Clément Nizak

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), as well as Rama Ranganathan (U Chicago), Martin Weigt (CQSB-Sorbonne Université), Jorge Fernandez de Cossio Diaz (IPhT-CEA-Saclay), Guido Uguzzoni (IRIG-CEA Grenoble).

PhD students:

• Matilde Pattanaro
• Shoichi Yip

Biorxiv, Google Scholar

Peer-reviewed articles:

2025

• 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 Comp Biol, vol. 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.

2013

• S. Modi, C. Nizak, S. Surana, S. Halder, and Y. Krishnan, “Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell.” Nature Nanotechnology, vol. 8, no. 6, pp. 459–467, Jun. 2013.

2012

• S. Moutel, C. Nizak, and F. Perez, “Selection and use of intracellular antibodies (intrabodies).” Methods Mol. Biol., vol. 907, pp. 667–679, Jul. 2012.

2011

• M. Iosin, T. Scheul, C. Nizak, O. Stephan, S. Astilean, and P. Baldeck, “Laser microstructuration of three-dimensional enzyme reactors in microfluidic channels” Microfluid Nanofluid, vol. 10, no. 3, pp. 685–690, Mar. 2011.

2010

• S. Adiba, C. Nizak, M. van Baalen, E. Denamur, and F. Depaulis, “From grazing resistance to pathogenesis: the coincidental evolution of virulence factors,” PLoS ONE, vol. 5, no. 8, p. e11882, 2010.
• O. Vielemeyer, C. Nizak, A. J. Jimenez, A. Echard, B. Goud, J. Camonis, J.-C. Rain, and F. Perez, “Characterization of single chain antibody targets through yeast two hybrid.” BMC Biotechnol, vol. 10, p. 59, 2010.

2009

• O. Vielemeyer, H. Yuan, S. Moutel, R. Saint-Fort, D. Tang, C. Nizak, B. Goud, Y. Wang, and F. Perez, “Direct selection of monoclonal phosphospecific antibodies without prior phosphoamino acid mapping.” J Biol Chem, vol. 284, no. 31, pp. 20791–20795, Jul. 2009.
• S. Moutel, A. El Marjou, O. Vielemeyer, C. Nizak, P. Benaroch, S. Dübel, and F. Perez, “A multi-Fc-species system for recombinant antibody production.” BMC Biotechnol, vol. 9, p. 14, 2009.

2006

• C. Nizak, R. J. Fitzhenry, and R. H. Kessin, “Exploitation of other social amoebae by Dictyostelium caveatum.” PLoS ONE, vol. 2, no. 2, p. e212, Jan. 2007.
• E. del Nery, S. Miserey-Lenkei, T. Falguières, C. Nizak, L. Johannes, F. Perez, and B. Goud, “Rab6A and Rab6A' GTPases play non-overlapping roles in membrane trafficking.” Traffic, vol. 7, no. 4, pp. 394–407, Apr. 2006.
• R. Sannerud, M. Marie, C. Nizak, H. A. Dale, K. Pernet-Gallay, F. Perez, B. Goud, and J. Saraste, “Rab1 defines a novel pathway connecting the pre-Golgi intermediate compartment with the cell periphery.” Mol. Biol. Cell, vol. 17, no. 4, pp. 1514–1526, Apr. 2006.

2005

• C. Nizak, S. Moutel, B. Goud, and F. Perez, “Selection and application of recombinant antibodies as sensors of rab protein conformation” Meth Enzymol, vol. 403, pp. 135–153, 2005.

2004

• C. Nizak, R. Sougrat, F. Jollivet, A. Rambourg, B. Goud, and F. Perez, “Golgi inheritance under a block of anterograde and retrograde traffic.” Traffic, vol. 5, no. 4, pp. 284–299, Mar. 2004.

2003

• C. Nizak, S. Martin-Lluesma, S. Moutel, A. Roux, T. E. Kreis, B. Goud, and F. Perez, “Recombinant antibodies against subcellular fractions used to track endogenous Golgi protein dynamics in vivo.” Traffic, vol. 4, no. 11, pp. 739–753, Nov. 2003.
• C. Nizak, S. Monier, E. del Nery, S. Moutel, B. Goud, and F. Perez, “Recombinant antibodies to the small GTPase Rab6 as conformation sensors.” Science, vol. 300, no. 5621, pp. 984–987, May 2003.

2002

• F. Perez, K. Pernet-Gallay, C. Nizak, H. V. Goodson, T. E. Kreis, and B. Goud, “CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family.” J Cell Biol, vol. 156, no. 4, pp. 631–642, Feb. 2002.