LBNC | Laboratory of Biological Network Characterization

Publications

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
HTML

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
HTML

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
HTML
ACS Synthetic Biology, DOI: 10.1021/acssynbio.3c00390
HTML

68. On biochemical constructors and synthetic cells

Sebastian Josef Maerkl
Interface Focus, DOI: 10.1098/rsfs.2023.0014
HTML

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
HTML
Applications in Plant Sciences, DOI: 10.1002/aps3.11529
HTML

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
HTML
ACS Synthetic Biology, DOI: 10.1021/acssynbio.2c00453
HTML

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
HTML
Scientific Reports, DOI: 10.1038/s41598-022-25895-8
HTML

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
HTML
PLoS One, DOI: 10.1371/journal.pone.0283149
HTML

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
HTML
PNAS, DOI: 10.1073/pnas.2212151120
HTML

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
HTML

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
HTML

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
HTML
Frontiers in Biotechnology and Bioengineering, DOI: 10.3389/fbioe.2022.918659
HTML

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
HTML
Nature Communications, DOI: 10.1038/s41467-022-32971-0
HTML

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
HTML
PLoS One, DOI: 10.1371/journal.pone.0272663
HTML

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
HTML
ACS Sensors, DOI: 10.1021/acssensors.1c01935
HTML

56. OnePot PURE Cell-Free System

Laura Grasemann*, Barbora Lavickova*, M. Carolina Elizondo-Cantú and Sebastian J. Maerkl
JoVE, DOI: 10.3791/62625
HTML

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
HTML
BioDesign Research, DOI: 10.34133/2021/2968181
HTML

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
HTML
PNAS, DOI: 10.1073/pnas.2025289118
HTML

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
HTML
Advanced Materials, DOI: 10.1002/adma.202104581
HTML

52. A partially self-regenerating synthetic cell

Barbora Lavickova, Nadanai Laohakunakorn, and Sebastian J. Maerkl
bioRxiv, DOI: 10.1101/2020.07.03.185900
HTML
Nature Communications, DOI: 10.1038/s41467-020-20180-6
HTML

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
HTML

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
HTML
Frontiers in Biotechnology and Bioengineering DOI: 10.3389/fbioe.2020.00213
HTML

49. How single-cell immunology is benefitting from microfluidic technologies.

Fabien Jammes and Sebastian J. Maerkl
Preprint DOI: 10.5281/zenodo.3529331
HTML
Microsystems and Nanoengineering DOI: 10.1038/s41378-020-0140-8
HTML

48. Microfluidic systems for cancer diagnostics.

Jose L. Garcia-Cordero and Sebastian J. Maerkl
Preprint DOI: 10.5281/zenodo.3521198
HTML
Current Opinion in Biotechnology DOI: 10.1016/j.copbio.2019.11.022
HTML

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
HTML

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
HTML PDF
Methods in Molecular Biology DOI: 10.1007/978-1-0716-1032-9_9
HTML

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.
HTML PDF

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
HTML PDF
ACS Synthetic Biology DOI: 10.1021/acssynbio.8b00427
Featured: Most Read Articles List.
HTML PDF

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

Zoe Swank*, Nadanai Laohakunakorn* and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/247627
HTML PDF
PNAS DOI: 10.1073/pnas.1816591116
Featured: EPFL News, EurekAlert, Phys.org, ScienceDaily.
HTML PDF

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
HTML PDF
Scientific Reports DOI: 10.1038/s41598-018-26542-x
HTML PDF

41. Microfluidic Transfection for High-Throughput Mammalian Protein Expression.

Kristina Woodruff and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/200261
HTML PDF
Methods in Molecular Biology DOI: 10.1007/978-1-4939-8730-6_13
HTML

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
HTML PDF
Analytical Chemistry. DOI: 10.1021/acs.analchem.7b04099
HTML PDF

39. A microfluidic biodisplay.

Francesca Volpetti*, Ekaterina Petrova* and Sebastian J. Maerkl
bioRxiv DOI: 10.1101/112110
HTML PDF
ACS Synthetic Biology. DOI: 10.1021/acssynbio.7b00088
HTML PDF

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
HTML PDF

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
HTML PDF

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

Kristina Woodruff and Sebastian J. Maerkl
Scientific Reports DOI: 10.1038/srep23937
HTML PDF

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
HTML PDF

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
HTML PDF
Nucleic Acids Research DOI: 10.1093/nar/gkv1497
HTML PDF

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
HTML PDF
ACS Synthetic Biology. DOI: 10.1021/acssynbio.6b00017
HTML PDF

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
HTML PDF
eLife. DOI: 10.7554/eLife.09771
HTML PDF

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
HTML PDF ResearchGate

30. A microfluidic platform for high-throughput multiplexed protein quantitation.

Volpetti F., Garcia-Cordero J.L. and Maerkl S.J.
arXiv arXiv:1410.5377v1
HTML PDF
PLoS One. DOI: 10.1371/journal.pone.0117744
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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.
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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

HTML PDF ResearchGate

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
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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
HTML PDF ResearchGate

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

HTML PDF

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

HTML PDF

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
HTML PDF

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
HTML PDF

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
HTML PDF

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
HTML PDF

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

HTML PDF

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.

HTML PDF

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.

HTML PDF

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

HTML PDF

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
HTML PDF

9. Experimental strategies for studying transcription factor-DNA binding specificities.

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

HTML PDF

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

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

HTML PDF

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
HTML PDF

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

HTML PDF

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

HTML PDF

4. Integration column: Microfluidic high-throughput screening.

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

HTML PDF

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
HTML PDF

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
HTML PDF

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)
HTML PDF