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Deniz Pekin
tr  Visiting Scientist - IECB
Former Group Members



pekin [at] crpp-bordeaux.cnrs.fr (+33) 55-684-3029
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Education & Career

08/2013 - ... Post-Doc
Droplets, Membranes and Interfaces - MPI for Dynamics and Self-Organisation 		Goettingen, Germany de 
2010 - 2013 Ph.D. in Molecular Diagnostics
Topic: Quantitative detection of sequence variants in tumor DNA, usingdroplet based microfluidics
Adviser: Dr. Valerie Abecassis-Taly
University of Strasbourg 		Strasbourg, France fr 
2009 Master of Science in Molecular and Structural Biology
Topic: Genetical Diagnostics- Developpment of a new strategy based on the model of KRAS oncogene
Adviser: Dr. Valerie Abecassis-Taly
University of Strasbourg 		Strasbourg, France fr 
2008 Bachelor of Science in Biochenistry and Molecular Biology
University of Strasbourg 		Strasbourg, France fr 

PhD Thesis

Development of Novel Droplet-based Microfluidic Strategies for the Molecular Diagnosis of Cancer
D. Pekin
University of Strasbourg, Ecole Doctorale de Sciences Chimiques, 2013

Group Publications

Confining Trypanosoma brucei in emulsion droplets reveals population variabilities in division rates and improves in vitro cultivation
S. Oldenburg, L. Buisson, T. Beneyton, D. Pekin, M. Thonnus, F. Bringaud, L. Riviere and J.-C. Baret
Scientific Reports, 11, 18192 (2021) 		pdfOpen Access
From Compartmentalization of Bacteria within Inorganic Macrocellular Beads to the Assembly of Microbial Consortia
A. Roucher, M. Morvan, D. Pekin, M. Depardieu, J.-L. Blin, V. Schmitt, M. Konrad, J.-C. Baret and R. Backov
Advanced Biosystems, 2, 1700233 (2018) 		pdfOpen Access
High-Content Screening of Plankton Alkaline Phosphatase Activity in Microfluidics
M. Girault, T. Beneyton, D. Pekin, L. Buisson, S. Bichon, C. Charbonnier, Y. del Amo, and J.-C. Baret
Analytical Chemistry 90 (6), 4174-4181 (2018) 		pdf
Digital PCR compartmentalization. I. Single molecule detection of rare mutations
K. Perez-Toralla, D. Pekin, J.-F. Bartolo, F. Garlan, P. Nizard, P. Laurent-Puig, J.-C. Baret and V. Taly
Medecine Sciences 31 : 84-92 (2015) 		pdfOpen Access
Stabilisers for water-in-fluorinated-oil dispersions: key properties for microfluidic applications
P. Gruner, B. Riechers, L. A. Chacòn Orellana, Q. Brosseau, F. Maes, T. Beneyton, D. Pekin, J.-C. Baret
Current opinion in colloid and interface science, 20, 3, 183-191 (2015) 		pdfOpen Access
Dynamics of molecular transport by surfactants in emulsions
Y. Skhiri, P. Gruner, B. Semin, Q. Brosseau, D. Pekin, L. Mazutis, V. Goust, F. Kleinschmidt, A. El Harrak, J.B. Hutchison, E. Mayot, J.-F. Bartolo, A.D. Griffiths, V. Taly, J.-C. Baret
Soft Matter 8, 10618-10627 (2012) 		pdf
Quantitative and sensitive detection of rare mutations using droplet-based microfluidics
D. Pekin, Y. Skhiri, J.-C. Baret, D. Le Corre, L. Mazutis, C. Ben Salem, F. Millot, A. El Harrak, J.B. Hutchison, J.W. Larson, D.R. Link, P. Laurent-Puig, A.D. Griffiths and V. Taly
Lab Chip 11, 2156-2166 (2011)

Other Publications

Droplet-Based Microfluidics Digital PCR for the Detection of KRAS Mutations
D. Pekin, V. Taly
Methods Mol Biol., 1547:143-164
Multiplex Detection of KRAS Mutations Using Passive Droplet Fusion
D. Pekin, V. Taly
Methods Mol Biol., 1547:133-142
Clinical relevance of KRAS-mutated subclones detected with picodroplet digital PCR in advanced colorectal cancer treated with anti-EGFR therapy
P. Laurent-Puig, D. Pekin, C. Normand, S.K. Kotsopoulos, P. Nizard, K. Perez-Toralla, R. Rowell, J. Olson, P. Srinivasan, D. Le Corre, T. Hor, Z. El Harrak, X. Li, D.R. Link, O. Bouché, J.F. Emile, B. Landi, V. Boige, J.B. Hutchison, V. Taly
Clin Cancer Res., 1;21(5):1087-97.
Multiplex Picodroplet Digital PCR for quantitative assessment of DNA integrity in clinical samples
A. Didelot, S. K. Kotsopoulos, A. Lupo, D. Pekin, X. Li, I. Atochi, P. Srinivasan, Q. Zhong, J. Olson, D. R. Link, P. Laurent- Puig, H. Blons, J. B. Hutchison and V. Taly
Clin Chem. 2013 May;59(5):815-23. doi: 10.1373/clinchem.2012.193409. Epub 2013 Feb 12.
Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from plasma of colorectal cancer patients
V. Taly, D. Pekin, L. Benhaim, S.K. Kotsopoulos, D. Le Corre, Q. Zhong, X. Li, I. Atochin, H. Gang, J.B. Hutchison, D. R. Link, A.D. Griffiths, K. Palier, H. Blons, O. Bouch, J.-F. Emile and P. Laurent-Puig
Clin Chem 2013.
Biomarker detection in microdroplets
V. Taly, D. Pekin, A.E. Abed, P. Laurent-Puig
Trends Mom Med 2012, 18(7), 405-16.

Proceedings

Picoliter droplet-based digital PCR for the quantitative and sensitive detection of rare mutations and the assessment of DNA integrity
D. Pekin, A. Didelot, S.K. Kotsopoulos, J.-C. Baret, D. Le Corre, B. Hutchison, D.R. Link, P. Laurent-Puig, A.D. Griffiths, and V. Taly.
Proceedings of the 3rd European Conference on Microfluidics - Microfluidics 2012 - Heidelberg, December 3-5, 2012.
Quantitative detection of circulating tumor DNA in plasma samples by droplet digital PCR
D. Pekin,S. Kotsopoulos,L. Xinyu, I. Atochin, H. Gang, D. Le Corre, L. Benhaim, J.B. Hutchison, D.R. Link, H. Blons, P. Laurent-Puig, and V. Taly
The 16th International conference on miniaturized systems for Chemistry and Life Science (MicroTas 2012). Oct. 28- Nov. 1, 2012. Okinawa. Japan.
Multiplex highly sensitive detection of cancer biomarkers in biological samples
D. Pekin, Y. Skhiri, J.-C. Baret,D. Le Corre, L. Mazutis, C. Ben Salem, A. El Abed, J.B. Hutchison, D.R. Link, A.D. Griffiths, P. Laurent-Puig, and V. Taly
2011 In: Proceedings of the 15th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS), 2011, p. 665-667. ISBN: 978-0-9798064-4-5.
Multiplex highly sensitive detection of Cancer Biomarkers in biological samples
D. Pekin, S. Kotsopoulos, H. Gang, Q. Zhong, J.-C. Baret, D. Le Corre, A. El Abed, J.B. Hutchison, D. Link, J. Larson, A. Griffiths, P. Laurent-Puig and V. Taly. Invited by Raindance Technologies.
Association of Molecular Pathology (AMP) 2011 Annual meeting workshop. 19 November 2011, Dallas, US.
Emulsion PCR in microfluidics for the quantitative detection of rare mutations: Towards an application in cancer diagnostics
D. Pekin, Y. Skhiri, J.-C. Baret, D. Le Corre, L. Mazutis, C. Ben Salem, A. El Abed, J.B. Hutchison, D. Link, J. Larson, A. Griffiths, P. Laurent-Puig and V. Taly.
GDR 2825- New Approaches in Protein Directed Evolution. October 11-12th 2011. Ax-les-thermes, France.
Droplet-based microfluidics for the quantitative detection of rare mutations
D. Pekin, Y. Skhiri, J.-C. Baret, D. Le Corre, L. Mazutis, C. Ben Salem, A. El Abed, J.B. Hutchison, D.R. Link, A.D. Griffiths, P. Laurent-Puig, and V. Taly.
2010 In: Proceedings of the 14th international Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS), 2010, p. 58-60. ISBN: 978-0-9798064-3-8
All group publications ...
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