Ten years of tension: single-molecule DNA mechanics, Nature, vol.74, issue.6921, pp.423-430, 2003. ,
DOI : 10.1038/nature01405
The micromechanics of DNA Phys, World, vol.16, pp.37-41, 2003. ,
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads, Science, vol.258, issue.5085, pp.1122-1128, 1992. ,
DOI : 10.1126/science.1439819
Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules, Science, vol.271, issue.5250, p.795, 1996. ,
DOI : 10.1126/science.271.5250.795
DNA strand separation studied by single molecule force measurements Phys, Rev. E, vol.58, pp.2386-94, 1998. ,
Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips, Biophysical Journal, vol.82, issue.3, pp.1537-53, 2002. ,
DOI : 10.1016/S0006-3495(02)75506-9
URL : http://doi.org/10.1016/s0006-3495(02)75506-9
Rotational Drag on DNA: A Single Molecule Experiment, Physical Review Letters, vol.88, issue.24, p.248102, 2002. ,
DOI : 10.1103/PhysRevLett.88.248102
Dynamics of the DNA Duplex Formation Studied by Single Molecule Force Measurements, Biophysical Journal, vol.87, issue.5, pp.3388-96, 2004. ,
DOI : 10.1529/biophysj.104.039776
URL : https://hal.archives-ouvertes.fr/hal-00004440
Force-Dependent Fragility in RNA Hairpins, Physical Review Letters, vol.96, issue.21, p.218301, 2006. ,
DOI : 10.1103/PhysRevLett.96.218301
Force Unfolding Kinetics of RNA using Optical Tweezers. II. Modeling Experiments, Biophysical Journal, vol.92, issue.9, p.3010, 2007. ,
DOI : 10.1529/biophysj.106.094243
Reversible Unfolding of Single RNA Molecules by Mechanical Force, Science, vol.292, issue.5517, pp.733-740, 2001. ,
DOI : 10.1126/science.1058498
Measurement of the Phase Diagram of DNA Unzipping in the Temperature-Force Plane, Physical Review Letters, vol.93, issue.7, p.78101, 2004. ,
DOI : 10.1103/PhysRevLett.93.078101
Pause Point Spectra in DNA Constant-Force Unzipping, Biophysical Journal, vol.88, issue.4, pp.2752-65, 2005. ,
DOI : 10.1529/biophysj.104.047340
Replication by a single DNA polymerase of a stretched single-stranded DNA, Proc. Natl Acad. Sci, p.12002, 2000. ,
DOI : 10.1073/pnas.97.22.12002
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations, Science, vol.299, issue.5607, pp.682-688, 2003. ,
DOI : 10.1126/science.1079700
Combined optical trapping and single-molecule fluorescence, J. Biol, vol.2, 2003. ,
DOI : 10.1038/nmeth714
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1483847
Unzipping Kinetics of Double-Stranded DNA in a Nanopore, Physical Review Letters, vol.90, issue.23, p.238101, 2003. ,
DOI : 10.1103/PhysRevLett.90.238101
DNA mechanics as a tool to probe helicase and translocase activity, Nucleic Acids Research, vol.34, issue.15, p.4232, 2006. ,
DOI : 10.1093/nar/gkl451
URL : https://hal.archives-ouvertes.fr/hal-00867953
Single molecule statistics and the polynucleotide unzipping transition Phys, Rev. E, vol.65, p.31917, 2002. ,
Probing DNA and RNA single molecules with a double optical tweezer Eur, Phys. J. E, vol.19, pp.311-318, 2006. ,
Passive All-Optical Force Clamp for High-Resolution Laser Trapping, Physical Review Letters, vol.95, issue.20, p.208102, 2005. ,
DOI : 10.1103/PhysRevLett.95.208102
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1357091
Force and kinetic barriers to initiation of DNA unzipping Phys. Rev, p.41907, 2002. ,
Verification of the Crooks fluctuation theorem and recovery of RNA folding free energies, Nature, vol.15, issue.7056, p.231, 2005. ,
DOI : 10.1063/1.1363668
Inference of DNA Sequences from Mechanical Unzipping: An Ideal-Case Study, Physical Review Letters, vol.96, issue.12, p.128102, 2006. ,
DOI : 10.1103/PhysRevLett.96.128102
Single-Molecule DNA Sequencing of a Viral Genome, Science, vol.320, issue.5872, p.106, 2008. ,
DOI : 10.1126/science.1150427
Physical limits on the mechanical measurement of the secondary structure of bio-molecules Europhys, Lett, vol.31, p.335, 1995. ,
Calculating nucleic acid secondary structure, Current Opinion in Structural Biology, vol.10, issue.3, pp.303-313, 2000. ,
DOI : 10.1016/S0959-440X(00)00088-9
A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers, The Journal of Chemical Physics, vol.21, issue.7, pp.1272-80 ,
DOI : 10.1063/1.1699180
Infotassi: un algoritmo di ricerca senza gradienti, La Sapienza, 2007. ,
Structural transitions of encapsidated polyelectrolytes, The European Physical Journal E, vol.59, issue.3, pp.323-334, 2008. ,
DOI : 10.1140/epje/i2007-10301-6
Observation of a single-beam gradient force optical trap for dielectric particles, Optics Letters, vol.11, issue.5, pp.288-290, 1986. ,
DOI : 10.1364/OL.11.000288
Enzymic synthesis of deoxyribonucleic acid. XXXIV. Termination of chain growth by a 2',3'-dideoxyribonucleotide, Biochemistry, vol.8, issue.12, pp.4897-4904, 1969. ,
DOI : 10.1021/bi00840a037
Neural correlations, population coding and computation, Nature Reviews Neuroscience, vol.2, issue.5, pp.358-366, 2006. ,
DOI : 10.1038/nrn1888
Inference of DNA Sequences from Mechanical Unzipping: An Ideal-Case Study, Physical Review Letters, vol.96, issue.12, p.128102, 2006. ,
DOI : 10.1103/PhysRevLett.96.128102
Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case, Physical Review E, vol.75, issue.1, p.11904, 2007. ,
DOI : 10.1103/PhysRevE.75.011904
URL : https://hal.archives-ouvertes.fr/hal-00142549
Olfactory search at high Reynolds number, Proceedings of the National Academy of Sciences, p.12589, 2002. ,
DOI : 10.1073/pnas.192393499
Dynamical modeling of molecular constructions and setups for DNA unzipping, Physical Biology, vol.6, issue.2, p.25003, 2009. ,
DOI : 10.1088/1478-3975/6/2/025003
On the trajectories and performance of Infotaxis, an information-based greedy search algorithm, EPL (Europhysics Letters), vol.94, issue.2, 2011. ,
DOI : 10.1209/0295-5075/94/20005
URL : https://hal.archives-ouvertes.fr/hal-00526241
Chemotaxis in Bacteria, Annual Review of Biophysics and Bioengineering, vol.4, issue.1, pp.119-136, 1975. ,
DOI : 10.1146/annurev.bb.04.060175.001003
A Physicist Looks at Bacterial Chemotaxis, Cold Spring Harbor Symposium on Quantitative Biology, pp.1-9, 1988. ,
DOI : 10.1101/SQB.1988.053.01.003
Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements, Biophysical Journal, vol.76, issue.1, pp.409-413, 1999. ,
DOI : 10.1016/S0006-3495(99)77207-3
Predicting DNA duplex stability from the base sequence., Proceedings of the National Academy of Sciences, p.3746, 1986. ,
DOI : 10.1073/pnas.83.11.3746
Excluded Volume Effects on Polymer Chains Confined to Spherical Surfaces, Macromolecules, vol.38, issue.4, pp.1469-1477, 2005. ,
DOI : 10.1021/ma048989n
Continuous base identification for single-molecule nanopore DNA sequencing, Nature Nanotechnology, vol.19, issue.4, pp.265-270, 2009. ,
DOI : 10.1038/nnano.2009.12
Force and kinetic barriers to unzipping of the DNA double helix, Proceedings of the National Academy of Sciences, p.8608, 2001. ,
DOI : 10.1073/pnas.151257598
Slow nucleic acid unzipping kinetics from sequence-defined barriers, The European Physical Journal E - Soft Matter, vol.10, issue.2, pp.153-161, 2003. ,
DOI : 10.1140/epje/e2003-00019-8
URL : http://arxiv.org/abs/cond-mat/0207609
Neuronal couplings between retinal ganglion cells inferred by efficient inverse statistical physics methods Theory of the melting transition of synthetic polynucleotides: Evaluation of the stacking free energy*, Proceedings of the National Academy of Sciences, pp.14058-14059, 1964. ,
Dynamic holographic optical tweezers, Optics Communications, vol.207, issue.1-6, pp.1-6, 2002. ,
DOI : 10.1016/S0030-4018(02)01524-9
DNA unzipped under a constant force exhibits multiple metastable intermediates, Proceedings of the National Academy of Sciences, p.1694, 2003. ,
DOI : 10.1073/pnas.262789199
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149895
The Theory of polymer dynamics. Numeéro 73 in International Series of Monographs on Physics, 1986. ,
Stochastic Gene Expression in a Single Cell, Science, vol.297, issue.5584, p.1183, 2002. ,
DOI : 10.1126/science.1070919
Principles of polymer chemistry. George Fisher Baker non-resident lectureship in chemistry at Cornell University, 1953. ,
Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation, The American Journal of Human Genetics, vol.79, issue.3, pp.500-513, 1980. ,
DOI : 10.1086/507471
Strong synaptic transmission impact by copy number variations in schizophrenia, Proceedings of the National Academy of Sciences, p.10584, 2010. ,
DOI : 10.1073/pnas.1000274107
Magnetic Tweezers: Micromanipulation and Force Measurement at the Molecular Level, Biophysical Journal, vol.82, issue.6, pp.3314-3329, 2002. ,
DOI : 10.1016/S0006-3495(02)75672-5
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology, BIBLIOGRAPHY 135 BIBLIOGRAPHY [Huguet 09] J. M. Huguet, N. Forns & F. Ritort. Statistical properties of metastable intermediates in DNA unzipping. Physical review letters, pp.2310-248106, 2001. ,
DOI : 10.1126/science.1065889
Single-molecule derivation of salt dependent base-pair free energies in DNA, Proceedings of the National Academy of Sciences, p.15431, 2010. ,
DOI : 10.1073/pnas.1001454107
Detection of large-scale variation in the human genome, Nature Genetics, vol.10, issue.9, pp.949-951, 2004. ,
DOI : 10.1038/ng1307
Theory of the Elastic Properties of Rubber, The Journal of Chemical Physics, vol.11, issue.10, p.455, 1943. ,
DOI : 10.1063/1.1723785
Generalized Integrate-and-Fire Models of Neuronal Activity Approximate Spike Trains of a Detailed Model to a High Degree of Accuracy, Journal of Neurophysiology, vol.92, issue.2, p.959, 2004. ,
DOI : 10.1152/jn.00190.2004
Initiation of slime mold aggregation viewed as an instability, Journal of Theoretical Biology, vol.26, issue.3, pp.399-415, 1970. ,
DOI : 10.1016/0022-5193(70)90092-5
Comparative analysis of copy number variation detection methods and database construction, BMC Genetics, vol.12, issue.1, p.29, 2011. ,
DOI : 10.1038/jhg.2009.68
Brownian motion in a field of force and the diffusion model of chemical reactions, Physica, vol.7, issue.4, pp.284-304, 1940. ,
DOI : 10.1016/S0031-8914(40)90098-2
Beziehungen zwischen elastischen Konstanten und Dehnungsdoppelbrechung hochelastischer Stoffe, Kolloid-Zeitschrift, vol.101, issue.3, pp.248-271, 1942. ,
DOI : 10.1007/BF01793684
A review of the methods for signal estimation in stochastic diffusion leaky integrate-and-fire neuronal models, Biological Cybernetics, vol.1, issue.2, pp.253-262, 2008. ,
DOI : 10.1007/s00422-008-0237-x
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations, Science, vol.299, issue.5607, p.682, 2003. ,
DOI : 10.1126/science.1079700
Information theory, inference, and learning algorithms, 2005. ,
Interference and crosstalk in double optical tweezers using a single laser source, Review of Scientific Instruments, vol.79, issue.8, pp.83103-3224, 2005. ,
DOI : 10.1063/1.2957652
Bending and twisting elasticity of DNA, Macromolecules, vol.27, issue.4, pp.981-988, 1994. ,
DOI : 10.1021/ma00082a015
Stretching DNA, Macromolecules, vol.28, issue.26, pp.8759-8770, 1995. ,
DOI : 10.1021/ma00130a008
Chasing information to search in random environments, Journal of Physics A: Mathematical and Theoretical, vol.42, issue.43, p.434009, 2009. ,
DOI : 10.1088/1751-8113/42/43/434009
URL : https://hal.archives-ouvertes.fr/hal-00539327
A new method for sequencing DNA., Proceedings of the National Academy of Sciences, p.560, 1977. ,
DOI : 10.1073/pnas.74.2.560
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding, Genome Research, vol.19, issue.9, pp.1527-1541, 2009. ,
DOI : 10.1101/gr.091868.109
Fast inference of interactions in assemblies of stochastic integrate-and-fire neurons from spike recordings, Journal of Computational Neuroscience, vol.93, issue.2, pp.1-29 ,
DOI : 10.1007/s10827-010-0306-8
URL : https://hal.archives-ouvertes.fr/hal-00569388
Torsional directed walks, entropic elasticity, and DNA twist stiffness, Proceedings of the National Academy of Sciences, p.14418, 1997. ,
DOI : 10.1073/pnas.94.26.14418
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC25005
Investigating the thermodynamics of small biosystems with optical tweezers, Physica E: Lowdimensional Systems and Nanostructures, pp.666-671, 2010. ,
DOI : 10.1016/j.physe.2009.06.055
Specific Enzymatic Amplification of DNA In Vitro: The Polymerase Chain Reaction, Cold Spring Harbor Symposia on Quantitative Biology, vol.51, issue.0, p.263, 1986. ,
DOI : 10.1101/SQB.1986.051.01.032
Maximum Likelihood Estimation of a Stochastic Integrate-and-Fire Neural Encoding Model, Neural Computation, vol.79, issue.2, pp.2533-2561, 2004. ,
DOI : 10.1103/PhysRevE.68.011901
The most likely voltage path and large deviations approximations for integrate-and-fire neurons, Journal of Computational Neuroscience, vol.21, issue.1, pp.71-87, 2006. ,
DOI : 10.1007/s10827-006-7200-4
Numerical recipes in fortran 77. the art of scientific computing, 1986. ,
Dictyostelium discoideum, a new species of slime mold from decaying forest leaves, Journal of Agricultural Research, vol.50, pp.135-147, 1935. ,
Pseudoplasmodium formation and organization in Dictyostelium discoideum, Journal of the Elisha Mitchell Scientific Society, vol.56, pp.241-282, 1940. ,
Real-Time DNA Sequencing Using Detection of Pyrophosphate Release, Analytical Biochemistry, vol.242, issue.1, pp.84-89, 1996. ,
DOI : 10.1006/abio.1996.0432
A sequencing method based on real-time pyrophosphate, Science, vol.281, issue.5375, pp.363-365, 1998. ,
A Theory of the Linear Viscoelastic Properties of Dilute Solutions of Coiling Polymers, Journal of Chemical Physics, vol.21, pp.1272-1280, 1953. ,
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase, Journal of Molecular Biology, vol.94, issue.3, pp.441-446, 1975. ,
DOI : 10.1016/0022-2836(75)90213-2
DNA sequencing with chain-terminating inhibitors, Proceedings of the National Academy of Sciences, p.5463, 1977. ,
DOI : 10.1073/pnas.74.12.5463
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC431765
Large-Scale Copy Number Polymorphism in the Human Genome, Science, vol.305, issue.5683, pp.525-445, 2004. ,
DOI : 10.1126/science.1098918
Temporal comparisons in bacterial chemotaxis., Proceedings of the National Academy of Sciences, pp.8987-8991, 1986. ,
DOI : 10.1073/pnas.83.23.8987
Aggregation in Cellular Slime Moulds: in vitro Isolation of Acrasin, Nature, vol.103, issue.4361, pp.975-977, 1953. ,
DOI : 10.1002/jez.1401060102
Copy number variations and cancer susceptibility, Current Opinion in Oncology, vol.22, issue.1, p.55, 2010. ,
DOI : 10.1097/CCO.0b013e328333dca4
On the connected-charges Thomson problem, Europhysics Letters (EPL), vol.75, issue.4, p.631, 2006. ,
DOI : 10.1209/epl/i2006-10146-1
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads, Science, vol.258, issue.5085, pp.1122-1126, 1992. ,
DOI : 10.1126/science.1439819
Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules, Science, vol.271, issue.5250, p.795, 1996. ,
DOI : 10.1126/science.271.5250.795
Versuch einer mathematischen Theorie des Koagulationeskinetik kolloider Lösungen, Zeitschrift für physicalische Chimie, pp.129-168, 1917. ,
A strategy of DNA sequencing employing computer programs, Nucleic Acids Research, vol.6, issue.7, p.2601, 1979. ,
DOI : 10.1093/nar/6.7.2601
On the Effect of the Internal Friction of Fluids on the Motion of Pendulums, Transactions of the Cambridge Philosophical Society, vol.IX, pp.8-1851 ,
DOI : 10.1017/CBO9780511702266.002
Tourette syndrome is associated with recurrent exonic copy number variants, Neurology, vol.74, issue.20, p.1583, 2010. ,
DOI : 10.1212/WNL.0b013e3181e0f147
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2876824
Advances in network electrophysiology: using multi-electrode arrays, 2006. ,
DOI : 10.1007/b136263
Estimation of Secondary Structure in Ribonucleic Acids, Nature, vol.5, issue.5293, pp.362-367, 1971. ,
DOI : 10.1038/230362a0
Improved Estimation of Secondary Structure in Ribonucleic Acids, BIBLIOGRAPHY 139 BIBLIOGRAPHY [Uhlenbeck 30] G. E. Uhlenbeck & L. S. Ornstein. On the theory of the Brownian motion. Physical Review, pp.40-41, 1930. ,
DOI : 10.1038/newbio246040a0
Private communication, 2007. ,
???Infotaxis??? as a strategy for searching without gradients, Nature, vol.5, issue.7126, pp.406-409, 2007. ,
DOI : 10.1038/nature05464
Reiterative responses to single strands of odor promote sustained upwind flight and odor source location by moths., Proceedings of the National Academy of Sciences, p.5756, 1994. ,
DOI : 10.1073/pnas.91.13.5756
Error Bounds for Convolutional Codes and an Asymptotically Optimum Decoding Algorithm, IEEE Transactions on Information Theory, vol.13, issue.2, pp.260-269, 1967. ,
DOI : 10.1142/9789814287517_0004
A New Semiconductor Photocell Using Lateral Photoeffect, Proceedings of the IRE, pp.474-483, 1957. ,
DOI : 10.1109/JRPROC.1957.278435
Ligase chain reaction (LCR)--overview and applications., Genome Research, vol.3, issue.4, p.51, 1994. ,
DOI : 10.1101/gr.3.4.S51
URL : http://genome.cshlp.org/cgi/content/short/3/4/S51
Direct Measurement of the Full, Sequence-Dependent Folding Landscape of a Nucleic Acid, Science, vol.314, issue.5801, p.1001, 2006. ,
DOI : 10.1126/science.1133601
Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins, Proceedings of the National Academy of Sciences, pp.6190-6195, 2006. ,
DOI : 10.1073/pnas.0511048103
The ligation amplification reaction (LAR)???Amplification of specific DNA sequences using sequential rounds of template-dependent ligation, Genomics, vol.4, issue.4, pp.560-569, 1989. ,
DOI : 10.1016/0888-7543(89)90280-2
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data, Bioinformatics, vol.21, issue.1, p.71, 2005. ,
DOI : 10.1093/bioinformatics/bth463