Recent Publications

Recent Journal Papers

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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Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infection

L. A. Meirelles; E. Vayena; A. Debache; E. Schmidt; T. Rossy et al. 

Nature microbiology. 2024. Vol. 9, num. 12, p. 3284 – 3303. DOI : 10.1038/s41564-024-01842-3.

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Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites

M. Maurizio; M. Masid; K. Woods; R. Caldelari; J. G. Doench et al. 

Nature communications. 2024. Vol. 15, num. 1. DOI : 10.1038/s41467-024-50405-x.

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RIP1 inhibition protects retinal ganglion cells in glaucoma models of ocular injury

B. k. Kim; T. Goncharov; S. A. Archaimbault; F. Roudnicky; J. D. Webster et al. 

CELL DEATH AND DIFFERENTIATION. 2024. DOI : 10.1038/s41418-024-01390-7.

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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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