Publications 2013

Cytokinin signalling inhibitory fields provide robustness to phyllotaxis

Besnard F., Refahi Y., Morin V., Marteaux B., Brunoud G., Chambrier P., Rozier F., Mirabet V., Legrand J., Lainé S., Thévenon E., Farcot E., Cellier C., Das P., Bishopp A., Dumas R., Parcy F., Helariutta Y., Boudaoud A., Godin C., Traas J., Guédon Y., Vernoux T.
Nature 505(7483):417-21, 2013
Url : http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12791.html
PDF : http://www.nature.com/nature/journal/vaop/ncurrent/pdf/nature12791.pdf

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

N. Philippe, E. Bou Samara, A. Boureux, F. Rufflé, Q. Bai, A. Mancheron, J. Devos, E. Rivals, T. Commes
Nucleic Acids Res. (NAR), 42(5):2820-2832, 2013
URL : http://nar.oxfordjournals.org/content/42/5/2820
PDF : http://nar.oxfordjournals.org/content/42/5/2820.full.pdf

Detecting and measuring selection from gene frequency data

Vitalis R., Gautier M., Dawson K.J., Beaumont M.A.
Genetics 196(3):799-817, 2013
URL : http://www.genetics.org/content/196/3/799
PDF : http://www.genetics.org/content/196/3/799.full.pdf

RepeatsDB: a database of tandem repeat protein structures

Di Domenico T., Potenza E., Walsh I., Gonzalo Parra R., Giollo M., Minervini G., Piovesan D., Ihsan A., Ferrari C., Kajava A.V., Tosatto S.C.
Nucleic Acids Res.(NAR) 42(Database issue):D352-357, 2013
URL : http://nar.oxfordjournals.org/content/42/D1/D352
PDF : http://nar.oxfordjournals.org/content/42/D1/D352.full.pdf

Reconciliation-based detection of co-evolving gene families

Chan, Y.-C., Ranwez, V. and Scornavacca, C.
BMC Bioinformatics 14:332, 2013
URL : http://www.biomedcentral.com/1471-2105/14/332
PDF : http://www.biomedcentral.com/content/pdf/1471-2105-14-332.pdf

Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods

Algebraic Dataflows for Big Data Analysis

Dias J., Ogasawara E., De Oliveira D., Porto F., Valduriez P., Mattoso M.
IEEE BigData'2013 : International Conference on Big Data, 2013
Url : http://hal-lirmm.ccsd.cnrs.fr/lirmm-00857221

Whole Genome Mapping and Re-Organization of the Nuclear and Mitochondrial Genomes of Babesia microti Isolates

Cornillot E., Dassouli A., Garg A., Pachikara N., Randazzo S., Depoix D., Carcy B., Delbecq S., Frutos R, Silva JC., Sutton R., Krause PJ., Mamoun CB.
PLoS One 8(9): e72657, 2013
Url : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762879/

The origin and molecular epidemiology of HIV

Peeters M., Jung M., Ayouba A.
Expert Review of Anti-infective Therapy 11(9):885-896, 2013
URL : http://www.expert-reviews.com/doi/abs/10.1586/14787210.2013.825443

Effect of charged residues in the N-domain of Sup35 protein on prion [PSI+] stability and propagation

Bondarev S.A., Shchepachev V.V., Kajava A.V. and Zhouravleva G.A.
J Biol Chem. 288(40):28503-13, 2013
URL : http://www.ncbi.nlm.nih.gov/pubmed/23965990
PDF (Author version) : http://www.ibc-montpellier.fr/images/IBC/publi/2013-J. Biol. Chem.Bondarev.pdf

Exegeses on maximum genetic differentiation

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

Frange P., Meyer L., Jung M., Goujard C., Zucman D., Abel S., Hochedez P., Gousset M., Gascuel O., Rouzioux C., Chaix M-L. for the ANRS PRIMO Cohort Study Group
PLoS One 8(7):e69144, 2013
Url : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069144
PDF : http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0069144&representation=PDF

Genetic structure and evolution of the Leishmania genus in Africa and Eurasia: what does MLSA tell us

F. El Baidouri, S. Brisse, V. Berry, F. Chevenet, L. Diancourt, F. Pratlong, P. Marty, C. Ravel
PLOS Neglected Tropical Diseases 7(6): e2255, 2013
URL : http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0002255
PDF : http://www.plosntds.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pntd.0002255&representation=PDF

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data

Välimäki N., Rivals E.
ISBRA'2013: International Symposium on Bioinformatics Research and Applications
Springer Verlag LNBI 7875:237-248, 2013
Url : http://hal-lirmm.ccsd.cnrs.fr/lirmm-00806103
PDF : http://hal-lirmm.ccsd.cnrs.fr/docs/00/80/61/03/PDF/cgka-RR-2013.pdf

Embryonic stem cells or induced pluripotent stem cells? A DNA integrity perspective

Bai Q., Desprat R., Klein B., Lemaitre J-M., De Vos J.
Current Gene Therapy 13(2):93-8, 2013
Url : http://www.ncbi.nlm.nih.gov/pubmed/23317057

Profile Diversity in Search and Recommendation

Servajean M., Pacitti E., Amer-Yahia S., Neveu P.
SRS'13: International Workshop on Social Recommender Systems 2013
ACM Digital Library WWW'13 Companion:973:980, 2013
Url : http://hal-lirmm.ccsd.cnrs.fr/lirmm-00806676
PDF : http://dl.acm.org/citation.cfm?id=2488094

Chiron: A Parallel Engine for Algebraic Scientific Workflows

Ogasawara E., Dias J., Silva V., Chirigati F., De Oliveira D., Porto F., Mattoso M., Valduriez P.
Journal of Concurrency and Computation: Practice and Experience 25(16):2327-2341, 2013
Url : http://hal-lirmm.ccsd.cnrs.fr/lirmm-00806557

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

Wollbrett J., Larmande P., de Lamotte F. and Ruiz M.
BMC Bioinformatics 14:126, 2013
Url : http://www.biomedcentral.com/1471-2105/14/126
PDF : http://www.biomedcentral.com/content/pdf/1471-2105-14-126.pdf

Reconciliation and local gene tree rearrangement can be of mutual profit

Nguyen T. H., Ranwez V., Pointet S., Arigon Chifolleau A-M., Doyon J-P. and Berry V.
Algorithms for Molecular Biology 8:12 2013
Url : http://www.almob.org/content/8/1/12/abstract

CRAC: an integrated approach to the analysis of RNA-seq reads

Philippe N., Salson M., Commes T., Rivals E.
Genome Biology 14(3):R30, 2013 [epub]
Url : http://genomebiology.com/content/14/3/R30

Bayesian computation via empirical likelihood

Mengerson K.L., Pudlo P., Robert C. P.
Proceedings of the National Academy of Sciences 110(4):1321-1326, 2013
Url : http://www.pnas.org/content/110/4/1321

Searching for Virus Phylotypes

Chevenet F., Jung M., Peeters M., De Oliveira T., Gascuel O.
Bioinformatics 29(5): 561-570, 2013
Url : http://bioinformatics.oxfordjournals.org/content/29/5/561
PDF : http://bioinformatics.oxfordjournals.org/content/early/2013/01/16/bioinformatics.btt010.full.pdf

The Flux-Based PIN Allocation Mechanism Can Generate Either Canalyzed or Diffuse Distribution Patterns Depending on Geometry and Boundary Conditions