Evolution

Our current research focuses on enzymes and antibodies as experimental models to tackle fundamental questions related to bio-molecule function and evolution. Our large-scale experiments are based on droplet microfluidics, phage display and high-throughput DNA sequencing technologies, and downstream statistical analysis. Our approaches are strongly motivated by computational analysis of genomic data and theory inspired by statistical physics.

We work in close collaboration with Olivier Rivoire (Statistical Biology, Gulliver-ESPCI).

Current Group:

- CNRS researcher: Clément Nizak

- PhD students: Shoichi Yip, Matilde Pattanaro

- M1 intern: Cerdane Vayssier

Past members

- Postdoc: Viktor Zahoransky

- PhD student: Angelo Charry, Amaury Paveyranne

- M1 interns: Claire Hülsemann, Capucine Samama, Mirka Abbes, Timothé Lucas

Recent publications

2025

• 1.D. Genettais, C. Bernard, F. Geoffroy, C. Nizak* & S. Adiba*. Continuous emergence of phototaxis in Dictyostelium discoideum. PLOS One 20, e0321614 (2025). (* corres. authors).

2024

• J. Fernandez-de-Cossio-Diaz, G. Uguzzoni, K. Ricard, F. Anselmi, C. Nizak*, A. Pagnani*, O. Rivoire*, Inference and design of antibody specificity: From experiments to models and back. PLOS Comput. Biol. 20, e1012522 (2024) (* corres. authors).

2021

• S. Schulz, S. Boyer, M. Smerlak, S. Cocco, R. Monasson, C. Nizak*, O. Rivoire*, "Parameters and determinants of responses to selection in antibody libraries." PLoS Comp Bio, vol. 17, no. 3, p. e1008751, 2021 (* corres. authors).

2020

• A. Gerard, A. Woolfe, G. Mottet, M. Reichen, C. Castrillon, V. Menrath, S. Ellouze, A. Poitou, R. Doineau, L. Briseño-Roa, P. Canales-Herrerias, P. Mary, G. Rose, C. Ortega, M. Delince, S. Essono, B. Jia, B. Iannascoli, O. Richard-LeGoff, R. Kumar, Y. Pousse, B. Shen, K. Grosselin, B. Saudemont, A. Sautel-Caillé, A. Godina, S. McNamara, K. Eyer, G. Millot, J. Baudry, P. England, C. Nizak, A. Jensen, A. Griffiths, and C. Brenan, "High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics." Nature Biotechnology, vol. 38, no. 6, pp. 715-721, 2020.

2018

• S. Moutel, C. Nizak, and F. Perez, “Selection and Use of Intracellular Antibodies.,” Methods Mol. Biol., vol. 1827, no. 9, pp. 491–503, 2018.

2017

• K. Eyer, R.C.L. Doineau, C.E. Castrillon, L. Briseño-Roa, V. Menrath, G. Mottet, P. England, A. Godina, E. Brient-Litzler, C. Nizak, A. Jensen, A.D. Griffiths, J. Bibette, P. Bruhns, and J. Baudry, "Single-cell deep phenotyping of IgG-secreting cells for high-resolution immune monitoring." Nature Biotechnology, vol 35, pp. 977–982, Oct 2017.
• J. Fenneteau, D. Chauvin, A.D. Griffiths, C. Nizak, and J. Cossy, "Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays." Chem Comm vol. 53, no. 39, pp. 5437-5440, May 2017.

2016

• S. Boyer, D. Biswas, A. Kumar Soshee, C. Nizak, and O. Rivoire, "Hierarchy and extremes in selections from pools of randomized proteins." PNAS, vol. 113, no.13, pp. 3482–3487, Mar 2016.

2014

• D. Dubravcic, M. van Baalen, and C. Nizak, “An evolutionarily significant unicellular strategy in response to starvation in Dictyostelium social amoebae.” F1000Res, vol. 3, p. 133, Dec. 2014.
• P. Jain, A. Soshee, S. S. Narayanan, J. Sharma, C. Girard, E. Dujardin, and C. Nizak, “Selection of Arginine-Rich Anti-Gold Antibodies Engineered for Plasmonic Colloid Self-Assembly.” J. Phys. Chem. C, vol. 118, no. 26, pp. 14502–14510, Jun. 2014.
• S. Modi, S. Halder, C. Nizak, and Y. Krishnan, “Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways.” Nanoscale, vol. 6, no. 2, pp. 1144–1152, Jan. 2014.
• A. Soshee, S. Zürcher, N. D. Spencer, A. Halperin, and C. Nizak, “General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires.” Biomacromolecules, vol. 15, no. 1, pp. 113–121, Jan. 2014.