Publications 2016

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

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

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

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

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

Reliable ABC model choice via random forests

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

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

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