R. Prill, R. Vogel, G. Cecchi, G. Altan-bonnet, and G. Stolovitzky, Noise-Driven Causal Inference in Biomolecular Networks):e0125777. https, PLoS ONE, vol.10, issue.6, p.26030907, 2015.

S. Affeldt, L. Verny, and H. Isambert, 3off2: A network reconstruction algorithm based on 2-point and 3-point information statistics, BMC Bioinformatics, vol.6, issue.12, 2016.
DOI : 10.1002/9781118032770

URL : https://hal.archives-ouvertes.fr/hal-01260480

M. Dunlop, R. Cox, J. Levine, R. Murray, and M. Elowitz, Regulatory activity revealed by dynamic correlations in gene expression noise, Nature Genetics, vol.149, issue.12, pp.1493-1498, 2008.
DOI : 10.1038/msb4100050

D. Kiviet, P. Nghe, N. Walker, S. Boulineau, V. Sunderlikova et al., Stochasticity of metabolism and growth at the single-cell level, Nature, vol.108, issue.7522, pp.376-25186725, 2014.
DOI : 10.1073/pnas.1100059108

C. Granger, Investigating Causal Relations by Econometric Models and Cross-spectral Methods, Econometrica, vol.37, issue.3, pp.424-438, 1969.
DOI : 10.2307/1912791

T. Schreiber, Measuring Information Transfer, Physical Review Letters, vol.23, issue.2, pp.461-10991308, 2000.
DOI : 10.1088/0305-4470/23/8/008

M. Wibral, N. Pampu, V. Priesemann, F. Siebenhühner, H. Seiwert et al., Measuring Information-Transfer Delays, PLoS ONE, vol.10, issue.119, pp.55809-23468850, 2013.
DOI : 10.1371/journal.pone.0055809.t002

URL : https://doi.org/10.1371/journal.pone.0055809

J. Pahle, A. Green, C. Dixon, and U. Kummer, Information transfer in signaling pathways: A study using coupled simulated and experimental data, BMC Bioinformatics, vol.9, issue.1, pp.139-18318909, 2008.
DOI : 10.1186/1471-2105-9-139

R. Vicente, M. Wibral, M. Lindner, and G. Pipa, Transfer entropy???a model-free measure of effective connectivity for the neurosciences, Journal of Computational Neuroscience, vol.18, issue.2, pp.45-67, 2011.
DOI : 10.1002/cne.920180503

T. Lizier and M. Prokopenko, Differentiating information transfer and causal effect, The European Physical Journal B, vol.73, issue.4, pp.605-615, 2010.
DOI : 10.1140/epjb/e2010-00034-5

URL : http://arxiv.org/pdf/0812.4373

D. Hartich, A. Barato, and U. Seifert, Sensory capacity: An information theoretical measure of the performance of a sensor, Physical Review E, vol.93, issue.2, pp.22116-26986297, 2016.
DOI : 10.1007/978-3-642-14394-6

S. Tusch, A. Kundu, G. Verley, T. Blondel, V. Miralles et al., Energy versus Information Based Estimations of Dissipation Using a Pair of Magnetic Colloidal Particles, Physical Review Letters, vol.112, issue.18, pp.180604-24856685, 2014.
DOI : 10.1209/0295-5075/87/60005

URL : https://hal.archives-ouvertes.fr/hal-01230025

J. Lizier and . Jidt, JIDT: An Information-Theoretic Toolkit for Studying the Dynamics of Complex Systems, Frontiers in Robotics and AI, vol.9, issue.11, p.11, 2014.
DOI : 10.1371/journal.pone.0102833

J. Parrondo, J. Horowitz, and T. Sagawa, Thermodynamics of information, Nature Physics, vol.89, issue.2, p.131, 2015.
DOI : 10.1103/PhysRevE.89.052102

J. Horowitz and M. Esposito, Thermodynamics with Continuous Information Flow, Physical Review X, vol.4, issue.3, p.31015, 2014.
DOI : 10.1103/PhysRevB.79.193407

URL : http://doi.org/10.1103/physrevx.4.031015

J. Horowitz and H. Sandberg, Second-law-like inequalities with information and their interpretations, New Journal of Physics, vol.16, issue.12, p.125007, 2014.
DOI : 10.1088/1367-2630/16/12/125007

URL : http://iopscience.iop.org/article/10.1088/1367-2630/16/12/125007/pdf

D. Hartich, A. Barato, and U. Seifert, Stochastic thermodynamics of bipartite systems: transfer entropy inequalities and a Maxwell???s demon interpretation, Journal of Statistical Mechanics: Theory and Experiment, vol.2014, issue.2, pp.1742-5468, 2014.
DOI : 10.1088/1742-5468/2014/02/P02016

A. Allahverdyan, D. Janzing, and G. Mahler, Thermodynamic efficiency of information and heat flow(09):P09011. https://doi.org/10, J Stat Mech, vol.09, pp.1742-5468, 1088.

C. Bowsher and P. Swain, Identifying sources of variation and the flow of information in biochemical networks, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.1320-1328, 2012.
DOI : 10.1073/pnas.162041399

K. Kim and H. Qian, Entropy Production of Brownian Macromolecules with Inertia, Physical Review Letters, vol.243, issue.12, pp.120602-15447247, 2004.
DOI : 10.1007/BF01394858

T. Munakata and M. Rosinberg, Feedback cooling, measurement errors, and entropy production, P06014. https, p.6014, 2013.
DOI : 10.1088/1742-5468/2013/06/P06014

URL : http://arxiv.org/pdf/1303.2269

T. Sauer, Computational solution of stochastic differential equations, Wiley Interdisciplinary Reviews: Computational Statistics, vol.112, issue.5, pp.362-371, 2013.
DOI : 10.1007/s00211-008-0200-8

D. Monteoliva and L. Diambra, Information propagation in a noisy gene cascade, Physical Review E, vol.96, issue.1, p.12403, 2017.
DOI : 10.1073/pnas.79.4.1129

S. Ito and T. Sagawa, Maxwell???s demon in biochemical signal transduction with feedback loop, Nature Communications, vol.4, p.7498, 2014.
DOI : 10.1103/PhysRevLett.104.218103

L. Barnett and A. Seth, Detectability of Granger causality for subsampled continuous-time neurophysiological processes, Journal of Neuroscience Methods, vol.275, pp.93-121, 2017.
DOI : 10.1016/j.jneumeth.2016.10.016

N. Tishby, F. Pereira, and W. Bialek, The Information bottleneck. arXiv preprint physics/0004057, 2000.

F. Tostevin and P. Ten-wolde, Mutual Information between Input and Output Trajectories of Biochemical Networks, Physical Review Letters, vol.27, issue.21, 2009.
DOI : 10.1073/pnas.0705463105

T. Kobayashi and Y. Sughiyama, Fluctuation Relations of Fitness and Information in Population Dynamics, Physical Review Letters, vol.115, issue.23, pp.238102-26684143, 2015.
DOI : 10.1126/science.1227946

N. Halabi, O. Rivoire, S. Leibler, and R. Ranganathan, Protein Sectors: Evolutionary Units of Three-Dimensional Structure, Cell, vol.138, issue.4, pp.774-786, 2009.
DOI : 10.1016/j.cell.2009.07.038

D. Smith, A. Lapedes, J. De-jong, T. Bestebroer, G. Rimmelzwaan et al., Mapping the Antigenic and Genetic Evolution of Influenza Virus, Science, vol.305, issue.5682, pp.371-376, 2004.
DOI : 10.1126/science.1097211

M. Lässig, V. Mustonen, and A. Walczak, Predicting evolution, Nature Ecology & Evolution, vol.5, issue.3, pp.1-9, 2017.
DOI : 10.1038/nature12053

H. Risken, The Fokker-Planck equation, 1989.