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Items: 1 to 50 of 86

1.

Alignment-free Clustering of UMI Tagged DNA Molecules.

Orabi B, Erhan E, McConeghy B, Volik SV, Le Bihan S, Bell R, Collins CC, Chauve C, Hach F.

Bioinformatics. 2018 Oct 23. doi: 10.1093/bioinformatics/bty888. [Epub ahead of print]

PMID:
30351359
2.

Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework.

Luhmann N, Chauve C, Stoye J, Wittler R.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Nov-Dec;15(6):2094-2100. doi: 10.1109/TCBB.2018.2816034. Epub 2018 Mar 15.

PMID:
29993816
3.

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Anselmetti Y, Duchemin W, Tannier E, Chauve C, Bérard S.

BMC Genomics. 2018 May 9;19(Suppl 2):96. doi: 10.1186/s12864-018-4466-7.

4.

Beaver Fever: Whole-Genome Characterization of Waterborne Outbreak and Sporadic Isolates To Study the Zoonotic Transmission of Giardiasis.

Tsui CK, Miller R, Uyaguari-Diaz M, Tang P, Chauve C, Hsiao W, Isaac-Renton J, Prystajecky N.

mSphere. 2018 Apr 25;3(2). pii: e00090-18. doi: 10.1128/mSphere.00090-18. Print 2018 Apr 25.

5.

flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry.

Lux M, Brinkman RR, Chauve C, Laing A, Lorenc A, Abeler-Dörner L, Hammer B.

Bioinformatics. 2018 Jul 1;34(13):2245-2253. doi: 10.1093/bioinformatics/bty082.

6.

MentaLiST - A fast MLST caller for large MLST schemes.

Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L.

Microb Genom. 2018 Jan 10. doi: 10.1099/mgen.0.000146. [Epub ahead of print]

7.

Comparative Methods for Reconstructing Ancient Genome Organization.

Anselmetti Y, Luhmann N, Bérard S, Tannier E, Chauve C.

Methods Mol Biol. 2018;1704:343-362. doi: 10.1007/978-1-4939-7463-4_13.

PMID:
29277873
8.

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes.

Luhmann N, Doerr D, Chauve C.

Microb Genom. 2017 Jul 8;3(9):e000123. doi: 10.1099/mgen.0.000123. eCollection 2017 Sep.

9.

LRCstats, a tool for evaluating long reads correction methods.

La S, Haghshenas E, Chauve C.

Bioinformatics. 2017 Nov 15;33(22):3652-3654. doi: 10.1093/bioinformatics/btx489.

PMID:
29036421
10.

Correction to: ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Oct 6;18(1):188. doi: 10.1186/s13059-017-1327-7. No abstract available.

11.

ReMixT: clone-specific genomic structure estimation in cancer.

McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP.

Genome Biol. 2017 Jul 27;18(1):140. doi: 10.1186/s13059-017-1267-2. Erratum in: Genome Biol. 2017 Oct 6;18(1):188.

12.

Gene Tree Construction and Correction Using SuperTree and Reconciliation.

Lafond M, Chauve C, El-Mabrouk N, Ouangraoua A.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1560-1570. doi: 10.1109/TCBB.2017.2720581. Epub 2017 Jun 27.

PMID:
28678712
13.

The gene family-free median of three.

Doerr D, Balaban M, Feijão P, Chauve C.

Algorithms Mol Biol. 2017 May 26;12:14. doi: 10.1186/s13015-017-0106-z. eCollection 2017.

14.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E.

Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069.

15.

The SCJ Small Parsimony Problem for Weighted Gene Adjacencies.

Luhmann N, Lafond M, Thevenin A, Ouangraoua A, Wittler R, Chauve C.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Jan 31. doi: 10.1109/TCBB.2017.2661761. [Epub ahead of print]

PMID:
28166504
16.

CoLoRMap: Correcting Long Reads by Mapping short reads.

Haghshenas E, Hach F, Sahinalp SC, Chauve C.

Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463.

PMID:
27587673
17.

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.

Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26.

PMID:
27153713
18.

The BRaliBase dent-a tale of benchmark design and interpretation.

Löwes B, Chauve C, Ponty Y, Giegerich R.

Brief Bioinform. 2017 Mar 1;18(2):306-311. doi: 10.1093/bib/bbw022.

19.

Algorithms and Complexity Results for Genome Mapping Problems.

Rajaraman A, Zanetti JP, Manuch J, Chauve C.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):418-430. doi: 10.1109/TCBB.2016.2528239. Epub 2016 Feb 11.

PMID:
26887011
20.

Evolution of genes neighborhood within reconciled phylogenies: an ensemble approach.

Chauve C, Ponty Y, Zanetti J.

BMC Bioinformatics. 2015;16 Suppl 19:S6. doi: 10.1186/1471-2105-16-S19-S6. Epub 2015 Dec 16.

21.

Ancestral gene synteny reconstruction improves extant species scaffolding.

Anselmetti Y, Berry V, Chauve C, Chateau A, Tannier E, Bérard S.

BMC Genomics. 2015;16 Suppl 10:S11. doi: 10.1186/1471-2164-16-S10-S11. Epub 2015 Oct 2.

22.

Chaining sequence/structure seeds for computing RNA similarity.

Bourgeade L, Chauve C, Allali J.

J Comput Biol. 2015 Mar;22(3):205-17. doi: 10.1089/cmb.2014.0283.

PMID:
25768236
23.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ.

Science. 2015 Jan 2;347(6217):1258522. doi: 10.1126/science.1258522. Epub 2014 Nov 27.

24.

Polytomy refinement for the correction of dubious duplications in gene trees.

Lafond M, Chauve C, Dondi R, El-Mabrouk N.

Bioinformatics. 2014 Sep 1;30(17):i519-26. doi: 10.1093/bioinformatics/btu463.

25.

FPSAC: fast phylogenetic scaffolding of ancient contigs.

Rajaraman A, Tannier E, Chauve C.

Bioinformatics. 2013 Dec 1;29(23):2987-94. doi: 10.1093/bioinformatics/btt527. Epub 2013 Sep 24.

PMID:
24068034
26.

Linearization of ancestral multichromosomal genomes.

Maňuch J, Patterson M, Wittler R, Chauve C, Tannier E.

BMC Bioinformatics. 2012;13 Suppl 19:S11. doi: 10.1186/1471-2105-13-S19-S11. Epub 2012 Dec 19.

27.

ANGES: reconstructing ANcestral GEnomeS maps.

Jones BR, Rajaraman A, Tannier E, Chauve C.

Bioinformatics. 2012 Sep 15;28(18):2388-90. doi: 10.1093/bioinformatics/bts457. Epub 2012 Jul 20.

PMID:
22820205
28.

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms.

Allali J, Saule C, Chauve C, d'Aubenton-Carafa Y, Denise A, Drevet C, Ferraro P, Gautheret D, Herrbach C, Leclerc F, de Monte A, Ouangraoua A, Sagot MF, Termier M, Thermes C, Touzet H.

Adv Bioinformatics. 2012;2012:893048. doi: 10.1155/2012/893048. Epub 2012 May 23.

29.

Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes.

Wittler R, Chauve C.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S21. doi: 10.1186/1471-2105-12-S9-S21.

30.

A 2-approximation for the minimum duplication speciation problem.

Ouangraoua A, Swenson KM, Chauve C.

J Comput Biol. 2011 Sep;18(9):1041-53. doi: 10.1089/cmb.2011.0108.

PMID:
21899414
31.

Reconstructing the architecture of the ancestral amniote genome.

Ouangraoua A, Tannier E, Chauve C.

Bioinformatics. 2011 Oct 1;27(19):2664-71. doi: 10.1093/bioinformatics/btr461. Epub 2011 Aug 16.

PMID:
21846735
32.
33.

Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

Gavranović H, Chauve C, Salse J, Tannier E.

Bioinformatics. 2011 Jul 1;27(13):i257-65. doi: 10.1093/bioinformatics/btr224.

34.

An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework.

Doyon JP, Hamel S, Chauve C.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):26-39. doi: 10.1109/TCBB.2011.64. Epub 2011 Mar 30.

PMID:
21464510
35.

Branch-and-bound approach for parsimonious inference of a species tree from a set of gene family trees.

Doyon JP, Chauve C.

Adv Exp Med Biol. 2011;696:287-95. doi: 10.1007/978-1-4419-7046-6_29.

PMID:
21431569
36.

Minimal conflicting sets for the consecutive ones property in ancestral genome reconstruction.

Chauve C, Hausd UU, Stephen T, You VP.

J Comput Biol. 2010 Sep;17(9):1167-81. doi: 10.1089/cmb.2010.0113.

PMID:
20874402
37.

Yeast ancestral genome reconstructions: the possibilities of computational methods II.

Chauve C, Gavranovic H, Ouangraoua A, Tannier E.

J Comput Biol. 2010 Sep;17(9):1097-112. doi: 10.1089/cmb.2010.0092.

PMID:
20874398
38.

Diversity of phylogenetic information according to the locus and the taxonomic level: an example from a parasitic mesostigmatid mite genus.

Roy L, Dowling AP, Chauve CM, Buronfosse T.

Int J Mol Sci. 2010 Apr 13;11(4):1704-34. doi: 10.3390/ijms11041704.

39.

Computation of perfect DCJ rearrangement scenarios with linear and circular chromosomes.

Bérard S, Chateau A, Chauve C, Paul C, Tannier E.

J Comput Biol. 2009 Oct;16(10):1287-309. doi: 10.1089/cmb.2009.0088.

PMID:
19803733
40.

Space of gene/species trees reconciliations and parsimonious models.

Doyon JP, Chauve C, Hamel S.

J Comput Biol. 2009 Oct;16(10):1399-418. doi: 10.1089/cmb.2009.0095.

PMID:
19754270
41.

Flock management and histomoniasis in free-range turkeys in France: description and search for potential risk factors.

Callait-Cardinal MP, Gilot-Fromont E, Chossat L, Gonthier A, Chauve C, Zenner L.

Epidemiol Infect. 2010 Mar;138(3):353-63. doi: 10.1017/S0950268809990562. Epub 2009 Aug 10.

PMID:
19664306
42.

Monitoring of Dermanyssus gallinae in free-range poultry farms.

Zenner L, Bon G, Chauve C, Nemoz C, Lubac S.

Exp Appl Acarol. 2009 Jun;48(1-2):157-66. doi: 10.1007/s10493-009-9253-3. Epub 2009 Feb 28.

PMID:
19252824
43.

Exploration of the susceptibility of AChE from the poultry red mite Dermanyssus gallinae (Acari: Mesostigmata) to organophosphates in field isolates from France.

Roy L, Chauve C, Delaporte J, Inizan G, Buronfosse T.

Exp Appl Acarol. 2009 Jun;48(1-2):19-30. doi: 10.1007/s10493-009-9249-z. Epub 2009 Feb 13.

PMID:
19214761
44.

Molecular phylogenetic assessment of host range in five Dermanyssus species.

Roy L, Dowling AP, Chauve CM, Lesna I, Sabelis MW, Buronfosse T.

Exp Appl Acarol. 2009 Jun;48(1-2):115-42. doi: 10.1007/s10493-008-9231-1. Epub 2009 Jan 22.

PMID:
19160062
45.

Delimiting species boundaries within Dermanyssus Dugès, 1834 (Acari:Dermanyssidae) using a total evidence approach.

Roy L, Dowling AP, Chauve CM, Buronfosse T.

Mol Phylogenet Evol. 2009 Mar;50(3):446-70. doi: 10.1016/j.ympev.2008.11.012. Epub 2008 Nov 27.

PMID:
19059487
46.

A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.

Chauve C, Tannier E.

PLoS Comput Biol. 2008 Nov;4(11):e1000234. doi: 10.1371/journal.pcbi.1000234. Epub 2008 Nov 28.

47.

Bacterial taxa associated with the hematophagous mite Dermanyssus gallinae detected by 16S rRNA PCR amplification and TTGE fingerprinting.

Valiente Moro C, Thioulouse J, Chauve C, Normand P, Zenner L.

Res Microbiol. 2009 Jan-Feb;160(1):63-70. doi: 10.1016/j.resmic.2008.10.006. Epub 2008 Nov 6.

PMID:
19027065
48.

Gene family evolution by duplication, speciation, and loss.

Chauve C, Doyon JP, El-Mabrouk N.

J Comput Biol. 2008 Oct;15(8):1043-62. doi: 10.1089/cmb.2008.0054.

PMID:
18781833
49.

Comparing genomes with duplications: a computational complexity point of view.

Blin G, Chauve C, Fertin G, Rizzi R, Vialette S.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Oct-Dec;4(4):523-34.

PMID:
17975264
50.

Incidence of histomonosis in turkeys in France since the bans of dimetridazole and nifursol.

Callait-Cardinal MP, Leroux S, Venereau E, Chauve CM, Le Pottier G, Zenner L.

Vet Rec. 2007 Oct 27;161(17):581-5.

PMID:
17965368

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