Profile picture

Sebastian Maerkl

Nationalité: German

EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne

EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne

EPFL STI IBI-STI LBNC
BM 1141 (Bâtiment BM)
Station 17
1015 Lausanne

Formation

PhD

| Biochemistry and Molecular Biophysics

2008 – 2008 California Institute of Technology

B.Sc.

| Biology

2001 – 2001 Fairleigh-Dickinson University

B.Sc.

| Chemistry

2001 – 2001 Fairleigh-Dickinson University

2025

De novo design of phosphorylation-induced protein switches for synthetic signaling in cells

S. BuckleyY. MiaoM. IdrisP. LeeL. Scheller  et al.

2025

Evolving Infectious Disease Dynamics Shape School-based Intervention Effectiveness

J. Perez-SaezM. BellonJ. LesslerJ. BerthelotE. B. Hodcroft  et al.

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

F. LiA. K. BaranwalS. J. Maerkl

Nature Communications. 2025. DOI : 10.1038/s41467-025-61671-8.

Long-Term Protein Synthesis with PURE in a Mesoscale Dialysis System

L. Roset JuliàL. GrasemannF. StellacciS. J. Maerkl

ACS synthetic biology. 2025. DOI : 10.1021/acssynbio.4c00618.

Targeting protein-ligand neosurfaces with a generalizable deep learning tool

A. MarchandS. BuckleyA. SchneuingM. PacesaM. Elia  et al.

NATURE. 2025. DOI : 10.1038/s41586-024-08435-4.

2024

Regulatory Components for Bacterial Cell-Free Systems Engineering

P.-W. LeeS. J. Maerkl

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

R. B. GaneshS. J. Maerkl

ACS SYNTHETIC BIOLOGY. 2024. DOI : 10.1021/acssynbio.4c00304.

Nature-inspired recycling of a protein mixture into a green fluorescent protein-based hydrogel

L. Roset JuliàS. J. MaerklF. Stellacci

RSC Sustainability. 2024. DOI : 10.1039/d4su00212a.

A comprehensive review of Microfluidic approaches in cell-free synthetic biology

A. K. BaranwalS. Maerkl

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

S. Cheng / S. Maerkl (Dir.)

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

L. S. Grasemann / S. Maerkl (Dir.)

Lausanne, EPFL, 2024. DOI : 10.5075/epfl-thesis-10321.

2023

C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System

L. GrasemannP. Thiel PizarroS. J. Maerkl

Acs Synthetic Biology. 2023. DOI : 10.1021/acssynbio.3c00390.

On biochemical constructors and synthetic cells

S. J. Maerkl

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

J. SelzN. R. AdamC. E. M. MagriniF. M. MontandonS. Buerki  et al.

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

G. MichielinF. ArefiO. PuhachM. BellonP. Sattonnet-Roche  et al.

Plos One. 2023. DOI : 10.1371/journal.pone.0283149.

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

H. M. YipS. ChengE. J. OlsonM. A. CroneS. J. Maerkl

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

G. MichielinS. J. Maerkl

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

B. LavickovaL. GrasemannS. J. Maerkl

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

A. ShaheinM. Lopez-MaloI. IstominE. J. OlsonS. Cheng  et al.

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

E. LortheM. BellonG. MichielinJ. BerthelotM.-E. Zaballa  et al.

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

J. TischlerZ. SwankH.-A. HsiungS. VianelloM. P. Lutolf  et al.

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

R. B. GaneshS. J. Maerkl

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

E. LortheM. BellonJ. BerthelotG. MichielinA. G. L'Huillier  et al.

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

F. JammesJ. SchmidtG. CoukosS. J. Maerkl

Acs Sensors. 2022. DOI : 10.1021/acssensors.1c01935.

Systematic analysis of biomolecular binding reactions using microfluidic systems

A. Shahein / S. Maerkl (Dir.)

Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-10441.

High-throughput Microfluidic Platforms for S. cerevisiae Single Cell Studies

H. M. Yip / S. Maerkl (Dir.)

Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9312.

2021

Nature-Inspired Circular-Economy Recycling for Proteins: Proof of Concept

S. GiaveriA. M. SchmittL. Roset JuliaV. ScamarcioA. Murello  et al.

Advanced Materials. 2021. DOI : 10.1002/adma.202104581.

OnePot PURE Cell-Free System

L. GrasemannB. LavickovaM. C. Elizondo-CantuS. J. Maerkl

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

Z. SwankG. MichielinH. M. YipP. CohenD. O. Andrey  et al.

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

B. Lavickova / S. Maerkl (Dir.)

Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8286.

An autonomous microfluidic device for identification and analysis of individual clinically-relevant mammalian cells

F. L. C. R. Jammes / S. Maerkl (Dir.)

Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8751.

Microfluidics and cell-free synthetic biology in the development of new diagnostic and therapeutic platforms

G. Michielin / S. Maerkl (Dir.)

Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8385.

2020

A partially self-regenerating synthetic cell

B. LavickovaN. LaohakunakornS. J. Maerkl

Nature Communications. 2020. DOI : 10.1038/s41467-020-20180-6.

Microfluidic systems for cancer diagnostics

J. L. Garcia-CorderoS. J. Maerkl

Current Opinion In Biotechnology. 2020. DOI : 10.1016/j.copbio.2019.11.022.

How single-cell immunology is benefiting from microfluidic technologies

F. C. JammesS. J. Maerkl

Microsystems & Nanoengineering. 2020. DOI : 10.1038/s41378-020-0140-8.

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

P. BhedaD. Aguilar-GomezN. B. BeckerJ. BeckerE. Stavrou  et al.

Molecular Cell. 2020. DOI : 10.1016/j.molcel.2020.04.016.

Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology

N. LaohakunakornL. GrasemannB. LavickovaG. MichielinA. Shahein  et al.

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

Z. N. Swank / S. Maerkl (Dir.)

Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10123.

Microfluidic iMITOMI platform to study the architecture of low-affinity transcription factor binding site clusters

I. Istomin / S. Maerkl (Dir.)

Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7427.

2019

A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression

A. J. van der LindenM. YelleswarapuP. A. PietersZ. SwankW. T. S. Huck  et al.

Journal of Visualized Experiments. 2019. DOI : 10.3791/59655.

Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals

X. WanF. VolpettiE. PetrovaC. FrenchS. J. Maerkl  et al.

Nature Chemical Biology. 2019. DOI : 10.1038/s41589-019-0244-3.

Cell-free gene-regulatory network engineering with synthetic transcription factors

Z. SwankN. LaohakunakornS. J. Maerkl

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

B. LavickovaS. J. Maerkl

Acs Synthetic Biology. 2019. DOI : 10.1021/acssynbio.8b00427.

2018

Microfluidic Transfection for High-Throughput Mammalian Protein Expression

K. WoodruffS. J. Maerkl

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

J.-C. ChangZ. N. SwankO. KeiserS. MaerklE. Amstad

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

E. E. Petrova / S. Maerkl (Dir.)

Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8614.

2017

Microfluidic platforms for high-throughput mammalian cell printing, transfection, and dosage-dependent studies

K. P. Woodruff / S. Maerkl (Dir.)

Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7889.

A Microfluidic Biodisplay

F. VolpettiE. PetrovaS. J. Maerkl

Acs Synthetic Biology. 2017. DOI : 10.1021/acssynbio.7b00088.

High-throughput microfluidic platforms applied to immunoassay-based diagnostics and environmental monitoring

F. Volpetti / S. Maerkl (Dir.)

Lausanne, EPFL, 2017. DOI : 10.5075/epfl-thesis-7903.

A system, device and method for multiplexed biomarker diagnostics of ultra-low volume whole blood samples

S. J. MaerklF. PirainoF. Volpetti

WO2017102593 . 2017.

2016

A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing

K. WoodruffS. J. Maerkl

Scientific Reports. 2016. DOI : 10.1038/srep23937.

Integrating Gene Synthesis and MITOMI for Rapid Protein Engineering

M. C. Blackburn / S. Maerkl (Dir.)

Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6796.

Mechanically Induced Trapping of Molecular Interactions and Its Applications

J. L. Garcia-CorderoS. J. Maerkl

Journal of laboratory automation. 2016. DOI : 10.1177/2211068215578586.

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

M. C. BlackburnE. PetrovaB. E. CorreiaS. J. Maerkl

Nucleic Acids Research. 2016. DOI : 10.1093/nar/gkv1497.

Single Molecule Localization and Discrimination of DNA–Protein Complexes by Controlled Translocation Through Nanocapillaries

R. D. BulushevS. MarionE. PetrovaS. J. DavisS. J. Maerkl  et al.

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

L. L. De MaddalenaH. NiederholtmeyerM. TurtolaZ. N. SwankG. A. Belogurov  et al.

Acs Synthetic Biology. 2016. DOI : 10.1021/acssynbio.6b00017.

A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultralow Volume Samples

F. PirainoF. VolpettiC. WatsonS. J. Maerkl

Acs Nano. 2016. DOI : 10.1021/acsnano.5b07939.

2015

Rapid cell-free forward engineering of novel genetic ring oscillators

H. NiederholtmeyerZ. Z. SunY. HoriE. YeungA. Verpoorte  et al.

eLife. 2015. DOI : 10.7554/eLife.09771.

Implementation and Characterization of Dynamic Genetic Networks in Vitro

H. M. Niederholtmeyer / S. Maerkl (Dir.)

Lausanne, EPFL, 2015. DOI : 10.5075/epfl-thesis-6617.

High-throughput nanoimmunoassay chip

S. MaerklJ. L. Garcia-Cordero

US2015285794 ; EP2908949 ; WO2014060869 . 2015.

A microfluidic platform for high-throughput multiplexed protein quantitation

F. VolpettiJ. Garcia-CorderoS. J. Maerkl

PloS One. 2015. DOI : 10.1371/journal.pone.0117744.

2014

A 1024-sample serum analyzer chip for cancer diagnostics

J. L. Garcia-CorderoS. J. Maerkl

Lab On A Chip. 2014. DOI : 10.1039/c31c51153g.

Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array

J.-B. NobsS. J. Maerkl

Plos One. 2014. DOI : 10.1371/journal.pone.0093466.

LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in Serum

S. S. AcimovicM. A. OrtegaV. SanzJ. BerthelotJ. L. Garcia-Cordero  et al.

Nano Letters. 2014. DOI : 10.1021/nl500574n.

Automated long-term single cell analysis of Schizosaccharomyces pombe on a microfluidic microchemostat array

J.-B. Nobs / S. Maerkl (Dir.)

Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6196.

Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription

B. KnightS. KubikB. GhoshM. J. BruzzoneM. Geertz  et al.

Genes & Development. 2014. DOI : 10.1101/gad.244434.114.

2013

iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

S. RockelM. GeertzK. HensB. DeplanckeS. J. Maerkl

Nucleic Acids Research. 2013. DOI : 10.1093/nar/gks1323.

A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening

J. L. Garcia-CorderoC. NembriniA. StanoJ. A. HubbellS. J. Maerkl

Integrative Biology. 2013. DOI : 10.1039/c3ib20263a.

Multiplexed surface micropatterning of proteins with a pressure-modulated microfluidic button-membrane

J. L. Garcia-CorderoS. J. Maerkl

Chemical Communications (ChemComm). 2013. DOI : 10.1039/c2cc37740c.

A microfluidic live-cell imaging platform to study large collections of microbial genotypes

N. Dénervaud / S. MaerklF. Naef (Dir.)

Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5593.

Mapping the fine structure of a eukaryotic promoter input-output function

A. S. RajkumarN. DenervaudS. J. Maerkl

Nature Genetics. 2013. DOI : 10.1038/ng.2729.

Systematic Analysis of Yeast Gene Expression by Synthetic Promoter Libraries

A. S. Rajkumar / S. Maerkl (Dir.)

Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-6002.

Generating microarrays for protein interaction studies using microfluidic devices

S. Rockel / S. Maerkl (Dir.)

Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5592.

A chemostat array enables the spatio-temporal analysis of the yeast proteome

N. DénervaudJ. BeckerR. Delgado-GonzaloP. DamayA. S. Rajkumar  et al.

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

H. NiederholtmeyerV. StepanovaS. J. Maerkl

Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2013. DOI : 10.1073/pnas.1311166110.

Live mammalian cell arrays

K. P. WoodruffL. M. FidalgoS. GobaaM. LutolfS. Maerkl

Nature Methods. 2013. DOI : 10.1038/nmeth.2473.

2012

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

M. GeertzD. ShoreS. J. Maerkl

Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2012. DOI : 10.1073/pnas.1206011109.

Topology and dynamics of the zebrafish segmentation clock core circuit

C. SchröterS. AresL. G. MorelliA. IsakovaK. Hens  et al.

PLoS Biology. 2012. DOI : 10.1371/journal.pbio.1001364.

Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA-Binding Domain

R. K. ShultzabergerS. J. MaerklJ. F. KirschM. B. Eisen

Plos Genetics. 2012. DOI : 10.1371/journal.pgen.1002614.

Real-Time mRNA Measurement during an

H. NiederholtmeyerL. XuS. J. Maerkl

ACS Synthetic Biology. 2012. DOI : 10.1021/sb300104f.

Rapid Synthesis of Defined Eukaryotic Promoter Libraries

A. S. RajkumarS. J. Maerkl

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

B. Z. HeA. K. HollowayS. J. MaerklM. Kreitman

PLoS Genetics. 2011. DOI : 10.1371/journal.pgen.1002053.

MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction

S. RockelM. GeertzS. J. Maerkl

Gene Regulatory Networks. 2011. DOI : 10.1007/978-1-61779-292-2_6.

Next generation microfluidic platforms for high-throughput protein biochemistry

S. J. Maerkl

Current Opinion in Biotechnology. 2011. DOI : 10.1016/j.copbio.2010.08.010.

A High-Throughput Microfluidic Method for Generating and Characterizing Transcription Factor Mutant Libraries

M. GeertzS. RockelS. J. Maerkl

Synthetic Gene Networks. 2011. DOI : 10.1007/978-1-61779-412-4_6.

A software-programmable microfluidic device for automated biology

F. RabaneraL. MiguelS. J. Maerkl

Lab on a Chip. 2011. DOI : 10.1039/C0LC00537A.

2010

Experimental strategies for studying transcription factor-DNA binding specificities

M. GeertzS. J. Maerkl

Briefings in Functional Genomics. 2010. DOI : 10.1093/bfgp/elq023.

Software-reconfigurable universally-applicable microfluidic platform

L. M. FidalgoS. Maerkl

2010. p. 18 - ANYL.

2009

An in vitro microfluidic approach to generating protein-interaction networks

D. GerberS. J. MaerklS. R. Quake

Nature Methods. 2009. DOI : 10.1038/nmeth.1289.

Experimental determination of the evolvability of a transcription factor

S. MaerklS. Quake

Proceedings Of The National Academy Of Sciences Of The United States Of America (PNAS). 2009. DOI : 10.1073/pnas.0907688106.

Integration column: Microfluidic high-throughput screening

S. J. Maerkl

Integrative Biology. 2009. DOI : 10.1039/b819762h.

Integration of plasmonic trapping in a microfluidic environment

L. HuangO. J. F. MartinS. J. Maerkl

Optics Express. 2009. DOI : 10.1364/OE.17.006018.

2008

Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis

S. EinavD. GerberP. BrysonE. SklanM. Elazar  et al.

Nature Biotechnology. 2008. DOI : 10.1038/nbt.1490.

2007

A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors

S. MaerklS. Quake

Science. 2007. DOI : 10.1126/science.1131007.

2002

Microfluidic Large-Scale Integration

T. ThorsenS. MaerklS. Quake

Science. 2002. DOI : 10.1126/science.1076996.

Doctorant·es actuel·les

https://people.epfl.ch/309584?lang=fr, https://people.epfl.ch/328143?lang=fr, https://people.epfl.ch/350750?lang=fr, https://people.epfl.ch/385441?lang=fr

A dirigé les thèses EPFL de

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

Meltem Elitas, Johannes Becker, Zuzana Tatárová, Amanda Verpoorte, Simone Giaveri

Cours

Introduction to bioengineering

EE-526

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

EE-490(j)

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