Open Source Software Packages

“TherapySim” (released on December 25th, 2013 for Python; TherapySim website: is a Python package to predict potential therapeutic targets in signaling networks. Software can be downloaded at and the corresponding tutorials are available at

“CplexA” (latest version released on December 12th, 2012 for Mathematica, Python, and Matlab; first released on April 19th, 2010 for Mathematica; CplexA website: is a Mathematica, Python, and Matlab package to compute the probabilities and average properties of macromolecular assembly and its effects in gene regulation. Software can be downloaded at and the corresponding Mathematica, Matlab, and Python implementation tutorials are available at


Articles in journals

I. Jeddi and L. Saiz, Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors, Scientific Reports, 7, 1178 (2017).

J. Doudna, R. Bar-Ziv, J. Elf, V. Noireaux, J. Berro, L. Saiz, D. Vavylonis, J.-L. Faulon, and P. Fordyce, How Will Kinetics and Thermodynamics Inform Our Future Efforts to Understand and Build Biological Systems?, Cell Systems, 4, 144-146 (2017).

A. Keller, R.C. Gerkin, Y. Guan, A. Dhurandhar, G. Turu, B. Szalai, J.D. Mainland, Y. Ihara, C.W. Yu., R. Wolfinger, C. Vens, L. Schietgat, K. De Grave, R. Norel, G. Stolovitzky, G.A. Cecchi, L.B. Vosshall, P. Meyer, DREAM Olfaction Prediction Consortium (including L. Saiz), Predicting human olfactory perception from chemical features of odor molecules, Science, 355, 820-826 (2017).

J.M.G. Vilar and L. Saiz, Suppression and enhancement of transcriptional noise by DNA looping, Phys. Rev. E, 89, 062703 (2014).

S.K. Sinha and L. Saiz, Determinants of protein-ligand complex formation in the thyroid hormone receptor α: a Molecular Dynamics simulation study, Comp. Theor. Chem., 1038, 57-66 (2014).

Q. Mei and L. Saiz, Literature-based automated reconstruction, expansion, and refinement of the TGF-β superfamily ligand-receptor network, J. Membr. Biol., 247, 381-386 (2014).

D. Nicklas and L. Saiz, In silico identification of potential therapeutic targets in the TGF-β signal transduction pathway, Mol. BioSyst., 10 (3), 537-548 (2014).

D. Nicklas and L. Saiz, Characterization of negative feedback network motifs in the TGF-β signaling pathway, PLoS ONE, 8(12): e83531 (2013).

J.M.G. Vilar and L. Saiz, Reliable prediction of complex phenotypes from a modular design in free energy space: an extensive exploration of the lac operon, ACS Synthetic Biology, 2, 576–586 (2013).

D. Nicklas and L. Saiz, Computational modeling of smad-mediated negative feedback and crosstalk in the TGF-β superfamily network, J. R. Soc. Interface, 10, 20130363 (2013).

J.M.G. Vilar and L. Saiz, Systems Biophysics of Gene Expression, Biophys. J., 104, 2574-2585 (2013).

  • Chosen for Cell Press’ “Spotlight on Quantitative Cell Biology”, a selection of the best (recent) Biophysical Journal articles on the topic.
  • Awarded “Best of 2013”

L. Saiz, The physics of protein-DNA interaction networks in the control of gene expression, Journal of Physics: Condensed Matter, 24, 193102 (2012).

J.M.G. Vilar and L. Saiz, Trafficking coordinate description of intracellular transport control of signaling networks, Biophysical Journal, 101, 2315-2323 (2011).

  • Chosen as featured article in the Biophysical Journal.
  • Highlighted as featured article in the Biophysical Society Newsletter.

J.M.G. Vilar and L. Saiz, Control of gene expression by modulated self-assembly, Nucleic Acids Research, 39, 6854-6863 (2011). Supplementary Data: [pdf].

  • Highlighted as a featured article in Nucleic Acids Research (“featured articles represent the top 5% of papers in terms of originality, significance and scientific excellence”).

J.M.G. Vilar and L. Saiz, CplexA: a Mathematica package to study macromolecular-assembly control of gene expression, Bioinformatics, 26, 2060-2061 (2010). Supplementary Information: Supplementary Data files 1 [pdf] and 2 [nb].

L. Saiz and J.M.G. Vilar, Protein-protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression, IET Systems Biology, 2, 247-255 (2008).

L. Saiz and J.M.G. Vilar, Ab initio thermodynamic modeling of distal multisite transcription regulation, Nucleic Acids Research, 36, 726-731 (2008).

L. Saiz and J.M.G. Vilar, Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes, PLoS ONE, 2(4): e355. doi:10.1371/journal.pone.0000355 (2007).

S. Vemparala, L. Saiz, R.G. Eckenhoff, and M.L. Klein, Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles, Biophys. J., 91, 2815-2825 (2006).

J.M.G. Vilar and L. Saiz, Multiprotein DNA looping, Phys. Rev. Lett., 96, 238103 (2006).

L. Saiz and J.M.G. Vilar, DNA looping: the consequences and its control, Curr. Opin. Struct. Biol., 16, 344-350 (2006).

L. Saiz and J. M. G. Vilar, Stochastic dynamics of macromolecular-assembly networks, Molecular Systems Biology, 2, 2006.0024 (2006).

Leonor Saiz, J. Miguel Rubi, and Jose M.G. Vilar, Inferring the in vivo looping properties of DNA, Proc. Natl. Acad. Sci. USA, 102, 17642-17645 (2005).

Jose M.G. Vilar and Leonor Saiz, DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise, Current Opinion in Genetics & Development, 15, 136-144 (2005).

Leonor Saiz and M.L. Klein, The transmembrane domain of the acetylcholine receptor: Insights from simulations on synthetic peptide models, Biophys. J., 88, 959-970 (2005).

M. Pickholz, Leonor Saiz, and M.L. Klein, Concentration effects of volatile anesthetics on the properties of model membranes: A coarse-grain approach, Biophys. J., 88, 1524-1534 (2005).

Leonor Saiz, S. Bandyopadhyay, and M.L. Klein, Effect of the pore region of a transmembrane ion-channel on the physical properties of a simple membrane, J. Phys. Chem. B, 108, 2608-2613 (2004).

L. Koubi, Leonor Saiz, M. Tarek, D. Scharf, and M.L. Klein, Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer, J. Phys. Chem. B 107, 14500-14508 (2003).

Leonor Saiz, S. Bandyopadhyay, and M.L. Klein, Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations, Bioscience Reports 22, 151-173 (2002).

Leonor Saiz and M.L. Klein, Computer simulation studies of model biological membranes, Accounts of Chemical Research 35, 482-489 (2002).

E. Guardia, J. Marti, J.A. Padro, Leonor Saiz, and A.V. Komolkin, Dynamics in hydrogen bonded liquids: water and alcohols, J. Mol. Liq. 96-97, 3-17 (2002).

Leonor Saiz and M.L. Klein, Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations, J. Chem. Phys. 116, 3052-3057 (2002).

Leonor Saiz and M.L. Klein, Influence of highly polyunsaturated lipid acyl chains of biomembranes on the NMR order parameters, J. Am. Chem. Soc. 123, 7381-7387 (2001).

Leonor Saiz and M.L. Klein, Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations, Biophys. J. 81, 204-216 (2001). This work appears also on the cover of the July 2001 issue of the Biophys. J.

Leonor Saiz, J. M. G. Vilar, and J. Miguel Rubi, Field-induced force-suppression in ferromagnetic colloids, Physica A 293, 51-58 (2001).

Leonor Saiz, J.A. Padro, and E. Guardia, Structure of liquid ethylene glycol: A molecular dynamics simulation study with different force fields, J. Chem. Phys. 114, 3187-3199 (2001).

L. Saiz, E. Guardia, and J.A. Padro, Dielectric properties of liquid ethanol. A computer simulation study, J. Chem. Phys. 113, 2814-2822 (2000).

L. Saiz, J.A. Padro, and E. Guardia, Dynamics and hydrogen bonding in liquid ethanol, Mol. Phys. 97, 897-905 (1999).

J.A. Padro, L. Saiz, and E. Guardia, Hydrogen bonding in liquid alcohols: A computer simulation study, J. Molec. Structure 416, 243-248 (1997).

L. Saiz, J.A. Padro, and E. Guardia, Structure and dynamics of liquid ethanol, J. Phys. Chem. B 101, 78-86 (1997).


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