About the Authors
- Alexander Mitsos
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Affiliation Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Ioannis N. Melas
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Affiliation Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
- Paraskeuas Siminelakis
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Affiliation Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
- Aikaterini D. Chairakaki
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Affiliation Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
- Julio Saez-Rodriguez
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Affiliations Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Leonidas G. Alexopoulos
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* E-mail: leo@mail.ntua.gr
Affiliation Department of Mechanical Engineering, National Technical University of Athens, Athens, Greece
Competing Interests
The authors have declared that no competing interests exist.
Author Contributions
Conceived and designed the experiments: LGA. Performed the experiments: INM ADC LGA. Analyzed the data: INM PS ADC LGA. Contributed reagents/materials/analysis tools: AM JSR LGA. Wrote the paper: AM LGA. Conceived and formulated the integer linear program for the more efficient presentation of the Boolean model: AM. Implemented the formulation and linked to commercial solvers: AM. Provided access to commercial solvers (license-based): AM. Secondary inventor of the methodology for drug effects via drug-induced pathway alterations: AM. Wrote parts of the manuscript (mostly the computational part): AM. Run the computational case studies under the supervision of Alexopoulos and Mitsos: INM PS. Prepared the figures of the manuscript under the supervision of Alexopoulos: INM PS. Provided data/tools of previous approach for optimization of Boolean networks with genetic algorithm (GA): JSR. Assisted in the reformulation of the Boolean model and in the comparison with the GA approach: JSR. Edited the manuscript: JSR. Initiated and led the project and collaborations: LGA. Conceived the idea of using more sophisticated computational methods for fitting of experimental data after his initial discussion with AM: LGA. Provided the facilities and materials for the experiments: LGA. Main inventor of the methodology for finding drug effects via drug-induced pathway alteration: LGA. Wrote most of the paper: LGA.