Recent Publications

Recent Journal Papers

COBRAxy: Constraint-based metabolic modelling in Galaxy

F. Lapi; L. Milazzo; L. Lin; I. Rizzo; B. Galuzzi et al. 

Bioinformatics. 2025. DOI : 10.1093/bioinformatics/btaf670.

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Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production

B. Narayanan; W. Jiang; S. Wang; J. Sáez-Sáez; D. Weilandt et al. 

METABOLIC ENGINEERING. 2025. Vol. 91, p. 430 – 441. DOI : 10.1016/j.ymben.2025.06.008.

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Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

A. Sveshnikova; O. Oftadeh; V. Hatzimanikatis 

Nature Communications. 2025. Vol. 16, num. 1. DOI : 10.1038/s41467-025-59827-7.

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The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

I. Toumpe; S. Choudhury; V. Hatzimanikatis; L. Miskovic 

ACS SYNTHETIC BIOLOGY. 2025. DOI : 10.1021/acssynbio.4c00868.

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Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine

E. Vayena; L. Fuchs; H. M. Peyhani; K. Lagoda; B. Nguyen et al. 

PLOS COMPUTATIONAL BIOLOGY. 2025. Vol. 21, num. 3. DOI : 10.1371/journal.pcbi.1012869.

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Recent Conference Papers, Poster and Talks

SYSTEMS BIOLOGY APPROACHES ALLOW INVESTIGATING THE SIGNALING AND METABOLIC REPROGRAMMING OF T CELLS

M. Masid; V. Hatzimanikatis; G. Coukos 

2023. Asian Transplantation Week (ATW)/ Annual congress of the Korean-Society-for-Transplantation (KST), Seoul, SOUTH KOREA, NOV 17-19, 2022. p. A20 – A20.

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A NON-CD25-BINDING IL-2 VARIANT FOR THE EXPANSION OR ENGINEERING OF T CELLS THAT CONFER SUPERIOR TUMOR CONTROL

Y. O. Miranda; M. Masid; C. J. Luna; G. M. Montalvo Bereau; T. Muller et al. 

2023. Asian Transplantation Week (ATW)/ Annual congress of the Korean-Society-for-Transplantation (KST), Seoul, SOUTH KOREA, NOV 17-19, 2022. p. A21 – A22.

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Machine Learning for Uncertainty Reduction in Biochemical Kinetic Models

L. Miskovic; J. Beal; M. Moret; V. Hatzimanikatis 

5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, USA, October 14-16, 2018.

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