LBNC | Laboratory of Biological Network Characterization

Publications

75. Regulatory Components for Bacterial Cell-Free Systems Engineering.

Pao-Wan Lee and Sebastian J. Maerkl
ACS Synthetic Biology, DOI: 10.1021/acssynbio.4c00574
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74. Long-term protein synthesis with PURE in a mesoscale dialysis system.

Laura Roset Julià, Laura Grasemann, Francesco Stellacci and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2024.09.09.611992
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73. Nature-Inspired Recycling of a Protein Mixture into a Green Fluorescent Protein-based hydrogel.

Laura Roset Julià, Sebastian J. Maerkl and Francesco Stellacci
RSC Sustainability, DOI: 10.1039/D4SU00212A
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72. A comprehensive review of microfluidic approaches in cell-free synthetic biology.

Amogh Kumar Baranwal and Sebastian J. Maerkl
Frontiers in Synthetic Biology, DOI: 10.3389/fsybi.2024.1397533
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71. Targeting protein-ligand neosurfaces using a generalizable deep learning approach

Anthony Marchand, Stephen Buckley, Arne Schneuing, Martin Pacesa, Pablo Gainza, Evgenia Elizarova, Rebecca M. Neeser, Pao-Wan Lee, Luc Reymond, Maddalena Elia, Leo Scheller, Sandrine Georgeon, Joseph Schmidt, Philippe Schwaller, Sebastian J. Maerkl, Michael Bronstein, Bruno E. Correia
bioRxiv, DOI: 10.1101/2024.03.25.585721
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70. Towards self-regeneration: exploring the limits of protein synthesis in the PURE cell-free transcription-translation system

Ragunathan Bava Ganesh and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2024.04.03.587879
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ACS Synthetic Biology, DOI: 10.1021/acssynbio.4c00304
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69. C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System

Laura Grasemann, Paula Thiel Pizarro and Sebastian J Maerkl
bioRxiv, DOI: 10.1101/2023.06.26.546530
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ACS Synthetic Biology, DOI: 10.1021/acssynbio.3c00390
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68. On biochemical constructors and synthetic cells

Sebastian Josef Maerkl
Interface Focus, DOI: 10.1098/rsfs.2023.0014
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67. A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical survey and monitoring

Jonathan Selz, Nicolas R. Adam, Celine E.M. Magrini, Fulvia Malvido Montandon, Sven Buerki, and Sebastian Josef Maerkl
bioRxiv, DOI: 10.1101/2023.01.09.523204
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Applications in Plant Sciences, DOI: 10.1002/aps3.11529
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66. Improved cell-free transcription-translation reactions in microfluidic chemostats augmented with hydrogel membranes for continuous small molecule dialysis

Barbora Lavickova, Laura Grasemann, and Sebastian J Maerkl
bioRxiv, DOI: 10.1101/2022.08.23.504913
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ACS Synthetic Biology, DOI: 10.1021/acssynbio.2c00453
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65. Direct encapsulation of biomolecules in semi-permeable microcapsules produced with double-emulsions

Grégoire Michielin and Sebastian J Maerkl
bioRxiv, DOI: 10.1101/2022.06.23.497329
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Scientific Reports, DOI: 10.1038/s41598-022-25895-8
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64. 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

Grégoire Michielin, Fatemeh Arefi, Olha Puhach, Mathilde Bellon, Pascale Sattonnet, Arnaud L'Huillier, Isabella Eckerle, Benjamin Meyer, and Sebastian J Maerkl
medRxiv, DOI: 10.1101/2022.06.09.22276142
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PLoS One, DOI: 10.1371/journal.pone.0283149
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63. Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Hon Ming Yip, Shiyu Cheng, Evan J. Olson, Michael Crone, and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2022.05.26.493535
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PNAS, DOI: 10.1073/pnas.2212151120
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62. An automated do-it-yourself system for dynamic stem cell and organoid culture in standard multi-well plates

Julia Tischler, Zoe Swank, Hao-An Hsiung, Stefano Vianello, Matthias P Lutolf and Sebastian J Maerkl
Cell Reports Methods, DOI: 10.1016/j.crmeth.2022.100244
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61. Epidemiological investigation of a SARS-CoV-2 Omicron variant outbreak in a primary school

Elsa Lorthe, Mathilde Bellon, Julie Berthelot, Grégoire Michielin, Arnaud G. L’Huillier, Klara M. Posfay-Barbe, Andrew S. Azman, Idris Guessous, Sebastian J. Maerkl, Isabella Eckerle, and Silvia Stringhini
The Lancet Infectious Diseases, DOI: 10.1016/S1473-3099(22)00267-5
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60. Biochemistry of aminoacyl tRNA synthetase and tRNAs and their engineering for cell-free and synthetic cell applications

Ragunathan Bava Ganesh, and Sebastian J. Maerkl
Zenodo.org, DOI: 10.5281/zenodo.6452569
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Frontiers in Biotechnology and Bioengineering, DOI: 10.3389/fbioe.2022.918659
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59. Systematic analysis of low-affinity transcription factor binding site clusters in vitro and in vivo establishes their functional relevance

Amir Shahein, Maria López-Malo, Ivan Istomin, Evan J. Olson, Shiyu Cheng and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2021.12.17.473130
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Nature Communications, DOI: 10.1038/s41467-022-32971-0
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58. Epidemiological, virological and serological investigation into a SARS-CoV-2 outbreak (Alpha variant) in a primary school in Geneva, Switzerland: a prospective longitudinal study

Elsa Lorthe, Mathilde Bellon, Grégoire Michielin, Julie Berthelot, María-Eugenia Zaballa, Francesco Pennacchio, Meriem Bekliz, Florian Laubscher, Fatemeh Arefi, Javier Perez-Saez, Andrew S Azman, Arnaud G L’Huillier, Klara M Posfay-Barbe, Laurent Kaiser, Idris Guessous, Sebastian Maerkl, Isabella Eckerle, Silvia Stringhini, SEROCoV-Schools Study Group
medRxiv, DOI: 10.1101/2021.10.26.21265509
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PLoS One, DOI: 10.1371/journal.pone.0272663
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57. High-throughput single-cell TCR - pMHC dissociation rate measurements performed by an autonomous microfluidic cellular processing unit

Fabien Jammes, Julien Schmidt, George Coukos and Sebastian J. Maerkl
BioRxiv, DOI: 10.1101/2021.06.30.450499
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ACS Sensors, DOI: 10.1021/acssensors.1c01935
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56. OnePot PURE Cell-Free System

Laura Grasemann*, Barbora Lavickova*, M. Carolina Elizondo-Cantú and Sebastian J. Maerkl
JoVE, DOI: 10.3791/62625
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55. CFPU: a cell-free processing unit for high-throughput, automated in vitro circuit characterization

Zoe Swank and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2020.12.04.411470
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BioDesign Research, DOI: 10.34133/2021/2968181
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54. A high-throughput microfluidic nano-immunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultra-low volume dried blood samples

Zoe Swank, Grégoire Michielin, Hon Ming Yip, Patrick Cohen, Diego O. Andrey, Nicolas Vuilleumier, Laurent Kaiser, Isabella Eckerle*, Benjamin J. Meyer*, and Sebastian J. Maerkl*
medRxiv, DOI: 10.1101/2020.10.07.20208280
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PNAS, DOI: 10.1073/pnas.2025289118
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53. Nature-inspired Circular-economy Recycling (NaCRe) for Proteins: Proof of Concept

Simone Giaveri, Adeline M. Schmitt, Laura Roset Julia, Anna Murello, Laure Menin, Daniel Ortiz, Luc Patiny, Sreenath Bolisetty, Raffaele Mezzenga, Sebastian J. Maerkl*, Francesco Stellacci*
bioRxiv, DOI: 10.1101/2020.09.23.309799
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Advanced Materials, DOI: 10.1002/adma.202104581
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52. A partially self-regenerating synthetic cell

Barbora Lavickova, Nadanai Laohakunakorn, and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2020.07.03.185900
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Nature Communications, DOI: 10.1038/s41467-020-20180-6
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51. Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

Poonam Bheda, Diana Aguilar-Gomez, Nils B. Becker, Johannes Becker, Emmanouil Stavrou, Igor Kukhtevich, Thomas Hoefer, Sebastian J. Maerkl, Gilles Charvin, Carsten Marr, Antonis Kirmizis, and Robert Schneider
Molecular Cell, DOI: 10.1016/j.molcel.2020.04.016
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50. Bottom-up construction of complex biological systems with cell-free synthetic biology

Nadanai Laohakunakorn, Laura Grasemann, Barbora Lavickova, Gregoire Michielin, Amir Shahein, Zoe Swank, and Sebastian J. Maerkl
Preprint DOI: 10.5281/zenodo.3591964
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Frontiers in Biotechnology and Bioengineering DOI: 10.3389/fbioe.2020.00213
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49. How single-cell immunology is benefitting from microfluidic technologies.

Fabien Jammes and Sebastian J. Maerkl
Preprint DOI: 10.5281/zenodo.3529331
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Microsystems and Nanoengineering DOI: 10.1038/s41378-020-0140-8
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48. Microfluidic systems for cancer diagnostics.

Jose L. Garcia-Cordero and Sebastian J. Maerkl
Preprint DOI: 10.5281/zenodo.3521198
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Current Opinion in Biotechnology DOI: 10.1016/j.copbio.2019.11.022
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47. A Multilayer Microfluidic Platform for the Conduction of Prolonged Cell-Free Gene Expression.

Ardjan J. van der Linden, Maaruthy Yelleswarapu, Pascal A. Pieters, Zoe Swank, Wilhlem T.S. Huck, Sebastian J. Maerkl and Tom F.A. de Greef
Jove
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46. Steady-state cell-free gene expression with microfluidic chemostats.

Nadanai Laohakunakorn, Barbora Lavickova, Zoe Swank, Julie Laurent, and Sebastian J. Maerkl
protocols.io DOI: 10.17504/protocols.io.46wgzfe
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Methods in Molecular Biology DOI: 10.1007/978-1-0716-1032-9_9
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45. Cascaded amplifying circuits enable ultrasensitive cellular sensors for toxic metals.

Xinyi Wan, Francesca Volpetti, Ekaterina Petrova, Chris French, Sebastian J. Maerkl and Baojun Wang
Nature Chemical Biology DOI: 10.1038/s41589-019-0244-3
Featured: U. Edinburgh News, EurekAlert, Phys.org, Yahoo! News.
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44. A simple, robust, and low-cost method to produce the PURE cell - free system.

Barbora Lavickova and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/420570
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ACS Synthetic Biology DOI: 10.1021/acssynbio.8b00427
Featured: Most Read Articles List.
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43. Cell-free gene regulatory network engineering with synthetic transcription factors.

Zoe Swank*, Nadanai Laohakunakorn* and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/247627
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PNAS DOI: 10.1073/pnas.1816591116
Featured: EPFL News, EurekAlert, Phys.org, ScienceDaily.
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42. Microfluidic device for on-chip mixing and encapsulation of lysates.

Jui-Cha Chang, Zoe Swank, Oliver Keiser, Sebastian J. Maerkl, and Esther Amstad
bioRxiv DOI: 10.1101/247627
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Scientific Reports DOI: 10.1038/s41598-018-26542-x
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41. Microfluidic Transfection for High-Throughput Mammalian Protein Expression.

Kristina Woodruff and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/200261
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Methods in Molecular Biology DOI: 10.1007/978-1-4939-8730-6_13
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40. A microfluidic module for real-time generation of complex multi-molecule temporal concentration profiles.

Kristina Woodruff and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/119701
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Analytical Chemistry. DOI: 10.1021/acs.analchem.7b04099
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39. A microfluidic biodisplay.

Francesca Volpetti*, Ekaterina Petrova* and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/112110
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ACS Synthetic Biology. DOI: 10.1021/acssynbio.7b00088
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38. Single Molecule Localisation and Discrimination of DNA-Protein Complexes by Controlled Translocation Through Nanocapillaries.

Roman D. Bulushev*, Sanjin Marion*, Ekaterina Petrova*, Sebastian James Davis, Sebastian J. Maerkl and Aleksandra Radenovic
Nano Letters DOI: 10.1021/acs.nanolett.6b04165
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37. Microfluidic co-culture platform to quantify chemotaxis of primary stem cells

Zuzana Tatarova, Jean-Paul Abbuehl, Sebastian Maerkl and Joerg Huelsken
LOC DOI: 10.1039/C6LC00236F
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36. A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing.

Kristina Woodruff and Sebastian J. Maerkl
Scientific Reports DOI: 10.1038/srep23937
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35. A Digital-Analog Microfluidic Platform for Patient-Centric Multiplexed Biomarker Diagnostics of Ultra-Low Volume Samples.

Francesco Piraino*, Francesca Volpetti*, Craig Watson, and Sebastian J. Maerkl
ACS Nano DOI: 10.1021/acsnano.5b07939
Featured in: EurekAlert, The Times of India, RTS, SwissInfo, gizmag, EPFL News
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34. Integrating Gene Synthesis and Microfluidic Protein Analysis for Rapid Protein Engineering.

Matthew C Blackburn, Ekaterina Petrova, Bruno E Correia, Sebastian J. Maerkl
bioRxiv. DOI: 10.1101/025239
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Nucleic Acids Research DOI: 10.1093/nar/gkv1497
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33. GreA and GreB enhance Escherichia coli RNA polymerase transcription rate in a reconstituted transcription-translation system.

Lea L. De Maddalena, Henrike Niederholtmeyer, Matti Turtola, Zoe Swank, Georgiy A. Belogurov, Sebastian J. Maerkl
bioRxiv. DOI: 10.1101/024604
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ACS Synthetic Biology. DOI: 10.1021/acssynbio.6b00017
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32. Rapid cell-free forward engineering of novel genetic ring oscillators

Henrike Niederholtmeyer*, Zachary Sun*, Yutaka Hori, Enoch Yeung, Amanda Verpoorte, Richard M Murray and Sebastian J Maerkl
bioRxiv. DOI: 10.1101/018317
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eLife. DOI: 10.7554/eLife.09771
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31. Mechanically Induced Trapping of Molecular Interactions and Its Applications.

Garcia-Cordero J.L. and Maerkl S.J.
Journal of Laboratory Automation. DOI: 10.1177/2211068215578586
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30. A microfluidic platform for high-throughput multiplexed protein quantitation.

Volpetti F., Garcia-Cordero J.L. and Maerkl S.J.
arXiv arXiv:1410.5377v1
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PLoS One. DOI: 10.1371/journal.pone.0117744
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29. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription.

Knight B., Kubik S., Ghosh B., Bruzzone M.J., Geertz M., Martin V., Denervaud N., Jacquet P., Ozkan B., Rougemont J., Maerkl S.J., Naef F., and Shore D.
Genes & Development. DOI: 10.1101/gad.244434.114
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28. LSPR Chip for Parallel, Rapid, and Sensitive Detection of Cancer Markers in Serum.

Acimovic S.S., Ortega M.A., Sanz V., Berthelot J., Garcia-Cordero J.L., Renger J., Maerkl S.J., Kreuzer M., and Quidant R.
Nano Letters. DOI: 10.1021/nl500574n
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27. Long-Term Single Cell Analysis of S. pombe on a Microfluidic Microchemostat Array.

Nobs J.B. and Maerkl S.J.
PLoS One. DOI: 10.1371/journal.pone.0093466.
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26. A 1,024-sample serum analyzer chip for cancer diagnostics.

Garcia-Cordero J.L. and Maerkl S.J.
Lab on a Chip. DOI: 10.1039/C3LC51153G.
Featured in: LOC Top 10%, ChemistryWorld, LOC most downloaded articles, Lab on a Chip Blog
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25. Implementation of cell-free biological networks at steady-state.

Niederholtmeyer H., Stepanova V., and Maerkl S.J.
PNAS 110(40):15985-15990. DOI: 10.1073/pnas.1311166110

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

Denervaud N., Becker J., Delgado-Gonzalo R., Damay P., Rajkumar A.S., Unser M., Shore D., Naef F. and Maerkl S.J.
PNAS 110(39):15614-15619. DOI:10.1073/pnas.1308265110
Featured in: LOC Research Highlights, Molecular Systems Biology Editor's Selection, GenomeWeb
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23. Mapping the fine structure of a eukaryotic promoter input-output function.

Rajkumar A., Dénervaud N., and Maerkl S.J.
Nature Genetics 45(10):1207-1215. DOI:10.1038/ng.2729
Featured in: Nature Methods, EPFL News, Scicasts, MedicalExpress, Radio Canada
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22. Live Mammalian Cell Arrays.

Woodruff K.*, Fidalgo L.M.*, Gobaa S., Lutolf M.P., and Maerkl S.J.
Nature Methods 10(6):550-552. DOI:10.1038/nmeth.2473.
Highlighted in: Faculty of 1000
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21. A high-throughput nanoimmunoassay chip applied to large-scale vaccine adjuvant screening.

Garcia-Cordero J.L., Nembrini C., Stano A., Hubbell J.A., and Maerkl S.J.
Integrative Biology 5(4):650-658. DOI: 10.1039/C3IB20263A
Featured in: Inside Front Cover, Most Read Articles, Top Ten Most Accessed Papers in Q2 2013
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20. Real-time mRNA measurement during an in vitro transcription and translation reaction using binary probes.

Niederholtmeyer H., Xu L. and Maerkl S.J.
ACS Synthetic Biology 2(8):411-417. doi: 10.1021/sb300104f

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

Rockel S., Geertz M., Hens K., Deplancke B. and Maerkl S.J.
Nucleic Acids Research 41(4):e52. doi:10.1093/nar/gks1323

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

Garcia-Cordero J.L. and Maerkl S.J.
Chem. Commun 49(13):1264-1266. doi:10.1039/C2CC37740C
Featured in: Inside Front Cover
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17. Massively Parallel Measurements of Molecular Interaction Kinetics on a Microfluidic Platform.

Geertz M., Shore D., and Maerkl S.J.
PNAS 109(41):16540-16545. doi:10.1073/pnas.1206011109
Featured in: Radio Canada, EPFL News, Science Daily, American Society for Biochemistry and Molecular Biology Blog, Phys.org
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16. Topology and Dynamics of the Zebrafish Segmentation Clock Core Circuit.

Schroeter C, Ares S., Morelli L.G., Isakova A., Hens K., Soroldoni D., Gajewski M., Juelicher F., Maerkl S.J., Deplancke B., and Oates A.
PLoS Biology 10(7): e1001364. doi:10.1371/journal.pbio.1001364
Highlighted in: Nature Reviews Genetics
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15. Rapid Synthesis Of Defined Eukaryotic Promoter Libraries.

Rajkumar A.S. and Maerkl S.J.
ACS Synthetic Biology 1(10):483-490. doi:10.1021/sb300045j
Highlighted in: Top 5 most read articles
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14. Probing the Informational and Regulatory Plasticity of a Transcription Factor DNA–Binding Domain.

Shultzaberger R.K., Maerkl S.J., Kirsch J.F., Eisen M.B.
PLoS Genetics, 8(3): e1002614. doi:10.1371/journal.pgen.1002614

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13. A high-throughput microfluidic method for generating and characterizing transcription factor mutant libraries.

Geertz M., Rockel S., and Maerkl S.J.
Methods in Molecular Biology, 813:107-23.

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12. MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor-DNA Interaction.

Rockel S., Geertz M., and Maerkl S.J.
Methods in Molecular Biology, 786:97-114.

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11. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules

He B., Holloway A., Maerkl S.J. and Kreitman M.
PLoS Genetics, 7:p. e1002053

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10. A software-programmable microfluidic device for automated biology.

Fidalgo L.M. and Maerkl S.J.
Lab on a Chip, 11:p. 1612.
Featured in: Top 10 most accessed paper in March 2011
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9. Experimental strategies for studying transcription factor-DNA binding specificities.

Geertz M. and Maerkl S.J.
Briefings in Functional Genomics.

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8. Next generation microfluidic platforms for high-throughput protein biochemistry.

Maerkl, S.J.
Current Opinion in Biotechnology, Sep 8

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7. Experimental determination of the evolvability of a transcription factor.

Maerkl, S.J. and Quake S.R.
PNAS, 106(44):p. 18650-5
Highlighted in: Faculty of 1000
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6. Integration of plasmonic trapping in a microfluidic environment.

Huang, L., S.J. Maerkl, and Martin O.J.
Optics Express, 17(8): p. 6018-24

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5. An in vitro microfluidic approach to generating protein-interaction networks.

Gerber, D., S.J. Maerkl, and Quake S.R.
Nature Methods, 6(1): p. 71-4

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4. Integration column: Microfluidic high-throughput screening.

Maerkl, S.J.
Integrative Biology, 1(1): p. 19-29

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

Einav, S.*, D. Gerber*, P.D. Bryson, E.H. Sklan, M. Elazar, S.J. Maerkl, J.S. Glenn, and Quake S.R.
Nature Biotechnology, 26(9): p. 1019-1027
Featured in: Cover, Chemistry World
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2. A systems approach to measuring the binding energy landscapes of transcription factors.

Maerkl, S.J. and Quake S.R.
Science, 315(5809): p. 233-237
Highlighted in: Scientific American, Chemical & Engineering News, HHMI News, Nature Methods, Biopolymers
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1. Microfluidic large-scale integration.

Thorsen, T., S.J. Maerkl, and Quake S.R.
Science, 298(5593): p. 580-584
Highlighted in: Cover, Science Express, Highlighted in: Faculty of 1000, Chemical & Engineering News, Nature Science Update, Technology Research News, Science Watch Top 10, ESI-Topics: Microfluidic Devices Top 10 papers (2007)
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