Bakker Biotech is a specialist consultancy in vaccine and bioprocess development

Services

Experience

Publications

Publications

 

Main research themes

 

  • Viral vaccine process development, with a strong focus on Sabin-strain based inactivated polio vaccine (process design, scale‑down, cost reduction, biosafety, and technology transfer).

  • Bioprocess engineering and modeling, including air‑lift and rocking bioreactors, hydrodynamics, oxygen and mass transfer, and kinetic models for adherent Vero cells and virus production.
  • Analytical and process control tools for IPV (D‑antigen ELISA, isoelectric focusing, multivariate data analysis, data‑driven bioprocess optimization).
  • Broader viral and vector platforms, including rotavirus vaccines, adenoviral vectors for gene therapy and vaccines, and CHO‑based expression of complex viral glycoproteins and difficult‑to‑express proteins.
  • Translation to clinical evaluation, with multiple phase I trials on the safety, immunogenicity, and antigen‑sparing potential of Sabin‑based IPV, including studies with and without aluminum adjuvant and mucosal adjuvants.

 

 

 

Career trajectory and evolution

 

 

  • Early career (1990–1999): Focused on bioreactor design, air‑lift loop cascades, oxygen transfer, immobilized cells and enzyme systems, and early work on cell growth and shear sensitivity, establishing a strong bioprocess engineering foundation.

 

  • Transition phase (2000–2010): Gained experience from R&D to large-scale GMP manufacturing team-management. Shift from food/bioprocess applications to human vaccines, including fast ELISAs, multivariate analysis of historical IPV production data, and early work on process understanding and control.

 

  • sIPV and global health phase (2010–2016): Intensive work on Sabin‑IPV development, process scale‑down and scale‑up, cell line selection for viral vaccine production, antigen standardization, and clinical evaluation of Sabin‑based IPV in adults and infants, closely aligned with polio‑eradication and biosafety goals.

 

  • Platform and innovation phase (2017–2022): Expansion into animal‑component‑free production, data‑driven upstream process optimization, and novel vector and vaccine platforms (rotavirus, adenoviral vectors, manufacturing cost‑effectiveness), as well as stable high‑yield expression systems for complex antigens.

 

  • Recent diversification (2022–2025): Contributions to cardiovascular gene therapy vectors, HIV Env glycoprotein expression, CHO vector platforms, and upstream fixed‑bed bioreactor technologies for Sabin-IPV, plus a 2025 scoping review on Schistosoma mansoni vaccines demonstrating broader engagement with parasitic vaccine development.

 

 

Peer-reviewed scientific publications

 

  1. Houlder EL, Ferreira da Silva L, van Diepen A, Amaral MS, Wilson RA, Hokke CH, Roestenberg M, Bakker WA: Pre-clinical studies of Schistosoma mansoni vaccines: a scoping review. PLoS neglected tropical diseases, 19(6), e0012956
  2. Hamidi A, Willemsen M, Robert T, Drugmand JC, Ballmann MZ, Velthof P, Verdurmen H, Pinto AC, Pronk J, Palladino L, Havenga M, Yallop C, Bakker WAM: Sabin inactivated polio vaccine upstream process development using fixed-bed bioreactor technology. Vaccine 2025, 53:126950. DOI: 10.1016/j.vaccine.2025.126950.
  3. Opmeer L, Gazzoli I, Ballmann M, Willemsen M, Voshol GP, Grudniewska-Lawton M, Havenga M, Yallop C, Hamidi A, Gillissen G, Bakker WAM: High throughput AS LNA qPCR method for the detection of a specific mutation in poliovirus vaccine strains. Vaccine 2024, 42(9):2475-2484. DOI: 10.1016/j.vaccine.2024.01.103.
  4. Brown SD, Klimi E, Bakker WAM, Beqqali A, Baker AH: Non-coding RNAs to treat vascular smooth muscle cell dysfunction. Br J Pharmacol 2024. DOI: 10.1111/bph.16409.
  5. Suarez-Zuluaga DA, van der Pol LA, van 't Oever AG, Bakker WAM, Thomassen YE: Development of an animal component free production process for Sabin inactivated polio vaccine. Vaccine X 2022, 12:100223. DOI: 10.1016/j.jvacx.2022.100223.
  6. Schwartze JT, Havenga M, Bakker WAM, Bradshaw AC, Nicklin SA: Adenoviral vectors for cardiovascular gene therapy applications: a clinical and industry perspective. J Mol Med (Berl) 2022, 100(6):875-901. DOI: 10.1007/s00109-022-02208-0.
  7. Luthra A, Spanjaard RA, Cheema S, Veith N, Kober L, Wang Y, Jing T, Zhao Y, Hoeksema F, Yallop C, Havenga M, Bakker WAM: STEP(R) vectors for rapid generation of stable transfected CHO cell pools and clones with high expression levels and product quality homogeneity of difficult-to-express proteins. Protein Expr Purif 2021, 186:105920. DOI: 10.1016/j.pep.2021.105920.
  8. Luthra A, Cheema S, Whitney S, Bakker WAM, Sandalon Z, Richardson J, Yallop C, Havenga M: Stable, high yield expression of gp145 Env glycoprotein from HIV-1 in mammalian cells. Biologicals 2021, 73:16-23. DOI: 10.1016/j.biologicals.2021.07.004.
  9. Hamidi A, Hoeksema F, Velthof P, Lemckert A, Gillissen G, Luitjens A, Bines JE, Pullagurla SR, Kumar P, Volkin DB, Joshi SB, Havenga M, Bakker WAM, Yallop C: Developing a manufacturing process to deliver a cost effective and stable liquid human rotavirus vaccine. Vaccine 2021, 39(15):2048-2059. DOI: 10.1016/j.vaccine.2021.03.033.
  10. Ballmann MZ, Raus S, Engelhart R, Kajan GL, Beqqali A, Hadoke PWF, van der Zalm C, Papp T, John L, Khan S, Boedhoe S, Danskog K, Frangsmyr L, Custers J, Bakker WAM, van der Schaar HM, Arnberg N, Lemckert AAC, Havenga M, Baker AH: Human AdV-20-42-42, a Promising Novel Adenoviral Vector for Gene Therapy and Vaccine Product Development. J Virol 2021, 95(22):e0038721. DOI: 10.1128/JVI.00387-21.
  11. Suarez-Zuluaga DA, Borchert D, Driessen NN, Bakker WAM, Thomassen YE: Accelerating bioprocess development by analysis of all available data: A USP case study. Vaccine 2019, 37(47):7081-7089. DOI: 10.1016/j.vaccine.2019.07.026.
  12. Jiang Y, van der Welle JE, Rubingh O, van Eikenhorst G, Bakker WAM, Thomassen YE: Kinetic model for adherent Vero cell growth and poliovirus production in batch bioreactors. Process Biochem 2019, 81:156-164. DOI: 10.1016/j.procbio.2019.03.010.
  13. Okayasu H, Sein C, Hamidi A, Bakker WA, Sutter RW: Development of inactivated poliovirus vaccine from Sabin strains: A progress report. Biologicals 2016, 44(6):581-587. DOI: 10.1016/j.biologicals.2016.08.005.
  14. Ursache RV, Thomassen YE, van Eikenhorst G, Verheijen PJ, Bakker WA: Mathematical model of adherent Vero cell growth and poliovirus production in animal component free medium. Bioprocess Biosyst Eng 2015, 38(3):543-555. DOI: 10.1007/s00449-014-1294-2.
  15. Thomassen YE, Bakker WA: sIPV process development for costs reduction. Vaccine 2015, 33(35):4307-4312. DOI: 10.1016/j.vaccine.2015.03.076.
  16. Oosterhoff D, van de Weerd G, van Eikenhorst G, de Gruijl TD, van der Pol LA, Bakker WA: Hematopoietic cancer cell lines can support replication of Sabin poliovirus type 1. Biomed Res Int 2015, 2015:358462. DOI: 10.1155/2015/358462.
  17. Verdijk P, Rots NY, van Oijen MG, Weldon WC, Oberste MS, Okayasu H, Sutter RW, Bakker WA: Safety and immunogenicity of a primary series of Sabin-IPV with and without aluminum hydroxide in infants. Vaccine 2014, 32(39):4938-4944. DOI: 10.1016/j.vaccine.2014.07.029.
  18. van Eikenhorst G, Thomassen YE, van der Pol LA, Bakker WA: Assessment of mass transfer and mixing in rigid lab-scale disposable bioreactors at low power input levels. Biotechnol Prog 2014, 30(6):1269-1276. DOI: 10.1002/btpr.1981.
  19. van der Pol LA, Bakker WAM: How to choose the correct cell line for producing your viral vaccine: what is important? Pharmaceutical Bioprocessing 2014, 2(3):207-210. DOI: 10.4155/pbp.14.19.
  20. Thomassen YE, Rubingh O, Wijffels RH, van der Pol LA, Bakker WA: Improved poliovirus D-antigen yields by application of different Vero cell cultivation methods. Vaccine 2014, 32(24):2782-2788. DOI: 10.1016/j.vaccine.2014.02.022.
  21. Steil BP, Jorquera P, Westdijk J, Bakker WA, Johnston RE, Barro M: A mucosal adjuvant for the inactivated poliovirus vaccine. Vaccine 2014, 32(5):558-563. DOI: 10.1016/j.vaccine.2013.11.101.
  22. Resik S, Tejeda A, Fonseca M, Alemani N, Diaz M, Martinez Y, Garcia G, Okayasu H, Burton A, Bakker WA, Verdijk P, Sutter RW: Reactogenicity and immunogenicity of inactivated poliovirus vaccine produced from Sabin strains: a phase I Trial in healthy adults in Cuba. Vaccine 2014, 32(42):5399-5404. DOI: 10.1016/j.vaccine.2014.07.109.
  23. Westdijk J, Koedam P, Barro M, Steil BP, Collin N, Vedvick TS, Bakker WA, van der Ley P, Kersten G: Antigen sparing with adjuvanted inactivated polio vaccine based on Sabin strains. Vaccine 2013, 31(9):1298-1304. DOI: 10.1016/j.vaccine.2012.12.076.
  24. Vlecken DH, Pelgrim RP, Ruminski S, Bakker WA, van der Pol LA: Comparison of initial feasibility of host cell lines for viral vaccine production. J Virol Methods 2013, 193(1):28-41. DOI: 10.1016/j.jviromet.2013.04.020.
  25. Verdijk P, Rots NY, van Oijen MG, Oberste MS, Boog CJ, Okayasu H, Sutter RW, Bakker WA: Safety and immunogenicity of inactivated poliovirus vaccine based on Sabin strains with and without aluminum hydroxide: a phase I trial in healthy adults. Vaccine 2013, 31(47):5531-5536. DOI: 10.1016/j.vaccine.2013.09.021.
  26. Thomassen YE, van Eikenhorst G, van der Pol LA, Bakker WA: Isoelectric point determination of live polioviruses by capillary isoelectric focusing with whole column imaging detection. Anal Chem 2013, 85(12):6089-6094. DOI: 10.1021/ac400968q.
  27. Thomassen YE, van 't Oever AG, Vinke M, Spiekstra A, Wijffels RH, van der Pol LA, Bakker WA: Scale-down of the inactivated polio vaccine production process. Biotechnol Bioeng 2013, 110(5):1354-1365. DOI: 10.1002/bit.24798.
  28. Thomassen YE, van 't Oever AG, van Oijen MG, Wijffels RH, van der Pol LA, Bakker WA: Next generation inactivated polio vaccine manufacturing to support post polio-eradication biosafety goals. PLoS One 2013, 8(12):e83374. DOI: 10.1371/journal.pone.0083374.
  29. Sanders BP, Edo-Matas D, Custers JH, Koldijk MH, Klaren V, Turk M, Luitjens A, Bakker WA, Uytdehaag F, Goudsmit J, Lewis JA, Schuitemaker H: PER.C6((R)) cells as a serum-free suspension cell platform for the production of high titer poliovirus: a potential low cost of goods option for world supply of inactivated poliovirus vaccine. Vaccine 2013, 31(5):850-856. DOI: 10.1016/j.vaccine.2012.10.070.
  30. Thomassen YE, van der Welle JE, van Eikenhorst G, van der Pol LA, Bakker WA: Transfer of an adherent Vero cell culture method between two different rocking motion type bioreactors with respect to cell growth and metabolic rates. Process Biochemistry 2012, 47(2):288-296.
  31. ten Have R, Thomassen YE, Hamzink MR, Bakker WA, Nijst OE, Kersten G, Zomer G: Development of a fast ELISA for quantifying polio D-antigen in in-process samples. Biologicals 2012, 40(1):84-87. DOI: 10.1016/j.biologicals.2011.11.004.
  32. Hamidi A, Bakker WA: Innovative IPV from attenuated Sabin poliovirus or newly designed alternative seed strains. Pharm Pat Anal 2012, 1(5):589-599. DOI: 10.4155/ppa.12.70.
  33. Westdijk J, Brugmans D, Martin J, van't Oever A, Bakker WA, Levels L, Kersten G: Characterization and standardization of Sabin based inactivated polio vaccine: proposal for a new antigen unit for inactivated polio vaccines. Vaccine 2011, 29(18):3390-3397. DOI: 10.1016/j.vaccine.2011.02.085.
  34. Verdijk P, Rots NY, Bakker WA: Clinical development of a novel inactivated poliomyelitis vaccine based on attenuated Sabin poliovirus strains. Expert Rev Vaccines 2011, 10(5):635-644. DOI: 10.1586/erv.11.51.
  35. Bakker WA, Thomassen YE, van't Oever AG, Westdijk J, van Oijen MG, Sundermann LC, van't Veld P, Sleeman E, van Nimwegen FW, Hamidi A, Kersten GF, van den Heuvel N, Hendriks JT, van der Pol LA: Inactivated polio vaccine development for technology transfer using attenuated Sabin poliovirus strains to shift from Salk-IPV to Sabin-IPV. Vaccine 2011, 29(41):7188-7196. DOI: 10.1016/j.vaccine.2011.05.079.
  36. Thomassen YE, van Sprang EN, van der Pol LA, Bakker WA: Multivariate data analysis on historical IPV production data for better process understanding and future improvements. Biotechnol Bioeng 2010, 107(1):96-104. DOI: 10.1002/bit.22788.
  37. Soethout EC, Bakker WA, van Dam RH, Rots NY, Boog CJ: Phacilitate, Barcelona Vaccine Forum 2010: focus on correlates of protection against influenza. Hum Vaccin 2010, 6(12):964-965. DOI: 10.4161/hv.6.12.13218.
  38. Houben JH, Bakker WA, Keizer G: Effect of trisodium phosphate on slip and textural properties of hog and sheep natural sausage casings. Meat Sci 2005, 69(2):209-214. DOI: 10.1016/j.meatsci.2004.06.023.
  39. Bakker WA, Houben JH, Koolmees PA, Bindrich U, Sprehe L: Effect of initial mild curing, with additives, of hog and sheep sausage casings on their microbial quality and mechanical properties after storage at difference temperatures. Meat Sci 1999, 51(2):163-174. DOI: 10.1016/s0309-1740(98)00118-1.
  40. Bakker WAM, Overdevest PEM, Beeftink HH, Tramper J, de Gooijer CD: Serial air-lift bioreactors for the approximation of aerated plug flow. Trends in Biotechnology 1997, 15(7):264-269. DOI: 10.1016/s0167-7799(97)01053-6.
  41. de Gooijer CD, Bakker WAM, Beeftink HH, Tramper J: Bioreactors in series: An overview of design procedures and practical applications. Enzyme and Microbial Technology 1996, 18(3):202-219. DOI: 10.1016/0141-0229(95)00090-9.
  42. Bakker WA, Schafer T, Beeftink HH, Tramper J, De Gooijer CD: Hybridomas in a bioreactor cascade: modeling and determination of growth and death kinetics. Cytotechnology 1996, 21(3):263-277. DOI: 10.1007/BF00365349.
  43. Bakker WA, Kers P, Beeftink HH, Tramper J, de Gooijer CD: Nitrite conversion by immobilized Nitrobacter agilis cells in an air-lift loop bioreactor cascade: effects of combined substrate and product inhibition. Journal of fermentation and bioengineering 1996, 81(5):390-393. DOI: 10.1016/0922-338X(96)85138-5.
  44. Bakker W, Den Hertog M, Tramper J, De Gooijer C: Oxygen transfer in a multiple air-lift loop reactor. Bioprocess Engineering 1995, 12(4):167-172. DOI: 10.1007/s004490050101.
  45. Bakker WA, Knitel JT, Tramper J, de Gooijer CD: Sucrose conversion by immobilized invertase in a multiple air-lift loop bioreactor. Biotechnol Prog 1994, 10(3):277-283. DOI: 10.1021/bp00027a007.
  46. Bakker WA, van Can HJ, Tramper J, de Gooijer CD: Hydrodynamics and mixing in a multiple air-lift loop reactor. Biotechnol Bioeng 1993, 42(8):994-1001. DOI: 10.1002/bit.260420810.
  47. van der Pol L, Bakker WA, Tramper J: Effect of low serum concentrations (0%-2.5%) on growth, production, and shear sensitivity of hybridoma cells. Biotechnol Bioeng 1992, 40(1):179-182. DOI: 10.1002/bit.260400125.

Wilfried Bakker

Contact

 
For requests and information please send an e-mail to: info@bakkerbiotech.nl
 
 
Wilfried Bakker, PhD
Founder, CEO and Principal Consultant
 
 
BAKKER BIOTECH B.V.
KvK: 99081474
BTW: NL868786202B01