1. Parmaki S, Vyrides I, Vasquez MI, Hartman V, Zacharia I, Hadjiadamou I, Barbeitos CBM, Ferreira FC, Afonso CAM, Drouza C, Michalis Koutinas. 2018. Bioconversion of alkaloids to high-value chemicals: Comparative analysis of newly isolated lupanine degrading strains. Chemosphere, 193:50-59. 
2. Koutinas M, Yiangou C, Osório NM, Ioannou K, Canet A, Valero F, Ferreira-Dias S. 2018. Application of commercial and non-commercial immobilized lipases for biocatalytic production of ethyl lactate in organic solvents. Bioresource Technology, 247:496-503. 

3. Patsalou M, Menikea KK, Makri E, Vasquez MI, Drouza C, Koutinas M. 2017. Development of a citrus peel-based biorefinery strategy for the production of succinic acid. Journal of Cleaner Production, 166:706-716. 
4. Papadaki A, Androutsopoulos N, Patsalou M, Koutinas M, Kopsahelis N, Papanikolaou S, Koutinas AA. 2017. Biotechnological production of fumaric acid: The effect of morphology of Rhizopus arrhizus NRRL 2582. Fermentation, 3:33. 
5. Tsipa A, Koutinas M, Vernardis SI, Mantalaris A. 2017. The impact of succinate trace on pWW0 and ortho-cleavage pathway transcription in Pseudomonas putida mt-2 during toluene biodegradation. Bioresource Technology, 234:397-405. 
6. Patsalou M, Koutinas M. 2017. Food waste valorization for the production of added-value commodities: Focus on citrus peel waste as a feedstock for sustainable biorefineries. In: Municipal solid waste: Management strategies, challenges and future directions. Commack: Nova Science Publishers, Inc., ISBN: 978-1-53611-865-0. 
7. Pateraki C, Patsalou M, Vlysidis A, Kopsahelis N, Webb C, Koutinas AA, Koutinas M. 2016. Actinobacillus succinogenes: Advances on succinic acid production and prospects for development of integrated biorefineries. Biochemical Engineering Journal, 112:285-303. 
8. Tsipa A, Koutinas M, Pistikopoulos EN, Mantalaris A. 2016. Transcriptional kinetics of the cross-talk between the ortho-cleavage and TOL pathways of toluene biodegradation in Pseudomonas putida mt-2. Journal of Biotechnology, 228:112-123. 
9. Koutinas M, Patsalou M, Stavrinou S, Vyrides I. 2016. High temperature alcoholic fermentation of orange peel by the newly isolated thermotolerant Pichia kudriavzevii KVMP10. Letters in Applied Microbiology 62:75-83. 

10. Vyrides I, Agathangelou M, Dimitriou R, Souroullas K, Salamex A, Ioannou A, Koutinas M. 2015. Novel Halomonas sp. B15 isolated from Larnaca Salt Lake in Cyprus that generates vanillin and vanillic acid from ferulic acid. World Journal of Microbiology and Biotechnology 31:1291-1296. 
11. Drakou E-M, Koutinas M, Pantelides I, Tsolakidou M, Vyrides I. 2015. Insights into the metabolic basis of the halotolerant Pseudomonas aeruginosa strain LVD-10 during toluene biodegradation. International Biodeterioration & Biodegradation 99:85-94. 

12. Turon X, Venus J, Arshadi M, Koutinas M, Lin CSK, Koutinas A. 2014. Food waste and byproduct valorization through bio-processing: Opportunities and challenges. Bioresources 9:5774-5777. 
13. Koutinas M, Menelaou M, Nicolaou EN. 2014. Development of a hybrid fermentation-enzymatic bioprocess for the production of ethyl lactate from dairy waste. Bioresource Technology 165:343-349. 
14. Koutinas M, Kiparissides A, Pistikopoulos EN, Mantalaris A. 2012. Bioprocess systems engineering: transferring traditional process engineering principles to industrial biotechnology. Computational and Structural Biotechnology Journal 3:e201210022. 

15. Koutinas M, Kiparissides A, Lam M-C, Silva-Rocha R, Godinho M, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2011. Imroving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid. Biochemical Engineering Journal 55:108-118. 
16. Koutinas M, Kiparissides A, Silva-Rocha R, Lam M-C, Martins dos Santos VAP, de Lorenzo V, Pistikopoulos EN, Mantalaris A. 2011. Linking genes to microbial growth kinetics – an integrated biochemical systems engineering approach. Metabolic Engineering 13:401-413. 
17. Kiparissides A, Koutinas M, Kontoravdi C, Mantalaris A, Pistikopoulos EN. 2011. „Closing the loop‟ in biological systems modelling - from the in silico to the in vitro. Automatica 47:1147-1155. 
18. Kiparissides A, Koutinas M, Moss T, Newman J, Pistikopoulos EN, Mantalaris A. 2011. Modelling the delta1/notch1 pathway; in search of the mediator(s) of neural stem cell differentiation. PLoS One 6:e14668. 
19. Koutinas M, Lam M-C, Kiparissides A, Silva-Rocha R, Godinho M, Livingston AG, Pistikopoulos EN, de Lorenzo V, Martins dos Santos VAP, Mantalaris A. 2010. The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environmental Microbiology 12:1705-1718. 
20. Koutinas M, Baptista IIR, Meniconi A, Peeva LG, Mantalaris A, Castro PML, Livingston AG. 2007. The use of an oil-absorber-bioscrubber system during biodegradation of sequentially alternating loadings of 1,2-dichloroethane and fluorobenzene in a waste gas. Chemical Engineering Science 62:5989-6001. 

21. Koutinas M, Baptista IIR, Peeva LG, Ferreira Jorge RM, Livingston AG. 2007. The use of an oil absorber as a strategy to overcome starvation periods in degrading 1,2-dichloroethane in waste gas. Biotechnology and Bioengineering 96:673-686. 
22. Koutinas M, Martin J, Peeva LG, Mantalaris A, Livingston AG. 2006. An oil-absorber-bioscrubber system to stabilise biotreatment of pollutants present in waste gas. Fluctuating loads of 1,2-dichloroethane. Environmental Science and Technology 40:595-602. 
23. Koutinas M, Peeva LG, Livingston AG. 2005. An attempt to compare the performance of bioscrubbers and biotrickling filters for degradation of ethyl acetate in gas streams. Journal of Chemical Technology and Biotechnology 80:1252-1260. 
24. Kiparissides Α, Koutinas Μ, Pistikopoulos ΕΝ, Mantalaris Α. 2011. Model development and analysis of mammalian cell culture systems. In: Dynamic process modelling. pp: 403-440. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA. ISBN: 978-3-527-31696-0. 

Conference papers with review 

25. Koutinas M, Kiparissides A, Lam M-C, Silva-Rocha R, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2010. Combining genetic circuit and microbial growth kinetic models: a challenge for biological modelling. Computer-Aided Chemical Engineering 28:301-306. 
26. Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2011. Predicting microbial growth kinetics with the use of genetic circuit models. Computer-Aided Chemical Engineering 29:1321-1325. 
27. Patsalou M, Pateraki C, Vasquez M, Drouza C, Koutinas M. 2016. Bioprocess development for the production of succinic acid from orange peel waste. 4th International Conference on Sustainable Solid Waste Management (CYPRUS 2016), Limassol, Cyprus, 23-25 June 2016. 
28. Papadaki A, Kopsahelis N, Patsalou M, Koutinas M, Papanikolaou S, Koutinas AA. 2017. Fumaric acid production through valorization of molasses and soybean cake derived from biodiesel and sugarcane industries. 5th International Conference on Sustainable Solid Waste Management (ATHENS 2017), Athens, Greece, 21-24 June 2017. 

Conference and workshop presentations 
As Assistant Professor at Cyprus University of Technology 

1. Koutinas M. 2017. Food waste valorization for the production of added-value commodities: Focus on citrus peel waste as a feedstock for sustainable biorefineries. Mediterranean Workshop 2017, Naples, Italy, 23-24 October 2017, (invited oral - Koutinas M). 
2. Tsipa A, Vernardis SI, Koutinas M, Pistikopoulos EN, Mantalaris A. 2015. How genetic circuit kinetics is connected to prediction of bioprocess performance? The special case of Pseudomonas putida mt-2. Focused Meeting 2017: 16th International Conference on Pseudomonas, Liverpool, UK, 5-9 September 2017, (poster - Tsipa A). 
3. Papadaki A, Kopsahelis N, Patsalou M, Koutinas M, Papanikolaou S, Koutinas AA. 2017. Fumaric acid production through valorization of molasses and soybean cake derived from biodiesel and sugarcane industries. 5th International Conference on Sustainable Solid Waste Management (ATHENS 2017), Athens, Greece, 21-24 June 2017, (oral - Papadaki A). 
4. Koutinas M. 2017. Screening for biocatalysts producing added-value commodities from alkaloids: The case of lupanine. Workshop – Closing the loop on valorization of food processing wastewater containing alkaloids: The lupanine case. Milan, Italy, 29 May 2017, (invited oral - Koutinas M). 
5. Parmaki S, Vyrides I, Andreou V, Hartman V, Drouza C, Koutinas M. 2017. Valorization of alkaloid containing wastewater through the isolation of microorganisms converting lupanine into added-value products. 7th International Forum on Industrial Bioprocesses (IFIBiop2017), Wuxi, China, 21-24 May 2017, (oral - Parmaki S). 
6. Yiangou C, Ferreira-Dias S, Ioannou K, Osorio NM, Canet A, Valero F, Koutinas M. 2017. Application of lipases from Candida antarctica B and Candida rugosa for the production of ethyl lactate from cheese whey. 7th International Forum on Industrial Bioprocesses (IFIBiop2017), Wuxi, China, 21-24 May 2017, (invited oral - Koutinas M). 
7. Koutinas M. 2016. Biochemical systems engineering: A systems approach for the production of chemicals, biofuels and biopolymers from waste and biomass. NIREAS Speaker Series – When Ideas Flow, NIREAS International Water Research Center, University of Cyprus, 12 October 2016, (invited oral - Koutinas M). 
8. Yiangou C, Ferreira-Dias S, Ioannou K, Osorio NM, Canet A, Valero F, Koutinas M. 2016. Green solvent biosynthesis by esterification of lactic acid and ethanol in different biocatalysts and organic media. Workshop - The future of food waste: Challenges and opportunities for valorisation in Europe. Wageningen, The Netherlands, 20-21 Sept 2016, (poster - Koutinas M). 

9. Patsalou M, Vasquez M, Drouza C, Koutinas M. 2016. Bioprocess development for the production of succinic acid from orange peel waste. 4th International Conference on Sustainable Solid Waste Management (CYPRUS 2016), Limassol, Cyprus, 23-25 June 2016, (oral - Patsalou M). 

As Lecturer at Cyprus University of Technology 

10. Koutinas M, Pashali P, Loizou E, Nicolaou E, Vasquez MI, Vyrides I. 2015. Contaminants on the Horizon: Bioprocess development for the treatment of ionic liquid-polluted industrial effluents. New Horizons in Biotechnology (NHBT 2015), Trivandrum, India, 22-25 November 2015, (invited oral - Koutinas M). 
11. Patsalou M, Drouza C, Koutinas M. 2015. Development of an orange peel-based biorefinery strategy for the production of succinic acid. Development of pilot scale or integrated bioprocesses based on refining of food supply chain wastes (WG2 Workshop of COST Action TD1203), Potsdam, Germany, 29-30 Sept 2015, (oral - Koutinas M). 
12. Tsipa A, Koutinas M, Mantalaris A, Pistikopoulos EN. 2015. Prediction of double substrate microbial growth kinetics through transcriptional regulation: an integrated experimental/modelling approach on Pseudomonas putida mt-2. 2015 AIChE Annual Meeting, Salt Lake City, Utah, USA, 8-13 November 2015, (oral - Tsipa A). 
13. Tsipa A, Vernardis SI, Koutinas M, Pistikopoulos EN, Mantalaris A. 2015. Effect of succinate traces on TOL plasmid and chromosomal metabolic pathways of Pseudomonas putida mt-2 growing on toluene. Recent Technologies in Microbiology (RTM’15), Birmingham, UK, 5 June 2015, (poster - Tsipa A). 
14. Tsipa A, Koutinas M, Mantalaris A, Pistikopoulos EN. 2014. Development of a new paradigm in biochemical engineering: predicting the genetic regulation of aromatic pollutants degradation. 2014 AIChE Annual Meeting, Atlanta, Georgia, USA, 16-21 November 2014, (oral - Tsipa A). 
15. Koutinas M. 2014. Industrial food waste valorisation processes. 2nd Training School of COST Action ES1202, Nicosia, Cyprus, 29-31 Oct 2014, (invited oral - Koutinas M). 
16. Patsalou M, Koutinas M. 2014. Development of an orange peel based biorefinery strategy for the production of succinic acid. 10th European Symposium on Biochemical Engineering Sciences and 6th International Forum on Industrial Bioprocesses (in collaboration with ACS), Lille, France, 7-10 September 2014, (oral - Koutinas M). 

17. Koutinas M, Menelaou M, Nicolaou EN. 2014. Bioprocess development for the production of ethyl lactate from dairy waste. 18th Green Chemistry & Engineering Conference (ACS-GC&E), North Bethesda, Washington D.C., Maryland, USA, 17-19 June 2014, (invited oral - Koutinas M). 
18. Koutinas M, Menelaou M, Nicolaou EN. 2014. Development of a two-stage bioprocess for the production of the green solvent ethyl lactate from dairy waste. 2nd Workshop of the COST Action TD1203, Toulouse, France, 21-22 January 2014, (oral - Koutinas M). 
19. Koutinas M, Menelaou M, Nicolaou EN. 2013. Valorization of cheese dairy wastes for the production of the “green” solvent ethyl lactate. International Conference on Advances in Biotechnology and Bioinformatics 2013 (ICABB-2013) and X Convention of Biotech Research Society, Pune, India, 25-27 November 2013, (invited oral - Koutinas M). 
20. Koutinas M, Menelaou M, Nicolaou EN. 2013. Development of a two-stage bioprocess for the production of the “green” solvent ethyl lactate from dairy wastes. International Conference on Health, Environment and Industrial Biotechnology (BioSangam-2013), Allahabad, India, 21-23 November 2013, (invited oral - Koutinas M). 
21. Koutinas M. 2013. A biochemical systems engineering approach for the production of added-value chemicals from renewable resources. 1st Working Group 2 meeting entitled Bioprocessing, COST Action TD1203, Athens, Greece, 12 April 2013, (oral - Koutinas M). 
22. Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2012. Let‟s go upstream! Gene regulation as a path from traditional to advanced growth kinetic models. 5th International Conference on Industrial Bioprocesses, Taipei, Taiwan, 7-10 October 2012, (invited oral - Koutinas M). 

As Research Associate and PhD student at Imperial College London 

23. Mantalaris A, Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN. 2011. Linking genes to microbial growth kinetics: An integrated biochemical systems engineering approach. 13th International Conference on Pseudomonas, Sydney, Australia, 4-7 September 2011, (invited oral – Mantalaris A). 
24. Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2011. Integrating gene regulatory and metabolic models to predict microbial growth kinetics. 7th GRACM International Congress on Computational Mechanics, Athens, Greece, 30 June - 2 July 2011, (oral - Koutinas M). 

25. Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2011. Predicting microbial growth kinetics with the use of genetic circuit models. 21st European Symposium on Computer Aided Process Engineering – ESCAPE-21, Chalkidiki, Greece, 29 May - 1 June 2011, (poster - Koutinas M). 
26. Koutinas M, Kiparissides A, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2010. Advancing microbial growth kinetic models with the use of genetic modeling. 2010 AIChE Annual Meeting, Salt Lake City, Utah, USA, 7-12 November 2010, (oral - Koutinas M). 
27. Koutinas M, Kiparissides A, Lam M-C, Silva-Rocha R, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2010. Establishment of a modelling framework for the development of optimised biocatalysts. Metabolic Engineering VIII: Metabolic Engineering for Green Growth, Jeju Island, South Korea, 13-17 June 2010, (poster - Koutinas M). 
28. Koutinas M, Kiparissides A, Lam M-C, Silva-Rocha R, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2010. Combining genetic circuit and microbial growth kinetic models: a challenge for biological modelling. 20th European Symposium on Computer Aided Process Engineering – ESCAPE-20, Ischia, Naples, Italy, 6-9 June 2010, (oral -Koutinas M). 
29. Koutinas M, Lam M-C, Kiparissides A, Silva-Rocha R, Godinho M, de Lorenzo V, Pistikopoulos EN, Martins dos Santos VAP, Mantalaris A. 2009. Model driven decisions for the understanding and optimisation of microorganisms genetic circuits: an application in biodegradation of aromatic compounds. 7th Panhellenic Scientific Chemical Engineering Conference, University of Patras, Patras, Greece, 3-5 June 2009, (oral - Koutinas M). 
30. Koutinas M, Lam M-C, Kiparissides A, Silva-Rocha R, Godinho M, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2009. A systems engineering approach to understanding genetic circuits: model driven decisions for the improvement of aromatic compounds decomposition by TOL. 2nd SysMO Evaluation Conference, Vienna, Austria, 19-20 May 2009, (poster - Koutinas M). 
31. Baptista IIR, Koutinas M, Mantalaris A, Livingston AG. 2008. Revealing microbial strain dynamics case study in an oil-absorber-bioscrubber system. Proceedings of the 2008 AIChE Annual Meeting, Philadelphia, PA, USA, 15-21 November 2008, pp.35a, (oral - Baptista IIR). 
32. Lam M-C, Koutinas M, Kiparissides A, Godinho M, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2008. Formal design tools for synthetic biology – engineering the building blocks of genetic circuit in Pseudomonas putida. Synthetic Biology 4.0, Hong 

Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong 10-12 October 2008, (oral - Lam M-C). 
33. Lam M-C, Koutinas M, Kiparissides A, Godinho M, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2008. Towards a model of the biodegradation network in Pseudomonas putida: in silico study of functional units responsible for the degradation of aromatics. Synthetic Biology 4.0, Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong 10-12 October 2008, (poster - Lam M-C). 
34. Koutinas M, Lam M-C, Kiparissides A, Silva-Rocha R, Godinho M, de Lorenzo V, Martins dos Santos VAP, Pistikopoulos EN, Mantalaris A. 2008. A systems engineering approach to understanding genetic circuits: model driven decisions for the improvement of aromatic compounds decomposition by TOL. 1st SysMO Evaluation Conference, Bad Honnef, Germany, 30 June-2 July 2008, (poster - Koutinas M). 
35. Koutinas M, Baptista IIR, Meniconi A, Peeva LG, Mantalaris A, Castro PML, Livingston AG. 2006. Microbial dynamics and bioreactor stability in an oil-absorber-bioscrubber system exposed to an alternating sequence of 1,2-dichloroethane and fluorobenzene. Proceedings of the 2006 AIChE Annual Meeting, San Francisco, California, USA, 12-17 November 2006, pp.299s, (poster - Baptista IIR). 
36. Koutinas M, Martin J, Peeva LG, Mantalaris A, Livingston AG. 2005. Sunflower oil-absorber-bioscrubber system for treatment of 1,2-dichloroethane waste-gas shock loads, Proceedings of the Third European Bioremediation Conference, Chania, Greece, 4-7 July 2005, pp.205, (oral - Koutinas M). 
37. Koutinas M, Peeva LG, Livingston AG. 2004. Bioscrubber and biotrickling filter: performance comparison under ethyl acetate vapour detoxification. 10th International Summer School of Chemical Engineering, Varna, Bulgaria, 24-31 May 2004, pp.240, (oral - Koutinas M).