Publications

Book chapter

Parallel Computations with DNA-encoded Chemical Reaction Networks.
Gines G., Genot A.J., Rondelez Y., Visions of DNA Nanotechnology at 40 for the Next 40, ed. Springer, 2023 (PDF) 

Programmable Ultrasensitive Molecular Amplifier for Digital and Multiplex MicroRNA Quantification
Rondelez Y., Gines G.*, MicroRNA Detection and Target Identification, Methods in Molecular Biology ed. Springer Protocol, 2023.

Programming Spatiotemporal Patterns with DNA‐Based Circuits
Van Der Hofstadt M., Gines G., Galas J.-C., Estevez-Torres A., DNA- and RNA-Based Computing Systems, ed. Wiley-VCH, 2021 (PDF)

Peer-reviewed articles

19 Functional analysis of single enzymes using programmable molecular circuits
Gines G.*, Espada R., Dramé-Maigné A., Baccouche A., Larrouy N., Rondelez Y., Nature Nanotechnology, 2024.

18 In vitro enzyme self-selection using molecular programs
Dramé-Maigné A., Espada R., McCallum G., Sieskind R., Gines G, Rondelez Y., ACS Synthetic Biology, 2024.

17 Silicon chambers for enhanced incubation and imaging of microfluidic droplets
Lobato-Dauzier N., Deteix R., Gines G., Baccouche A., Hapsanto B.N., Okumura S., Mariette G., Belharet D., Queste S., Jalabert L., Denoual M., Rondelez Y., Toshiyoshi  H., Fujita H., Kim S.H., Fujii T., Genot A.J., Lab on a Chip, 2023.

16 Molecular Computation for Molecular Classification
Kieffer C., Genot A.J., Rondelez Y.*, Gines G.*, Advanced Biology, 2023 (PDF)

15 Nonlinear decision-making with enzymatic neural networks
Okumura S., Gines G., Lobato-Dauzier N., Baccouche A., Deteix R., Fujii T., Rondelez Y., A.J. Genot A.J., Nature, 2022

Research Briefing: A deep artificial neural network powered by enzymes

14 Signal-on/signal-off bead-based assays for the multiplexed monitoring of base excision repair activities by flow cytometry – Paper in Forefront
Gines G*., Brusa C., Saint-Pierre C., Gasparutto D., Analytical and Bioanalytical Chemistry, 2022 (PDF, SI)

13 A small-molecule chemical interface for molecular programs
Shenshin V., Lescanne C., Gines G., Rondelez Y., Nucleic Acids Research, 2021 (PDF, SI)

12 Advances in multiplexed techniques for the detection and quantification
of microRNAs
Jet T., Gines G.*, Rondelez Y., Taly V.*, Chemical Society Reviews, 2021 (PDF)

11 Multiplex digital microRNA detection using cross-inhibitory DNA circuits
Rondelez Y., Gines G.*, ACS Sensors, 2020 (PDF, SI) – Editor’s choice

10 Isothermal digital detection of microRNAs using background-free molecular circuit
Gines G.†, Menezes R.†, Nara K., Kirstetter A.-S., Taly V., Rondelez Y., Science Advances, 2020 (PDF) † both authors contributed equally

9 Emergence of isothermal amplification technologies for microRNA biosensing: applications to liquid biopsies.
Gines G., Menezes R., Xiao W., Rondelez Y., Taly V., Molecular Aspect of Medecine, 2020 (PDF)

8 Streamlined digital bioassays with a 3D printed sample changer
Menezes R., Dramé-Maigné A., Taly V., Rondelez Y., Gines G.*, Analyst, 2019 (PDF)

7 Spatiotemporal control of DNA-based chemical reaction network via electrochemical activation in microfluidics
Kurylo I., Gines G., Rondelez Y., Coffinier Y., Vlandas A., Scientific Reports, 2018 (PDF)

6 Synthesis and materialization of a reaction-diffusion French flag pattern
Zadorin A.S., Rondelez Y., Gines G., Dilhal V., Urtel G., Zambrano A., Galas J-C., Esteves-Torres A., Nature Chemistry, 2017 (PDF)

5 Microscopic agents programmed by DNA circuits
Gines G., Zadorin, A.S., Galas, J.-C., Fujii, T., Estevez-Torres, A., Rondelez, Y., Nature Nanotechnology, 2017 (PDF)

News&Views: Nanosystem: Programmed communication
Kandere-Grzybowska K., Grzybowski B.A., Nature Nanotechnology, 2017.

4 Boosting functionality of synthetic DNA circuits with tailored deactivation
Montagne, K., Gines, G., Fujii, T., Rondelez, Y.,”, Nature Communication, 2016 (PDF)

3 Tuning Optical Properties of Functionalized Gold Nanorods through Controlled Interactions with Organic Semiconductors
Ferrier R.C, Gines G., Gasparutto D, Pépin-Donat B., Rannou P., Composto R.J., The Journal of Physical Chemistry, 2015 (PDF)

2 A multiplex assay based on encoded microbeads conjugated to DNA nanobeacons to monitor base excision repair activities by flow cytometry
Gines G., Saint-Pierre C., Gasparutto D., Biosensors and Bioelectronics, 2014 (PDF)

1 On-bead fluorescent DNA nanoprobes to analyze base excision repair activities
Gines G., Saint-Pierre C., Gasparutto D., Analytica Chemica Acta, 2014 (PDF)

Proceedings

Emergence of structures from parasitic species in a spatially distributed molecular system
Aubert-Kato N., Gines G., Fujii T., Rondelez Y., ALIFE 2021, 2021

Evolutionary Optimization of Self-Assembly in Swarm of Bio-micro-robots
Aubert-Kato N., Bredeche N., Cazenille L., Dinh H., Fosseprez C., Gines G., Kawamata I., Hagiya M., Rondelez Y., GECCO2017 59–66., Berlin, 2017 (nominated for the best paper award)

On-support fluorescent assays based on functionalized oligonucleotides to monitor specific DNA repair activities
Gines, G., Flaender, M., Desiron, C., Saint-Pierre, C., Gasparutto, D.,”. Collection Czechoslov Chemical Communication. 12, 327–329., ČeskýKrumlov, 2011

Thesis manuscript

On beads fluorescent assays based on functionalized DNA nanoprobes : new biosensors to monitor specific DNA repair activities
Gines G., Thesis manuscript, 2013.