Groningen Biomolecular Sciences and Biotechnology Institute

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  • 2024

    Analysis of cGMP Signaling in Dictyostelium

    van Haastert, P. J. M., Keizer-Gunnink, I. & Kortholt, A., 3-Jul-2024, Dictyostelium discoideum: Methods and Protocols. Kimmel, A. R. (ed.). Humana Press, p. 177-194 18 p. (Methods in molecular biology (Clifton, N.J.); vol. 2814).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • GRminusRD: A Sensitive Assay to Detect Activation Processes at the Plasma Membrane in Living Cells

    van Haastert, P. J. M., Keizer-Gunnink, I. & Kortholt, A., 3-Jul-2024, Dictyostelium discoideum: Methods and protocols. Kimmel, A. R. (ed.). Humana Press, p. 133-147 15 p. (Methods in molecular biology (Clifton, N.J.); vol. 2814).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Morphological assessment of liposomes by microscopy

    Stuart, M. C. A., 2024, Liposomes in Drug Delivery: What, where, how and when to Deliver. Antimisiaris, S. G. (ed.). Elsevier, p. 71-87 17 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    1 Citation (Scopus)

  • Pseudopod Tracking and Statistics During Cell Movement in Buffer and Chemotaxis

    van Haastert, P. J. M., 2024, Cell Motility and Chemotaxis: Methods and Protocols. Beta, C. & Martinez-Torres, C. (eds.). Humana, New York, NY, Vol. 2828. p. 185-204 20 p. (Methods in molecular biology; vol. 2828).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • RNA structure probing, dynamics, and folding

    Incarnato, D., 5-Jul-2024, RNA as a Drug Target: The Next Frontier for Medicinal Chemistry. Schneekloth, J., Pettersson, M., Mannhold, R., Buschmann, H. & Holenz, J. (eds.). Wiley-VCH Verlag GmbH & Co. KGaA, p. 7-28 22 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Transfer Learning from Synthetic Data for Cell Segmentation and Tracking

    Milias Argeitis, A. & Kruitbosch, H., Apr-2024, Frontiers in Bioimage Informatics Methodology. Zhou, J., Peng, H. & Rapsomaniki, M. (eds.). World Scientific Publishing, (Series on Language Processing, Pattern Recognition, and Intelligent Systems; vol. 8).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • 2023

    Super-Resolution Imaging of Peroxisomal Proteins Using STED Nanoscopy

    de Lange, E. M. F. & Vlijm, R., 24-Mar-2023, Peroxisomes: Methods and protocols. Schrader, M. (ed.). 2nd ed. Humana Press, p. 65-84 20 p. (Methods in molecular biology (Clifton, N.J.); vol. 2643).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    1 Citation (Scopus)
    130 Downloads (Pure)
  • 2022

    Membrane transport of cobalamin

    Nijland, M., Martínez Felices, J. M., Slotboom, D. J. & Thangaratnarajah, C., 22-Mar-2022, Vitamins and Hormones. Litwack, G. (ed.). ACADEMIC PRESS INC ELSEVIER SCIENCE, p. 121-148 28 p. (Vitamins and Hormones; vol. 119).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    11 Citations (Scopus)

  • Methods to Analyze Motility in Eury- and Crenarchaea

    Patro, M., van Wolferen, M., Ye, X., Albers, S.-V. & Quax, T. E. F., 2022, Archaea: Methods and Protocols. Ferreira-Cerca, S. (ed.). Springer, p. 373-385 13 p. (Methods in molecular biology (Clifton, N.J.); vol. 2522).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Using Single-Molecule Optical Tweezers to Study the Conformational Cycle of the Hsp90 Molecular Chaperone

    Tych, K. & Rief, M., 6-Sept-2022, Optical Tweezers. Humana, New York, NY, Vol. 2478. p. 401-425 25 p. (Methods in molecular biology (Clifton, N.J.)).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    3 Citations (Scopus)
  • 2021

    Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell

    Mantovanelli, L., Gaastra, B. F. & Poolman, B., 2021, Current Topics in Membranes: New Methods and Sensors for Membrane and Cell Volume Research. Model, M. A. & Levitan, I. (eds.). ACADEMIC PRESS INC ELSEVIER SCIENCE, Vol. 88. p. 1-54 54 p. (Current Topics in Membranes).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    11 Citations (Scopus)
    307 Downloads (Pure)

  • Modes of Flavin-Based Catalysis

    Cibulka, R. & Fraaije, M. W., 1-Jan-2021, Flavin-Based Catalysis: Principles and Applications. Cibulka, R. & Fraaije, M. W. (eds.). Wiley, p. 97-124 28 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    9 Citations (Scopus)
    227 Downloads (Pure)

  • Natural Flavins: Occurrence, Role, and Noncanonical Chemistry

    Drenth, J. & Fraaije, M. W., 1-Jan-2021, Flavin-Based Catalysis: Principles and Applications. Cibulka, R. & M. W. F. (eds.). Wiley, p. 29-65 37 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    6 Citations (Scopus)
    190 Downloads (Pure)

  • Optimizing the linker length for fusing an alcohol dehydrogenase with a cyclohexanone monooxygenase

    Gran-Scheuch, A., Aalbers, F., Woudstra, Y., Parra, L. & Fraaije, M. W., 2021, Linkers in Biomacromolecules. Merkx, M. (ed.). Elsevier, Vol. 647. p. 107-143 37 p. (Methods in Enzymology).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    8 Citations (Scopus)

  • Preparation of Cytolysin A (ClyA) Nanopores

    Galenkamp, N. S., Van Meervelt, V., Mutter, N. L., van der Heide, N. J., Wloka, C. & Maglia, G., 2021, Nanopore Technology: Methods in Molecular Biology. Fahie , M. A. (ed.). New York: Humana Press, p. 11-18 8 p. (Methods in Molecular Biology; vol. 2186).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    6 Citations (Scopus)

  • Preparation of Fragaceatoxin C (FraC) Nanopores

    Mutter, N. L., Huang, G., van der Heide, N. J., Lucas, F. L. R., Galenkamp, N. S., Maglia, G. & Wloka, C., 2021, Nanopore Technology: Methods in Molecular Biology. Fahie, M. A. (ed.). New York: Humana Press, p. 3-10 8 p. (Methods in Molecular Biology; vol. 2186).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    7 Citations (Scopus)

  • Protocol for Simulations of PEGylated Proteins with Martini 3

    Grünewald, F., Kroon, P. C., Souza, P. C. T. & Marrink, S. J., 2021, Structural Genomics. Chen , Y. W. & Yiu , C. B. (eds.). New York: Humana Press, p. 315-335 21 p. (Methods in Molecular Biology; vol. 2199).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    14 Citations (Scopus)

  • Real-Time Monitoring of APC /C-Mediated Substrate Degradation Using Xenopus laevis Egg Extracts

    Kamenz, J., Qiao, R., Yang, Q. & Ferrell, J. E., 2021, Methods in Molecular Biology. Humana Press, p. 29-38 10 p. (Methods in Molecular Biology; vol. 2329).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • RNA Framework for Assaying the Structure of RNAs by High-Throughput Sequencing

    Marinus, T. & Incarnato, D., 2021, RNA Bioinformatics. Picardi , E. (ed.). New York: Humana, New York, NY, p. 63-76 14 p. (Methods in Molecular Biology; vol. 2284).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    2 Citations (Scopus)
    186 Downloads (Pure)

  • RNA Post-Transcriptional Modification Mapping Data Analysis Using RNA Framework

    Manfredonia, I. & Incarnato, D., 4-Jun-2021, RNA Modifications. Methods in Molecular Biology. McMahon, M. (ed.). Springer, p. 3-13 11 p. (Methods in Molecular Biology; vol. 2298).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    5 Citations (Scopus)
  • 2020

    Collision Cross Section Calculations Using HPCCS

    Heerdt, G., Zanotto, L., Souza, P. C. T., Araujo, G. & Skaf, M. S., 2020, Ion Mobility-Mass Spectrometry. Paglia , G. & Astarita , G. (eds.). New York: Humana Press, Vol. 2084. p. 297-310 14 p. (Methods in Molecular Biology).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    10 Citations (Scopus)

  • Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs

    Kalienkova, V., Alvadia, C., Clerico Mosina, V. & Paulino, C., 2020, Expression, Purification, and Structural Biology of Membrane Proteins. Perez, C. & Maier, T. (eds.). New York: Humana, New York, NY, p. 245-273 29 p. (Methods in Molecular Biology; vol. 2127).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    8 Citations (Scopus)

  • The multipurpose family of flavoprotein oxidases

    Martin, C., Binda, C., Fraaije, M. W. & Mattevi, A., 2020, Flavin-Dependent Enzymes : Mechanisms, Structures and Applications. Chaiyen, P. & Tamanoi, F. (eds.). Elsevier, Vol. 47. p. 63-86 24 p. (The Enzymes).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    20 Citations (Scopus)

  • Vanillyl alcohol oxidase

    Ewing, T. A., Gygli, G., Fraaije, M. W. & van Berkel, W. J. H., 2020, Flavin-Dependent Enzymes : Mechanisms, Structures and Applications. Chaiyen, P. & Tamanoi, F. (eds.). Elsevier, Vol. 47. p. 87-116 30 p. (The Enzymes).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    26 Citations (Scopus)
  • 2019

    A Practical View of the Martini Force Field

    Bruininks, B. M. H., Souza, P. C. T. & Marrink, S. J., 2019, Biomolecular Simulations: Methods in Molecular Biology. Bonomi, M. & Camilloni, C. (eds.). Humana, NY: Springer, p. 105-127 23 p. (Methods in Molecular Biology; vol. 2022).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    40 Citations (Scopus)

  • Systems Genetics for Evolutionary Studies

    Prins, P., Smant, G., Arends, D., Mulligan, M. K., Williams, R. W. & Jansen, R. C., 2019, Evolutionary Genomics. Anisimova, M. (ed.). Springer, p. 635-652 18 p. (Methods in Molecular Biology; vol. 1910).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    129 Downloads (Pure)
  • 2018

    Biophysical Analysis of Sec-Mediated Protein Translocation in Nanodiscs

    Koch, S., Driessen, A. & Kedrov, A., Jan-2018, Advances in Biomembranes and Lipid Self-Assembly. Elsevier, (Advances in Biomembranes and Lipid Self-Assembly; vol. 27).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    3 Citations (Scopus)

  • Experimental Protocols for Generating Focused Mutant Libraries and Screening for Thermostable Proteins

    Fürst, M., Martin, C., Lončar, N. & Fraaije, M., 2018, Enzymes in Synthetic Biology. Scrutton, N. (ed.). Academic Press, p. 151-187 37 p. (Methods in Enzymology; vol. 608).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    13 Citations (Scopus)
    290 Downloads (Pure)

  • Genome Editing in Penicillium chrysogenum Using Cas9 Ribonucleoprotein Particles

    Pohl, C., Mózsik, L., Driessen, A. J. M., Bovenberg, R. A. L. & Nygård, Y. I., May-2018, Synthetic biology: Methods and Protocols. Braman, J. C. (ed.). New York: Humana Press, p. 213-232 20 p. (Methods in Molecular Biology; vol. 1772).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    18 Citations (Scopus)
    213 Downloads (Pure)

  • Organization of photosynthetic membrane proteins into supercomplexes

    Boekema, E. & Semchonok, D., Feb-2018, Light Harvesting in Photosynthesis. Croce, R., van Grondelle, R., van Amerongen, H. & van Stokkum, I. (eds.). 1 ed. Boca Raton, FL: CRC Press, Taylor and Francis Group, Vol. 1. p. 207-217 11 p. (Foundation of Biochemistry and Biophysics).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Organization of Plant Photosystem II and Photosystem I Supercomplexes

    Kouril, R., Nosek, L., Semchonok, D., Boekema, E. & Ilík, P., 21-Feb-2018, Membrane Protein Complexes: Structure and Function. Harris, J. R. & Boekema, E. J. (eds.). 1 ed. Singapore: Springer Nature, Vol. 87. p. 259-286 28 p. (Subcellular Biochemistry; vol. 87).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    18 Citations (Scopus)
  • 2017

    A Computational Library Design Protocol for Rapid Improvement of Protein Stability: FRESCO

    Wijma, H., Fürst, M. & Janssen, D., 31-Oct-2017, Protein Engineering: Methods and Protocols. Clifton, N. J. (ed.). New York, NY: Humana Press, Vol. 1685. p. 69-85 7 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    62 Citations (Scopus)

  • Analysis of protein dynamics during cytokinesis in budding yeast

    Okada, S., Wloka, C. & Bi, E., 2017, Cytokinesis. Echard, A. (ed.). 1 ed. Elsevier, p. 25-45 21 p. (Methods in Cell Biology; vol. 137).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    7 Citations (Scopus)

  • Archaeal Surface Structures and Their Role in Communication with the Extracellular Environment

    Albers, S.-V. & Quax, T. E. F., 2017, Biocommunication of Archaea. Witzany, G. (ed.). Springer, p. 67-84 18 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Bacterial gangs: United and strong by means of quorum sensing

    Kuipers, O. & Kovacs, A., 2017, Mighty microbes: the amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H., Willemsen, P. & Biemans, C. (eds.). 1 ed. Castricum; The Netherlands: Microcanon Foundation, Vol. 1. p. 71-73 3 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    Open Access
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    8 Downloads (Pure)

  • Computational microscopy of mitochondrial membranes

    Arnarez, C. & Marrink, S. J., 1-Jan-2017, Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena. Hauppauge, New York: Nova Science Publishers, Inc, Hauppauge, NY, USA. , p. 1-20 20 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

  • Detection of Ubiquitinated Peroxisomal Proteins in Yeast

    Danda, N. & Williams, C., 14-Apr-2017, Peroxisomes. Springer, Vol. 1595. p. 233-241 9 p. (Methods in Molecular Biology; vol. 1595).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

  • Expanding the Repertoire of Flavoenzyme-Based Biocatalysis

    Nguyen, Q. T., Mattevi, A. & Fraaije, M. W., 15-Aug-2017, Future Directions in Biocatalysis: Second Edition. Matsuda, T. (ed.). 2nd ed. Elsevier, p. 119-133 15 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    2 Citations (Scopus)

  • Microscopes: Essential instruments in microbiology research

    van der Klei, I. & Veenhuis, M., 2017, Mighty microbes: the amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H., Willemsen, P. & Biemans, C. (eds.). 1 ed. Castricum, The Netherlands: Microcanon Foundation, Vol. 1. p. 41-44 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

  • Synthetic Biology: From engineering living systems to the bottom=up construction of synthetic cells

    Poolman, B. & Noireaux, V., 2017, Mighty Microbes: the amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H., Willemsen, P. & Biemans, C. (eds.). 1 ed. The Netherlands: Microcanon Foundation, Vol. 1. p. 215-217 3 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    Open Access
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    28 Downloads (Pure)

  • The Canonical and Accessory Sec System of Gram-positive Bacteria

    Prabudiansyah, I. & Driessen, A. J. M., 2017, Protein and Sugar Export and Assembly in Gram-positive Bacteria . Bagnoli, F. & Rappuoli, R. (eds.). Cham, Switzerland: Springer, p. 45-67 23 p. (Current Topics in Microbiology and Immunology; vol. 404).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    16 Citations (Scopus)
  • 2016

    De invloed op ons brein

    El Aidy, S., 2016, Ons microbioom: Wat betekenen bacteriën voor onze gezondheid?. Kleerebezem, M., Hoekstra, W. & van de Graaf, A. (eds.). 4 ed. Zutphen: Stichting Biowetenschappen en Maatschappij, Vol. 35. p. 54-57 4 p. (Cahier Biowetenschappen en Maatschappij).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Popular

  • Discovery and Engineering of Enzymes for Peptide Synthesis and Activation

    Toplak, A., Arif, M. I., Wu, B. & Janssen, D. B., 13-May-2016, Green Biocatalysis. Patel, R. N. (ed.). Wiley, p. 397-420 24 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    2 Citations (Scopus)

  • In Silico Screening of Enzyme Variants by Molecular Dynamics Simulation

    Wijma, H., 2016, Understanding enzymes: Function, design, engineering, and analysis. Svendsen, A. (ed.). Singapore: Pan Stanford Publishing Pte. Ltd., p. 805-833 29 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    2 Citations (Scopus)

  • Microbiome to Brain: Unravelling the Multidirectional Axes of Communication

    El Aidy, S., Stilling, R., Dinan, T. G. & Cryan, J. F., 2016, Microbial Endocrinology: Interkingdom Signalling in Infectious Diseases and Health. Lyte, M. (ed.). 2 ed. Springer International Publishing AG, Vol. 874. p. 301-336 36 p. (Advances in Experimental Medicine and Biology; vol. 874).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

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    48 Citations (Scopus)
    552 Downloads (Pure)

  • Recent Developments in Flavin-Based Catalysis: Enzymatic Sulfoxidation

    Brondani, P. B., Fraaije, M. W. & Gonzalo, G. D., 13-May-2016, Green Biocatalysis. Patel, R. N. (ed.). Wiley, p. 149-164 16 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic › peer-review

    Open Access
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    11 Citations (Scopus)
    795 Downloads (Pure)

  • Size exclusion chromatography with multi-angle laser light scattering (SEC-MALLS) to determine protein oligomeric states

    Guskov, A. & Slotboom, D., Jan-2016, From molecules to living organisms: an interplay between biology and physics: Lecture Notes of the Les Houches School of Physics: Volume 102, July 2014. Pebay-Peyroula, E., Nury, H., Parcy, F., Ruigrok, R. W. H., Ziegler, C. & Cugliandolo, L. F. (eds.). Oxford: Oxford University Press, p. 169-183 15 p. (Lecture Notes of the Les Houches School of Physics; vol. 102).

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    Open Access
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    108 Downloads (Pure)
  • 2015

    ABC Importers

    Swier, L. J. Y. M., Slotboom, D. & Poolman, B., 17-Dec-2015, ABC Transporters - 40 Years on. George, A. M. (ed.). 1 ed. Cham: Springer, Vol. 1. p. 3-36 34 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

    9 Citations (Scopus)

  • Baeyer-Villiger oxidations

    de Gonzalo, G., van Berkel, W. J. H. & Fraaije, M., 2015, Science of Synthesis: Biocatalysis in Organic Synthesis. Faber, K., Fessner, W.-D. & Turner, N. J. (eds.). Stuttgart: Thieme, Vol. 3. p. 187-234 48 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic

  • Oxidation using alcohol oxidases

    Ewing, T. A., Fraaije, M. & van Berkel, W. J. H., 2015, Science of Synthesis: Biocatalysis in Organic Synthesis. Faber, K., Fessner, W.-D. & Turner, N. J. (eds.). Stuttgart: Thieme, Vol. 3. p. 157-185 29 p.

    Research output: Chapter in Book/Report/Conference proceeding › Chapter › Academic