Publications 2015

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

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

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

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

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