Metabolic control of nitrogen fixation in rhizobium-legume symbioses

CCM Schulte, K Borah, RM Wheatley, JJ Terpolilli… - Science …, 2021 - science.org
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which
catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite …

Computational strategies for a system-level understanding of metabolism

P Cazzaniga, C Damiani, D Besozzi, R Colombo… - Metabolites, 2014 - mdpi.com
Cell metabolism is the biochemical machinery that provides energy and building blocks to
sustain life. Understanding its fine regulation is of pivotal relevance in several fields, from …

Flux sampling is a powerful tool to study metabolism under changing environmental conditions

HA Herrmann, BC Dyson, L Vass… - NPJ systems biology …, 2019 - nature.com
The development of high-throughput 'omic techniques has sparked a rising interest in
genome-scale metabolic models, with applications ranging from disease diagnostics to crop …

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

C Damiani, D Maspero, M Di Filippo… - PLoS computational …, 2019 - journals.plos.org
Metabolic reprogramming is a general feature of cancer cells. Regrettably, the
comprehensive quantification of metabolites in biological specimens does not promptly …

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell …

C Damiani, R Colombo, D Gaglio… - PLoS computational …, 2017 - journals.plos.org
Cancer cells share several metabolic traits, including aerobic production of lactate from
glucose (Warburg effect), extensive glutamine utilization and impaired mitochondrial …

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation

M Di Filippo, D Pescini, BG Galuzzi… - PLoS computational …, 2022 - journals.plos.org
Metabolism is directly and indirectly fine-tuned by a complex web of interacting regulatory
mechanisms that fall into two major classes. On the one hand, the expression level of the …

Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models

M Di Filippo, R Colombo, C Damiani, D Pescini… - … biology and chemistry, 2016 - Elsevier
The metabolic rearrangements occurring in cancer cells can be effectively investigated with
a Systems Biology approach supported by metabolic network modeling. We here present …

popFBA: tackling intratumour heterogeneity with Flux Balance Analysis

C Damiani, M Di Filippo, D Pescini, D Maspero… - …, 2017 - academic.oup.com
Motivation Intratumour heterogeneity poses many challenges to the treatment of cancer.
Unfortunately, the transcriptional and metabolic information retrieved by currently available …

Linking alterations in metabolic fluxes with shifts in metabolite levels by means of kinetic modeling

C Damiani, R Colombo, M Di Filippo, D Pescini… - Advances in Artificial …, 2017 - Springer
The links between metabolic dysfunctions and various diseases or pathological conditions
are being increasingly revealed. This revival of interest in cellular metabolism has pushed …

‐Omics and Clinical Data Integration

G De Sanctis, R Colombo, C Damiani… - Integration of Omics …, 2018 - Wiley Online Library
Many high‐throughput post‐genomics (‐omics) technologies have been developed to
unravel cellular complexity and to investigate biological systems. Each‐omics technology …