Clément Nizak

30
Documents

Présentation

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

I work at ESPCI Paris in collaboration with Andrew Griffiths (Laboratory of Biochemistry) and at CIRB-College de France in collaboration with Olivier Rivoire (Statistical Biology).

I teach part of the Systems Biology course at ESPCI and the ICFP Masters program of ENS Paris.

Publications

Publications

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Inference and design of antibody specificity: From experiments to models and back

Jorge Fernandez-De-Cossio-Diaz , Guido Uguzzoni , Kévin Ricard , Francesca Anselmi , Clément Nizak et al.
PLoS Computational Biology, 2024, 20 (10), pp.e1012522. ⟨10.1371/journal.pcbi.1012522⟩
Article dans une revue hal-04778023 v2
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Parameters and determinants of responses to selection in antibody libraries

Steven Schulz , Sébastien Boyer , Matteo Smerlak , Simona Cocco , Rémi Monasson et al.
PLoS Computational Biology, 2021, 17 (3), pp.e1008751. ⟨10.1371/journal.pcbi.1008751⟩
Article dans une revue hal-03190048 v2
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High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics

Annabelle Gérard , Adam Woolfe , Guillaume Mottet , Marcel Reichen , Carlos Castrillón et al.
Nature Biotechnology, 2020, 38, pp.715-721. ⟨10.1038/s41587-020-0466-7⟩
Article dans une revue pasteur-02505776 v1

Single-cell deep phenotyping of IgG-secreting cells for high-resolution immune monitoring

Klaus Eyer , Raphaël C L Doineau , Carlos E Castrillon , Luis Briseño-Roa , Vera Menrath et al.
Nature Biotechnology, 2017, 35 (10), pp.977 - 982. ⟨10.1038/nbt.3964⟩
Article dans une revue hal-01639647 v1

Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays

Johan Fenneteau , Dany Chauvin , Andrew D. Griffiths , Clément Nizak , Janine Cossy
Chemical Communications, 2017, 53 (39), pp.5437-5440. ⟨10.1039/c7cc01506b⟩
Article dans une revue hal-02104894 v1

Hierarchy and extremes in selections from pools of randomized proteins

Sébastien Boyer , Dipanwita Biswas , Ananda Kumar Soshee , Natale Scaramozzino , Clément Nizak et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (13), pp.3482-3487. ⟨10.1073/pnas.1517813113⟩
Article dans une revue hal-04128959 v1

Hierarchy and extremes in selections from pools of randomized proteins

Sébastien Boyer , Dipanwita Biswas , Anandakumar Soshee , Natate Scaramozzino , Clément Nizak et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, ⟨10.1073/pnas.1517813113⟩
Article dans une revue hal-01301847 v1
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An evolutionarily significant unicellular strategy in response to starvation in social amoebae Dictyostelium social amoebae [version 2; referees: 2 approved]

Darja Dubravcic , Minus van Baalen , Clément Nizak
F1000Research, 2014, 3, pp.133. ⟨10.12688/f1000research.4218.2⟩
Article dans une revue hal-02392322 v1

An evolutionarily significant unicellular strategy in response to starvation stress in Dictyostelium social amoebae

Darja Dubravcic , Minus van Baalen , Clément Nizak
F1000Research, 2014, 3, pp.133. ⟨10.12688/f1000research.4218.1⟩
Article dans une revue hal-01064077 v1

Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways

Souvik Modi , S. Haider , Clément Nizak , Yamuna Krishnan
Nanoscale, 2014, 6 (2), pp.1144-52. ⟨10.1039/c3nr03769j⟩
Article dans une revue hal-00959788 v1
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Selection of Arginine-Rich Anti-Gold Antibodies Engineered for Plasmonic Colloid Self-Assembly

Purvi Jain , Anandakumar Soshee , S.Shankara Narayanan , Jadab Sharma , Christian Girard et al.
Journal of Physical Chemistry C, 2014, 118 (26), 10.1021/jp502118n. ⟨10.1021/jp502118n⟩
Article dans une revue hal-00983923 v3

General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires

Anandakumar Soshee , Stefan Zürcher , N. Spencer , A. Halperin , Clément Nizak
Biomacromolecules, 2014, 15 (1), pp.113-21. ⟨10.1021/bm401360y⟩
Article dans une revue hal-00959789 v1

Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell.

Souvik Modi , Clément Nizak , Sunaina Surana , Saheli Halder , Yamuna Krishnan
Nature Nanotechnology, 2013, 8 (6), pp.459-67. ⟨10.1038/nnano.2013.92⟩
Article dans une revue hal-00832208 v1

Selection and use of intracellular antibodies (intrabodies).

Sandrine Moutel , Clément Nizak , Franck Perez
Methods in Molecular Biology, 2012, 907, pp.667-79. ⟨10.1007/978-1-61779-974-7_37⟩
Article dans une revue hal-00728051 v1

Laser microstructuration of three-dimensional enzyme reactors in microfluidic channels

Monica Iosin , Teodora Scheul , Clément Nizak , Olivier Stephan , Simion Astilean et al.
Microfluidics and Nanofluidics, 2011, 10 (3), pp.685-690. ⟨10.1007/s10404-010-0698-9⟩
Article dans une revue istex hal-00728055 v1
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From Grazing Resistance to Pathogenesis: The Coincidental Evolution of Virulence Factors

Sandrine Adiba , Clément Nizak , Minus van Baalen , Erick Denamur , Frantz Depaulis
PLoS ONE, 2010, 5 (8), pp.e11882. ⟨10.1371/journal.pone.0011882⟩
Article dans une revue hal-00528524 v1
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Characterization of single chain antibody targets through yeast two hybrid.

Ole Vielemeyer , Clément Nizak , Ana Joaquina Jimenez , Arnaud Echard , Bruno Goud et al.
BMC Biotechnology, 2010, 10 (1), pp.59. ⟨10.1186/1472-6750-10-59⟩
Article dans une revue inserm-00617227 v1

Direct selection of monoclonal phosphospecific antibodies without prior phosphoamino acid mapping

O. Vielemeyer , H. Yuan , S. Moutel , R. Saint-Fort , D. Tang et al.
Journal of Biological Chemistry, 2009, pp.PMID: 19473967
Article dans une revue hal-00565193 v1

A multi-Fc-species system for recombinant antibody production

S. Moutel , A. El Marjou , O. Vielemeyer , Clément Nizak , P. Benaroch et al.
BMC Biotechnology, 2009, pp.PMID: 19245715
Article dans une revue hal-00565195 v1

Exploitation of other social amoebae by Dictyostelium caveatum

Clément Nizak , Rj Fitzhenry , Rh Kessin
PLoS ONE, 2007, pp.PMID: 17299592
Article dans une revue hal-00565197 v1

Rab1 defines a novel pathway connecting the pre-Golgi intermediate compartment with the cell periphery

R. Sannerud , M. Marie , Clément Nizak , Ha Dale , Karin Pernet-Gallay et al.
Molecular Biology of the Cell, 2006, pp.PMID: 16421253
Article dans une revue hal-00565238 v1

Rab6A and Rab6A' GTPases play non-overlapping roles in membrane trafficking

E. del Nery , S. Miserey-Lenkei , T. Falguières , Clément Nizak , Ludger Johannes et al.
Traffic, 2006, pp.PMID: 16536738
Article dans une revue hal-00565201 v1

Selection and application of recombinant antibodies as sensors of rab protein conformation

Clément Nizak , S. Moutel , Bruno Goud , Franck Perez
Methods in Enzymology, 2005, pp.PMID: 16473583
Article dans une revue hal-00565236 v1

Golgi inheritance under a block of anterograde and retrograde traffic

Clément Nizak , R. Sougrat , F. Jollivet , A. Rambourg , Bruno Goud et al.
Traffic, 2004, pp.PMID: 15030570
Article dans une revue hal-00565237 v1

Recombinant antibodies to the small GTPase Rab6 as conformation sensors

Clément Nizak , Solange Monier , Elaine del Nery , Sandrine Moutel , Bruno Goud et al.
Science, 2003, 300 (5621), pp.PMID: 12738866. ⟨10.1126/science.1083911⟩
Article dans une revue hal-00565240 v1

Recombinant antibodies against subcellular fractions used to track endogenous Golgi protein dynamics in vivo

Clément Nizak , S. Martin-Lluesma , S. Moutel , A. Roux , Te Kreis et al.
Traffic, 2003, pp.PMID: 14617357
Article dans une revue hal-00565239 v1

CLIPR-59, a new trans-Golgi/TGN cytoplasmic linker protein belonging to the CLIP-170 family

Franck Perez , Karin Pernet-Gallay , Clément Nizak , Hv Goodson , Te Kreis et al.
Journal of Cell Biology, 2002, pp.PMID: 11854307
Article dans une revue hal-00565241 v1

Selection and Use of Intracellular Antibodies

Sandrine Moutel , Clément Nizak , Franck Perez
Methods in molecular biology, pp.491-503, 2018
Chapitre d'ouvrage hal-02104898 v1