This page presents the main research outputs of the group, including peer-reviewed scientific publications and research software developed in close connection with our experimental and methodological work. Together, these outputs reflect our commitment to quantitative science, reproducibility, and open research practices in microfluidics, droplets, and immunology.

A short selection of publications representative of our core research directions in microfluidics, droplet-based systems, biophysics and immunology:

  • Alcanivorax borkumensis biofilms enhance oil degradation by interfacial tubulation
    Science (2023)

  • Phenotyping polarization dynamics of immune cells using a lipid droplet–cell pairing microfluidic platform
    Cell Reports Methods (2022)

  • A multiparametric, quantitative and high-throughput assay to determine the influence of target size on phagocytic uptake
    Biophysical Journal (2019)

  • Design of a microfluidic and microscopic toolbox for the ultra-wide spatio-temporal study of plant protoplast development and physiology.
    Plant Methods (2019)

(See full publication list below.)

Publications

The complete and up-to-date list of publications is maintained below.

In Preparation

[44] Targeted fluorescent lipid microparticles for quantitative measurement of phagosomal pH. \ C. Pompili1, H. Uhl, S. Michelis, B. Dumat, J.-M. Mallet, J. Fattaccioli, F. Niedergang*
Methods & Protocols Book – Exocytosis and Endocytosis (2026)

[43] Lipid droplet–based passive tracking to probe tissue dynamics in lymph node slices
L. Bruno, H. Uhl, L. Vimeux, M. Karnat, J-F Rupprecht, E. Donnadieu, J. Fattaccioli and P. Pierobon
Methods in Molecular Biology : Real-Time Imaging of Immune Cells (2026)

2025

[42] Targeted fluorescent lipid microparticles for quantitative measurement of phagosomal pH.
S. Michelis, H. Uhl, F. Niedergang, J. Fattaccioli, B. Dumat*, J.-M. Mallet*
BioRxiv (2025) doi \

[41] A. Chargueraud, L. Kool, J. Fattaccioli*.
Fully integrated automatic microfluidic setup for immobilization, analysis and non-selective release of particles
Micro and Nano Engineering, Accepted (2025, In Press) doi

[40] L. Huang, R. Lopes Dos Santos, S. Labdi, G. Lamour, O. Maciejak, M. Malo, J. Fattaccioli, C. Campillo.
A microfluidic platform for actin-based membrane remodeling reveals the stabilizing role of branched actin networks on lipid microdomains
Small Science (2025) doi

[39] L. Bogdziewiez, R. Froeling, P. Schoppl, J. Juquel3, J. Antoniadi, V. Skalicky, A. Mathey, J. Fattaccioli, J. Sprakel, S. Verger.
The Q-Warg Pipeline: A Robust and Versatile Workflow for Quantitative Analysis of Protoplast Culture Conditions
Plant Direct - Accepted for publication (2025) doi

[38] E. Lu, W. Flores Cisternas, H. UHL, A. Chargueraud, Q. Grimal, G. Renaud, J.-G. Minonzio, J. Fattaccioli*.
Assessing ultrasonic and optical flow velocimetry in a millifluidic device using oil-in-water emulsions as blood mimicking fluid
Micro and Nano Engineering, 100298 (2025) DOI

[37] N. Ruyssen*, G. Fina, R. Allena, M.C. Jullien, J. Fattaccioli.
Spanwise dispersion optimizes the efficiency of dense microfluidic trap arrays
Computers & Fluids - 106643 (2025) DOI

2024

[36] C. Hu , E. Lu, L. Lacour, N. Delsuc, B. Bresson, J.-M. Mallet, J. Fattaccioli.
Shaping, Degradation And Drug Release Of Biosourced Particles Made From Acrylated Vegetable Oils
ChemRxiv (2024) Link

[35] M. Prudhomme, C. Lakhdar, J. Fattaccioli, F. Chollet*
Functionalization of microbubbles in a microfluidic chip for biosensing applications
Biomedical Microdevices 26, 39 (2024). URL

[34] B. Cocom-Chan, H. Khakzad, M. Konate, D. Isui-Aguilar, C. Bello, C. Valencia-Gallardo 5-8 , Y. Zarrouk , J. Fattaccioli, A. Mauviel, D. Javelaud, G. Tran Van Nhieu
IpaA reveals distinct modes of vinculin activation during Shigella invasion and cell-matrix adhesion
Life Science Alliance 7 (8) e202302418. URL {:target=”_blank”}

[33] S. Michelis, C. Pompili, B. Dumat, F. Niedergang, J. Fattaccioli, J.-M. Mallet. FRET-sensing of receptor binding at the interface of targeted biomimetic microparticles functionalized with tunable fluorescent lipids
ACS Applied Bio Materials (2024) In Press URL \

2023

[32] M. Prasad, N. Obana, S.-Z. Lin, K. Sakai, C. Blanch-Mercader, J. Prost, N. Nomura, J.-F. Rupprecht*, J. Fattaccioli*, A. S. Utada*
*Alcanivorax borkumensis Biofilms Enhance Oil Degradation By Interfacial Tubulation
Science 381,748-753 (2023). DOI:10.1126/science.adf3345 URL

Perspective : Bacteria stretch and bend oil to feed their appetite T. McGenity and P.-P. Laissue URL

News in Physics Today : How bacteria help clean up oil spills URL

[31] J. Pineau, L. Pinon, J. Fattaccioli* , P. Pierobon* (2023). Functionalized Lipid Droplets and Microfluidics Approach to Study Immune Cell Polarity In Vitro. In: Baldari, C.T., Dustin, M.L. (eds) The Immune Synapse. Methods in Molecular Biology, vol 2654. Humana, New York, NY. DOI

2022

[30] L. Pinon , N. Ruyssen , J. Pineau , O. Mesdjian , D. Cuvelier , R. Allena , S. Asnacios , A. Asnacios , P. Pierobon* , and J. Fattaccioli*. Phenotyping Polarization Dynamics Of Immune Cells Using A Lipid Droplet – Cell Pairing Microfluidic Platform.
Cell Reports Methods (2022) DOI (In press).

[29] J. Pineau, L. Pinon, O. Mesdjian, J. Fattaccioli, A.-M. Lennon-Duménil, P. Pierobon* . Microtubules restrict F-actin polymerization to the immune synapse via GEF-H1 to maintain polarity in lymphocytes.
eLife (2022) [DOI]

2021

[28] O. Mesdjian‡, N. Ruyssen‡, M.-C. Jullien, R. Allena, J. Fattaccioli*. Enhancing the capture efficiency and homogeneity of single-layer flow-through trapping microfluidic devices using oblique hydrodynamic streams.
Microfluidics and Nanofluidics, 25, 91 (2021) [doi]
Post-review preprint avaiable on the ArXiv (2021) [url]

2019

[27] B. Dumat‡, L. Montel‡, P. Matton, L. Pinon, L. Cattiaux, J. Fattaccioli*, J.M. Mallet*. Mannose-coated fluorescent emulsion droplets: specific biosensors for Mannose Receptor-induced phagocytosis.
ACS Applied Bio Materials., 2, 11, 5118-5126 (2019) [doi]
‡: equal contribution to the work

[26] K. Sakai, F. Charlot, T. Le Saux, S. Bonhomme, F. Nogué, J.C. Palauqui*, J. Fattaccioli*. 
Design of a microfluidic and microscopic toolbox for the ultra-wide spatio-temporal study of plant protoplast development and physiology.
Plant Methods, 15, n° 19 (2019) [doi]
Preprint available on BioRxiv [Link to BioRXiv]
Highlighted in the french magazine La Recherche (Nov. 2019) [url][pdf]

[25] L. Montel, L. Pinon,  J. Fattaccioli*. 
A multiparametric, quantitative and high-throughput assay to determine the influence of target size on phagocytic uptake.
Biophys. J., 117 (3) pp. 408-419 (2019) [doi]
Preprint available on BioRxiv (2019) [Link to BioRXiv]

[24] C. Vié, J. Fattaccioli*, P. Jacq*
Introducing digital microfluidics concepts in chemistry using a macroscopic droplet generator.  
Journal of Chemical Education. 96 (4), pp. 797-800 (2019) [pdf][doi]

[23] M. Prasad, N. Obana, K. Sakai, Y. Nakayama, S. Miyazaki, M. Toyofuku, J. Fattaccioli, N. Nomura, A.S. Utada*
Point mutations lead to increased levels of c-di-GMP and phenotypic changes to colony biofilm morphology in Alcanivorax borkumensis SK2.
Microbes and Environnements. 34 (1) pp. 104-107 (2019) [doi][pdf]

2018

[22] L. Pinon, L. Montel, O. Mesdjian, M. Bernard, A. Michel, C. Ménager, J. Fattaccioli*. Kinetically-enhanced fabrication of homogeneous biomimetic and functional emulsion droplets.
Langmuir, 34 (50), pp 15319–15326  (2018) [doi][url]

[21] F.M. Allioux*, P. Kapruwan, N. Milne, L. Kong, J. Fattaccioli, Y. Chen, L.F. Dumée*. Electro-capture of heavy metal ions with carbon cloth integrated microfluidic devices.
Sep. Purif. Technol., 194, pp. 26-32 (2018) [doi]

2016

[20] S. Quignard*, G. Frébourg, Y. Chen, J. Fattaccioli.
*Nanometric emulsions encapsulating solid particles as alternative carriers for intracellular delivery.
Nanomedicine, 11 (16), 2059-2072 (2016) [pdf].

[19] D. Molino, S. Quignard, C. Gruget, F. Pincet, Y. Chen, M. Piel, J. Fattaccioli*.
On-chip quantitative measurement of mechanical stresses during cell migration with emulsion droplets.
Scientific Reports 6, 29113 (2016)[pdf][doi].

[18] O. Mesdjian, Y. Chen, J. Fattaccioli*
Luminescent and Absorptive Metal-Coated Emulsions for Micro-Velocimetry
Microelectronic Engineering 158, 69-74 (2016). [pdf][doi].

2015

[17] K. Ben M’Barek, D. Molino, S. Quignard, Y. Chen, P. Chavrier and J. Fattaccioli*
Phagocytosis of Immunoglobulin-Coated Emulsion Droplets
Biomaterials 51, 270-277  (2015). [pdf][doi]

2014

[16] S. Quignard, Y. Chen, M. d’Ischia and J. Fattaccioli*
UV-induced fluorescence of polydopamine-coated emulsion droplets.
ChemPlusChem 79 (9),  1254-1257 (2014). [pdf][doi]
Article highlighted in Wiley-VCH Hot Topics – Surfaces and Interfaces. [link]

[15] G.M. Nocera, K. Ben M’Barek, D.G. Bazzoli, G. Fraux, M. Bontems-Van Heijenoort, J. Chokki, S. Georgeault, Y. Chen, and J. Fattaccioli*
Fluorescent microparticles fabrication through chemical coating of O/W emulsion droplets with a thin metallic film.
RSC Advances 4 (23), 11564 – 11568 (2014). [pdf][doi]

[14] C. Longuet, A. Yamada, Y. Chen, D. Baigl and J. Fattaccioli*
Spatially-Controlled Crystallization in Microfluidics Chambers
Journal of Crystal Growth 386  pp. 179-182 (2014). [pdf][doi]

2013

[13]  J. Fattaccioli. Méthode de dépôt de de polymère sur des particules liquides.
Patent Number : PCT/FR2014/050461 (2013). [url]

2012

[12] JH Park, J. Fattaccioli, H. Fujita and BJ Kim.
Fabrication of Aluminum/Alumina Patterns Using Localized Anodization of Aluminum.
Int. J. of Precision Eng. And Manuf. 5 (13) pp. 765-770 (2012). [pdf][doi]

2009

[11] C. Bottier, J. Fattaccioli, M.C. Tahran, R. Yokokawa, F.O. Morin, D. Collard and H. Fujita.
Active Transport of Oil Droplets along Oriented Microtubules by Kinesin Molecular Motors.
Lab on a Chip, 9:1694-1700 (2009) [pdf][doi]

[10] K. Nakamura, T. Sonobe, H. Fujita, B.J. Kim, J. Fattaccioli
Cylindrical coil, cylindrical micromotor and production method of cylindrical coil
Patent Number : JP2009247191 (A) [pdf]

[9] J.H. Park, J. Fattaccioli, N. Takama, H. Fujita, and B.J. Kim
Localized Anodization of Aluminum for the Formation of High Aspect Ratio Aluminum/Alumina Patterns
Asian Society for Precision Engineering and Nanotechnology Conference
ASPEN’2009 [pdf][url]

[8] J. Fattaccioli, A. Ikeda, J.G. Kim, N. Takama and B.J. Kim
Visual Observation of a PDMS Tip in Liquid Microcontact Printing
22st IEEE International Conference on Micro Electro Mechanical Systems
IEEE MEMS’2009 Conference Proceedings, pp. 681-684 [pdf][doi]

[7] S. Akiyama, Y. T. Cheng, J. Fattaccioli, N. Takama, P. Löw, C. Bergaud and B. J. Kim
Surface-Temperature Control of Silicon Nanowires in Dry and Liquid Conditions
22st IEEE International Conference on Micro Electro Mechanical Systems
IEEE MEMS’2009 Conference Proceedings, pp. 567-570 [pdf][doi]

2008

[6] Y.T. Cheng, J. Fattaccioli, S. Akiyama, N. Takama, Y. Akagi, S.J. Cho, and B.J. Kim.
Surface-temperature mapping on suspended silicon nanowire using fluorescent thermometry under dry and liquid conditions
Micro and Nano Engineering Conference 2008 (MNE 2008) [pdf][url]

[5] C. Bottier, M.C. Tahran, J. Fattaccioli, F.O. Morin, B.J. Kim and H. Fujita.
Direct Transportation and Electrofusion of Oil Droplets in a Microfluidic Device
21st IEEE International Conference on Micro Electro Mechanical Systems
IEEE MEMS’2008 Conference Proceedings, pp. 563-566 [pdf][doi]

[4] J. Fattaccioli*, J. Baudry, E. Bertrand, C. Goubault, N. Henry and J. Bibette.
Size and Fluorescence Measurements of Individual Droplets by Flow Cytometry.
Soft Matter, 5:2232-2238 (2008) [pdf][doi]

[3] J. Fattaccioli*, J. Baudry, F. Brochard-Wyart, N. Henry and J. Bibette
Specific Wetting Probed With Biomimetic Droplets
Soft Matter, 4, 2434–2440 (2008) [pdf][doi]

[2] M. Goutayer, I. Texier-Nogues, J. Fattaccioli and J. Bibette.
Émulsions fluorescentes pour l’imagerie optique.
Patent Number : WO2008125747 (A2) [pdf]

2005

[1] S. K. Mandal, N. Lequeux, B. Rotenberg, M. Tramier, J. Fattaccioli, J. Bibette and B. Dubertret
Encapsulation of Magnetic and Fluorescent Nanoparticles in Emulsion Droplets
Langmuir, 21 pp. 4175-4179 (2005) [pdf][doi]

Research Software and Open Tools

We develop open-source and custom software tools in direct support of our research activities in image analysis, microfluidics, and data science. These tools are designed to enable quantitative analysis, facilitate reproducibility, and support both research and training activities.

You can find most of the codes developed or and used in publications on our Github account

Background removal from time-lapse image stacks:

Novikova, A., Sima, D., Laïmouche, L., & Fattaccioli, J. (2024).
Zenodo. https://doi.org/10.5281/zenodo.10626975

Github repo : https://github.com/FattaccioliLab/Background-Removal-Plugin—ImageJ

Open science and reuse

Whenever possible, software tools, scripts, and notebooks are shared through open repositories or teaching material. This approach supports open science, method sharing, and lifelong learning programs in microfluidics.