Publications 2014

Evolutionary link between metazoan RHIM motif and prion-forming domain of fungal heterokaryon incompatibility factor Het-s/Het-S

Kajava A. V., K. Klopffleisch, S. Chen, and K. Hofmann
Scientific Reports 4:7436, 2014
URL : http://www.nature.com/srep/2014/141211/srep07436/full/srep07436.html
PDF : http://www.nature.com/srep/2014/141211/srep07436/pdf/srep07436.pdf

CompPhy: a web-based collaborative platform for comparing phylogenies

Fiorini N., Lefort V., Chevenet F., Berry V., Arigon Chifolleau A.M.
BMC Evolutionary Biology, 14:253, 2014
URL: http://www.biomedcentral.com/1471-2148/14/253
PDF: http://www.biomedcentral.com/content/pdf/s12862-014-0253-5.pdf

Plasmodium falciparum merozoite surface protein 2: epitope mapping and fine specificity of human antibody response against non-polymorphic domains

Balam S., Olugbile S., Servis C., Diakité M., D'Alessandro A., Frank G., Moret R., Nebie I., Tanner M., Felger I., Smith T., Kajava A., Spertini F., Corradin G.
Malaria Journal 13(1):510, 2014
URL : http://www.malariajournal.com/content/13/1/510
PDF : http://www.malariajournal.com/content/pdf/1475-2875-13-510.pdf

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Blanc-Mathieu R., Verhelst B., Derelle E., Rombauts S., Bouget F.Y., Carré I., Chateau A., Eyre-Walker A.C, Grimsley N., Moreau H., Piegu B., Rivals E., van de Peer Y., Schackwitz W., Piganeau G.
BMC Genomics, 15:1103, 2014
URL : http://www.biomedcentral.com/1471-2164/15/1103
PDF : http://www.biomedcentral.com/content/pdf/1471-2164-15-1103.pdf

High Plasma Concentrations of Sclerostin, an Inhibitor of the Wnt Signaling Pathway, in Young Horses Affected by Osteochondrosis

Serteyn D., Mendoza L., Sandersen C., Caudron I., Piquemal D., Chavatte-Palmer P., Lejeune J.P.
Open Journal of Orthopedics, 4(12):335-342, 2014
URL : http://www.scirp.org/Journal/PaperInformation.aspx?PaperID=52170
PDF : http://www.scirp.org/Journal/PaperDownload.aspx?paperID=52170

Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem

Chateau A., Giroudeau R.
Lecture Notes in Computer Science (AlCoB 2014), Springer, 8542:47-58, 2014
URL : http://link.springer.com/chapter/10.1007%2F978-3-319-07953-0_4
Author version : http://hal-lirmm.ccsd.cnrs.fr/lirmm-01007556

FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets

Cuong Cao Dang, Vinh Sy Le, Olivier Gascuel, Bart Hazes and Quang Si Le
BMC Bioinfomatics, 2014 [epub]
URL : http://www.biomedcentral.com/1471-2105/15/341/abstract
PDF : http://www.biomedcentral.com/content/pdf/1471-2105-15-341.pdf

BION2SEL: An Ontology-based Approach for the Selection of Molecular Biology Databases

Lichtnow D., Alves R., Pastor O., Burriel B., Palazzo Moreira de Oliveira J.
9th Brazilian Symposium on Bioinformatics (BSB), Springer Verlag, LNCS 8826:83-90, 2014.
URL: http://link.springer.com/chapter/10.1007%2F978-3-319-12418-6_11
PDF(Author version): http://sites.google.com/site/biofflows/workflows/bion2sel_bsb14.pdf

FUNN-MG: A metagenomic systems biology computational framework

Corrêa L., Alves R., Góes F., Chaparro C. and Thom L.  
9th  Brazilian Symposium on Bioinformatics (BSB), Springer Verlag, LNCS 8826:25-32, 2014.
URL: http://link.springer.com/chapter/10.1007%2F978-3-319-12418-6_4
PDF(Author version): http://sites.google.com/site/biofflows/functional-analysis/funnmg_bsb14.pdf

Towards an Ensemble Learning Strategy for Metagenomic Gene Prediction

Góes F., Alves R., Corrêa L., Chaparro C. and Thom L.
9th Brazilian Symposium on Bioinformatics (BSB), Springer Verlag, LNCS 8826:17-24, 2014.
URL : http://link.springer.com/chapter/10.1007%2F978-3-319-12418-6_3
PDF(Author version): http://sites.google.com/site/biofflows/gene-prediction/classmg_bsb14.pdf

Data-Centric Iteration in Dynamic Workflows

Jonas Dias, Gabriel Guerra, Fernando Rochinha, Alvaro Coutinho, Patrick Valduriez, Marta Mattoso
Future Generation Computer Systems, Elsevier, 46:114-126, 2014
URL : http://www.sciencedirect.com/science/article/pii/S0167739X14002155
PDF : https://hal.archives-ouvertes.fr/lirmm-01073638/document

Dynamic Workload-Based Partitioning Algorithms for Continuously Growing Databases

Liroz-Gistau M., Akbarinia R., Pacitti E., Porto F., Valduriez P.
Transactions on Large-Scale Data- and Knowledge-Centered Systems, 2014
URL : https://hal.archives-ouvertes.fr/lirmm-00906966v1
PDF : http://hal-lirmm.ccsd.cnrs.fr/docs/00/90/69/66/PDF/tldks.pdf

Layer Decomposition: An Effective Structure-based Approach for Scientific Workflow Similarity

Starlinger J., Cohen-Boulakia S., Khanna S., Davidson S., Leser U.
IEEE e-Science conference, 2014
URL : https://hal.archives-ouvertes.fr/hal-01066076v1
PDF : http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6972262&tag=1

Sequence and Annotation of the Apicoplast Genome of the Human Pathogen Babesia microti

Osteochondrosis-Related Gene Expression in Equine Leukocytes Differs among Affected Joints in Foals

Similarity Search for Scientific Workflows

Starlinger J., Brancotte B., Cohen-Boulakia S., Leser U.
Proceedings of the 40th International on Very Large Data Bases (VLDB 2014), 2014
URL : http://hal.inria.fr/hal-01066046
PDF : http://www.vldb.org/pvldb/vol7/p1143-starlinger.pdf

From Indexing Data Structures to de Bruijn Graphs

Cazaux B., Lecroq T., Rivals E.
25th Annual Symposium on Combinatorial Pattern Matching (CPM 2014), Springer Verlag, LNCS 8486:89-99, 2014.
URL : http://link.springer.com/chapter/10.1007/978-3-319-07566-2_10

Exploiting Diversification in Gossip-Based Recommendation

Servajean M., Pacitti E., Liroz-Gistau M., Amer-Yahia S., El Abbadi A.
Globe'2014: 7th International Conference, LNCS (8648):25-36, 2014
URL : http://link.springer.com/chapter/10.1007/978-3-319-10067-8_3

LoRDEC: accurate and efficient long read error correction

An Integer Linear Programming Approach for Genome Scaffolding

Briot N., Chateau A., Coletta R., de Givry S., Leleux P., Schiex T.
10th Workshop on Constraint-Based Methods for Bioinformatics (WCB), 2014
PDF : http://stoics.org.uk/wcb2014/papers/BriotN_etal_2014.pdf

Matrix inversions for chromosomal inversions: A method to construct summary statistics in complex coalescent models

Rousset F., Kirkpatrick M., Guerrero R.F.
Theoretical Population Biology, 97 : 1-10, 2014
URL : www.sciencedirect.com/science/article/pii/S0040580914000549
PDF : http://ac.els-cdn.com/S0040580914000549/...

Scientific Workflow Partitioning in Multi-site Clouds

Ji Liu, Esther Pacitti, Patrick Valduriez, Vitor Silva Souza, Marta Mattoso
BigDataCloud’2014: 3rd Workshop on Big Data Management in Clouds in conjunction with Euro-Pa
Lecture Notes in Computer Science, Springer, 8805 : 105-116, 2014.
URL : http://link.springer.com/chapter/10.1007/978-3-319-14325-5_10

Maximum likelihood inference of population size contractions from microsatellite data

Leblois R., Pudlo P., Néron J., Bertaux F., Beeravolua C. R., Vitalis R., Rousset F.
Molecular Biology and Evolution31(10):2805-23, 2014
URL : http://mbe.oxfordjournals.org/content/early/2014/07/11/molbev.msu212.long
PDF (Author version) : Maximum_likelihood_inference_of_population_size_contractions_from_microsatellite_data.pdf

Identification of a 20-Gene Expression-Based Risk Score as a Predictor of Clinical Outcome in Chronic Lymphocytic Leukemia Patients

Bou Samra E., Klein B., Commes T., Moreaux J.
BioMed Research International, 2014(2014):423174 [epub]
URL : http://www.hindawi.com/journals/bmri/2014/423174/
PDF : http://downloads.hindawi.com/journals/bmri/2014/423174.pdf

Plasmodium vivax Antigen Discovery Based on Alpha-Helical Coiled Coil Protein Motif

Céspedes N., Habel C., Lopez-Perez M., Castellanos A., Kajava A.V., Servis C., Felger I., Moret R., Arévalo-Herrera M., Corradin G., Herrera S.
Plos One, 9(6):e100440, 2014
URL : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0100440
PDF : http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0100440&representation=PDF

A modelling framework to simulate foliar fungal epidemics using functional-structural plant models

Garin G., Fournier C., Andrieu B., Houlès V., Robert C., Pradal C.
Annals of Botany, 2014 [epub]
Url: http://aob.oxfordjournals.org/content/early/2014/06/12/aob.mcu101.abstract

Identification of Divergent Protein Domains by Combining HMM-HMM Comparisons and Co-Occurrence Detection

Ghouila A., Florent I., Guerfali FZ., Terrapon N., Laouini D., Yahia S., Gascuel O., Bréhélin L.
Plos One 9(6):e95275, 2014
Url : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0095275
PDF : http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0095275&representation=PDF

Conformational Switching in PolyGln Amyloid Fibrils Resulting from a Single Amino Acid Insertion

Huang RK., Baxa U., Aldrian G., Ahmed AB., Wall JS., Mizuno N., Antzutkin O., Steven AC., Kajava AV.
Biophysical Journal 106(10):2134-42, 2014
Url : http://www.cell.com/biophysj/abstract/S0006-3495%2814%2900385-3

Using genotyping data to assign markers to their chromosome type and to infer the sex of individuals: a Bayesian model-based classifier

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

Cruaud A., Gautier M., Galan M., Foucaud J., Sauné L., Genson G., Dubois E., Nidelet S., Deuve T., Rasplus J.-Y.
Molecular Biology and Evolution, 31(5): 1272-1274, 2014
URL : http://mbe.oxfordjournals.org/content/31/5/1272

TRDistiller: A rapid filter for enrichment of sequence datasets with proteins containing tandem repeats

Richard F.D., Kajava A.V.
Journal of Structural Biology, 186(3) : 386-391, 2014
Url : http://www.sciencedirect.com/science/article/pii/S1047847714000665
PDF : http://ac.els-cdn.com/S1047847714000665/1-s2.0-S10478(...)

Predicting the ancestral character changes in a tree is typically easier than predicting the root state

Testing environmental and genetic effects in the presence of spatial autocorrelation

Deep conservation of human protein tandem repeats within the eukaryotes

Schaper E, Gascuel O, Anisimova M.
Molecular Biology and Evolution, 31(5) : 1132-1148, 2014
Url : http://mbe.oxfordjournals.org/content/31/5/1132.abstract
PDF : http://mbe.oxfordjournals.org/content/31/5/1132.full.pdf

Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots

Muraro D., Mellor N., Pound M.P., Help H., Lucas M., Chopard J., Byrne H.M., Godin C., Hodgman T.C., King J.R. et al
PNAS 111(2):857-862, 2014
URL : http://www.pnas.org/content/111/2/857.long
PDF : http://www.pnas.org/content/111/2/857.full.pdf

Diversity of Prdm9 Zinc Finger Array in Wild Mice Unravels New Facets of the Evolutionary Turnover of this Coding Minisatellite

Jérôme Buard, Eric Rivals, Denis Dunoyer de Segonzac, Charlotte Garres, Pierre Caminade, Bernard de Massy mail, Pierre Boursot
Plos One 9(1):e85021, 2014
Url : http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0085021
PDF : http://www.plosone.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0085021&representation=PDF

Origin and diversity of human retroviruses

Peeters M., D'Arc M., Delaporte E.
AIDS Reviews 16(1): 23-34, 2014
PDF : http://www.aidsreviews.com/files/2014_16_1_023-034.pdf

Drosophila Spag Is the Homolog of RNA Polymerase II-associated Protein 3 (RPAP3) and Recruits the Heat Shock Proteins 70 and 90 (Hsp70 and Hsp90) during the Assembly of Cellular Machineries

N. E. Benbahouche, I. Iliopoulos, I. Török, J. Marhold, J. Henri, A., V. Kajava, R. Farkaš, T. Kempf, M. Schnölzer, P. Meyer, I. Kiss, E. Bertrand , M. Mechler and B. Pradet-Balade
Journal of biologycal chemistry 289(9):6236-6247, 2014
URL : http://www.jbc.org/content/289/9/6236.long
PDF : http://www.jbc.org/content/289/9/6236.full.pdf

DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

Cornuet J.-M., Pudlo P., Veyssier J., Dehne-Garcia A., Gautier M., Leblois R., Marin J.-M., Estoup A.
Bioinformatics, 30(8) : 1187-1189, 2014
Url : http://bioinformatics.oxfordjournals.org/content/30/8/1187

Relevant statistics for Bayesian model choice

Marin J.-M., Pillai N. S., Robert C. P., Rousseau J.
Journal of the Royal Statistical Society : Series B, 76(5) : 833-859, 2014
Url : http://onlinelibrary.wiley.com/doi/10.1111/rssb.12056/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/rssb.12056/pdf