Sebastian Maerkl
Nationalité: German
EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne
+41 21 693 11 61
+41 21 693 78 35
Office: BM 1141
EPFL › STI › IBI-STI › LBNC
Site web: https://lbnc.epfl.ch/
EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne
+41 21 693 78 35
Office: BM 1141
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDBB-GE
Site web: https://go.epfl.ch/phd-edbb
Formation
PhD
| Biochemistry and Molecular Biophysics2008 – 2008 California Institute of Technology
B.Sc.
| Biology2001 – 2001 Fairleigh-Dickinson University
B.Sc.
| Chemistry2001 – 2001 Fairleigh-Dickinson University
2025
De novo design of phosphorylation-induced protein switches for synthetic signaling in cells
2025Evolving Infectious Disease Dynamics Shape School-based Intervention Effectiveness
NATURE COMMUNICATIONS. 2025. DOI : 10.1038/s41467-025-61925-5.Continuous in situ synthesis of a complete set of tRNAs sustains steady-state translation in a recombinant cell-free system
Nature Communications. 2025. DOI : 10.1038/s41467-025-61671-8.Long-Term Protein Synthesis with PURE in a Mesoscale Dialysis System
ACS synthetic biology. 2025. DOI : 10.1021/acssynbio.4c00618.Targeting protein-ligand neosurfaces with a generalizable deep learning tool
NATURE. 2025. DOI : 10.1038/s41586-024-08435-4.2024
Regulatory Components for Bacterial Cell-Free Systems Engineering
ACS SYNTHETIC BIOLOGY. 2024. DOI : 10.1021/acssynbio.4c00574.Towards Self-regeneration: Exploring the Limits of Protein Synthesis in the Protein Synthesis Using Recombinant Elements (PURE) Cell-free Transcription-Translation System
ACS SYNTHETIC BIOLOGY. 2024. DOI : 10.1021/acssynbio.4c00304.Nature-inspired recycling of a protein mixture into a green fluorescent protein-based hydrogel
RSC Sustainability. 2024. DOI : 10.1039/d4su00212a.A comprehensive review of Microfluidic approaches in cell-free synthetic biology
Frontiers in Synthetic Biology. 2024. DOI : 10.3389/fsybi.2024.1397533.Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10077.Advancing Cell-Free Synthetic Biology: From sustained PURE protein synthesis to an isothermal one-pot DNA replication system
Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10321.2023
C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System
Acs Synthetic Biology. 2023. DOI : 10.1021/acssynbio.3c00390.On biochemical constructors and synthetic cells
Interface Focus. 2023. DOI : 10.1098/rsfs.2023.0014.A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring
Applications In Plant Sciences. 2023. DOI : 10.1002/aps3.11529.Clinical sensitivity and specificity of a high-throughput microfluidic nano-immunoassay combined with capillary blood microsampling for the identification of anti-SARS-CoV-2 Spike IgG serostatus
Plos One. 2023. DOI : 10.1371/journal.pone.0283149.Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2023. DOI : 10.1073/pnas.2212151120.2022
Direct encapsulation of biomolecules in semi-permeable microcapsules produced with double-emulsions
Scientific Reports. 2022. DOI : 10.1038/s41598-022-25895-8.Improved Cell-Free Transcription-Translation Reactions in Microfluidic Chemostats Augmented with Hydrogel Membranes for Continuous Small Molecule Dialysis
Acs Synthetic Biology. 2022. DOI : 10.1021/acssynbio.2c00453.Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance
Nature Communications. 2022. DOI : 10.1038/s41467-022-32971-0.Epidemiological, virological and serological investigation of a SARS-CoV-2 outbreak (Alpha variant) in a primary school: A prospective longitudinal study
Plos One. 2022. DOI : 10.1371/journal.pone.0272663.An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates
Cell Reports Methods. 2022. DOI : 10.1016/j.crmeth.2022.100244.Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell Applications
Frontiers In Bioengineering And Biotechnology. 2022. DOI : 10.3389/fbioe.2022.918659.A SARS-CoV-2 omicron (B.1.1.529) variant outbreak in a primary school in Geneva, Switzerland
Lancet Infectious Diseases. 2022. DOI : 10.1016/S1473-3099(22)00267-5.p High-Throughput Single-Cell TCR-pMHC Dissociation Rate Measurements Performed by an Autonomous Microfluidic Cellular Processing Unit
Acs Sensors. 2022. DOI : 10.1021/acssensors.1c01935.High-throughput Microfluidic Platforms for S. cerevisiae Single Cell Studies
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9312.Systematic analysis of biomolecular binding reactions using microfluidic systems
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-10441.2021
Nature-Inspired Circular-Economy Recycling for Proteins: Proof of Concept
Advanced Materials. 2021. DOI : 10.1002/adma.202104581.OnePot PURE Cell-Free System
Jove-Journal Of Visualized Experiments. 2021. DOI : 10.3791/62625.A high-throughput microfluidic nanoimmunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultralow-volume blood samples
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2021. DOI : 10.1073/pnas.2025289118.Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8286.An autonomous microfluidic device for identification and analysis of individual clinically-relevant mammalian cells
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8751.Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platforms
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8385.2020
A partially self-regenerating synthetic cell
Nature Communications. 2020. DOI : 10.1038/s41467-020-20180-6.Microfluidic systems for cancer diagnostics
Current Opinion In Biotechnology. 2020. DOI : 10.1016/j.copbio.2019.11.022.How single-cell immunology is benefiting from microfluidic technologies
Microsystems & Nanoengineering. 2020. DOI : 10.1038/s41378-020-0140-8.Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory
Molecular Cell. 2020. DOI : 10.1016/j.molcel.2020.04.016.Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology
Frontiers In Bioengineering And Biotechnology. 2020. DOI : 10.3389/fbioe.2020.00213.High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuits
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10123.Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7427.2019
A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression
Journal of Visualized Experiments. 2019. DOI : 10.3791/59655.Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals
Nature Chemical Biology. 2019. DOI : 10.1038/s41589-019-0244-3.Cell-free gene-regulatory network engineering with synthetic transcription factors
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2019. DOI : 10.1073/pnas.1816591116.A Simple, Robust, and Low-Cost Method To Produce the PURE Cell Free System
Acs Synthetic Biology. 2019. DOI : 10.1021/acssynbio.8b00427.2018
Microfluidic Transfection for High-Throughput Mammalian Protein Expression
Methods in Molecular Biology. 2018. DOI : 10.1007/978-1-4939-8730-6_13.Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsions
Scientific Reports. 2018. DOI : 10.1038/s41598-018-26542-x.Development of microfluidic tools and methods for the biochemical characterization of scFv and Cas9 affinity reagents and their applications in molecular detection
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8614.2017
A system, device and method for multiplexed biomarker diagnostics of ultra-low volume whole blood samples
WO2017102593 . 2017.Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7889.A Microfluidic Biodisplay
Acs Synthetic Biology. 2017. DOI : 10.1021/acssynbio.7b00088.High-throughput microfluidic platforms applied to immunoassay-based diagnostics and environmental monitoring
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7903.2016
A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing
Scientific Reports. 2016. DOI : 10.1038/srep23937.Integrating Gene Synthesis and MITOMI for Rapid Protein Engineering
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6796.A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultralow Volume Samples
Acs Nano. 2016. DOI : 10.1021/acsnano.5b07939.Mechanically Induced Trapping of Molecular Interactions and Its Applications
Journal of laboratory automation. 2016. DOI : 10.1177/2211068215578586.Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries
Nano Letters. 2016. DOI : 10.1021/acs.nanolett.6b04165.GreA and GreB Enhance Expression of Escherichia coil RNA Polymerase Promoters in a Reconstituted Transcription-Translation System
Acs Synthetic Biology. 2016. DOI : 10.1021/acssynbio.6b00017.Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering
Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkv1497.2015
Rapid cell-free forward engineering of novel genetic ring oscillators
eLife. 2015. DOI : 10.7554/eLife.09771.Implementation and Characterization of Dynamic Genetic Networks in Vitro
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6617.High-throughput nanoimmunoassay chip
US2015285794 ; EP2908949 ; WO2014060869 . 2015.A microfluidic platform for high-throughput multiplexed protein quantitation
PloS One. 2015. DOI : 10.1371/journal.pone.0117744.2014
Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array
Plos One. 2014. DOI : 10.1371/journal.pone.0093466.A 1024-sample serum analyzer chip for cancer diagnostics
Lab On A Chip. 2014. DOI : 10.1039/c31c51153g.LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in Serum
Nano Letters. 2014. DOI : 10.1021/nl500574n.Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
Genes & Development. 2014. DOI : 10.1101/gad.244434.114.Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat array
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6196.2013
Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membrane
Chemical Communications (ChemComm). 2013. DOI : 10.1039/c2cc37740c.A microfluidic live-cell imaging platform to study large collections of microbial genotypes
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5593.iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks
Nucleic Acids Research. 2013. DOI : 10.1093/nar/gks1323.A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening
Integrative Biology. 2013. DOI : 10.1039/c3ib20263a.Systematic Analysis of Yeast Gene Expression by Synthetic Promoter Libraries
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-6002.Mapping the fine structure of a eukaryotic promoter input-output function
Nature Genetics. 2013. DOI : 10.1038/ng.2729.Generating microarrays for protein interaction studies using microfluidic devices
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5592.Live mammalian cell arrays
Nature Methods. 2013. DOI : 10.1038/nmeth.2473.A chemostat array enables the spatio-temporal analysis of the yeast proteome
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2013. DOI : 10.1073/pnas.1308265110.Implementation of cell-free biological networks at steady state
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2013. DOI : 10.1073/pnas.1311166110.2012
Topology and dynamics of the zebrafish segmentation clock core circuit
PLoS Biology. 2012. DOI : 10.1371/journal.pbio.1001364.Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2012. DOI : 10.1073/pnas.1206011109.Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA-Binding Domain
Plos Genetics. 2012. DOI : 10.1371/journal.pgen.1002614.Real-Time mRNA Measurement during an
ACS Synthetic Biology. 2012. DOI : 10.1021/sb300104f.Rapid Synthesis of Defined Eukaryotic Promoter Libraries
Acs Synthetic Biology. 2012. DOI : 10.1021/sb300045j.2011
Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules
PLoS Genetics. 2011. DOI : 10.1371/journal.pgen.1002053.A High-Throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant Libraries
Synthetic Gene Networks. 2011. DOI : 10.1007/978-1-61779-412-4_6.Next generation microfluidic platforms for high-throughput protein biochemistry
Current Opinion in Biotechnology. 2011. DOI : 10.1016/j.copbio.2010.08.010.A software-programmable microfluidic device for automated biology
Lab on a Chip. 2011. DOI : 10.1039/C0LC00537A.MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction
Gene Regulatory Networks. 2011. DOI : 10.1007/978-1-61779-292-2_6.2010
Experimental strategies for studying transcription factor-DNA binding specificities
Briefings in Functional Genomics. 2010. DOI : 10.1093/bfgp/elq023.Software-reconfigurable universally-applicable microfluidic platform
2010. p. 18 - ANYL.2009
An in vitro microfluidic approach to generating protein-interaction networks
Nature Methods. 2009. DOI : 10.1038/nmeth.1289.Integration column: Microfluidic high-throughput screening
Integrative Biology. 2009. DOI : 10.1039/b819762h.Experimental determination of the evolvability of a transcription factor
Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0907688106.Integration of plasmonic trapping in a microfluidic environment
Optics Express. 2009. DOI : 10.1364/OE.17.006018.2008
Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis
Nature Biotechnology. 2008. DOI : 10.1038/nbt.1490.2007
A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
Science. 2007. DOI : 10.1126/science.1131007.2002
Microfluidic Large-Scale Integration
Science. 2002. DOI : 10.1126/science.1076996.Enseignement et PhD
Current Phd
Amogh Kumar Baranwal, Pao-Wan Lee, Seyed Saeed Mottaghi, Ragunathan Bava Ganesh
Past Phd As Director
Nicolas Dénervaud, Sylvie Rockel, Jean-Bernard Nobs, Arun Stephen Rajkumar, Henrike Marie Niederholtmeyer, Matthew Christopher Blackburn, Kristina Pan Woodruff, Francesca Volpetti, Ekaterina Emilova Petrova, Zoe Newell Swank, Ivan Istomin, Grégoire Michielin, Fabien Jammes, Barbora Lavickova, Hon Ming Andrew Yip, Amir Shahein, Shiyu Cheng, Laura Grasemann
Past Phd As Codirector
Meltem Elitas, Johannes Becker, Zuzana Tatárová, Amanda Verpoorte, Simone Giaveri
Courses
Introduction to bioengineering
Ce cours offre aux étudiants en ingénierie une compréhension fondamentale de la bio-ingénierie, un domaine multidisciplinaire qui intègre les principes de la biologie, de la chimie et de l'ingénierie.
Lab on cell-free synthetic biology
Le cours de biologie synthétique acellulaire présente aux ingénieurs les techniques les plus couramment utilisées pour mener des travaux en biotechnologie et en bio-ingénierie. De plus, ce cours est une expérience de démocratisation de l'éducation et de la science ouverte en générant des ressources