2023

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.

Detailed record

View at publisher

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.

Detailed record

Full text – View at publisher

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.

Detailed record

Full text – View at publisher

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.

Detailed record

Full text – View at publisher

2022

Dynamic partitioning of branched-chain amino acids-derived nitrogen supports renal cancer progression

M. Sciacovelli; A. Dugourd; L. V. Jimenez; M. Yang; E. Nikitopoulou et al.

Nature Communications. 2022-12-20. Vol. 13, num. 1, p. 7830. DOI : 10.1038/s41467-022-35036-4.

Detailed record

Full text – View at publisher

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

D. R. Weilandt; P. Salvy; M. Masid; G. Fengos; R. Denhardt-Erikson et al.

Bioinformatics. 2022-12-10. DOI : 10.1093/bioinformatics/btac787.

Detailed record

Full text – View at publisher

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

E. Vayena; A. Chiappino-Pepe; H. MohammadiPeyhani; Y. Francioli; N. Hadadi et al.

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2022-11-15. Vol. 119, num. 46, p. e2211197119. DOI : 10.1073/pnas.2211197119.

Detailed record

View at publisher

Reconstructing Kinetic Models for Dynamical Studies of Metabolism using Generative Adversarial Networks

S. Choudhury; M. Moret; P. Salvy; D. Weilandt; V. Hatzimanikatis et al.

Nature Machine Intelligence. 2022-08-01. Vol. 4, num. 8, p. 710-719. DOI : 10.1038/s42256-022-00519-y.

Detailed record

Full text – View at publisher

ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds

A. Sveshnikova; H. MohammadiPeyhani; V. Hatzimanikatis

Metabolic Engineering. 2022-07-01. Vol. 72, p. 259-274. DOI : 10.1016/j.ymben.2022.03.013.

Detailed record

View at publisher

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

H. MohammadiPeyhani; J. Hafner; A. Sveshnikova; V. Viterbo; V. Hatzimanikatis

Nature Communications. 2022-03-23. Vol. 13, num. 1, p. 1560. DOI : 10.1038/s41467-022-29238-z.

Detailed record

Full text – View at publisher

2021

Editorial Overview: Mathematical modeling: It’s a matter of scale

S. D. Finley; V. Hatzimanikatis

Current Opinion In Systems Biology. 2021-12-01. Vol. 28, p. 100360. DOI : 10.1016/j.coisb.2021.100360.

Detailed record

View at publisher

An inverse method for mechanical characterization of heterogeneous diseased arteries using intravascular imaging

B. Narayanan; M. L. Olender; D. Marlevi; E. R. Edelman; F. R. Nezami

Scientific Reports. 2021-11-18. Vol. 11, num. 1, p. 22540. DOI : 10.1038/s41598-021-01874-3.

Detailed record

Full text – View at publisher

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

J. Hafner; V. Hatzimanikatis

Bioinformatics. 2021-10-15. Vol. 37, num. 20, p. 3560-3568. DOI : 10.1093/bioinformatics/btab368.

Detailed record

View at publisher

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

O. Oftadeh; P. Salvy; M. Masid; M. Curvat; L. Miskovic et al.

Nature Communications. 2021-08-09. Vol. 12, num. 1, p. 4790. DOI : 10.1038/s41467-021-25158-6.

Detailed record

Full text – View at publisher

NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism

H. Mohammadi Peyhani; A. Chiappino-Pepe; K. Haddadi; J. M. Hafner; N. Hadadi et al.

eLife. 2021-08-03. Vol. 10, p. e65543. DOI : 10.7554/eLife.65543.

Detailed record

Full text – View at publisher

The influence of the crowding assumptions in biofilm simulations

L. Angeles-Martinez; V. Hatzimanikatis

Plos Computational Biology. 2021-07-01. Vol. 17, num. 7, p. e1009158. DOI : 10.1371/journal.pcbi.1009158.

Detailed record

Full text – View at publisher

Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities

L. Angeles-Martinez; V. Hatzimanikatis

Plos Computational Biology. 2021-07-01. Vol. 17, num. 7, p. e1009140. DOI : 10.1371/journal.pcbi.1009140.

Detailed record

Full text – View at publisher

Development of Selective FXIa Inhibitors Based on Cyclic Peptides and Their Application for Safe Anticoagulation

V. Carle; Y. Wu; R. Mukherjee; X-D. Kong; C. Rogg et al.

Journal Of Medicinal Chemistry. 2021-05-27. Vol. 64, num. 10, p. 6802-6813. DOI : 10.1021/acs.jmedchem.1c00056.

Detailed record

Full text – View at publisher

Offset-Free Economic MPC Based on Modifier Adaptation: Investigation of Several Gradient-Estimation Techniques

M. Vaccari; D. Bonvin; F. Pelagagge; G. Pannocchia

Processes. 2021-05-01. Vol. 9, num. 5, p. 901. DOI : 10.3390/pr9050901.

Detailed record

Full text – View at publisher

Quantitative modeling of human metabolism: A call for a community effort

M. Masid Barcon; V. Hatzimanikatis

Current Opinion in Systems Biology. 2021-04-27. Vol. 26, p. 109-115. DOI : 10.1016/j.coisb.2021.04.008.

Detailed record

Full text – View at publisher

Constraint-based metabolic control analysis for rational strain engineering

S. Tsouka; M. Ataman; T. E. Hameri; L. Miskovic; V. Hatzimanikatis

Metabolic Engineering. 2021-04-22. Vol. 66, p. 191-203. DOI : 10.1016/j.ymben.2021.03.003.

Detailed record

Full text – View at publisher

The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli

T. Hameri; G. Fengos; V. Hatzimanikatis

Bmc Bioinformatics. 2021-03-20. Vol. 22, num. 1, p. 134. DOI : 10.1186/s12859-021-04066-y.

Detailed record

Full text – View at publisher

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

J. Hafner; J. Payne; H. MohammadiPeyhani; V. Hatzimanikatis; C. Smolke

Nature Communications. 2021-03-19. Vol. 12, num. 1, p. 1760. DOI : 10.1038/s41467-021-22022-5.

Detailed record

Full text – View at publisher

Emergence of diauxie as an optimal growth strategy under resource allocation constraints in cellular metabolism

P. Salvy; V. Hatzimanikatis

Proceedings Of The National Academy Of Sciences Of The United States Of America. 2021-02-23. Vol. 118, num. 8, p. e2013836118. DOI : 10.1073/pnas.2013836118.

Detailed record

Full text – View at publisher

The solubility parameters of carbon dioxide and ionic liquids: Are they an enigma?

C. Panayiotou; V. Hatzimanikatis

Fluid Phase Equilibria. 2021-01-01. Vol. 527, p. 112828. DOI : 10.1016/j.fluid.2020.112828.

Detailed record

View at publisher

2020

Mechanistic insights into bacterial metabolic reprogramming from omics-integrated genome-scale models

N. Hadadi; V. Pandey; A. Chiappino-Pepe; M. Morales; H. Gallart-Ayala et al.

Npj Systems Biology And Applications. 2020-12-01. Vol. 6, num. 1, p. 1. DOI : 10.1038/s41540-019-0121-4.

Detailed record

Full text – View at publisher

Real-time optimization of load sharing for gas compressors in the presence of uncertainty

P. Milosavljevic; A. G. Marchetti; A. Cortinovis; T. Faulwasser; M. Mercangoez et al.

Applied Energy. 2020-08-15. Vol. 272, p. 114883. DOI : 10.1016/j.apenergy.2020.114883.

Detailed record

View at publisher

Impact of multi-micronutrient supplementation on lipidemia of children and adolescents

A. Chakrabarti; M. Eiden; D. Morin-Rivron; N. Christinat; J. P. Monteiro et al.

Clinical Nutrition. 2020-07-01. Vol. 39, num. 7, p. 2211-2219. DOI : 10.1016/j.clnu.2019.09.010.

Detailed record

Full text – View at publisher

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

J. Hafner; H. MohammadiPeyhani; A. Sveshnikova; A. Scheidegger; V. Hatzimanikatis

Acs Synthetic Biology. 2020-06-19. Vol. 9, num. 6, p. 1479-1482. DOI : 10.1021/acssynbio.0c00052.

Detailed record

View at publisher

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

M. Masid; M. Ataman; V. Hatzimanikatis

Nature Communications. 2020-06-04. Vol. 11, num. 1, p. 2821. DOI : 10.1038/s41467-020-16549-2.

Detailed record

Full text – View at publisher

Revisiting the concept of extents for chemical reaction systems using an enthalpy balance

N. Ha Hoang; D. Rodrigues; D. Bonvin

Computers & Chemical Engineering. 2020-05-08. Vol. 136, p. 106652. DOI : 10.1016/j.compchemeng.2019.106652.

Detailed record

View at publisher

Visible light plays a significant role during bacterial inactivation by the photo-fenton process, even at sub-critical light intensities

R. Mosteo; A. Varon Lopez; D. Muzard; N. Benitez; S. Giannakis et al.

Water Research. 2020-05-01. Vol. 174, p. 115636. DOI : 10.1016/j.watres.2020.115636.

Detailed record

View at publisher

MEMOTE for standardized genome-scale metabolic model testing

C. Lieven; M. E. Beber; B. G. Olivier; F. T. Bergmann; M. Ataman et al.

Nature Biotechnology. 2020-03-02. Vol. 38, p. 272–276. DOI : 10.1038/s41587-020-0446-y.

Detailed record

Full text – View at publisher

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

S. Tsouka; V. Hatzimanikatis

Fems Yeast Research. 2020-03-01. Vol. 20, num. 2, p. foaa006. DOI : 10.1093/femsyr/foaa006.

Detailed record

Full text – View at publisher

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

M. Tokic; V. Hatzimanikatis; L. Miskovic

Biotechnology for Biofuels. 2020-02-28. Vol. 13, num. 33, p. 1-19. DOI : 10.1186/s13068-020-1665-7.

Detailed record

Full text – View at publisher

Modifier Adaptation as a Feedback Control Scheme

A. G. Marchetti; T. d. A. Ferreira; S. Costello; D. Bonvin

Industrial & Engineering Chemistry Research. 2020-02-12. Vol. 59, num. 6, p. 2261-2274. DOI : 10.1021/acs.iecr.9b04501.

Detailed record

View at publisher

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

A. Krishnan; J. Kloehn; M. Lunghi; A. Chiappino-Pepe; B. S. Waldman et al.

Cell Host & Microbe. 2020-02-12. Vol. 27, num. 2, p. 290-+. DOI : 10.1016/j.chom.2020.01.002.

Detailed record

View at publisher

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

P. Salvy; V. Hatzimanikatis

Nature Communications. 2020-01-13. Vol. 11, p. 30. DOI : 10.1038/s41467-019-13818-7.

Detailed record

Full text – View at publisher

A note on efficient computation of privileged directions in modifier adaptation

M. Singhal; A. G. Marchetti; T. Faulwasser; D. Bonvin

Computers & Chemical Engineering. 2020-01-04. Vol. 132, p. 106524. DOI : 10.1016/j.compchemeng.2019.106524.

Detailed record

View at publisher

2019

Statistical inference in ensemble modeling of cellular metabolism

T. E. Hameri; M-O. Boldi; V. Hatzimanikatis

PLoS Computational Biology. 2019-12-09. Vol. 15, num. 12, p. e1007536. DOI : 10.1371/journal.pcbi.1007536.

Detailed record

Full text – View at publisher

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage

R. R. Stanway; E. Bushell; A. Chiappino-Pepe; M. Roques; T. Sanderson et al.

Cell. 2019-11-14. Vol. 179, num. 5, p. 1112-1128.e26. DOI : 10.1016/j.cell.2019.10.030.

Detailed record

Full text – View at publisher

Accelerated and adaptive modifier-adaptation schemes for the real-time optimization of uncertain systems

R. Schneider; P. Milosavljevic; D. Bonvin

Journal Of Process Control. 2019-11-01. Vol. 83, p. 129-135. DOI : 10.1016/j.jprocont.2018.07.001.

Detailed record

View at publisher

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

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

PLOS Computational Biology. 2019-08-20. Vol. 15, num. 8, p. e1007242. DOI : 10.1371/journal.pcbi.1007242.

Detailed record

Full text – View at publisher

110th Anniversary: A Feature-Based Analysis of Static Real-Time Optimization Schemes

B. Srinivasan; D. Bonvin

Industrial & Engineering Chemistry Research. 2019-08-07. Vol. 58, num. 31, p. 14227-14238. DOI : 10.1021/acs.iecr.9b02327.

Detailed record

View at publisher

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

D. R. Weilandt; V. Hatzimanikatis

Biophysical Journal. 2019-07-23. Vol. 117, num. 2, p. 355-368. DOI : 10.1016/j.bpj.2019.06.017.

Detailed record

Full text – View at publisher

110th Anniversary: From Solubility Parameters to Predictive Equation-of-State Modeling

C. Panayiotou; I. Zuburtikudis; V. Hatzimanikatis

Industrial & Engineering Chemistry Research. 2019-07-17. Vol. 58, num. 28, p. 12787-12800. DOI : 10.1021/acs.iecr.9b02908.

Detailed record

View at publisher

Education in Process Systems Engineering: Why it matters more than ever and how it can be structured

I. T. Cameron; S. Engell; C. Georgakis; N. Asprion; D. Bonvin et al.

Computers & Chemical Engineering. 2019-07-12. Vol. 126, p. 102-112. DOI : 10.1016/j.compchemeng.2019.03.036.

Detailed record

View at publisher

Dynamic Optimization of Reaction Systems via Exact Parsimonious Input Parameterization

D. Rodrigues; D. Bonvin

Industrial & Engineering Chemistry Research. 2019-07-03. Vol. 58, num. 26, p. 11199-11212. DOI : 10.1021/acs.iecr.8b05512.

Detailed record

View at publisher

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

B. Borer; M. Ataman; V. Hatzimanikatis; D. Or

Plos Computational Biology. 2019-06-01. Vol. 15, num. 6, p. e1007127. DOI : 10.1371/journal.pcbi.1007127.

Detailed record

Full text – View at publisher

Discovery and validation of temporal patterns involved in human brain ketometabolism in cerebral microdialysis fluids of traumatic brain injury patients

M. Eiden; N. Christinat; A. Chakrabarti; S. Sonnay; J-P. Miroz et al.

Ebiomedicine. 2019-06-01. Vol. 44, p. 607-617. DOI : 10.1016/j.ebiom.2019.05.054.

Detailed record

Full text – View at publisher

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

V. Pandey; N. Hadadi; V. Hatzimanikatis

PLOS Computational Biology. 2019-05-13. Vol. 15, num. 5, p. e1007036. DOI : 10.1371/journal.pcbi.1007036.

Detailed record

Full text – View at publisher

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

L. Miskovic; M. Tokic; G. Savoglidis; V. Hatzimanikatis

Industrial & Engineering Chemistry Research. 2019-05-10. Vol. 58, num. 30, p. 13544–13554. DOI : 10.1021/acs.iecr.9b00818.

Detailed record

Full text – View at publisher

Distributed modifier-adaptation schemes for the real-time optimisation of uncertain interconnected systems

R. Schneider; P. Milosavljevic; D. Bonvin

International Journal Of Control. 2019-05-04. Vol. 92, num. 5, p. 1123-1136. DOI : 10.1080/00207179.2017.1383632.

Detailed record

View at publisher

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

V. Pandey; V. Hatzimanikatis

PLOS Computational Biology. 2019-04-19. Vol. 15, num. 4, p. e1006760. DOI : 10.1371/journal.pcbi.1006760.

Detailed record

Full text – View at publisher

Robust control of systems with sector nonlinearities via convex optimization: A data-driven approach

A. Nicoletti; A. Karimi

International Journal Of Robust And Nonlinear Control. 2019-03-25. Vol. 29, num. 5, p. 1361-1376. DOI : 10.1002/rnc.4439.

Detailed record

View at publisher

Incremental Parameter Estimation under Rank-Deficient Measurement Conditions

K. Villez; J. Billeter; D. Bonvin

Processes. 2019-02-01. Vol. 7, num. 2, p. 75. DOI : 10.3390/pr7020075.

Detailed record

Full text – View at publisher

A data-driven approach to model-reference control with applications to particle accelerator power converters

A. Nicoletti; M. Martino; A. Karimi

Control Engineering Practice. 2019-02-01. Vol. 83, p. 11-20. DOI : 10.1016/j.conengprac.2018.10.007.

Detailed record

View at publisher

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

C. List; Z. Hosseini; K. Lederballe Meibom; V. Hatzimanikatis; R. Bernier‐Latmani

Environmental Microbiology. 2019. Vol. 21, num. 10, p. 3548-3563. DOI : 10.1111/1462-2920.14640.

Detailed record

Full text – View at publisher

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

N. Hadadi; H. MohammadiPeyhani; L. Miskovic; M. Seijo; V. Hatzimanikatis

Proceedings of the National Academy of Sciences. 2019. p. 201818877. DOI : 10.1073/pnas.1818877116.

Detailed record

Full text – View at publisher

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

T. E. Hameri; G. Fengos; M. Ataman; L. Miskovic; V. Hatzimanikatis

Metabolic Engineering. 2019. Vol. 52, p. 29-41. DOI : 10.1016/j.ymben.2018.10.005.

Detailed record

Full text – View at publisher

2018

Nanoparticle Conjugation of Human Papillomavirus 16 E7-long Peptides Enhances Therapeutic Vaccine Efficacy against Solid Tumors in Mice

G. Galliverti; M. Tichet; S. Domingos-Pereira; S. Hauert; D. Nardelli-Haefliger et al.

Cancer Immunology Research. 2018-11-01. Vol. 6, num. 11, p. 1301-1313. DOI : 10.1158/2326-6066.CIR-18-0166.

Detailed record

View at publisher

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

M. Tokic; N. Hadadi; M. Ataman; D. Neves; B. E. Ebert et al.

ACS Synthetic Biology. 2018-07-18. Vol. 7, num. 8, p. 1858-1873. DOI : 10.1021/acssynbio.8b00049.

Detailed record

Full text – View at publisher

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

P. Salvy; G. Fengos; M. Ataman; T. Pathier; K. C. Soh et al.

Bioinformatics. 2018-07-02. p. 1-3. DOI : 10.1093/bioinformatics/bty499.

Detailed record

View at publisher

2017

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

L. C. Bryan; D. R. Weilandt; A. L. Bachmann; S. Kilic; C. C. Lechner et al.

Nucleic Acids Research. 2017. Vol. 45, num. 18, p. 10504–10517. DOI : 10.1093/nar/gkx697.

Detailed record

Full text – View at publisher

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

M. Ataman; D. F. H. Gardiol; G. Fengos; V. Hatzimanikatis

Plos Computational Biology. 2017. Vol. 13, num. 7, p. e1005444. DOI : 10.1371/journal.pcbi.1005444.

Detailed record

Full text – View at publisher

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

M. Ataman; V. Hatzimanikatis

Plos Computational Biology. 2017. Vol. 13, num. 7, p. e1005513. DOI : 10.1371/journal.pcbi.1005513.

Detailed record

Full text – View at publisher

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

M. A. Islam; N. Hadadi; M. Ataman; V. Hatzimanikatis; G. Stephanopoulos

Metabolic Engineering. 2017. Vol. 41, p. 173-181. DOI : 10.1016/j.ymben.2017.04.005.

Detailed record

View at publisher

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

Y. Berset; D. Merulla; A. Joublin; V. Hatzimanikatis; J. R. Van Der Meer

Acs Synthetic Biology. 2017. Vol. 6, num. 5, p. 862-874. DOI : 10.1021/acs.synbio.6b00364.

Detailed record

View at publisher

On Lewis acidity/basicity and hydrogen bonding in the equation-of-state approach

C. Panayiotou; S. Mastrogeorgopoulos; V. Hatzimanikatis

Journal Of Chemical Thermodynamics. 2017. Vol. 110, p. 3-15. DOI : 10.1016/j.jct.2017.02.003.

Detailed record

View at publisher

Redefining solubility parameters: Bulk and surface properties from unified molecular descriptors

C. Panayiotou; S. Mastrogeorgopoulos; D. Aslanidou; M. Avgidou; V. Hatzimanikatis

Journal Of Chemical Thermodynamics. 2017. Vol. 111, p. 207-220. DOI : 10.1016/j.jct.2017.03.035.

Detailed record

View at publisher

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

L. Miskovic; S. Alff-Tuomala; K. C. Soh; D. Barth; L. Salusjärvi et al.

Biotechology for Biofuels. 2017. Vol. 10, p. 166. DOI : 10.1186/s13068-017-0838-5.

Detailed record

Full text – View at publisher

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

A. Kiparissides; V. Hatzimanikatis

Metabolic Engineering. 2017. Vol. 39, p. 117-127. DOI : 10.1016/j.ymben.2016.11.006.

Detailed record

View at publisher

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

A. Chiappino Pepe; S. Tymoshenko; M. Ataman; D. Soldati-Favre; V. Hatzimanikatis

PLoS Computational Biology. 2017. Vol. 13, num. 3, p. e1005397. DOI : 10.1371/journal.pcbi.1005397.

Detailed record

Full text – View at publisher

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

N. Hadadi; J. Hafner; K. C. Soh; V. Hatzimanikatis

Biotechnology Journal. 2017. Vol. 12, num. 1, p. 1600464. DOI : 10.1002/biot.201600464.

Detailed record

View at publisher

2016

Principles of Systems Biology, No. 11

G. Wayne; A. Graves; D. Hassabis; S. Saha; C. A. Weber et al.

Cell Systems. 2016. Vol. 3, num. 5, p. 406-410. DOI : 10.1016/j.cels.2016.11.010.

Detailed record

View at publisher

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

C. Panayiotou; S. Mastrogeorgopoulos; M. Ataman; N. Hadadi; V. Hatzimanikatis

Physical Chemistry Chemical Physics. 2016. Vol. 18, num. 47, p. 32570-32592. DOI : 10.1039/c6cp06281d.

Detailed record

View at publisher

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

N. Hadadi; J. Hafner; A. Shajkofci; A. Zisaki; V. Hatzimanikatis

Acs Synthetic Biology. 2016. Vol. 5, num. 10, p. 1155-1166. DOI : 10.1021/acssynbio.6b00054.

Detailed record

View at publisher

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

J. Pinto Vieira; J. Racle; V. Hatzimanikatis

Biophysical Journal. 2016. Vol. 110, num. 9, p. 2120-2131. DOI : 10.1016/j.bpj.2016.04.004.

Detailed record

View at publisher

Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering

M. Morales; M. Ataman; S. Badr; S. Linster; I. Kourlimpinis et al.

Energy & Environmental Science. 2016. Vol. 9, num. 9, p. 2794-2805. DOI : 10.1039/c6ee00634e.

Detailed record

View at publisher

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

A. Isakova; Y. Berset; V. Hatzimanikatis; B. Deplancke

Journal Of Biological Chemistry. 2016. Vol. 291, num. 19, p. 10293-10306. DOI : 10.1074/jbc.M115.691154.

Detailed record

Full text – View at publisher

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

G. Savoglidis; A. X. D. S. Dos Santos; I. Riezman; P. Angelino; H. Riezman et al.

Metabolic Engineering. 2016. Vol. 37, p. 46-62. DOI : 10.1016/j.ymben.2016.04.002.

Detailed record

View at publisher

The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

L. A. Bultet; J. Aguilar Rodriguez; C. H. Ahrens; E. L. Ahrne; N. Ai et al.

Nucleic Acids Research. 2016. Vol. 44, num. D1, p. D27-D37. DOI : 10.1093/nar/gkv1310.

Detailed record

Full text – View at publisher

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

T. Dallavilla; L. Abrami; P. A. Sandoz; G. Savoglidis; V. Hatzimanikatis et al.

PLOS Computational Biology. 2016. Vol. 12, num. 2, p. e1004774. DOI : 10.1371/journal.pcbi.1004774.

Detailed record

Full text – View at publisher

Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models

S. Andreozzi; A. Charkrabarti; K. C. Soh; A. Burgard; T-H. Yang et al.

Metabolic Engineering. 2016. Vol. 35, p. 148-159. DOI : 10.1016/j.ymben.2016.01.009.

Detailed record

Full text – View at publisher

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

S. Andreozzi; L. Miskovic; V. Hatzimanikatis

Metabolic Engineering. 2016. Vol. 33, p. 158-168. DOI : 10.1016/j.ymben.2015.10.002.

Detailed record

Full text – View at publisher

2015

Do genome-scale models need exact solvers or clearer standards?

A. Ebrahim; E. Almaas; E. Bauer; A. Bordbar; A. P. Burgard et al.

Molecular Systems Biology. 2015. Vol. 11, num. 10, p. 831. DOI : 10.15252/msb.20156157.

Detailed record

View at publisher

Heading in the right direction: thermodynamics-based network analysis and pathway engineering

M. Ataman; V. Hatzimanikatis

Current Opinion in Biotechnology. 2015. Vol. 36, p. 176-182. DOI : 10.1016/j.copbio.2015.08.021.

Detailed record

View at publisher

Integrative approaches for signalling and metabolic networks

V. Hatzimanikatis; J. Saez-Rodriguez

Integrative Biology. 2015. Vol. 7, num. 8, p. 844-845. DOI : 10.1039/c5ib90030a.

Detailed record

View at publisher

Solvation quantities from a COSMO-RS equation of state

C. Panayiotou; I. Tsivintzelis; D. Aslanidou; V. Hatzimanikatis

Journal Of Chemical Thermodynamics. 2015. Vol. 90, p. 294-309. DOI : 10.1016/j.jct.2015.07.011.

Detailed record

View at publisher

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

L. Miskovic; M. Tokic; G. Fengos; V. Hatzimanikatis

Current Opinion in Biotechnology. 2015. Vol. 36, p. 146-153. DOI : 10.1016/j.copbio.2015.08.019.

Detailed record

Full text – View at publisher

Noise analysis of genome-scale protein synthesis using a discrete computational model of translation

J. Racle; A. J. Stefaniuk; V. Hatzimanikatis

The Journal of Chemical Physics. 2015. Vol. 143, num. 4, p. 044109. DOI : 10.1063/1.4926536.

Detailed record

Full text – View at publisher

Molecular thermodynamics of metabolism: quantum thermochemical calculations for key metabolites

N. Hadadi; M. Ataman; V. Hatzimanikatis; C. Panayiotou

Physical Chemistry Chemical Physics. 2015. Vol. 17, num. 16, p. 10438-10453. DOI : 10.1039/c4cp05825a.

Detailed record

View at publisher

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

S. Tymoshenko; R. D. Oppenheim; R. Agren; J. Nielsen; D. Soldati-Favre et al.

PLOS Computational Biology. 2015. Vol. 11, num. 5, p. e1004261. DOI : 10.1371/journal.pcbi.1004261.

Detailed record

Full text – View at publisher

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

A. Zisaki; L. Miskovic; V. Hatzimanikatis

Current Pharmaceutical Design. 2015. Vol. 21, num. 6, p. 806-822.

Detailed record

2014

Kinetic models in industrial biotechnology – Improving cell factory performance

J. Almquist; M. Cvijovic; V. Hatzimanikatis; J. Nielsen; M. Jirstrand

Metabolic Engineering. 2014. Vol. 24, p. 38-60. DOI : 10.1016/j.ymben.2014.03.007.

Detailed record

View at publisher

A computational framework for integration of lipidomics data into metabolic pathways

N. Hadadi; K. Cher Soh; M. Seijo; A. Zisaki; X. Guan et al.

Metabolic engineering. 2014. Vol. 23, p. 1-8. DOI : 10.1016/j.ymben.2013.12.007.

Detailed record

View at publisher

2013

Metabolic modeling in biotechnology and medical research

D. Mattanovich; V. Hatzimanikatis

Biotechnology Journal. 2013. Vol. 8, num. 9, p. 962-963. DOI : 10.1002/biot.201300378.

Detailed record

View at publisher

A Novel Pulse-Chase SILAC Strategy Measures Changes in Protein Decay and Synthesis Rates Induced by Perturbation of Proteostasis with an Hsp90 Inhibitor

I. Fierro-Monti; J. Racle; C. Hernandez; P. Waridel; V. Hatzimanikatis et al.

Plos One. 2013. Vol. 8, num. 11, p. e80423. DOI : 10.1371/journal.pone.0080423.

Detailed record

Full text – View at publisher

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

J. Racle; F. Picard; L. Girbal; M. Cocaign-Bousquet; V. Hatzimanikatis

Plos Computational Biology. 2013. Vol. 9, num. 10, p. e1003240. DOI : 10.1371/journal.pcbi.1003240.

Detailed record

Full text – View at publisher

Dynamic Impacts of the Inhibition of the Molecular Chaperone Hsp90 on the T-Cell Proteome Have Implications for Anti-Cancer Therapy

I. Fierro-Monti; P. Echeverria; J. Racle; C. Hernandez; D. Picard et al.

Plos One. 2013. Vol. 8, num. 11, p. e80425. DOI : 10.1371/journal.pone.0080425.

Detailed record

Full text – View at publisher