Dr. F. (Filipe) Branco dos Santos
Faculty of Science
Swammerdam Institute for Life Sciences
Visiting address
- Science Park 904
- Room number: C3.264
Postal address
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Postbus 94232
1090 GE Amsterdam
Contact details
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Publications
2024
Du, W., Meister, L. L., van Grinsven, T., & Branco dos Santos, F. (2024). Efficient Multiplex Genome Editing of the Cyanobacterium Synechocystis sp. PCC6803 via CRISPR-Cas12a. Biotechnology and Bioengineering, 122(3), 736-743. https://doi.org/10.1002/bit.28910 [details]
2023
- Guillaume, M. C., & Branco Dos Santos, F. (2023). Assessing and reducing phenotypic instability in cyanobacteria. Current Opinion in Biotechnology, 80, Article 102899. https://doi.org/10.1016/j.copbio.2023.102899 [details]
- Imbimbo, P., D'Elia, L., Corrado, I., Alvarez-Rivera, G., Marzocchella, A., Ibáñez, E., Pezzella, C., Branco dos Santos, F., & Monti, D. M. (2023). An Alternative Exploitation of Synechocystis sp. PCC6803: A Cascade Approach for the Recovery of High Added-Value Products. Molecules, 28(7), Article 3144. https://doi.org/10.3390/molecules28073144 [details]
- Mager, M., Pineda Hernandez, H., Brandenburg, F., López-Maury, L., McCormick, A. J., Nürnberg, D. J., Orthwein, T., Russo, D. A., Victoria, A. J., Wang, X., Zedler, J. A. Z., Branco Dos Santos, F., & Schmelling, N. M. (2023). Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synthetic Biology, 12(6), 1823-1835. https://doi.org/10.1021/acssynbio.3c00150 [details]
2021
- Battaglino, B., Du, W., Pagliano, C., Jongbloets, J. A., Re, A., Saracco, G., & Branco dos Santos, F. (2021). Channeling Anabolic Side Products toward the Production of Nonessential Metabolites: Stable Malate Production in Synechocystis sp. PCC6803. ACS Synthetic Biology, 10(12), 3518-3526. https://doi.org/10.1021/acssynbio.1c00440 [details]
- Shabestary, K., Hernández, H. P., Miao, R., Ljungqvist, E., Hallman, O., Sporre, E., Branco Dos Santos, F., & Hudson, E. P. (2021). Cycling between growth and production phases increases cyanobacteria bioproduction of lactate. Metabolic Engineering, 68, 131-141. https://doi.org/10.1016/j.ymben.2021.09.010 [details]
2020
- Caicedo-Burbano, P., Smit, T., Pineda Hernández, H., Du, W., & Branco dos Santos, F. (2020). Construction of Fully Segregated Genomic Libraries in Polyploid Organisms Such as Synechocystis sp. PCC 6803. ACS Synthetic Biology, 9(10), 2632-2638. Advance online publication. https://doi.org/10.1021/acssynbio.0c00353 [details]
- Ekkers, D. M., Branco Dos Santos, F., Mallon, C. A., Bruggeman, F., & van Doorn, G. S. (2020). The omnistat: A flexible continuous-culture system for prolonged experimental evolution. Methods in Ecology and Evolution, 11(8), 932-942. https://doi.org/10.1111/2041-210X.13403 [details]
- Wu, W., Du, W., Gallego, R. P., Hellingwerf, K. J., van der Woude, A. D., & Branco Dos Santos, F. (2020). Using osmotic stress to stabilize mannitol production in Synechocystis sp. PCC6803. Biotechnology for Biofuels, 13, Article 117. https://doi.org/10.1186/s13068-020-01755-3 [details]
2019
- Chen, Q., Arents, J., Schuurmans, J. M., Ganapathy, S., de Grip, W. J., Cheregi, O., Funk, C., Branco Dos Santos, F., & Hellingwerf, K. J. (2019). Functional Expression of Gloeobacter Rhodopsin in PSI-Less Synechocystis sp. PCC6803. Frontiers in Bioengineering and Biotechnology, 7, Article 67. https://doi.org/10.3389/fbioe.2019.00067 [details]
- Chen, Q., Arents, J., Schuurmans, J. M., Ganapathy, S., de Grip, W. J., Cheregi, O., Funk, C., Dos Santos, F. B., & Hellingwerf, K. J. (2019). Combining retinal-based and chlorophyll-based (oxygenic) photosynthesis: Proteorhodopsin expression increases growth rate and fitness of a ∆PSI strain of Synechocystis sp. PCC6803. Metabolic Engineering, 52, 68-76. https://doi.org/10.1016/j.ymben.2018.11.002 [details]
- Du, W., Jongbloets, J. A., Guillaume, M., van de Putte, B., Battaglino, B., Hellingwerf, K. J., & Branco Dos Santos, F. (2019). Exploiting Day- and Night-Time Metabolism of Synechocystis sp. PCC 6803 for Fitness-Coupled Fumarate Production around the Clock. ACS Synthetic Biology, 8(10), 2263-2269. https://doi.org/10.1021/acssynbio.9b00289 [details]
- Kristjansdottir, T., Bosma, E. F., Branco dos Santos, F., Özdemir, E., Herrgård, M. J., França, L., Ferreira, B., Nielsen, A. T., & Gudmundsson, S. (2019). A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Microbial Cell Factories, 18, Article 186. https://doi.org/10.1186/s12934-019-1229-3 [details]
- Price, C. E., Branco dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S-J., Montalban-Lopez, M., de Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B., & Kuipers, O. P. (2019). Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. BMC Evolutionary Biology, 19, Article 15. https://doi.org/10.1186/s12862-018-1331-x [details]
- Pérez, A. A., Chen, Q., Pineda Hernández, H., Branco Dos Santos, F., & Hellingwerf, K. J. (2019). On the use of oxygenic photosynthesis for the sustainable production of commodity chemicals. Physiologia Plantarum, 166(1), 413-427. https://doi.org/10.1111/ppl.12946 [details]
2018
- Acuña, A. M., van Alphen, P., Branco Dos Santos, F., van Grondelle, R., Hellingwerf, K. J., & van Stokkum, I. H. M. (2018). Spectrally decomposed dark-to-light transitions in Synechocystis sp. PCC 6803. Photosynthesis Research, 137(2), 307-320. https://doi.org/10.1007/s11120-018-0505-0 [details]
- Acuña, A. M., van Alphen, P., Branco Dos Santos, F., van Grondelle, R., Hellingwerf, K. J., & van Stokkum, I. H. M. (2018). Spectrally decomposed dark-to-light transitions in a PSI-deficient mutant of Synechocystis sp. PCC 6803. Biochimica et Biophysica Acta - Bioenergetics, 1859(2), 57-68. https://doi.org/10.1016/j.bbabio.2017.11.002 [details]
- Cordara, A., Manfredi, M., van Alphen, P., Marengo, E., Pirone, R., Saracco, G., Branco Dos Santos, F., Hellingwerf, K. J., & Pagliano, C. (2018). Response of the thylakoid proteome of Synechocystis sp. PCC 6803 to photohinibitory intensities of orange-red light. Plant physiology and biochemistry : PPB, 132, 524-534. https://doi.org/10.1016/j.plaphy.2018.10.002 [details]
- Cordara, A., Re, A., Pagliano, C., Van Alphen, P., Pirone, R., Saracco, G., Branco dos Santos, F., Hellingwerf, K., & Vasile, N. (2018). Analysis of the light intensity dependence of the growth of Synechocystis and of the light distribution in a photobioreactor energized by 635 nm light. PeerJ, 6, e5256. https://doi.org/10.7717/peerj.5256 [details]
- Du, W., Caicedo Burbano, P., Hellingwerf, K. J., & Branco Dos Santos, F. (2018). Challenges in the Application of Synthetic Biology Toward Synthesis of Commodity Products by Cyanobacteria via "Direct Conversion". In W. Zhang, & X. Song (Eds.), Synthetic Biology of Cyanobacteria (pp. 3-26). (Advances in Experimental Medicine and Biology; Vol. 1080). Springer. https://doi.org/10.1007/978-981-13-0854-3_1 [details]
- Du, W., Jongbloets, J. A., van Boxtel, C., Pineda Hernández, H., Lips, D., Oliver, B. G., Hellingwerf, K. J., & Branco Dos Santos, F. (2018). Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth. Biotechnology for Biofuels, 11, Article 38. https://doi.org/10.1186/s13068-018-1037-8 [details]
- Feenstra, K. A., Abeln, S., Westerhuis, J. A., Brancos dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J., & Heringa, J. (2018). Training for translation between disciplines: a philosophy for life and data sciences curricula. Bioinformatics, 34(13), i4–i12. https://doi.org/10.1093/bioinformatics/bty233 [details]
- Giera, M., Branco dos Santos, F., & Siuzdak, G. (2018). Metabolite-Induced Protein Expression Guided by Metabolomics and Systems Biology. Cell Metabolism, 27(2), 270-272. https://doi.org/10.1016/j.cmet.2018.01.002 [details]
- Lips, D., Schuurmans, J. M., Branco dos Santos, F., & Hellingwerf, K. J. (2018). Many ways towards 'solar fuel': quantitative analysis of the most promising strategies and the main challenges during scale-up. Energy and Environmental Science, 11(1), 10-22. https://doi.org/10.1039/c7ee02212c [details]
- van Alphen, P., Abedini Najafabadi, H., Branco Dos Santos, F., & Hellingwerf, K. J. (2018). Increasing the Photoautotrophic Growth Rate of Synechocystis sp. PCC 6803 by Identifying the Limitations of Its Cultivation. Biotechnology Journal, 13(8), Article 1700764. https://doi.org/10.1002/biot.201700764 [details]
2017
- Bachmann, H., Molenaar, D., Branco dos Santos, F., & Teusink, B. (2017). Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiology Reviews, 41(Supplement 1), S201-S219. https://doi.org/10.1093/femsre/fux024 [details]
- Branco dos Santos, F., Olivier, B. G., Boele, J., Smessaert, V., De Rop, P., Krumpochova, P., Klau, G. W., Giera, M., Dehottay, P., Teusink, B., & Goffin, P. (2017). Probing the genome-scale metabolic landscape of Bordetella pertussis, the causative agent of whooping cough. Applied and Environmental Microbiology, 83(21), Article e01528-17. Advance online publication. https://doi.org/10.1128/AEM.01528-17 [details]
- Carpine, R., Du, W., Olivieri, G., Pollio, A., Hellingwerf, K. J., Marzocchella, A., & Branco dos Santos, F. (2017). Genetic engineering of Synechocystis sp. PCC6803 for poly-β-hydroxybutyrate overproduction. Algal Research, 25, 117-127. https://doi.org/10.1016/j.algal.2017.05.013 [details]
- Du, W., Angermayr, S. A., Jongbloets, J. A., Molenaar, D., Bachmann, H., Hellingwerf, K. J., & Branco Dos Santos, F. (2017). Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis sp. PCC6803. ACS Synthetic Biology, 6(3), 395-401. https://doi.org/10.1021/acssynbio.6b00235 [details]
- Knaus, U. G., Hertzberger, R., Pircalabioru, G. G., Yousefi, S. P. M., & Branco dos Santos, F. (2017). Pathogen control at the intestinal mucosa - H2O2 to the rescue. Gut Microbes, 8(1), 67-74. https://doi.org/10.1080/19490976.2017.1279378 [details]
- McLeod, A., Mosleth, E. F., Rud, I., Branco Dos Santos, F., Snipen, L., Liland, K. H., & Axelsson, L. (2017). Effects of glucose availability in Lactobacillus sakei; metabolic change and regulation of the proteome and transcriptome. PLoS ONE, 12(11), Article e0187542. https://doi.org/10.1371/journal.pone.0187542 [details]
2016
- Bachmann, H., Bruggeman, F. J., Molenaar, D., Branco dos Santos, F., & Teusink, B. (2016). Public goods and metabolic strategies. Current opinion in microbiology, 31, 109-115. https://doi.org/10.1016/j.mib.2016.03.007 [details]
- Savakis, P., Tan, X., Qiao, C., Song, K., Hellingwerf, K. J., & Branco dos Santos, F. (2016). Slr1670 from Synechocystis sp. PCC 6803 Is Required for the Re-assimilation of the Osmolyte Glucosylglycerol. Frontiers in Microbiology, 7, Article 1350. https://doi.org/10.3389/fmicb.2016.01350 [details]
2015
- Goel, A., Eckhardt, T. H., Puri, P., de Jong, A., Branco dos Santos, F., Giera, M., Fusetti, F., de Vos, W. M., Kok, J., Poolman, B., Molenaar, D., Kuipers, O. P., & Teusink, B. (2015). Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect? Molecular Microbiology, 97(1), 77-92. https://doi.org/10.1111/mmi.13012 [details]
2013
- Bachmann, H., Fischlechner, M., Rabbers, I., Barfa, N., Branco dos Santos, F., Molenaar, D., & Teusink, B. (2013). Availability of public goods shapes the evolution of competing metabolic strategies. Proceedings of the National Academy of Sciences of the United States of America, 110(35), 14302-14307. Advance online publication. https://doi.org/10.1073/pnas.1308523110 [details]
- Branco dos Santos, F., de Vos, W. M., & Teusink, B. (2013). Towards metagenome-scale models for industrial applications - the case of Lactic Acid Bacteria. Current Opinion in Biotechnology, 24(2), 200-206. Advance online publication. https://doi.org/10.1016/j.copbio.2012.11.003 [details]
2011
- Santos, F., Spinler, J. K., Saulnier, D. M. A., Molenaar, D., Teusink, B., de Vos, W. M., Versalovic, J., & Hugenholtz, J. (2011). Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis. Microbial Cell Factories, 10, Article 55. https://doi.org/10.1186/1475-2859-10-55, https://doi.org/10.1186/1475-2859-10-55 [details]
- Saulnier, D. M., Santos, F., Roos, S., Mistretta, T. A., Spinler, J. K., Molenaar, D., Teusink, B., & Versalovic, J. (2011). Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PLoS ONE, 6(4). https://doi.org/10.1371/journal.pone.0018783 [details]
2015
- Savakis, P., Tan, X., Du, W., Branco dos Santos, F., Lu, X., & Hellingwerf, K. J. (2015). Photosynthetic production of glycerol by a recombinant cyanobacterium. Journal of Biotechnology, 195, 46-51. Advance online publication. https://doi.org/10.1016/j.jbiotec.2014.12.015 [details]
2014
- Branco dos Santos, F., Du, W., & Hellingwerf, K. J. (2014). Synechocystis: not just a plug-bug for CO2, but a green E. coli. Frontiers in Bioengineering and Biotechnology, 2, Article 36. https://doi.org/10.3389/fbioe.2014.00036 [details]
2024
2021
- Caicedo Burbano, S. P. (2021). Improving the synthetic biology toolbox of Synechocystis sp. PCC 6803. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
- Wu, W. (2021). Photoautotrophic overproduction of mannitol in Synechocystis sp. PCC6803 using osmotic pressure as a driving force. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
2019
2018
2017
- Chen, Q. (2017). Engineering retinal-based phototrophy via a complementary photosystem in Synechocystis sp. PCC6803. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
- van Alphen, P. (2017). Physiological studies to optimize growth of the prototype biosolar cell factory Synechocystis sp. PCC6803. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
2019
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., Branco Dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM8 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086689.v1
- Price, C. E., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Berkhout, J., Bruggeman, F. J., Montalban-Lopez, M., Kok, J., Molenaar, D., Poolman, B., Teusink, B., Kuipers, O. P., Branco Dos Santos, F., Goel, A., Marrink, S.-J. & De Jong, A. (2019). Additional file 1: of Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength. Figshare. https://doi.org/10.6084/m9.figshare.7576595.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., Branco Dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM5 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086662.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., Branco Dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM1 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086632.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., Branco Dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM4 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086653.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM3 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086644.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM2 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086638.v1
- Kristjansdottir, T., Ferreira, B., Nielsen, A. T., Gudmundsson, S., Bosma, E. F., dos Santos, F., Özdemir, E., Herrgård, M. J. & França, L. (2019). MOESM6 of A metabolic reconstruction of Lactobacillus reuteri JCM 1112 and analysis of its potential as a cell factory. Figshare. https://doi.org/10.6084/m9.figshare.10086671.v1
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Ancillary activities
- No ancillary activities
Du, W., Meister, L. L., van Grinsven, T., & Branco dos Santos, F. (2024). Efficient Multiplex Genome Editing of the Cyanobacterium Synechocystis sp. PCC6803 via CRISPR-Cas12a. Biotechnology and Bioengineering, 122(3), 736-743.