Publications

Likelihood-free model choice

Marin J-M, Pudlo P., Estoup A., Robert C.
Handbook of Approximate Bayesian Computation, Chapman and Hall/CRC, 2017
URL : https://arxiv.org/pdf/1503.07689.pdf

Ribo-seq enlightens codon usage bias

Neurotoxicity of a Biopesticide Analog on Zebrafish Larvae at Nanomolar Concentrations

Nasri A, Valverde AJ, Roche DB, Desrumaux C, Clair P, Beyrem H, Chaloin L, Ghysen A, Perrier V.
International Journal of Molecular Sciences 17 (12): 2137, 2016
URL : http://www.mdpi.com/1422-0067/17/12/2137
PDF : http://www.mdpi.com/1422-0067/17/12/2137/pdf

Phylogenetic incongruence through the lens of Monadic Second Order logic

Kelk S., van Iersel L., Scornavacca C., Weller M.
Journal of Graph Algorithms and Applications 20(2):189–215, 2016
URL : https://arxiv.org/abs/1503.00368
PDF : https://arxiv.org/pdf/1503.00368v1.pdf

ecceTERA : Comprehensive gene tree-species tree reconciliation using parsimony

Jacox E., Chauve C., Szollosi G. J., Ponty Y., Scornavacca C.
Bioinformatics 31(6):841–848, 2016
URL : https://doi.org/10.1093/bioinformatics/btw105

On the fixed parameter tractability of agreement-based phylogenetic distances

Bordewich M., Scornavacca C., Tokac N., Weller M.
Journal of Mathematical Biology 74:239-257, 2017
URL : http://link.springer.com/article/10.1007%2Fs00285-016-1023-3

Colib'read on Galaxy: A tools suite dedicated to biological information extraction from raw NGS reads

Le Bras Y., Collin O., Monjeaud C., Lacroix V., Rivals E., Lemaitre C., Miele V., Sacomoto G., Marchet C., Cazaux B., Zine El Aabidine A., Salmela L., Alves-Carvalho S., Andrieux A., Uricaru R., Peterlongo P.
GigaScience 5:9, 2016
URL : https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0105-2
PDF : http://download.springer.com/static/pdf/460/art%253A10.1186%252Fs13742-015-0105-2.pdf

Linking indexing data structures to de Bruijn graphs: Construction and update

The summary-likelihood method and its implementation in the Infusion package

Rousset F., Gouy A., Martinez-Almoyna C., Courtiol A.
Molecular Ecology Resources, 17:110–119, 2017
URL : http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12627/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12627/pdf

Dengue Vaccine: Considerations before Rollout in Colombia

Villabona-Arenas C.J., Ocazionez Jimenez R.E., Jimenez Silva C.L.
PLoS Neglected Tropical Diseases 10(6):e0004653, 2016
URL : http://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0004653
PDF : http://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0004653&type=printable

Phylodynamics of the major HIV-1 CRF02_AG African lineages and its global dissemination

Mir D., Jung M., Delatorre E., Vidal N., Peeters M., Bello G.
Infection, Genetics and Evolution 46:190-199, 2016
URL : http://www.sciencedirect.com/science/article/pii/S1567134816301897
PDF : http://ac.els-cdn.com/S1567134816301897/1-s2.0-S1567134816301897-main.pdf

Primate immunodeficiency virus classification and nomenclature: Review

Foley BT, Leitner T, Paraskevis D, Peeters M.
Infection, Genetics and Evolution 46:150-158, 2016
URL : http://www.sciencedirect.com/science/article/pii/S1567134816304270
PDF : http://ac.els-cdn.com/S1567134816304270/1-s2.0-S1567134816304270-main.pdf

Short Communication: High Viral Load and Multidrug Resistance Due to Late Switch to Second-Line Regimens Could Be a Major Obstacle to Reach the 90-90-90 UNAIDS Objectives in Sub-Saharan Africa

Guichet E., Aghokeng A., Serrano L., Bado G., Toure-Kane C., Eymard-Duvernay S., Villabona-Arenas C.J., Delaporte E., Ciaffi L., Peeters M.
AIDS Research and Human Retroviruses 32(12):1159-1162, 2016
URL : http://online.liebertpub.com/doi/10.1089/aid.2016.0010
PDF : http://online.liebertpub.com/doi/pdf/10.1089/aid.2016.0010

Resampling: an improvement of Importance Sampling in varying population size models

Merle C., Leblois R., Rousset F., Pudlo P.
Theor. Pop. Biol., 2016
URL : https://arxiv.org/abs/1603.07237
PDF : https://arxiv.org/pdf/1603.07237v1.pdf

Genomic analyses inform on migration events during the peopling of Eurasia

Pagani L., Lawson D.J., Jagoda E., Mörseburg A., Eriksson A., Mitt M., Clemente F., Hudjashov G., DeGiorgio M., Saag L., Wall J.D., Cardona A., Mägi R., Sayres M.A., Kaewert S., Inchley C., Scheib C.L., Järve M., Karmin M., Jacobs G.S., Antao T., Iliescu F.M., Kushniarevich A., Ayub Q., Tyler-Smith C., Xue Y., Yunusbayev B., Tambets K., Mallick C.B., Saag L., Pocheshkhova E., Andriadze G., Muller C., Westaway M.C., Lambert D.M., Zoraqi G., Turdikulova S., Dalimova D., Sabitov Z., Sultana G.N., Lachance J., Tishkoff S., Momynaliev K., Isakova J., Damba L.D., Gubina M., Nymadawa P., Evseeva I., Atramentova L., Utevska O., Ricaut F.X., Brucato N., Sudoyo H., Letellier T., Cox M.P., Barashkov N.A., Škaro V., Mulahasanovic L., Primorac D., Sahakyan H., Mormina M., Eichstaedt C.A., Lichman D.V., Abdullah S., Chaubey G., Wee J.T., Mihailov E., Karunas A., Litvinov S., Khusainova R., Ekomasova N., Akhmetova V., Khidiyatova I., Marjanović D., Yepiskoposyan L., Behar D.M., Balanovska E., Metspalu A., Derenko M., Malyarchuk B., Voevoda M., Fedorova S.A., Osipova L.P., Lahr M.M., Gerbault P., Leavesley M., Migliano A.B., Petraglia M., Balanovsky O., Khusnutdinova E.K., Metspalu E., Thomas M.G., Manica A., Nielsen R., Villems R., Willerslev E., Kivisild T., Metspalu M.
Nature 538(7624):238-242, 2016
URL : http://www.nature.com/nature/journal/v538/n7624/full/nature19792.html
PDF : http://www.nature.com/nature/journal/v538/n7624/pdf/nature19792.pdf

Black rat invasion of inland Sahel: insights from interviews and population genetics in South Western Niger

Berthier K., Garba M., Leblois R., Navascues M., Tatard C., Gauthier P., Gagaré S., Piry S., Dalecky A., Loiseau A., Dobigny G.
Biological Journal of the Linean Society 119:748–765, 2016
URL : http://onlinelibrary.wiley.com/doi/10.1111/bij.12836/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/bij.12836/epdf

A stochastic multicellular model identifies biological watermarks from disorders in self-organized patterns of phyllotaxis

Refahi Y., Brunoud G., Farcot E., Jean-Marie A., Pulkkinen M., Vernoux T., Godin C.
Elife 5 pii: e14093, 2016
URL : https://elifesciences.org/content/5/e14093
PDF : https://elifesciences.org/content/5/e14093-download.pdf

Phyllotaxis: from patterns of organogenesis at the meristem to shoot architecture

Galvan-Ampudia C.S., Chaumeret A.M., Godin C., Vernoux T.
Wiley Interdisciplinary Reviews: Developmental Biology 5(4):460-473, 2016
URL : http://onlinelibrary.wiley.com/doi/10.1002/wdev.231/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1002/wdev.231/epdf

Global genetic diversity of the Plasmodium vivax transmission-blocking vaccine candidate Pvs48/45

Vallejo A.F., Martinez N.L., Tobon A., Alger J., Lacerda M.V., Kajava A.V., Arévalo-Herrera M., Herrera S.
Malaria Journal 15:202, 2016
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828788/
PDF : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828788/pdf/12936_2016_Article_1263.pdf

In-depth analysis of HIV-1 Drug Resistance Mutations in HIV-infected individuals failing first-line regimens in West and Central Africa

Villabona-Arenas C.J., Vidal N., Guichet E., Serrano L., Delaporte E., Gascuel O., Peeters M.
AIDS, 30(17):2577-2589, 2016
URL : http://journals.lww.com/aidsonline/Abstract/2016/11130/In_depth_analysis_of_HIV_1_drug_resistance.3.aspx

The combinatorics of overlapping genes

Lebre S., Gascuel O.
Journal of Theoretical Biology, 2016    [epub]
URL : https://arxiv.org/abs/1602.04971
PDF : https://arxiv.org/ftp/arxiv/papers/1602/1602.04971.pdf

A ‘stochastic safety radius’ for distance-based tree reconstruction

Gascuel O., Steel M.
Algorithmica 74(4):1386-1403, 2016
URL : http://link.springer.com/article/10.1007/s00453-015-0005-y

Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic

Cassan E., Arigon-Chifolleau A.M., Mesnard J.M., Gross A., Gascuel O.
Proc. National Academy of Science USA (PNAS) 113(41):11537-11542, 2016
URL : http://www.pnas.org/content/113/41/11537.full
PDF : http://www.pnas.org/content/113/41/11537.full.pdf

AgroLD API : Une architecture orientée services pour l'extraction de connaissances dans la base de données liées AgroLD

Ngompe G.T., Venkatesan A., El Hassouni N., Ruiz M., Larmande P.
RSTI série Ingénierie des Systèmes d'Information 28, 2016
URL : http://isi.revuesonline.com/article.jsp?articleId=37163
PDF : https://hal.archives-ouvertes.fr/hal-01411532/document

Assisted transcriptome reconstruction and splicing orthology

Blanquart S., Varré J.-S., Guertin P., Perrin A., Bergeron A., Swenson K. M.
BMC Genomics, 17(10):157-164, 2016.
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123294/

InfraPhenoGrid: A scientific workflow infrastructure for plant phenomics on the Grid

Pradal C., Artzet S., Chopard J., Dupuis D., Fournier C., Mielewczik M., Nègre V., Neveu P., Parigot D., Valduriez P., Cohen-Boulakia S.
Future Generation Computer Systems
, 67:341-353, 2016
URL : http://www.sciencedirect.com/science/article/pii/S0167739X16301820

Computational pan-genomics: status, promises and challenges

Marschall T., Marz M., Abeel T., Dijkstra L., Dutilh B. E., Ghaffaari A., Kersey P., Kloosterman W. P., Makinen V., Novak A. M., Paten B., Porubsky D., Rivals E., Alkan C., Baaijens J. A., De Bakker P. I. W., Boeva V., Bonnal R. J. P., Chiaromonte F., Chikhi R., Ciccarelli F. D., Cijvat R., Datema E., Van Duijn C. M., Eichler E. E., Ernst C., Eskin E., Garrison E.,El-Kebir M., Klau G. W., Korbel J. O., Lameijer E-W., Langmead B., Martin M., Medvedev P, Mu J. C., Neerincx P., Ouwens K., Peterlongo P., Pisanti N., Rahmann S., Raphael B., Reinert K., De Ridder D., De Ridder J., Schlesner M., Schulz-Trieglaff O., Sanders A. D., Sheikhizadeh S., Shneider C., Smit S., Valenzuela D., Wang J., Wessels L., Zhang Y., Guryev V., Vandin F., Ye K., Schönhuth A.
Briefings in Bioinformatics, 2016
URL : http://bib.oxfordjournals.org/content/early/2016/10/19/bib.bbw089
PDF : http://bib.oxfordjournals.org/content/early/2016/10/19/bib.bbw089.full.pdf

Accurate self-correction of errors in long reads using de Bruijn graphs

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

Gambette P., Van Iersel L., Kelk S., Pardi F., Scornavacca C.
Bulletin of Mathematical Biology 78(9): 1773-1795, 2016
URL : http://link.springer.com/article/10.1007/s11538-016-0199-4

Models and Algorithms for Genome Rearrangement with Positional Constraints

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

Paladin L., Hirsh L., Piovesan D., Andrade-Navarro M. A., Kajava A. V. , Tosatto S.C.E.
Nucleid Acids Research (Database issue) 45(D1):D308-D312, 2016
URL : http://nar.oxfordjournals.org/content/45/D1/D308
PDF : http://nar.oxfordjournals.org/content/45/D1/D308.full.pdf

DisProt 7.0: a major update of the database of disordered proteins

Damiano Piovesan, Francesco Tabaro, Ivan Mičetić, Marco Necci, Federica Quaglia, Christopher J. Oldfield, Maria Cristina Aspromonte, Norman E. Davey, Radoslav Davidović, Zsuzsanna Dosztányi, Arne Elofsson, Alessandra Gasparini, András Hatos, Andrey V. Kajava, Lajos Kalmar, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Eva Schad, Antoine Schramm, Beata Szabo, Agnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljković, Salvador Ventura, Wim Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa and Silvio C.E. Tosatto
Nucleic Acids Research (Database issue) 45(D1): D219-D227, 2016
URL : http://nar.oxfordjournals.org/content/45/D1/D219
PDF : http://nar.oxfordjournals.org/content/45/D1/D219.full.pdf

On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs

Beaumeunier S., Audoux J., Boureux A., Ruffle F., Commes T., Philippe N., Alves R.
BioData Mining, 9:34, 2016
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5090896/
PDF : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5090896/pdf/13040_2016_Article_112.pdf

Long non-coding RNAs in human early embryonic development and their potential in ART

Bouckenheimer J., Assou S., Riquier S., Hou C., Philippe N., Sansac C., Lavabre-Bertrand T., Commes T., Lemaître JM., Boureux A., De Vos J.
Human Reproduction Update 23(1):19-40, 2016
URL : http://humupd.oxfordjournals.org/content/23/1/19.abstract
PDF : http://humupd.oxfordjournals.org/content/23/1/19.full.pdf+html

Online Input Data Reduction in Scientific Workflows

Souza R., Silva V., Coutinho A., Valduriez P., Mattoso M.
ACM SIGHPC & IEEE 11th Workshop on Workflows in Support of Large-scale Science, in conjunction with SC2016, 2016
URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01400538
PDF : http://ceur-ws.org/Vol-1800/paper6.pdf

Managing Hot Metadata for Scientific Workflows on Multisite Clouds

Pineda-Morales L., Liu J., Costany A., Pacitti E., Antoniu G., Valduriez P., Mattoso M.
Proceeding IEEE Big Data Conference 390-397, 2016
URL : https://hal.inria.fr/hal-01395715
PDF : https://hal.inria.fr/hal-01395715/document

Database System Support of Simulation Data

Lustosa H., Porto F., Blanco P., Valduriez P.
Proceedings of the VLDB Endowment (PVLDB), 9(13) : 1329-1340, 2016
URL : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01363738
PDF : http://www.vldb.org/pvldb/vol9/p1329-lustosa.pdf

Inferring gene duplications, transfers and losses can be done in a discrete framework

Ranwez V., Scornavacca C., Doyon JP., Berry V.
Journal of Mathematical Biology, 72(7):1811-1844, 2016
URL : http://link.springer.com/article/10.1007%2Fs00285-015-0930-z
PDF : http://download.springer.com/static/pdf/709/art%253A10.1007%252Fs00285-015-0930-z.pdf

CSAM: Compressed SAM format

Cánovas R., Moffat A., Turpin A.
Bioinformatics 32(24): 3709-3716, 2016
URL : https://academic.oup.com/bioinformatics/article/32/24/3709/2525655/CSAM-Compressed-SAM-format

Deciphering the wisent demographic and adaptive histories from individual whole-genome sequences

Gautier M, Moazami-Goudarzi K, Leveziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L
Molecular Biology and Evolution 33(11):2801-2814, 2016
URL : http://mbe.oxfordjournals.org/content/33/11/2801
PDF: http://mbe.oxfordjournals.org/content/33/11/2801.full.pdf

Superstring Graph: A New Approach for Genome Assembly

Cazaux B., Sacomoto G., Rivals E.
Algorithmic Aspects in Information and Management LNCS 9778:39-52
URL : http://link.springer.com/chapter/10.1007%2F978-3-319-41168-2_4
PDF : http://link.springer.com/content/pdf/10.1007%2F978-3-319-41168-2_4.pdf

Read mapping on de Bruijn graphs

Limasset A., Cazaux B., Rivals E., Peterlongo P.
BMC Bioinformatics 17:237, 2016
URL : http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1103-9

Gigwa—Genotype investigator for genome-wide analyses

Sempéré G., Philippe F., Dereeper A., Ruiz M., Sarah G., Larmande P.
GigaScience 5:25, 2016
URL : https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0131-8
PDF : http://download.springer.com/static/pdf/814/art%253A10.1186%252Fs13742-016-0131-8.pdf

Development of a knowledge system for Big Data: Case study to plant phenotyping data

Le Ngoc L., Tireau A., Venkatesan A., Neveu P., Larmande P.
Proceedings of the 6th International Conference on Web Intelligence, Mining and Semantics, art. 27, 2016
URL : http://dl.acm.org/citation.cfm?id=2912869
PDF : https://hal.archives-ouvertes.fr/hal-01411565

A targeted immunomic approach identifies diagnostic antigens in the human pathogen Babesia microti

Cornillot E., Dassouli A., Pachikara N., Lawres L., Renard I., Francois C., Randazzo S., Brès V., Garg A., Brancato J., Pazzi J.E., Pablo J., Hung C., Teng A., Shandling A.D., Huynh V.T., Krause P.J., Lepore T., Delbecq S., Hermanson G., Liang X., Williams S., Molina D.M., Ben Mamoun C.
Transfusion 56(8):2085-2099, 2016
URL : http://onlinelibrary.wiley.com/doi/10.1111/trf.13640/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/trf.13640/epdf

A linear time algorithm for shortest cyclic cover of strings

In silico Identification and Characterization of Protein-Ligand Binding Sites

Roche DB., McGuffin LJ.
Methods in Molecular Biology, 1414:1-21, 2016
URL : http://link.springer.com/protocol/10.1007%2F978-1-4939-3569-7_1
PDF (Author version) : FunFOLD3_326633_1_En_1_Chapter_Author.pdf

Discovery of hantavirus circulating among Rattus rattus in French Mayotte island, Indian Ocean

Filippone C., Castel G., Murri S., Beaulieux F., Ermonval M., Jallet C., Wise EL., Ellis RJ., Marston DA., McElhinney LM., Fooks AR., Desvars A., Halos L., Vourc'h G., Marianneau P., Tordo N.
Journal of General Virology, 97(5):1060-1065, 2016
URL : http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000440

Multi-Objective Scheduling of Scientific Workflows in Multisite Clouds

Liu J., Pacitti E., Valduriez P., Mattoso M.
Future Generation Computer Systems, 63:76-95, 2016
URL : http://www.sciencedirect.com/science/article/pii/S0167739X16300917
PDF : https://hal-lirmm.ccsd.cnrs.fr/lirmm-01342203

Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences

Shortest DNA cyclic cover in compressed space

Cazaux B., Canovas R., Rivals E.
Data Compression Conference (DCC), IEEE Computer Society Press, 536-545, 2016
PDF : http://www.lirmm.fr/~rivals/PUBLI/FILES/Cazaux-etal-DCC-2016.pdf

Aligning the unalignable : bacteriophage whole genome alignments

Fast and accurate branch lengths estimation for phylogenomic trees

Binet M., Gascuel O., Scornavacca C., P Douzery EJ., Pardi F.
BMC Bioinformatics 17(1):23, 2016
URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705742/
PDF : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4705742/pdf/12859_2015_Article_821.pdf

Subtelomere organization in the genome of the microsporidian Encephalitozoon cuniculi: patterns of repeated sequences and physicochemical signatures

Dia N., Lavie L., Faye N., Méténier G., Yeramian E., Duroure C., Toguebaye BS., Frutos R., Niang MN., Vivarès CP., Ben Mamoun C., Cornillot E.
BMC Genomics 17(1):34, 2016
URL : http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1920-7
PDF : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704409/pdf/12864_2015_Article_1920.pdf

A Survey of Data-Intensive Scientific Workflow Management

Liu J., Pacitti E., Valduriez P., Mattoso M.
Journal of Grid Computing 13(4):457-493, 2015
URL : http://link.springer.com/article/10.1007/s10723-015-9329-8

Distance-Based Phylogeny Reconstruction: Safety and Edge Radius

Gascuel O., Pardi F., Truszkowski J.
Encyclopedia of Algorithms, 2015
URL : http://link.springer.com/referenceworkentry/10.1007/978-3-642-27848-8_115-2

Reliable ABC model choice via random forests

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality

Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods

Roche D.B., Brackenridge D.A., McGuffin L.J.
International Journal of Molecular Sciences 16(12) : 29829-29842, 2015
URL : http://www.mdpi.com/1422-0067/16/12/29829
PDF : http://www.mdpi.com/1422-0067/16/12/26202/pdf

Exact approaches for scaffolding

Weller M., Chateau A., Giroudeau R.
BMC Bioinformatics 16(Suppl 14):S2, 2015
URL : http://www.biomedcentral.com/1471-2105/16/S14/S2
PDF : http://www.biomedcentral.com/content/pdf/1471-2105-16-S14-S2.pdf

A complexity and approximation framework for the maximization scaffolding problem

Chateau A., Giroudeau R.
Theoretical Computer Science, 595 92:106, 2015
URL : http://www.sciencedirect.com/science/article/pii/S0304397515005332

Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets

Huber K., Van Iersel L., Moulton V., Scornavacca C., Wu T.
Algorithmica 2015
PDF : http://paperity.org/p/74099078/reconstructing-phylogenetic-level-1-networks-from-nondense-binet-and-trinet-sets

Efficient algorithms for reconciling gene trees and species networks via duplication and loss events

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

SylvX: a viewer for phylogenetic tree reconciliations

Chevenet F., Doyon J-P., Scornavacca C., Jacox E., Jousselin E., Berry V.
Bioinformatics 32(4):608-610, 2016
URL : http://bioinformatics.oxfordjournals.org/content/early/2015/10/28/bioinformatics.btv625.abstract

Toolbox for Protein Structure Prediction

Roche DB, McGuffin LJ
Methods in Molecular Biololgy 1369:363-77, 2016
URL : http://link.springer.com/protocol/10.1007%2F978-1-4939-3145-3_23
PDF (Author Version) : Proofs_Toolbox_for_protein_structure_prediction_325589_1_En_23_Chapter_Author.pdf

Rank aggregation with ties: Experiments and Analysis

Brancotte B., Yang B., Blin G., Cohen-Boulakia S., Denise A. et al.
VLDB Endowment (PVLDB),  2015 [Proceedings]
URL : https://hal.archives-ouvertes.fr/hal-01165336/document
PDF : http://www.vldb.org/pvldb/vol8/p1202-brancotte.pdf

OpenAlea: Scientific Workflows Combining Data Analysis and Simulation

Pradal C., Fournier C., Valduriez P., Cohen-Boulakia S.
SSDBM 2015: 27th International Conference on Scientific and Statistical Database Management, 2015 [Proceedings]
URL : https://hal.archives-ouvertes.fr/hal-01166298

Effective and Efficient Similarity Search in Scientific Workflow Repositories

Starlinger J., Cohen-Boulakia S., Khanna S., Davidson S., Leser U.
Future Generation Computer Systems, Elsevier, 2015
URL : https://hal.archives-ouvertes.fr/hal-01170597/
PDF : http://ac.els-cdn.com/S0167739X15002228/1-s2.0-S0167739X15002228-main.pdf

Complete Genome and Phylogeny of Puumala Hantavirus Isolates Circulating in France

Castel G., Couteaudier M., Sauvage F, Pons J-B., Murri S., Plyusnina A., Pontier D., Cosson J-F., Plyusnin A., Marianneau P., Tordo N.
Viruses 7(10) : 5476-5488, 2015
URL : http://www.mdpi.com/1999-4915/7/10/5476
PDF : http://www.mdpi.com/1999-4915/7/10/2884/pdf

A randomized, placebo-controlled phase III trial of masitinib plus gemcitabine in the treatment of advanced pancreatic cancer

Deplanque G, Demarchi M, Hebbar M, Flynn P, Melichar B, Atkins J, Nowara E, Moyé L, Piquemal D, Ritter D, Dubreuil P, Mansfield CD, Acin Y, Moussy A, Hermine O, Hammel P.
Annals of Oncology, 26(6):1194-200, 2015
URL : http://annonc.oxfordjournals.org/content/26/6/1194.long
PDF : http://annonc.oxfordjournals.org/content/26/6/1194.full.pdf

The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings

Cazaux B., Rivals E.
Distcrete Applied Mathematics 212:48-60, 2015
URL : http://www.sciencedirect.com/science/article/pii/S0166218X15002899
PDF : http://ac.els-cdn.com/S0166218X15002899/...

An assessment of the amount of untapped fold level novelty in under-sampled areas of the tree of life

Roche D. B., Brüls T.
Scientific Reports 5:14717, 2015
URL : http://www.nature.com/articles/srep14717
PDF : http://www.nature.com/articles/srep14717.pdf

Single substitution in bacteriophage T4 RNase H alters the ratio between its exo- and endonuclease activities

Kholoda N., Sivogrivova D., Latypova O., Mayorova S., Kuznitsyna R., Kajava A.V., Shlyapnikova M., Granovskya I.
Mutation Research 781(2015):49–57, 2015
URL : http://www.sciencedirect.com/science/article/pii/S0027510715300440
PDF : http://ac.els-cdn.com/S0027510715300440/1-s2.0-S0027510715300440-main.pdf

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

Lefort V., Desper R., Gascuel O.
Molecular Biology & Evolution 32(10): 2798-2800, 2015
URL : http://mbe.oxfordjournals.org/content/32/10/2798.long
PDF : http://mbe.oxfordjournals.org/content/32/10/2798.full.pdf

Fast dating using least-squares criteria and algorithms

To TH., Jung M., Lycett S., Gascuel O.
Systematic Biology 65(1): 82-97, 2016
URL : http://sysbio.oxfordjournals.org/content/65/1/82
PDF : http://sysbio.oxfordjournals.org/content/65/1/82.full.pdf

Ancestral gene synteny reconstruction improves extant species scaffolding

Anselmetti Y., Berry V., Chauve C., Chateau A., Tannier E., Berard S.
Genomcis, Procs of the 13th Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics, 2015
URL : http://biorxiv.org/content/early/2015/07/23/023085
PDF : http://biorxiv.org/content/biorxiv/early/2015/07/23/023085.full.pdf

A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK

Mourad R., Chevennet F., Dunn DT., Fearnhill E., Delpech V., Asboe D., Gascuel O., Hue S.; UK HIV Drug Resistance Database & the Collaborative HIV, Anti-HIV Drug Resistance Network
AIDS (London, England), 29(15):1917-1925, 2015
URL : http://www.ncbi.nlm.nih.gov/pubmed/26355570

HIV-1 group O infection in Cameroon from 2006 to 2013: Prevalence, genetic diversity, evolution and public health challenges

Villabona-Arenasa C.J., Domyeumc J., Mouachaa F., Butela C., Delaporte E., Peeters M., Mpoudi-Ngolec E.,Fobang Aghokenga A.
Infection, Genetics and Evolution 36:210-216, 2015
URL : http://www.sciencedirect.com/science/article/pii/S1567134815003731

TAPO: A combined method for the identification of tandem repeats in protein structures

Do Viet P., Roche D. B., Kajava A. K.
FEBS Letters, 589(19 Pt A):2611-2619, 2015
URL : http://www.sciencedirect.com/science/article/pii/S0014579315007255
PDF : (Author Version) TAPO_FEBSLetters2015.pdf

Analyzing Related Raw Data Files through Dataflows

Silva Souza V., De Oliveira D., Valduriez P., Mattoso M.
Concurrency and Computation: Practice and Experience, 28(8), 2528:2545, 2016
URL : http://onlinelibrary.wiley.com/doi/10.1002/cpe.3616/full

Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions

L. Ramya, N. Gautham, L. Chaloin, A.V. Kajava
Proteins 83(9):1654-1664, 2015
URL : http://onlinelibrary.wiley.com/doi/10.1002/prot.24851/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1002/prot.24851/epdf

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

Chang J-M, Di Tommaso P., Lefort V., Gascuel O., Notredame C.
Nucleic Acids Research 43(w1): w3-w6, 2015
URL : http://nar.oxfordjournals.org/content/43/W1/W3.long
PDF : http://nar.oxfordjournals.org/content/43/W1/W3.full.pdf

A structure-based approach to predict predisposition to amyloidosis

Ahmed A.B., Znassi N., Château M-T., Kajava A.V.
Alzheimer's & Dementia, 11(6):681-690, 2015
URL : http://www.sciencedirect.com/science/article/pii/S1552526014024662
PDF : http://www.sciencedirect.com/science/article...

Evolution of proteasome regulators in Eukaryotes

P. Fort, A. V. Kajava, F. Delsuc, O. Coux
Genome Biology and Evolution 7(15) : 1363-1379, 2015
URL : http://gbe.oxfordjournals.org/content/7/5/1363.long
PDF : http://gbe.oxfordjournals.org/content/early/2015/05/04/gbe.evv068.long

YOC, a new strategy for pairwise alignment of collinear genomes

R. Uricaru, C. Michotey, H. Chiapello, E. Rivals
BMC Bioinformatics, 16:111, 2015
URL : http://www.biomedcentral.com/1471-2105/16/111/abstract
PDF : http://www.biomedcentral.com/content/pdf/s12859-015-0530-3.pdf

Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

Pardi F., Scornavacca C.
PLoS Computational Biology 11(4): e1004135, 2015
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388854/
PDF : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388854/pdf/pcbi.1004135.pdf

Molecular characterization of a new mosaic Simian Immunodeficiency Virus in a naturally infected tantalus monkey (Chlorocebus tantalus) from Cameroon: a challenge to the virus-host co-evolution of SIVagm in African green monkeys

Ayouba A., Njouom R., Chia JE., Ahuka-Mundeke S., Kfutwah A., Ngole EM., Nerrienet E., Delaporte E., Peeters M.
Infect Genet Evol. 30:65-73 2015
URL : http://www.sciencedirect.com/science/article/pii/S1567134814004511
PDF : http://ac.els-cdn.com/S1567134814004511/1-s2.0-S1567134814004511-main.pdf

IntFOLD : an integrated server for modelling protein structures and functions from amino acid sequences

McGuffin L. J., Atkins J. D., Salehe B. R., Shuid A.N., Roche D. B.
Nucleic Acids Res. (NAR), 43(w1):w169-w173 2015
URL : http://nar.oxfordjournals.org/content/43/W1/W169.abstract?etoc
PDF : http://nar.oxfordjournals.org/content/43/W1/W169.full.pdf

Origin of the HIV-1 group O epidemic in western lowland gorillas

D'arc M, Ayoubaa A., Estebana A., Learn G.H., Boué V, Liegeois F., Etienne L., Tagg N., Leendertz F.H., Boesch C., Madinda N.F., Robbins M.M., Gray M., Cournil A., Ooms M., Letko M., Simon V.A., Sharp P.M., Hahn B.H., Delaporte E., Mpoudi Ngole E., Peeters M.
PNAS 112(11):1343-1352, 2015
URL : http://www.pnas.org/content/112/11/E1343
PDF : http://www.pnas.org/content/112/11/E1343.full.pdf

Age-dependent expression of osteochondrosis-related genes in equine leukocytes

Mendoza L, Piquemal D, Lejeune JP, Vander Heyden L, Noguier F, Bruno R, Sandersen C, Serteyn D.
Vet Rec Open. 2(1):e000058, 2015
URL : http://vetrecordopen.bmj.com/content/2/1/e000058.full
PDF : http://vetrecordopen.bmj.com/content/2/1/e000058.full.pdf

Root System Markup Language: Toward a Unified Root Architecture Description Language

Lobet G., Pound M.P., Diener J., Pradal C., Draye X., Godin C., Javaux M., Leitner D., Meunier F., Nacry P., Pridmore T.P., Schnepf A
Plant Physiology, 167(3):617-627, 2015
URL : http://www.plantphysiol.org/content/167/3/617
PDF : http://www.plantphysiol.org/content/167/3/617.full.pdf

A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution

Boudon F., Chopard J., Ali O., Gilles B., Hamant O., Boudaoud A., Traas J.,Godin C.
PLOS Computational biology, 11(1): e1003950, 2015
URL : http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003950
PDF : http://www.ploscompbiol.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pcbi.1003950&representation=PDF

Profile Diversity for Query Processing using User Recommendations

Maximilien Servajean, Reza Akbarinia, Esther Pacitti, Sihem Amer-Yahia
Information Systems, Elsevier, 48 : 44-63, 2015
URL : http://www.sciencedirect.com/science/article/pii/S030643791400132X
PDF : http://ac.els-cdn.com.gate6.inist.fr/S030643791400132X(...)

Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Ferchaud A.-L., Eudeline, R. , Arnal, V., Cheylan, M., Pottier, G., Leblois, R. and Crochet. P.-A.
Molecular Ecology, 24: 192–207, 2015
URL : http://onlinelibrary.wiley.com/doi/10.1111/mec.13011/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1111/mec.13011/epdf

Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree

Cazaux B., Lecroq T., Rivals E.
9th International Conference on Language and Automata Theory and Applications (LATA), Springer Verlag, LNCS 8977:109-120, 2015
URL : http://link.springer.com/chapter/10.1007%2F978-3-319-15579-1_8

Mathematical and Computational Evolutionary Biology (2013)

The ancient Yakuts: a population genetic enigma

Keyser C., Hollard C., Gonzalez A., Fausser L., Rivals E., Alexeev A., Riberon A., Crubézy E., Ludes B.
Philosophical Transactions of the Royal Society series B, 370(1660), 2015
URL : http://rstb.royalsocietypublishing.org/content/370/1660/20130385.long

The enzymatic nature of an anonymous protein sequence cannot reliably be inferred from superfamily level structural information alone

Roche D.B., Brüls T.                                    
Protein Science24(5):643-50, 2015
URL : http://onlinelibrary.wiley.com/doi/10.1002/pro.2635/abstract
PDF : http://onlinelibrary.wiley.com/doi/10.1002/pro.2635/pdf

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