Recent Publications

Recent Journal Papers

Rational strain design with minimal phenotype perturbation

B. Narayanan; D. R. Weilandt; M. Masid; L. Miskovic; V. Hatzimanikatis 

Nature Communications. 2024-01-24. Vol. 15, num. 1, p. 723. DOI : 10.1038/s41467-024-44831-0.

Metabolic interaction models recapitulate leaf microbiota ecology

M. Schafer; A. R. Pacheco; R. Kunzler; M. Bortfeld-Miller; C. M. Field et al. 

Science. 2023-07-07. Vol. 381, num. 6653, p. eadf5121. DOI : 10.1126/science.adf5121.

Dynamics of CLIMP-63 S-acylation control ER morphology

P. A. Sandoz; R. A. Denhardt-Eriksson; L. Abrami; L. A. Abriata; G. Spreemann et al. 

Nature Communications. 2023-01-17. Vol. 14, num. 1. DOI : 10.1038/s41467-023-35921-6.

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

A. Sahin; D. R. Weilandt; V. Hatzimanikatis 

Nature Communications. 2023-05-05. Vol. 14, num. 1. DOI : 10.1038/s41467-023-38159-4.

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

S. Choudhury; B. Narayanan; M. Moret; V. Hatzimanikatis; L. Miskovic 

2023. DOI : 10.1101/2023.02.21.529387.

Recent Conference Papers, Poster and Talks

Systematic reduction of genome-scale models for the study of metabolic phenotypes of human cells

M. Masid Barcon; M. Ataman; V. Hatzimanikatis 

Constraint-Based Reconstruction and Analysis (COBRA) 2018, Seattle, USA, 14-16 October 2018.

Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.

M. Masid Barcon; V. K. Pandey; V. Hatzimanikatis 

European Conference on Computational Biology (ECCB) 2018, Athens, 8-12 September 2018.

Modeling CLiMP-63 spatio-temporal distribution and its interplay with Post-translational modification

R. A. Denhardt-Eriksson; P. Sandoz; L. Gouzi Abrami; S. Ho; B. Kunz 

5th Conference on Constraint-Based Reconstruction and Analysis, Seattle, United States of America, October 14-16, 2018.

Identification of the enzymes responsible for diverse phenotypic states of yeast lipid metabolism using comprehensive mechanistic models

S. Tsouka 

Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018), Seattle, USA, 14-16/10/2018.

ETFL: A Formulation of ME-Models Accounting for Expression and Thermodynamics in Constraint-Based Models

P. G. R. Salvy 

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