Fields of expertise
BiographyProf. 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.
Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevanceNature 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 studyPlos One. 2022-08-17. DOI : 10.1371/journal.pone.0272663.
Biochemistry of Aminoacyl tRNA Synthetase and tRNAs and Their Engineering for Cell-Free and Synthetic Cell ApplicationsFrontiers 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, SwitzerlandLancet 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 UnitAcs Sensors. 2022-01-10. DOI : 10.1021/acssensors.1c01935.
Systematic analysis of biomolecular binding reactions using microfluidic systemsLausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-10441.
Nature-Inspired Circular-Economy Recycling for Proteins: Proof of ConceptAdvanced Materials. 2021-09-23. DOI : 10.1002/adma.202104581.
OnePot PURE Cell-Free SystemJove-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 samplesProceedings 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 cellsLausanne, 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 reactorsLausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8286.
Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platformsLausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8385.
A partially self-regenerating synthetic cellNature Communications. 2020-12-11. DOI : 10.1038/s41467-020-20180-6.
Microfluidic systems for cancer diagnosticsCurrent Opinion In Biotechnology. 2020-10-01. DOI : 10.1016/j.copbio.2019.11.022.
How single-cell immunology is benefiting from microfluidic technologiesMicrosystems & Nanoengineering. 2020-07-13. DOI : 10.1038/s41378-020-0140-8.
Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction MemoryMolecular Cell. 2020-06-04. DOI : 10.1016/j.molcel.2020.04.016.
Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic BiologyFrontiers 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 clustersLausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7427.
High-throughput microfluidic platforms for characterizing and engineering cell-free gene regulatory circuitsLausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10123.
A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene ExpressionJournal of Visualized Experiments. 2019-10-06. DOI : 10.3791/59655.
Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metalsNature Chemical Biology. 2019-05-01. DOI : 10.1038/s41589-019-0244-3.
Cell-free gene-regulatory network engineering with synthetic transcription factorsProceedings 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 SystemAcs Synthetic Biology. 2019-02-01. DOI : 10.1021/acssynbio.8b00427.
Microfluidic Transfection for High-Throughput Mammalian Protein ExpressionMethods 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 ProfilesANALYTICAL 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 detectionLausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8614.
Microfluidic device for real-time formulation of reagents and their subsequent encapsulation into double emulsionsScientific Reports. 2018. DOI : 10.1038/s41598-018-26542-x.
A Microfluidic BiodisplayAcs Synthetic Biology. 2017. DOI : 10.1021/acssynbio.7b00088.
High-throughput microfluidic platforms applied to immunoassay-based diagnostics and environmental monitoringLausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7903.
Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studiesLausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7889.
A system, device and method for multiplexed biomarker diagnostics of ultra-low volume whole blood samplesWO2017102593 . 2017.
A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and CulturingScientific Reports. 2016-03-31. DOI : 10.1038/srep23937.
Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through NanocapillariesNano Letters. 2016. DOI : 10.1021/acs.nanolett.6b04165.
GreA and GreB Enhance Expression of Escherichia coil RNA Polymerase Promoters in a Reconstituted Transcription-Translation SystemAcs Synthetic Biology. 2016. DOI : 10.1021/acssynbio.6b00017.
Microfluidic co-culture platform to quantify chemotaxis of primary stem cellsLab On A Chip. 2016. DOI : 10.1039/c6lc00236f.
Integrating gene synthesis and microfluidic protein analysis for rapid protein engineeringNucleic Acids Research. 2016. DOI : 10.1093/nar/gkv1497.
A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultralow Volume SamplesAcs Nano. 2016. DOI : 10.1021/acsnano.5b07939.
Integrating Gene Synthesis and MITOMI for Rapid Protein EngineeringLausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6796.
Mechanically Induced Trapping of Molecular Interactions and Its ApplicationsJournal of laboratory automation. 2016. DOI : 10.1177/2211068215578586.
Rapid cell-free forward engineering of novel genetic ring oscillatorseLife. 2015-10-02. DOI : 10.7554/eLife.09771.
High-throughput nanoimmunoassay chipUS2015285794 ; EP2908949 ; WO2014060869 . 2015.
Implementation and Characterization of Dynamic Genetic Networks in VitroLausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6617.
A microfluidic platform for high-throughput multiplexed protein quantitationPloS One. 2015. DOI : 10.1371/journal.pone.0117744.
Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat arrayLausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6196.
Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcriptionGenes & Development. 2014. DOI : 10.1101/gad.244434.114.
A 1024-sample serum analyzer chip for cancer diagnosticsLab On A Chip. 2014. DOI : 10.1039/c31c51153g.
LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in SerumNano Letters. 2014. DOI : 10.1021/nl500574n.
Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat ArrayPlos One. 2014. DOI : 10.1371/journal.pone.0093466.
Systematic Analysis of Yeast Gene Expression by Synthetic Promoter LibrariesLausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-6002.
Implementation of cell-free biological networks at steady stateProceedings 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 functionNature Genetics. 2013. DOI : 10.1038/ng.2729.
A chemostat array enables the spatio-temporal analysis of the yeast proteomeProceedings 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 networksNucleic Acids Research. 2013. DOI : 10.1093/nar/gks1323.
Live mammalian cell arraysNature Methods. 2013. DOI : 10.1038/nmeth.2473.
A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screeningIntegrative Biology. 2013. DOI : 10.1039/c3ib20263a.
Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membraneChemical Communications. 2013. DOI : 10.1039/c2cc37740c.
A microfluidic live-cell imaging platform to study large collections of microbial genotypesLausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5593.
Generating microarrays for protein interaction studies using microfluidic devicesLausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5592.
Topology and dynamics of the zebrafish segmentation clock core circuitPLoS Biology. 2012. DOI : 10.1371/journal.pbio.1001364.
Real-Time mRNA Measurement during anACS Synthetic Biology. 2012. DOI : 10.1021/sb300104f.
Massively parallel measurements of molecular interaction kinetics on a microfluidic platformProceedings Of The National Academy Of Sciences Of The United States Of America. 2012. DOI : 10.1073/pnas.1206011109.
Rapid Synthesis of Defined Eukaryotic Promoter LibrariesAcs Synthetic Biology. 2012. DOI : 10.1021/sb300045j.
Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA-Binding DomainPlos Genetics. 2012. DOI : 10.1371/journal.pgen.1002614.
MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA InteractionGene Regulatory Networks. 2011. DOI : 10.1007/978-1-61779-292-2_6.
A High-Throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant LibrariesSynthetic 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 ModulesPLoS Genetics. 2011. DOI : 10.1371/journal.pgen.1002053.
A software-programmable microfluidic device for automated biologyLab on a Chip. 2011. DOI : 10.1039/C0LC00537A.
Next generation microfluidic platforms for high-throughput protein biochemistryCurrent Opinion in Biotechnology. 2011. DOI : 10.1016/j.copbio.2010.08.010.
Software-reconfigurable universally-applicable microfluidic platform2010. p. 18-ANYL.
Experimental strategies for studying transcription factor-DNA binding specificitiesBriefings in Functional Genomics. 2010. DOI : 10.1093/bfgp/elq023.
Integration of plasmonic trapping in a microfluidic environmentOptics Express. 2009. DOI : 10.1364/OE.17.006018.
Experimental determination of the evolvability of a transcription factorProceedings of the National Academy of Sciences of the United States of America. 2009. DOI : 10.1073/pnas.0907688106.
Integration column: Microfluidic high-throughput screeningIntegrative Biology. 2009. DOI : 10.1039/b819762h.
An in vitro microfluidic approach to generating protein-interaction networksNature Methods. 2009. DOI : 10.1038/nmeth.1289.
Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysisNature Biotechnology. 2008. DOI : 10.1038/nbt.1490.
A Systems Approach to Measuring the Binding Energy Landscapes of Transcription FactorsScience. 2007. DOI : 10.1126/science.1131007.
Microfluidic Large-Scale IntegrationScience. 2002. DOI : 10.1126/science.1076996.
Teaching & PhD
Life Sciences Engineering
Doctoral Program in Biotechnology and Bioengineering
Doctoral Program in Microsystems and Microelectronics