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Hénin J, Baaden M, Taly A.  2014.  Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. Membrane Proteins Production for Structural Analysis. :347–392.
Hénin J.  2021.  Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
Hénin J, Fiorin G., Chipot C, Klein ML.  2010.  Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables. J. Chem. Theory Comput.. 6:35–47.
Hénin J, Maigret B., Tarek M, Escrieut C., Fourmy D., Chipot C.  2006.  Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor. Biophys. J.. 90:1232–1240.
Hénin J, Shinoda W, Klein ML.  2008.  United-Atom Acyl Chains for CHARMM Phospholipids. J. Phys. Chem. B.. 112:7008–7015.
Hénin J, Chipot C.  2004.  Overcoming free energy barriers using unconstrained molecular dynamics simulations. J. Chem. Phys.. 121:2904–2914.
Hénin J, Tajkhorshid E, Schulten K, Chipot C.  2008.  Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF. Biophys. J.. 94:832–839.
Hénin J, Brannigan G, Dailey WP, Eckenhoff RG, Klein ML.  2010.  An atomistic model for simulations of the general anesthetic isoflurane. J. Phys. Chem. B. 114:604–612.
Hénin J, Pohorille A., Chipot C.  2005.  Insights into the recognition and association of transmembrane $\alpha$-helices. The free energy of $\alpha$-helix dimerization in glycophorin A. J. Am. Chem. Soc.. 127:8478–8484.
Hénin J, Salari R, Murlidaran S, Brannigan G.  2014.  A predicted binding site for cholesterol on the GABAA receptor.. Biophys. J.. 106:1938–1949.
Hénin J, Shinoda W, Klein ML.  2009.  Models for phosphatidylglycerol lipids put to a structural test. J. Phys. Chem. B. 113:6958–6963.
Hénin J, Chipot C.  2006.  Hydrogen-bonding patterns of cholesterol in lipid membranes. Chem. Phys. Lett.. 425:329–335.
Hénin J, Schulten K., Chipot C.  2006.  Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations. J. Phys. Chem. B. 110:16718–16723.