Sebastian Maerkl
Associate Professor
sebastian.maerkl@epfl.ch +41 21 693 78 35 http://lbnc.epfl.ch
Citizenship: German
EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne
+41 21 693 78 35
+41 21 693 11 61
Office:
BM 1141
EPFL
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Web site: Web site: https://lbnc.epfl.ch/
Fields of expertise
Biography
Prof. Maerkl received B.S. degrees in Biology and in Chemistry from Fairleigh-Dickinson University in 2001. He then joined the Biophysics and Biochemistry Department at the California Institute of Technology and contributed to the early development of microfluidic technology. For his graduate work Prof. Maerkl was awarded the Demetriades-Tsafka-Kokalis prize for the best Caltech PhD thesis in the field of Biotechnology. He was also awarded 1st place at the Innovator’s Challenge, a competition amongst inventors and entrepreneurs from Stanford University, UC Berkeley, and Caltech. After graduating in 2008, Prof. Maerkl accepted a position as an Assistant Professor at the Ecole Polytechnique Federale de Lausanne (EPFL) in the Institute of Bioengineering and the School of Engineering and was promoted to Associate Professor with tenure in 2015. In 2012 and received the Prix SSV – Ambition for dedication to teaching and promotion of EPFL students and the school at large. Prof. Maerkl was awarded an ERC Consolidator Grant, an HFSP Program Grant, a SystemsX.ch RTD grant, a SNF Sinergia grant, and a SNF NRP 78 Covid-19 research grant, amongst others. Prof. Maerkl published over 50 peer-reviewed publications and 6 patents, gave over 90 invited seminars, organised several international conferences and workshops, and serves as a reviewer for national and international funding agencies and journals. The lab hosted one Fulbright Scholar, two Whitaker and one Think Swiss Fellow. His lab is currently working at the interface of micro-engineering, systems biology, synthetic biology, and molecular diagnostics. Prof Maerkl started the EPFL iGEM team in 2008 and has been teaching and advising the teams from 2008 to 2020. During this period the EPFL teams won 8 Gold, 2 Silver, and 1 bronze medal and were awarded 5 prices. In 2019, the EPFL iGEM team became the Grand Prize Winner in the Overgrad category and the first Swiss team to have won the competition.Education
PhD
Biochemistry and Molecular Biophysics
California Institute of Technology
2008
B.Sc.
Biology
Fairleigh-Dickinson University
2001
B.Sc.
Chemistry
Fairleigh-Dickinson University
2001
Awards
First Place Innovators Challenge
Category: Biotechnology
2005
Demetriades-Tsafka-Kokkalis Prize in Biotechnology or Related Field
The prize honors annually the best Caltech Ph.D. thesis in the given category.
2008
Prix SSV - Ambition
EPFL prize for dedication to teaching and promotion of EPFL students and the school at large.
2012
HFSP Program Grant
2015
ERC Consolidator Grant
2016
iGEM Grand Prize Winner (overgrad)
2019
Publications
Infoscience publications
2024
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.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-10077.2023
C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System
Acs Synthetic Biology. 2023-09-20. DOI : 10.1021/acssynbio.3c00390.On biochemical constructors and synthetic cells
Interface Focus. 2023-08-11. 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. 2023-06-14. 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. 2023-03-23. 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. 2023-01-10. DOI : 10.1073/pnas.2212151120.2022
Direct encapsulation of biomolecules in semi-permeable microcapsules produced with double-emulsions
Scientific Reports. 2022-12-10. 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. 2022-12-07. 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. 2022-09-07. 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. 2022-08-17. 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. 2022-07-18. 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. 2022-07-01. 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. 2022-06-01. 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. 2022-01-10. 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. 2021-09-23. DOI : 10.1002/adma.202104581.OnePot PURE Cell-Free System
Jove-Journal Of Visualized Experiments. 2021-06-01. 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. 2021-05-04. DOI : 10.1073/pnas.2025289118.An autonomous microfluidic device for identification and analysis of individual clinically-relevant mammalian cells
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8751.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.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. 2020-12-11. DOI : 10.1038/s41467-020-20180-6.Microfluidic systems for cancer diagnostics
Current Opinion In Biotechnology. 2020-10-01. DOI : 10.1016/j.copbio.2019.11.022.How single-cell immunology is benefiting from microfluidic technologies
Microsystems & Nanoengineering. 2020-07-13. DOI : 10.1038/s41378-020-0140-8.Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory
Molecular Cell. 2020-06-04. 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. 2020-03-24. DOI : 10.3389/fbioe.2020.00213.Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7427.High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuits
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10123.2019
Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals
Nature Chemical Biology. 2019-05-01. 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. 2019-03-26. DOI : 10.1073/pnas.1816591116.A Simple, Robust, and Low-Cost Method To Produce the PURE Cell Free System
Acs Synthetic Biology. 2019-02-01. DOI : 10.1021/acssynbio.8b00427.A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression
Journal of Visualized Experiments. 2019-10-06. DOI : 10.3791/59655.2018
Microfluidic Transfection for High-Throughput Mammalian Protein Expression
Methods in Molecular Biology. 2018-09-22. DOI : 10.1007/978-1-4939-8730-6_13.Microfluidic Module for Real-Time Generation of Complex Multimolecule Temporal Concentration Profiles
ANALYTICAL CHEMISTRY. 2018. DOI : 10.1021/acs.analchem.7b04099.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.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.2017
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.Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies
Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7889.A system, device and method for multiplexed biomarker diagnostics of ultra-low volume whole blood samples
WO2017102593 . 2017.2016
A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing
Scientific Reports. 2016-03-31. DOI : 10.1038/srep23937.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.Microfluidic co-culture platform to quantify chemotaxis of primary stem cells
Lab On A Chip. 2016. DOI : 10.1039/c6lc00236f.Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering
Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkv1497.A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultralow Volume Samples
Acs Nano. 2016. DOI : 10.1021/acsnano.5b07939.Integrating Gene Synthesis and MITOMI for Rapid Protein Engineering
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6796.Mechanically Induced Trapping of Molecular Interactions and Its Applications
Journal of laboratory automation. 2016. DOI : 10.1177/2211068215578586.2015
Rapid cell-free forward engineering of novel genetic ring oscillators
eLife. 2015-10-02. DOI : 10.7554/eLife.09771.High-throughput nanoimmunoassay chip
US2015285794 ; EP2908949 ; WO2014060869 . 2015.Implementation and Characterization of Dynamic Genetic Networks in Vitro
Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6617.A microfluidic platform for high-throughput multiplexed protein quantitation
PloS One. 2015. DOI : 10.1371/journal.pone.0117744.2014
Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat array
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6196.Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription
Genes & Development. 2014. DOI : 10.1101/gad.244434.114.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.Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array
Plos One. 2014. DOI : 10.1371/journal.pone.0093466.2013
Systematic Analysis of Yeast Gene Expression by Synthetic Promoter Libraries
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-6002.Implementation of cell-free biological networks at steady state
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. DOI : 10.1073/pnas.1311166110.Mapping the fine structure of a eukaryotic promoter input-output function
Nature Genetics. 2013. DOI : 10.1038/ng.2729.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. 2013. DOI : 10.1073/pnas.1308265110.iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks
Nucleic Acids Research. 2013. DOI : 10.1093/nar/gks1323.Live mammalian cell arrays
Nature Methods. 2013. DOI : 10.1038/nmeth.2473.A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening
Integrative Biology. 2013. DOI : 10.1039/c3ib20263a.Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membrane
Chemical Communications. 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.Generating microarrays for protein interaction studies using microfluidic devices
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5592.2012
Topology and dynamics of the zebrafish segmentation clock core circuit
PLoS Biology. 2012. DOI : 10.1371/journal.pbio.1001364.Real-Time mRNA Measurement during an
ACS Synthetic Biology. 2012. DOI : 10.1021/sb300104f.Massively parallel measurements of molecular interaction kinetics on a microfluidic platform
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2012. DOI : 10.1073/pnas.1206011109.Rapid Synthesis of Defined Eukaryotic Promoter Libraries
Acs Synthetic Biology. 2012. DOI : 10.1021/sb300045j.Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA-Binding Domain
Plos Genetics. 2012. DOI : 10.1371/journal.pgen.1002614.2011
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.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.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 software-programmable microfluidic device for automated biology
Lab on a Chip. 2011. DOI : 10.1039/C0LC00537A.Next generation microfluidic platforms for high-throughput protein biochemistry
Current Opinion in Biotechnology. 2011. DOI : 10.1016/j.copbio.2010.08.010.2010
Software-reconfigurable universally-applicable microfluidic platform
2010. p. 18-ANYL.Experimental strategies for studying transcription factor-DNA binding specificities
Briefings in Functional Genomics. 2010. DOI : 10.1093/bfgp/elq023.2009
Integration of plasmonic trapping in a microfluidic environment
Optics Express. 2009. DOI : 10.1364/OE.17.006018.Experimental determination of the evolvability of a transcription factor
Proceedings of the National Academy of Sciences of the United States of America. 2009. DOI : 10.1073/pnas.0907688106.Integration column: Microfluidic high-throughput screening
Integrative Biology. 2009. DOI : 10.1039/b819762h.An in vitro microfluidic approach to generating protein-interaction networks
Nature Methods. 2009. DOI : 10.1038/nmeth.1289.2008
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.Teaching & PhD
Teaching
Electrical and Electronics Engineering