Thanks to smorfland for the colors...
More picts here.
Thanks to smorfland for the colors... More picts here. |
Most of my previous contributions are maintained here.
| [PDF] | Charif, D., Lobry, J.R. (2007) SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis in Structural approaches to sequence evolution: Molecules, networks, populations (U. Bastolla, M. Porto, H.E. Roman and M. Vendruscolo Eds.) Biological and Medical Physics, Biomedical Engineering. pp 207-232. [Link to last version] |
| [PDF] | Lobry, J.R., Necşulea, A. (2006) Synonymous Codon Usage and its Potential Link with Optimal Growth Temperature in Prokaryotes. Gene, 385:128-136. [ONLINE REPRODUCIBILITY] |
| [PDF] | Palmeira, L., Guéguen, L., Lobry, J.R. (2006) UV-targeted dinucleotides are not depleted in light-exposed Prokaryotic genomes. Molecular Biology and Evolution, 23:2214-2219. [ONLINE REPRODUCIBILITY] |
| [PDF] | Necşulea, A., Lobry, J.R. (2006) Revisiting the directional mutation pressure theory: the analysis of a particular genomic structure in Leishmania major. Gene, 385:28-40. [ONLINE REPRODUCIBILITY] |
| [PDF] | Peyron, F., Lobry, J.R., Musset, K., Ferrandiz, J., Gómez-Marín, J.E., Petersen, E., Meroni, V., Rausher, B., Mercier, C., Picot, S., Cesbron-Delauw, M.-F. (2006) Serotyping of Toxoplasma gondii in chronically infected pregnant women: predominance of type II in Europe and types I and III in Columbia (South America). Microbes and Infection, 8:2333-2340. [ONLINE REPRODUCIBILITY] |
| [PDF] | Sémon, M., Lobry, J.R., Duret, L. (2006) No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans. Molecular Biology and Evolution, 23:523-529. [ONLINE REPRODUCIBILITY] |
| [PDF] | Zagordi, O., Lobry, J.R. (2005) Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons. Gene, 347:175-182. [DATASET] [arXiv] [ONLINE REPRODUCIBILITY] |
| [PDF] | Charif, D., Thioulouse, J., Lobry, J.R., Perrière, G. (2005) Online Synonymous Codon Usage Analyses with the ade4 and seqinR packages Bioinformatics, 21:545-547. [ONLINE REPRODUCIBILITY] |
| [PDF] | Lobry, J.R. (2004) Life history traits and genome structure: aerobiosis and G+C content in bacteria. Lecture Notes in Computer Sciences, 3039:679-686. [ONLINE REPRODUCIBILITY] |
| [PDF] | Lobry, J.R., Chessel, D. (2003) Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria. Journal of Applied Genetics, 44:235-261. [DATASET] [ONLINE REPRODUCIBILITY] |
| [PDF] | Lobry, J.R., Louarn, J.-M. (2003) Polarization of prokaryotic chromosomes. Current Opinion in Microbiology, 6:101-108. |
| [PDF] | Lobry, J.R., Sueoka, N. (2002) Asymmetric directional mutation pressures in bacteria. Genome Biology, 3:research58.1-14. |
| [PDF] | Picardeau, M., Lobry, J.R., Hinnebusch, B.J. (2000) Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Research, 10:1594-1604. |
| [PDF] | Frank, A.C., Lobry, J.R. (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes, Bioinformatics, 16:560-561. |
| [PDF] | Lobry, J.R. (2000) The black hole of symmetric molecular evolution. Habilitation thesis defended on 20-JUL-2000 at the University Claude Bernard, Lyon I. Jury board: Siv Andersson (Uppsala University, Sweden), Antoine Danchin (Hong Kong University Pasteur Research centre, Hong Kong), Christian Gautier (University Claude Bernard, Lyon I, France), Jean-Michel Louarn (Paul Sabatier University, France), Noboru Sueoka (University of Colorado at Boulder, USA). |
| [PDF] | Lobry, J.R. (1999) A nice wrong model for the evolution of DNA base frequencies. Physica A, 273:100-103. |
| [PDF] | Lobry, J.R. (1999) Genomic landscapes. Microbiology Today, 26:164-165. |
| [PDF] | Kano-Sueoka, T., Lobry, J.R., Sueoka, N. (1999) Intra-strand biases in bacteriophage T4 genome. Gene, 238:59-64. |
| [PDF] | Frank, A.C., Lobry, J.R. (1999) Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 238:65-77. |
| [PDF] | Picardeau, M., Lobry, J.R., Hinnebusch, B.J. (1999) Physical mapping of an origin of bidirectional replication at the center of the Borrelia burgdorferi linear chromosome. Molecular Microbiology, 32:437-445. |
| [PDF] | Lobry, J.R., Lobry, C. (1999) Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant. Molecular Biology and Evolution, 16:719-723. |
| [PDF] | Charles, H., Mouchiroud, D., Lobry, J., Goncalves, I., Rahbe, Y. (1999) Gene size reduction in the bacterial aphid endosymbiont, Buchnera. Molecular Biology and Evolution, 16:1820-1822. |
| [ABS] | Perrière, G., Lobry, J.R. (1998) Asymmetrical coding sequence repartition and codon adaptation index values between leading and lagging strands in seven bacterial species. in Proceedings of the first international conference on bioinformatics of genome regulation and structure (Novosibirsk, Russia, August 24-31, 1998) 2:254-255. |
| [PDF] | Lobry, J.R. (1997) Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species. Gene, 205:309-316. [DATASET] |
| [PDF] | Galtier, N., Lobry, J.R. (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. Journal of Molecular Evolution, 44:632-636. [DATASET] [ONLINE REPRODUCIBILITY] |
| [PDF] | Perrière, G., Lobry, J.R., Thioulouse, J. (1996) Correspondence discriminant analysis: a multivariate method for comparing classes of protein and nucleic acids sequences. Computer Applications in the Biosciences, 12:519-524. [DATASET] [ONLINE REPRODUCIBILITY] |
| [PDF] | Lobry, J.R. (1996) A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie, 78:323-326. |
| [PDF] | Lobry, J.R. (1996) Origin of replication of Mycoplasma genitalium. Science, 262:745-746. |
| [PDF] | Lobry, J.R. (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Molecular Biology and Evolution, 13:660-665. |
| [PDF] | Lobry, J.R. (1995) Properties of a general model of DNA evolution under no-strand bias conditions. Journal of Molecular Evolution, 40:326-330; 41:680. [ONLINE REPRODUCIBILITY] |
| [NYT] | Thioulouse, J., Lobry, J.R. (1995) Co-inertia alaysis of amino-acid physico-chemical properties and protein composition with the ADE package. Computer Applications in the Biosciences, 11:321-329. [DATASET] [ONLINE REPRODUCIBILITY] |
| [NYT] | Lobry, J.R. (1995) Unexpected behaviour of Monod's bacterial growth model. pp 149-154 in Mathematical population dynamic: analysis of heterogeneity (Arino, O., Axelrod, D., Kimmel, M. eds). Wuerz, Winnipeg. |
| [PDF] | Rosso, L., Lobry, J.R., Bajard, S., Flandrois, J.-P. (1995) Convenient model to describe the combined effects of temperature and pH on microbial growth. Applied and Environmental Microbiology, 61:610-616. |
| [PDF] | Lobry, J.R., Gautier, C. (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Research, 22:3174-3180. [DATASET] [ONLINE REPRODUCIBILITY] |
| [PDF] | Rosso, L., Lobry, J.R., Flandrois, J.-P. (1993) An unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model. Journal of Theoretical Biology, 162:447-463. |
| [NYT] | Lobry, J.R., Carret, G., Flandrois, J.-P. (1992) Maintenance requirements of Escherichia coli ATCC 25922 in the presence of sub-inhibitory concentrations of various antibiotics. Journal of Antimicrobial Chemotherapy, 29:121-127. |
| [NYT] | Lobry, J.R., Flandrois, J.-P., Carret, G., Pavé, A. (1992) Monod's bacterial growth model revisited. Bulletin of Mathematical Biology, 54:117-122. |
| [PDF] | Lobry, J.R. (1991) Ré-évaluation de modèle de croissance de Monod. Effet des antibiotiques sur l’énergie de maintenance. PhD thesis defended on 9-SEP-1991 at the University Claude Bernard, Lyon I. Jury board: Arlette Cheruy, Jacques Demongeot, Jean-Pierre Flandrois, Emmanuel Jolivet, A. Pavé. |
| [NYT] | Carret, G., Flandrois, J.-P., Lobry, J.R. (1991) Biphasic kinetics of bacterial killing by quinolones. Journal of Antimicrobial Chemotherapy, 27:319-327. |
| [PDF] | Lobry, J.R., Flandrois, J.-P. (1991) Comparison of estimates of Monod's growth model from the same data set. Binary, 3:20-23. |
| [PDF] | Lobry, J.R., Rosso, L., Flandrois, J.-P. (1991) A FORTRAN subroutine for the determination of parameter confidence limits in non-linear Models. Binary, 3:86-93. [ONLINE REPRODUCIBILITY] |