1. EERIKÄINEN, T. 1986. Brewer's spent grain in high dietary fiber cereal products. M.Sc. thesis. Helsinki Univ. of Technology. (In Finnish).
2. EERIKÄINEN, T., LINKO, S. ja LINKO P. 1988. The potential of fuzzy logic in optimization and control. In: Automatic Control and Optimization of Food Processes. M. Renard and J.‑J. Bimbenet eds. Elsevier Applied Science Publishers, London, ss. 183-200.
3. EERIKÄINEN, T. 1987. Keittoekstruusion mallitus ja säätö. Säätötekniikan prosessisovellutukset, seminaariesitelmät 1987. Report 75, Eds. U. Kortela and M. Välisuo. Control Engineering Laboratory, Helsinki Univ. of Technology. (In Finnish).
4. EERIKÄINEN, T. and LINKO, P. 1987. Optimization and process control aspects of extrusion cooking bioreactors. Abstracts, 7th World Congress of Food Science and Technology, Singapore, 28. September - 2. October 1987, ss. 28-29.
5. EERIKÄINEN, T. and LINKO, P. 1988. Optimization and process control aspects of extrusion cooking bioreactors. Proceedings of the 7th World Congress of Food Science and Technology, vol.1, Advances in Post Harvest Technology, Food Processing and Packaging, 28.9.‑3.10., 1987 Singapore.
6. EERIKÄINEN, T. and LINKO, P. 1987. New approaches in extrusion cooking control. Poster, Symposium on Food Science and Technology in Finnish Chemical Congress 5.11. 1987, Helsinki; Abstract in Kemia‑Kemi 14(10b): 1051.
7. EERIKÄINEN, T. 1988. A novel approach to the simulation and control of an extrusion cooker bioreactor. Pages 25‑27 in Japan‑Finland Symposium on Automation Technologies and AI Applications for Bioprocesses. 10.‑11.3. 1988 RIKEN (The Institute of Physical and Chemical Research). RIKEN Symposium Preprints 87‑23.
8. EERIKÄINEN, T. and LINKO, P. 1988. Expert system in extrusion cooking control. Poster abstract: 8th International Cereal and Bread Congress 30.5.‑3.6. 1988, Lausanne, Switzerland.
9. EERIKÄINEN, T. and LINKO, P. 1989. New approaches in extrusion cooking control. In Proceedings of COST 91 bis Seminar HTST-Treatment - Severity of Processing and Influencing Parameters (K. O. Paulus, ed.), Helsinki, Finland, 5. November 1987, Bund für Lebensmittelrecht und Lebensmittelkunde, Bonn, FRG, 1989. ss. 48-53.
10. EERIKÄINEN, T. and LINKO, P. 1989. Extrusion Cooking modeling, control and optimization. In Extrusion Cooking. C. Mercier, P. Linko and M. Harper, eds, American Association of Cereal Chemistry, ss. 157‑204.
11. EERIKÄINEN, T. 1989. Fuzzy modeling and control in HTST‑ extrusion cooking. Licentiate’s thesis. Helsinki University of Technology, 9th of May 1989.
12. EERIKÄINEN, T. ja LINKO, P. 1989. Effect of wear in extrusion processing. In COST 91 bis Seminar Progress in Extrusion Cooking (K.O. Paulus and J.C. Cheftel, eds), 18‑19 May 1989, Montpellier, France. Bund für Lebensmittelrecht und Lebensmittelkunde, Bonn, Germany, ss. 53-63.
13. EERIKÄINEN, T., AARTS, R.J., SEPPÄ, L. ja LINKO, P. 1990. Object oriented fuzzy expert system as a tool for extrusion cooker control. In Processing and Quality of Foods, Vol. 1, High Temperature/Short Time (HTST) Processing: Guarantee for High Quality Food with Long Shelflife (P. Zeuthen, J.C. Cheftel, C. Eriksson, T.R. Gormley, P. Linko, K. Paulus, eds). London, 1990, Elsevier Applied Science, ss. 1.263 - 1.268.
14. EERIKÄINEN, T. 1990. Ekstruusiomenetelmä raekoon kasvatuksessa (Extrusion method in granulation). INSKO:n julkaisu 82‑90 XVI Jauheiden ja rakeiden prosessointi, (In Finnish).
15. AARTS R. J., SEPPÄ L., EERIKÄINEN T. AND LINKO P., 1990. A real-time expert system in extrusion cooker control. Teoksessa Engineering and Food, Vol. 1, Physical Properties and Process Control, eds. W. E. L. Spiess and H. Schubert, Elsevier Applied Science, London, ss. 909-918.
16. LINKO, P., AARTS, R.J. ja EERIKÄINEN, T. 1990. Extrusion Cooking modeling, control and optimization. Seoul International Food Extrusion Workshop '90, Korean Exhibition Center (KOEX), Seoul 23‑25 April 1990.
17. LINKO P., UEMURA K. and EERIKÄINEN T., 1992. Neural networks in fuzzy extrusion control. Proc. IChemE Conf. Food Engineering in a Computer Climate, Cambridge, UK, 30 March - 1 April, 1992, ss. 401-410.
18. LINKO P., UEMURA K., ZHU Y.-H. and EERIKÄINEN T., 1992. Application of neural network models in fuzzy extrusion control. Trans. IChemE Vol. 70, Part C, 131-137.
19. EERIKÄINEN, T., 1993. Artificial intelligence in extrusion cooking process modelling and control. Doctor of Technology Thesis. Helsinki University of Technology: Technical Biochemistry Report 2/1993.
20. EERIKÄINEN, T., LINKO, P., LINKO, S., SIIMES, T. and ZHU, Y.-H., 1993. Fuzzy and neural computing in food science and technology, Trends in Food Science and Technol., 4 (8), 237-242.
21. EERIKÄINEN, T., ZHU, Y.-H. and LINKO P., 1993. An expert system with fuzzy variables and neural network estimation. In Proceedings Volume 1 of EUFIT '93 - First European Congress on Fuzzy and Intelligent Technologies, Aachen, Germany, Sept. 7-10, 1993, ss. 202-208.
22. LINKO, P., EERIKÄINEN, T., LINKO, S. and ZHU, Y.-H., 1993. Artificial intelligence for the food industry. Proc. AIFA Conference 93 Artificial Intelligence for Agriculture and Food, October 26-28, Nimes, France. EC2, Paris, France, ss. 187-200.
23. ZHU, Y. H., EERIKÄINEN, T., SIIMES, T. and LINKO, P., 1993. Fuzzy neural networks in bioprocess control. In Abstract Books, 6th European Congress on Biotechnology, Florence, Italy, 11.-17. June 1993, Vol. 2 (1993) TU144.
24. EERIKÄINEN, T., LINKO, S., LINKO, P., SIIMES, T. ja ZHU, Y.-H., 1993. Tekoälyn mahdollisuudet elintarviketeknologiassa [The potential of artificial intelligence in food technology]. Kehittyvä Elintarvike 4(5) (1993) 8-12.
25. ZHU, Y.-H., LINKO, S., EERIKÄINEN, T. and LINKO, P., 1994. Neural networks in bioprocess engineering. In Proceedings of ICEF 6 (6th International Congress on Engineering and Food), 23.-27. May 1993, Chiba, Makuhari, Japan (T. Yano,R.Matsuno and K. Nakamura, eds). Blackie Academic & Professional, London, 1994, Part I, ss. 36-41.
26. EERIKÄINEN, T. and LINKO, P., 1994. AI-based techniques in food process control. In Fuzziness in Finland ‘94 (M. Hurme, V.A. Niskanen, P. Eklund and J.K. Mattila, eds) An International Symposium, 11.-13. 1. 1994, M/S Silja Symphony, Finland. Plant Design Report Series, Helsinki University of Technology, Laboratory of Chemical Engineering, Report No. 21 (1994), 3-15.
27. EERIKÄINEN, T., ZHU, Y.-H. and LINKO P., 1994. Neural Networks in Extrusion Process Identification and Control, Food Control, 5(2), 111-119.
28. LINKO, S., ZHU, Y.-H., EERIKÄINEN, T., SIIMES, T. and LINKO, P., 1994. Artificial intelligence in bioprocess modelling, estimation and control. Proceedings of Automatic Control of Food and Biological Processes (III), Paris, France, 25-26 October 1994. J.J. Bimbenet, E. Dumoulin and G. Trystram, eds. Developments in Food Science 36, 143-158.
29. EERIKÄINEN T., LINKO P., SEIBEL W. and SEILER K., 1994. Application de la modelisation boite noire, des systemes experts et du reseaux neuronaux a l'optimisation de la cuisson-extrusion (Application of black box modelling, expert systems and neural networks to extrusion process optimization). In Cuisson Extrusion (Extrusion Cooking), P. Colonna ja G. Della Valle, eds, INRA, Nantes Cedex, France ss. 355-389.
30. LINKO, P., SIIMES, T., KOSOLA, A., ZHU, Y.-H. and EERIKÄINEN, T., 1994. Hybrid fuzzy knowledge-based and neural systems for fed-batch baker's yeast bioprocess control. Proceedings of the Asian Control Conference, Volume 1 of 3, 27.-30. July, 1994, Tokyo, Japan, ss. 491-494.
31. LINKO P., KOSOLA, A., SIIMES, T., ZHU, Y.-H. and EERIKÄINEN, T., 1994. Hybrid fuzzy neural bioprocess control. In Proceedings of EUFIT '94 - Second European Congress on Intelligent Techniques and Soft Computing, Aachen, Germany, Sept. 20-23, 1994, ss. 84-90.
32. EERIKÄINEN, T. and LINKO P., 1995. Neural network based food extrusion cooker control. In Proceedings, EANN'95, Engineering Applications of Artificial Neural Networks (A. B. Bulsari and S. Kallio, eds), 21.-23. August, 1995, Finnish Artificial Intelligence Society, Espoo, Finland, ss. 473-476.
33. POUTANEN, K., MYLLYMÄKI, O., MYLLÄRINEN, P., SUORTTI, T., EERIKÄINEN, T., LINKO, P. and FORSSELL, P., 1995. Extrusion of starch-glycerol mixtures: Chemical and physical properties of the products. In Proceedings of 10 th International Conference on Problems of Cereal Processing, September 4.-6., 1995, Berlin, Germany.
34. LINKO, S., ZHU, Y.-H., EERIKÄINEN, T., KOSOLA, A., AND LINKO, P., 1995. Neurocontrol of bioprocessesses, RIKEN Symposium, 9th Finnish-Japanese Symposium on Bioprocess and Chemical Engineering, and Mechatronics, 8. June 1995, RIKEN, Wako, Japan, ss. 9-12.
35. EERIKÄINEN, T., KOSOLA, A., ZHU, Y.-H., LINKO, S. and LINKO, P., 1996. Food and bioprocess control with neural networks. In COST 93 Project 'Continuous Heat Treatmernt of Food' Report on Modelling and Control in Food Processes.
36. LINKO, P., EERIKÄINEN, T., MYLLYMÄKI, O., SUORTTI, T., LINKO, S., LINKO, Y.-Y., FORSELL, P. and POUTANEN, K., 1996. Developments in extrusion cooking technology for bioprocess applications in the 1990s. In Proceedings of 10th World Cereal and Bread Congress, 9.-12.6. 1996, Porto Carros.
37. MYLLYMÄKI, O., EERIKÄINEN, T., SUORTTI, T., FORSSELL, P., LINKO, P. and POUTANEN, K., 1997. Depolymerization of barley starch during extrusion in water-glycerol mixtures. Lebensmittel-Wissenschaft & Technologie 30 (4), 351-358.
38. EERIKÄINEN, T. and LINKO P., 1997. Novel developments in real-time monitoring and control of food processes. In Proceedings of ICEF 7, Seventh International Congress on Engineering and Food 13.-17.4. 1997, Brighton, England, Part 2, ss. M17-M20.
39. EERIKÄINEN, T., 1997. Fuzzy Logic and Neural Networks in Food and Bioprocesses. Plenary presentation in The First European Congress on Chemical Engineering, - ECCE-1, May 4-7, 1997, Florence, Italy, ss. 2687-2690.
40. EERIKÄINEN, T. and LEISOLA, M., 1998. Book-review: Snape, J.B., Dunn, I.J., Ingham, J. and Prenosil, J.E. Dynamics of Environmental Bioprocesses. Kemia-Kemi 25(8):724.
41. LEISOLA, M., EERIKÄINEN, T. and ARISTIDOU, A. 1999. Bioprosessitekniikka, tie koeputkesta tuotteeksi, Kemia-Kemi 26(8):629-632.
42. EERIKÄINEN, T. 1999. Bioteknisten prosessien mallintaminen, AEL-INSKO seminar Prosessien mallintaminen ja simulointi 11.-12.11. 1999, Y327403 XI/1-19 (In Finnish).
43. PASTINEN, O., JOKELA, J., EERIKÄINEN, T., SCHWABE, T. and LEISOLA, M., 2000. Cross-linked glucose isomerase crystals as a liquid chromatographic separation material,. Enzyme Microb. Tech. 26, 550-558.
44. EERIKÄINEN, T., HOME, V. and PASTINEN O., 2002. Biotechnical production of L-fucose and fucose containing polymer, Proceedings in: The Potra technology programme, Polymers for building the future, Annual seminar at Hanasaari 15.4.2002.
45. AITTOMÄKI, E., EERIKÄINEN, T., LEISOLA, M., OJAMO, H., SUOMINEN, I. ja vonWEYMARN, N., 2002. Bioprosessitekniikka, Porvoo 2002, Werner Söderström Osakeyhtiö, 445 s.
46. TKK-posteri Biotec 2002-näyttelyyn Wanha Satamassa 18.-19.9.2002.
47. EERIKÄINEN, T. and MESKANEN, E., 2003. Modelling and optimization of industrially interesting bacterial cultivations and their down stream unit processes, BCO WORKSHOP 26-27 May 2003, Comprehensive Analytical Techniques for Bioprocess and Environmental Analysis, Oulu, 2003. short presentation.
48. EERIKÄINEN, T., MESKANEN, E. and HOME, V., 2003. Modelling of Bacterial Bioreactor Cultivation. In Proceedings (and oral presentation) of 1st International Congress on Bioreactor Technology in Cell, Tissue Culture and Biomedical Applications, Tampere, Finland 14 - 18 July 2003, ss. 137-147.
49. MESKANEN, E. and EERIKÄINEN, T., 2003. Optimization of synthetic growth medium, P568, in Abstracts book (and poster) of 11th European Congress on Biotechnology 24 – 29 August 2003, Basel, Switzerland, s. 185.
50. EERIKÄINEN, T., 2004. Fukoosin ja fukoosia sisältävän polymeerin biotekninen tuotto, Tekes, Polymeerit tulevaisuuden rakentajina, Potra 2000-2003 loppuraportti, Teknologiaohjelmaraportti 1/2004, ss. 35-39.
51. KIVIHARJU, K.. and EERIKÄINEN, T., 2004. Freeze-drying of Bifidobacterium longum ATCC 15705. European Symposium on Biochemical Engineering Science 5, Stuttgart (Germany), 8.-11.9.2004. Stuttgart 2004, Institute of Biochemical Engineering, University of Stuttgart, s. 152.
52. KIVIHARJU, K., LEISOLA, M. and EERIKÄINEN, T., 2004. Optimization of Streptomyces peucetius var. caesius N47 cultivation and -rhodomycinone production using experimental designs and response surface methods, J. Ind. Microbiol. Biot. 31, 475-481.
53. EERIKÄINEN, T., 2004. Biotechnological production of L-fucose. In Proceedings (and oral presentation) of Japan-Finland Joint Seminar on New Aspects in Microbial Biotechnology, Kyoto, Japan, October 1-4, 2004, s. 42.
54. CESCUTTI, P., KALLIOINEN, A., IMPALLOMENI, G., TOFFANIN, R., POLLESELLO, P., LEISOLA, M. and EERIKÄINEN, T., 2005. Structure of the exopolysaccharide produced by Enterobacter amnigenus, Carbohyd. Res. 340, 439-447.
55. KIVIHARJU, K., LEISOLA, M. and EERIKÄINEN, T., 2005. Optimization of a Bifidobacterium longum ATCC 15707 production process, J. Biotechnol., 117, 299-308.
56. EERIKÄINEN, T., SALONEN, K., MESKANEN, E., MOILANEN, U., JOKILA J., JOKINEN, T., GOMEZ, F., DAHLBACKA, J. and KIVIHARJU, K., 2006. Measurement, modeling and optimization of bacterial bioprocesses, In Proceedings (and oral presentation) of FinMed 2006, 2nd International Conference on Bioreactor Technology in Cell, Tissue Culture and Biomedical Applications With an Additional Theme: Molecular Farming, FinMed 2006 Partnering Event, Saariselkä, Lapland, Finland 2006, March 27-31.
57. KIVIHARJU, K., SALONEN, K., LEISOLA, M. and EERIKÄINEN, T., 2006. Kinetic modeling of Streptomyces peucetius var. caesius N47 growth. In Proceedings of FinMed 2006, 2nd International Conference on Bioreactor Technology in Cell, Tissue Culture and Biomedical Applications With an Additional Theme: Molecular Farming, Saariselkä, Lapland, Finland 2006, March 27-31.
58. SALONEN K. and EERIKÄINEN, T., 2006. Data integration in a complex laboratory environment. In Proceedings of FinMed 2006, 2nd International Conference on Bioreactor Technology in Cell, Tissue Culture and Biomedical Applications With an Additional Theme: Molecular Farming, Saariselkä, Lapland, Finland 2006, March 27-31.
59. KIVIHARJU, K., SALONEN, K., LEISOLA, M., and EERIKÄINEN, T., 2006. Modeling and simulation of Streptomyces peucetius var. caesius N47 cultivation and ε-rhodomycinone production with kinetic equations and neural networks, J. Biotechnol. 126(3), 365-373.
60. KÄNSÄKOSKI, MARKKU, KURKINEN, MARIKA, VON WEYMARN, NIKLAS, NIEMELÄ, PENTTI, NEUBAUER, PETER, JUUSO, ESKO, EERIKÄINEN, TERO, TURUNEN, SEPPO, AHO, SIRKKA and SUHONEN, PIRKKO, 2006. Process analytical technology (PAT) needs and applications in the.bioprocess industry, VTT Working Papers 1459–7683 (URL: http://www.vtt.fi/publications/index.jsp).
61. KIVIHARJU, K., MOILANEN, U., LEISOLA, M., and EERIKÄINEN, T., 2007. A chemostat study of Streptomyces peucetius var. caesius N47, Applied Microbiology and Biotechnology 73:1267–1274.
62. KIVIHARJU, K., SALONEN, K., LEISOLA, M. and EERIKÄINEN, T., 2007. Kinetics of Bifidobacterium longum ATCC 15707 growth. Process Biochemistry. Vol. 42, nro 7, pp. 1140-1145.
63. SALONEN, K., KIVIHARJU, K. and EERIKÄINEN, T., Bioreactor Measurement and Simulation Environment, 10th International IFAC Symposium on Computer Applications in Biotechnology, Preprints Vol.1, June 4-6, 2007, Cancun, Mexico, ss. 279-284.
64. SALONEN, K., KIVIHARJU, K. and EERIKÄINEN, T. Integrated bioreactor measurement environment (Poster+abstract). The 14th Nordic Process Control Workshop, Espoo, Finland, 23.-25. Aug, 2007.
65. KIVIHARJU, K., SALONEN, K., MOILANEN, U., MESKANEN, E., LEISOLA, M. and EERIKÄINEN, T. 2007. On-line biomass measurements in bioreactor cultivations: comparison study of two on-line probes. Journal of Industrial Microbiology & Biotechnology, Vol. 34, nro 8, pp. 561-566.
66. KIVIHARJU, K., SALONEN, K., MOILANEN, U. and EERIKÄINEN, T., 2008. Biomass measurement on-line the performance of in situ measurements and software sensors, Journal of Industrial Microbiology & Biotechnology, 35(7), 657-665.
67. IGNATOVA, M., LYUBENOVA, V., EERIKÄINEN, T., SALONEN, K., KIVIHARJU, K., 2008. Software sensor of substrate kinetics and its application for control of a-amylase production by Bacillus subtilis, Compt. rend. Acad. bulg. Sci., 61(11), 1449-1458.
68. SALONEN, K., LEISOLA, M. and EERIKÄINEN, T., 2009. Multipoint Titration Method with a Variable Dose Implementation for Anaerobic Digestion Monitoring, Water Sci. Technol., 59(12), 2395-2403.
69. EERIKÄINEN, T., 2009. SKS:n Biotekniikan jaosto 30 vuotta. Kemia-Kemi , 2009.
70. EERIKÄINEN, T., WALLENIUS, J., HUUSKONEN, A., VUOKKO, H., VIDGREN, V., LONDESBOROUGH, J. and RAUTIO, J.J., 2010. Multivariate analysis of dynamic gene expression data from yeast fermentation. 14th International Biotechnology Symposium and Exhibition, IBS 2010, 14-18 September 2010, Rimini, Italy.
71. LYUBENOVA, V., IGNATOVA, M., SALONEN, K., KIVIHARJU, K. and EERIKÄINEN, T., 2011. Control of a-amylase production by Bacillus subtilis, Bioprocess. Biosyst. Eng. 34(3):367-74, (2011).
72. UUKSULAINEN, T., WALLENIUS, J., SALONEN, K., KIVIHARJU, K., PITKÄNEN, J.-P., and EERIKÄINEN, T. The effect of temperature and pH gradients on Lactobacillus rhamnosus GG: Viability and growth. Bioprocess and Biosystems Engineering (2011) (manuscript in preparation).
73. WALLENIUS, J., UUKSULAINEN, T., SALONEN, K., RAUTIO and EERIKÄINEN, T., The effect of temperature and pH gradients on Lactobacillus rhamnosus GG gene expression of stress related genes. Biotechnology Progress (2011) (submitted, manuscript number BTPR-10-0438).
74. WALLENIUS, J., BARTH, D. and EERIKÄINEN, T., The effects of pH oscillation on Lactobacillus rhamnosus GG batch cultivation. (manuscript in preparation)
75. BOZAUDI, M. , EERIKÄINEN, T., TURUNEN, O.and SHAMEHK, S., Effect of gamma irradiation and heat treatment on the artificial contamination of maize grains by Aspergillus flavus (manuscript in preparation).