Lobry Jean

seqinr: Biological Sequences Retrieval and Analysis

Delphine Charif, Simon Penel, Jean R Lobry, Anamaria Necsulea

DOI: 10.32614/CRAN.package.seqinr

2023

Software

see the publication

Oak masting drivers vary between populations depending on their climatic environments

Emilie Fleurot, Jean R Lobry, Vincent Boulanger, François Débias, Camille Mermet-Bouvier, Thomas Caignard...

Current Biology . 33 ( 6 ) : 1117-1124.e4

DOI: 10.1016/j.cub.2023.01.034

2023

Journal article

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The CV is dead, long live the CV !

Jean R Lobry, Marie‐claude Bel‐venner, Michał Bogdziewicz, Andrew Hacket‐pain, Samuel Venner

Methods in Ecology and Evolution .

DOI: 10.1111/2041-210X.14197

2023

Journal article

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Enseigner les recueil des données : explorer la variabilité biologique ... au chaud, dans une salle de cours

Anne-Béatrice Dufour, Jean R Lobry, Isabelle Amat

Statistique et Enseignement . 8 ( 2 ) : 79-85

2017

Journal article

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Estimating the Number of Contributors to Forensic DNA Mixtures: Does Maximum Likelihood Perform Better Than Maximum Allele Count?

Hinda Haned, Laurent Pène, J.R. Lobry, Anne-Béatrice Dufour, D. Pontier

Journal of Forensic Sciences . 56 ( 1 ) : 23-28

DOI: 10.1111/j.1556-4029.2010.01550.x

2011

Journal article

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Serotyping of Toxoplasma gondii: striking homogeneous pattern between symptomatic and asymptomatic infections within Europe and South America.

Stéphane Morisset, François Peyron, Jean R Lobry, Justus Garweg, Josette Ferrandiz, Karine Musset...

Microbes and Infection . 10 ( 7 ) : 742-7

DOI: 10.1016/j.micinf.2008.04.001

2008

Journal article

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From W.S. Gosset`s pieces of card (1908) to R software : analysing Macdonell`s dataset of 3000 criminals

Anne-Béatrice Dufour, J.R. Lobry

Biométrie Humaine et Anthropologie - revue de la Société de biométrie humaine . 26 : 33-39

2008

Journal article

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An agent-based model for predicting the prevalence of Trypanosoma cruzi I and II in their host and vector populations

H. Devillers, J.R. Lobry, F. Menu

Journal of Theoretical Biology . 255 : 307-315

2008

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

Molecular Biology and Evolution . 24 : 2169-2179

2007

Journal article

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SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis

D. Charif, J.R. Lobry

incollection . -- : 207-232

2007

Journal article

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A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

A. Necşulea, J.R. Lobry

incollection . 7 : 379-381

2007

Journal article

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Serotyping of Toxoplasma gondii in chronically infected pregnant women: predominance of type II in Europe and types I and III in Colombia (South America).

François Peyron, Jean R Lobry, Karine Musset, Josette Ferrandiz, Jorge Enrique Gomez-Marin, Eskild Petersen...

Microbes and Infection . 8 ( 9-10 ) : 2333-40

DOI: 10.1016/j.micinf.2006.03.023

2006

Journal article

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UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

L. Palmeira, Laurent Guéguen, J.R. Lobry

Molecular Biology and Evolution . 23 : 2214-2219

2006

Journal article

see the publication

Serotyping of Toxoplasma gondii in chronically infected pregnant women : predominance of type II in Europe and types I and III in Colombia (South America)

F. Peyron, J.R. Lobry, K. Musset, J. Ferrandiz, J.E. Gómez-Marín, E. Petersen...

Microbes and Infection . 8 : 2333-2340

2006

Journal article

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Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

J.R. Lobry, A. Necşulea

Gene . 385 : 128-136

2006

Journal article

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No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

M. Sémon, J.R. Lobry, L. Duret

Molecular Biology and Evolution . 23 : 523-529

2006

Journal article

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Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

A. Necşulea, J.R. Lobry

Gene . 385 : 28-40

2006

Journal article

see the publication

Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière

Bioinformatics . 21 : 545-547

2005

Journal article

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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

O. Zagordi, J.R. Lobry

Gene . 347 : 175-182

2005

Journal article

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Life history traits and genome structure: aerobiosis and G+C content in bacteria

J.R. Lobry

Lecture Notes in Computer Science . 3039 : 679-686

2004

Journal article

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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

O. Zagordi, J. R. Lobry

2004

Preprint

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Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria

J.R. Lobry, D. Chessel

Journal of Applied Genetics . 44 : 235-261

2003

Journal article

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Polarisation of prokaryotic chromosomes

J.R. Lobry, J.M. Louarn

Current Opinion in Microbiology . 6 : 101-108

2003

Journal article

see the publication

Asymmetric directional mutation pressures in bacteria

J.R. Lobry, N. Sueoka

Genome Biology . 26 : 1-14

2002

Journal article

see the publication

Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes

A.C. Frank, J.R. Lobry

Bioinformatics . 16 : 560-561

2000

Journal article

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Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids

M. Picardeau, J.R. Lobry, B.J. Hinnebusch

Genome Research . 10 : 1594-1604

2000

Journal article

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Genomic landscapes

Jean R Lobry

Microbiology Today . 26 : 164-165

1999

Journal article

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Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant

J.R. Lobry, C. Lobry

Molecular Biology and Evolution . 16 : 719-723

1999

Journal article

see the publication

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

A.C. Frank, J.R. Lobry

Gene . 238 : 65-77

1999

Journal article

see the publication

Intra-strand biases in bacteriophage T4 genome

T. Kano-Sueoka, J.R. Lobry, N. Sueoka

Gene . 238 : 59-64

1999

Journal article

see the publication

Publications

seqinr: Biological Sequences Retrieval and Analysis

Oak masting drivers vary between populations depending on their climatic environments

The CV is dead, long live the CV !

Enseigner les recueil des données : explorer la variabilité biologique ... au chaud, dans une salle de cours

Estimating the Number of Contributors to Forensic DNA Mixtures: Does Maximum Likelihood Perform Better Than Maximum Allele Count?

Serotyping of Toxoplasma gondii: striking homogeneous pattern between symptomatic and asymptomatic infections within Europe and South America.

From W.S. Gosset`s pieces of card (1908) to R software : analysing Macdonell`s dataset of 3000 criminals

An agent-based model for predicting the prevalence of Trypanosoma cruzi I and II in their host and vector populations

A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis

A New Method for Assessing the Effect of Replication on DNA Base Composition Asymmetry

Serotyping of Toxoplasma gondii in chronically infected pregnant women: predominance of type II in Europe and types I and III in Colombia (South America).

UV-Targeted Dinucleotides Are Not Depleted in Light-Exposed Prokaryotic Genomes

Serotyping of Toxoplasma gondii in chronically infected pregnant women : predominance of type II in Europe and types I and III in Colombia (South America)

Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans

Revisiting the directionnal mutation pressure theory : The analysis of a particular genomic structure in Leishmania major

Online synonymous codon usage analyses with the ade4 and seqinR packages

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

Life history traits and genome structure: aerobiosis and G+C content in bacteria

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

Internal correspondence analysis of codon and amino-acid usage in thermophilic bacteria

Polarisation of prokaryotic chromosomes

Asymmetric directional mutation pressures in bacteria

Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes

Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids

Genomic landscapes

Evolution of DNA base composition under no-strand-bias conditions when the substitution rates are not constant

Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms

Intra-strand biases in bacteriophage T4 genome