactivity and nominates drivers of degeneration

This study creates a perturbation atlas of mouse neural organoids to understand macroglial reactivity and identify drivers of degeneration.

Model-based inference of enzyme inhibitions from perturbation-induced metabolic dynamics

This paper introduces a computational framework to infer enzyme targets from metabolic perturbations using time-resolved metabolomics data.

Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis

The paper integrates metabolomics and genomics data to identify functional SNPs in Mycobacterium tuberculosis strains, revealing genetic basis for antibiotic sensitivity.

Charting the cross-functional map between transcription factors and cancer metabolism

The paper maps TF-metabolite associations in cancer using a combined computational-experimental framework, revealing diverse TF dependencies in carbon metabolism.

Resource misallocation as a mediator of fitness costs in antibiotic resistance.

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.

A framework for large-scale dynamic metabolome drug profiling in mammalian cells: a case study analysis of the anti-cancer drug dichloroacetate

This paper introduces a framework for large-scale dynamic metabolome drug profiling in mammalian cells, demonstrating its application to study dichloroacetate's toxic effects in ovarian cancer cell lines.

Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast

This study integrates metabolomics, phosphoproteomics, and transcriptomics data in yeast to identify regulatory mechanisms linking signaling kinases to metabolic changes.