Preprints
BAR-CAT: Targeted Recovery of Synthetic Genes via Barcode-Directed CRISPR-dCas9 Enrichment
Villegas NK, Tran MH, Keller A, Plesa C
bioRxiv 2025;. doi: 10.1101/2025.06.27.658158
bioRxiv preprint: 10.1101/2025.06.27.658158 - supplementary info
Optimizing in vitro Transcribed CRISPR-Cas9 Single-Guide RNA Libraries for Improved Uniformity and Affordability
Villegas NK, Gaudreault YR, Keller A, Kearns P, Stapleton JA, Plesa C
bioRxiv 2025;. doi: 10.1101/2025.03.24.644170
bioRxiv preprint: 10.1101/2025.03.24.644170 - supplementary info
Degenerate DropSynth for Simultaneous Assembly of Diverse Gene Libraries and Local Designed Mutants
Holston AS, Hinton SR, Lindley KA, Kearns NC, Plesa C.
bioRxiv 2023;. doi: 10.1101/2023.12.11.569291
bioRxiv preprint: 10.1101/2023.12.11.569291 - supplementary info - code - project website: dropsynth.org
Villegas NK, Tran MH, Keller A, Plesa C
bioRxiv 2025;. doi: 10.1101/2025.06.27.658158
bioRxiv preprint: 10.1101/2025.06.27.658158 - supplementary info
Optimizing in vitro Transcribed CRISPR-Cas9 Single-Guide RNA Libraries for Improved Uniformity and Affordability
Villegas NK, Gaudreault YR, Keller A, Kearns P, Stapleton JA, Plesa C
bioRxiv 2025;. doi: 10.1101/2025.03.24.644170
bioRxiv preprint: 10.1101/2025.03.24.644170 - supplementary info
Degenerate DropSynth for Simultaneous Assembly of Diverse Gene Libraries and Local Designed Mutants
Holston AS, Hinton SR, Lindley KA, Kearns NC, Plesa C.
bioRxiv 2023;. doi: 10.1101/2023.12.11.569291
bioRxiv preprint: 10.1101/2023.12.11.569291 - supplementary info - code - project website: dropsynth.org
Publications
See full list on Google Scholar
Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning
Romanowicz KJ, Resnick C, Hinton SR, Plesa C.
Sci. Adv. 11, eadw9178 (2025). DOI: 10.1126/sciadv.adw9178
bioRxiv preprint: 10.1101/2025.01.23.634126 - supplementary info - code
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Sidore AM*, Plesa C*, Samson JA, Kosuri S.
Nucleic Acids Res. 2020 Jul 21;. doi: 10.1093/nar/gkaa600
bioRxiv preprint: 10.1101/740977 - supplementary info - project website: dropsynth.org
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Plesa C*, Sidore AM*, Lubock N, Zhang D, Kosuri S.
Science. 2018 Jan 19;359(6373):343-347. doi: 10.1126/science.aao5167
bioRxiv preprint: 10.1101/163550 - supplementary info - code - project website: dropsynth.org
Direct observation of DNA knots using a solid-state nanopore
Plesa C, Verschueren D, Pud S, van der Torre J, Ruitenberg JW, Witteveen MJ, Jonsson MP, Grosberg AY, Rabin Y, Dekker C.
Nat Nanotechnol. 2016 Dec;11(12):1093-1097. doi: 10.1038/nnano.2016.153
Self-aligned plasmonic nanopores by optically controlled dielectric breakdown
S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M. P. Jonsson, and C. Dekker
Nano Letters 15 (10) pp 7112-7117, 2015. doi: 10.1021/acs.nanolett.5b03239
Single-molecule sensing with nanopores
M. Muthukumar, C. Plesa, and C. Dekker
Physics Today, 68 (8) 40, 2015 doi: 10.1063/PT.3.2881
DNA nanopore translocation in glutamate solutions
Plesa C, van Loo N, Dekker C.
Nanoscale. 2015 Aug 28;7(32):13605-9. doi: 10.1039/C5NR02793D
Detection of Individual Proteins Bound along DNA Using Solid-State Nanopores
Plesa C, Ruitenberg JW, Witteveen MJ, Dekker C.
Nano Lett. 2015 May 13;15(5):3153-8. doi: 10.1021/acs.nanolett.5b00249
Data analysis methods for solid-state nanopores
Plesa C, Dekker C.
Nanotechnology. 2015 Feb 27;26(8):084003. doi: 10.1088/0957-4484/26/8/084003
Velocity of DNA during translocation through a solid-state nanopore
Plesa C, van Loo N, Ketterer P, Dietz H, Dekker C.
Nano Lett. 2015 Jan 14;15(1):732-7. doi: 10.1021/nl504375c
Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores
C. Plesa, A.N. Ananth, V. Linko, C. Gu ̈lcher, A.J. Katan, H. Dietz, and C. Dekker
ACS Nano 8 (1), 35-43, 2013. doi: 10.1021/nn405045x
Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore
Plesa C, Cornelissen L, Tuijtel MW, Dekker C.
Nanotechnology. 2013 Nov 29;24(47):475101. doi: 10.1088/0957-4484/24/47/475101
Fast translocation of proteins through solid state nanopores
Plesa C, Kowalczyk SW, Zinsmeester R, Grosberg AY, Rabin Y, Dekker C.
Nano Lett. 2013 Feb 13;13(2):658-63. doi: 10.1021/nl3042678
Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography
X. J.A. Janssen, M.P. Jonsson, C. Plesa, G.V. Soni, C. Dekker and N.H. Dekker
Nanotechnology 23, 475302, 2012. doi: 10.1088/0957-4484/23/47/475302
Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
E.P. Lundberg, C. Plesa, L.M. Wilhelmsson, P. Lincoln, T. Brown, and B. Norden
ACS Nano 5 (9), 7565-7575, 2011. doi: 10.1021/nn202568q
Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning
Romanowicz KJ, Resnick C, Hinton SR, Plesa C.
Sci. Adv. 11, eadw9178 (2025). DOI: 10.1126/sciadv.adw9178
bioRxiv preprint: 10.1101/2025.01.23.634126 - supplementary info - code
DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions
Sidore AM*, Plesa C*, Samson JA, Kosuri S.
Nucleic Acids Res. 2020 Jul 21;. doi: 10.1093/nar/gkaa600
bioRxiv preprint: 10.1101/740977 - supplementary info - project website: dropsynth.org
Multiplexed Gene Synthesis in Emulsions for Exploring Protein Functional Landscapes
Plesa C*, Sidore AM*, Lubock N, Zhang D, Kosuri S.
Science. 2018 Jan 19;359(6373):343-347. doi: 10.1126/science.aao5167
bioRxiv preprint: 10.1101/163550 - supplementary info - code - project website: dropsynth.org
Direct observation of DNA knots using a solid-state nanopore
Plesa C, Verschueren D, Pud S, van der Torre J, Ruitenberg JW, Witteveen MJ, Jonsson MP, Grosberg AY, Rabin Y, Dekker C.
Nat Nanotechnol. 2016 Dec;11(12):1093-1097. doi: 10.1038/nnano.2016.153
Self-aligned plasmonic nanopores by optically controlled dielectric breakdown
S. Pud, D. Verschueren, N. Vukovic, C. Plesa, M. P. Jonsson, and C. Dekker
Nano Letters 15 (10) pp 7112-7117, 2015. doi: 10.1021/acs.nanolett.5b03239
Single-molecule sensing with nanopores
M. Muthukumar, C. Plesa, and C. Dekker
Physics Today, 68 (8) 40, 2015 doi: 10.1063/PT.3.2881
DNA nanopore translocation in glutamate solutions
Plesa C, van Loo N, Dekker C.
Nanoscale. 2015 Aug 28;7(32):13605-9. doi: 10.1039/C5NR02793D
Detection of Individual Proteins Bound along DNA Using Solid-State Nanopores
Plesa C, Ruitenberg JW, Witteveen MJ, Dekker C.
Nano Lett. 2015 May 13;15(5):3153-8. doi: 10.1021/acs.nanolett.5b00249
Data analysis methods for solid-state nanopores
Plesa C, Dekker C.
Nanotechnology. 2015 Feb 27;26(8):084003. doi: 10.1088/0957-4484/26/8/084003
Velocity of DNA during translocation through a solid-state nanopore
Plesa C, van Loo N, Ketterer P, Dietz H, Dekker C.
Nano Lett. 2015 Jan 14;15(1):732-7. doi: 10.1021/nl504375c
Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores
C. Plesa, A.N. Ananth, V. Linko, C. Gu ̈lcher, A.J. Katan, H. Dietz, and C. Dekker
ACS Nano 8 (1), 35-43, 2013. doi: 10.1021/nn405045x
Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore
Plesa C, Cornelissen L, Tuijtel MW, Dekker C.
Nanotechnology. 2013 Nov 29;24(47):475101. doi: 10.1088/0957-4484/24/47/475101
Fast translocation of proteins through solid state nanopores
Plesa C, Kowalczyk SW, Zinsmeester R, Grosberg AY, Rabin Y, Dekker C.
Nano Lett. 2013 Feb 13;13(2):658-63. doi: 10.1021/nl3042678
Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography
X. J.A. Janssen, M.P. Jonsson, C. Plesa, G.V. Soni, C. Dekker and N.H. Dekker
Nanotechnology 23, 475302, 2012. doi: 10.1088/0957-4484/23/47/475302
Nanofabrication Yields. Hybridization and Click-Fixation of Polycyclic DNA Nanoassemblies
E.P. Lundberg, C. Plesa, L.M. Wilhelmsson, P. Lincoln, T. Brown, and B. Norden
ACS Nano 5 (9), 7565-7575, 2011. doi: 10.1021/nn202568q