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Items: 1 to 50 of 91

1.

Exploring and Visualising Spaces of Tree Reconciliations.

Huber KT, Moulton V, Sagot MF, Sinaimeri B.

Syst Biol. 2018 Nov 10. doi: 10.1093/sysbio/syy075. [Epub ahead of print]

PMID:
30418649
2.

Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model.

Kyrkou I, Pusa T, Ellegaard-Jensen L, Sagot MF, Hansen LH.

Front Microbiol. 2018 Sep 12;9:2141. doi: 10.3389/fmicb.2018.02141. eCollection 2018. Review.

3.

An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets.

Ramos PIP, Fernández Do Porto D, Lanzarotti E, Sosa EJ, Burguener G, Pardo AM, Klein CC, Sagot MF, de Vasconcelos ATR, Gales AC, Marti M, Turjanski AG, Nicolás MF.

Sci Rep. 2018 Jul 17;8(1):10755. doi: 10.1038/s41598-018-28916-7.

4.

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny.

Urbini L, Sinaimeri B, Matias C, Sagot MF.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May 21. doi: 10.1109/TCBB.2018.2838667. [Epub ahead of print]

PMID:
29993554
5.

Fast-SG: an alignment-free algorithm for hybrid assembly.

Di Genova A, Ruz GA, Sagot MF, Maass A.

Gigascience. 2018 May 1;7(5). doi: 10.1093/gigascience/giy048.

6.

Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae.

Galvao Ferrarini M, Mucha SG, Parrot D, Meiffrein G, Ruggiero Bachega JF, Comte G, Zaha A, Sagot MF.

Mol Microbiol. 2018 Jun;108(6):683-696. doi: 10.1111/mmi.13957. Epub 2018 Apr 26.

PMID:
29624763
7.

OptPipe - a pipeline for optimizing metabolic engineering targets.

Hartmann A, Vila-Santa A, Kallscheuer N, Vogt M, Julien-Laferrière A, Sagot MF, Marienhagen J, Vinga S.

BMC Syst Biol. 2017 Dec 21;11(1):143. doi: 10.1186/s12918-017-0515-0.

8.

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V.

Algorithms Mol Biol. 2017 Feb 22;12:2. doi: 10.1186/s13015-017-0091-2. eCollection 2017.

9.

How Long Does Wolbachia Remain on Board?

Bailly-Bechet M, Martins-Simões P, Szöllosi GJ, Mialdea G, Sagot MF, Charlat S.

Mol Biol Evol. 2017 May 1;34(5):1183-1193. doi: 10.1093/molbev/msx073.

PMID:
28201740
10.

DegreeCox - a network-based regularization method for survival analysis.

Veríssimo A, Oliveira AL, Sagot MF, Vinga S.

BMC Bioinformatics. 2016 Dec 13;17(Suppl 16):449. doi: 10.1186/s12859-016-1310-4.

11.

Mycoplasma non-coding RNA: identification of small RNAs and targets.

Siqueira FM, de Morais GL, Higashi S, Beier LS, Breyer GM, de Sá Godinho CP, Sagot MF, Schrank IS, Zaha A, de Vasconcelos AT.

BMC Genomics. 2016 Oct 25;17(Suppl 8):743.

12.

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

Lopez-Maestre H, Brinza L, Marchet C, Kielbassa J, Bastien S, Boutigny M, Monnin D, Filali AE, Carareto CM, Vieira C, Picard F, Kremer N, Vavre F, Sagot MF, Lacroix V.

Nucleic Acids Res. 2016 Nov 2;44(19):e148. Epub 2016 Jul 25.

13.

Enumeration of minimal stoichiometric precursor sets in metabolic networks.

Andrade R, Wannagat M, Klein CC, Acuña V, Marchetti-Spaccamela A, Milreu PV, Stougie L, Sagot MF.

Algorithms Mol Biol. 2016 Sep 19;11:25. doi: 10.1186/s13015-016-0087-3. eCollection 2016.

14.

Human-modified habitats change patterns of population genetic structure and group relatedness in Peter's tent-roosting bats.

Sagot M, Phillips CD, Baker RJ, Stevens RD.

Ecol Evol. 2016 Jul 29;6(17):6050-63. doi: 10.1002/ece3.2255. eCollection 2016 Sep.

15.

A Combinatorial Algorithm for Microbial Consortia Synthetic Design.

Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A, Sagot MF.

Sci Rep. 2016 Jul 4;6:29182. doi: 10.1038/srep29182.

16.

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling.

Ferrarini MG, Siqueira FM, Mucha SG, Palama TL, Jobard É, Elena-Herrmann B, R Vasconcelos AT, Tardy F, Schrank IS, Zaha A, Sagot MF.

BMC Genomics. 2016 May 13;17:353. doi: 10.1186/s12864-016-2644-z.

17.

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs.

Sacomoto G, Lacroix V, Sagot MF.

Algorithms Mol Biol. 2015 Jun 27;10:20. doi: 10.1186/s13015-015-0046-4. eCollection 2015.

18.

Effects of roost specialization on extinction risk in bats.

Sagot M, Chaverri G.

Conserv Biol. 2015 Dec;29(6):1666-73. doi: 10.1111/cobi.12546. Epub 2015 Jun 16.

PMID:
26081600
19.

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data.

Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF.

BMC Bioinformatics. 2015 May 29;16:179. doi: 10.1186/s12859-015-0594-0.

20.

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci.

Rao Q, Rollat-Farnier PA, Zhu DT, Santos-Garcia D, Silva FJ, Moya A, Latorre A, Klein CC, Vavre F, Sagot MF, Liu SS, Mouton L, Wang XW.

BMC Genomics. 2015 Mar 21;16:226. doi: 10.1186/s12864-015-1379-6.

21.

MeDuSa: a multi-draft based scaffolder.

Bosi E, Donati B, Galardini M, Brunetti S, Sagot MF, Lió P, Crescenzi P, Fani R, Fondi M.

Bioinformatics. 2015 Aug 1;31(15):2443-51. doi: 10.1093/bioinformatics/btv171. Epub 2015 Mar 25.

PMID:
25810435
22.

Two host clades, two bacterial arsenals: evolution through gene losses in facultative endosymbionts.

Rollat-Farnier PA, Santos-Garcia D, Rao Q, Sagot MF, Silva FJ, Henri H, Zchori-Fein E, Latorre A, Moya A, Barbe V, Liu SS, Wang XW, Vavre F, Mouton L.

Genome Biol Evol. 2015 Feb 20;7(3):839-55. doi: 10.1093/gbe/evv030.

23.

EUCALYPT: efficient tree reconciliation enumerator.

Donati B, Baudet C, Sinaimeri B, Crescenzi P, Sagot MF.

Algorithms Mol Biol. 2015 Jan 23;10(1):3. doi: 10.1186/s13015-014-0031-3. eCollection 2015.

24.

Cophylogeny reconstruction via an approximate Bayesian computation.

Baudet C, Donati B, Sinaimeri B, Crescenzi P, Gautier C, Matias C, Sagot MF.

Syst Biol. 2015 May;64(3):416-31. doi: 10.1093/sysbio/syu129. Epub 2014 Dec 24.

25.

Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Azevedo-Martins AC, Machado AC, Klein CC, Ciapina L, Gonzaga L, Vasconcelos AT, Sagot MF, DE Souza W, Einicker-Lamas M, Galina A, Motta MC.

Parasitology. 2015 Feb;142(2):352-62. doi: 10.1017/S0031182014001139. Epub 2014 Aug 27.

26.

Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses.

Klein CC, Alves JM, Serrano MG, Buck GA, Vasconcelos AT, Sagot MF, Teixeira MM, Camargo EP, Motta MC.

PLoS One. 2013 Nov 19;8(11):e79786. doi: 10.1371/journal.pone.0079786. eCollection 2013.

27.

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.

Milreu PV, Klein CC, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF.

Bioinformatics. 2014 Jan 1;30(1):61-70. doi: 10.1093/bioinformatics/btt597. Epub 2013 Oct 27.

28.

Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers.

Alves JM, Klein CC, da Silva FM, Costa-Martins AG, Serrano MG, Buck GA, Vasconcelos AT, Sagot MF, Teixeira MM, Motta MC, Camargo EP.

BMC Evol Biol. 2013 Sep 9;13:190. doi: 10.1186/1471-2148-13-190.

29.

On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data.

Nor I, Engelstädter J, Duron O, Reuter M, Sagot MF, Charlat S.

Am Nat. 2013 Jul;182(1):E15-24. doi: 10.1086/670612.

PMID:
23778233
30.

Short and long-term genome stability analysis of prokaryotic genomes.

Brilli M, Liò P, Lacroix V, Sagot MF.

BMC Genomics. 2013 May 8;14:309. doi: 10.1186/1471-2164-14-309.

31.

Social calls produced within and near the roost in two species of tent-making bats, Dermanura watsoni and Ectophylla alba.

Gillam EH, Chaverri G, Montero K, Sagot M.

PLoS One. 2013 Apr 24;8(4):e61731. doi: 10.1371/journal.pone.0061731. Print 2013.

32.

Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family.

Motta MC, Martins AC, de Souza SS, Catta-Preta CM, Silva R, Klein CC, de Almeida LG, de Lima Cunha O, Ciapina LP, Brocchi M, Colabardini AC, de Araujo Lima B, Machado CR, de Almeida Soares CM, Probst CM, de Menezes CB, Thompson CE, Bartholomeu DC, Gradia DF, Pavoni DP, Grisard EC, Fantinatti-Garboggini F, Marchini FK, Rodrigues-Luiz GF, Wagner G, Goldman GH, Fietto JL, Elias MC, Goldman MH, Sagot MF, Pereira M, Stoco PH, de Mendonça-Neto RP, Teixeira SM, Maciel TE, de Oliveira Mendes TA, Ürményi TP, de Souza W, Schenkman S, de Vasconcelos AT.

PLoS One. 2013;8(4):e60209. doi: 10.1371/journal.pone.0060209. Epub 2013 Apr 3.

33.

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Mendes ND, Heyne S, Freitas AT, Sagot MF, Backofen R.

Bioinformatics. 2012 Dec 1;28(23):3034-41. doi: 10.1093/bioinformatics/bts574. Epub 2012 Oct 10.

34.

Exploration of the core metabolism of symbiotic bacteria.

Klein CC, Cottret L, Kielbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF.

BMC Genomics. 2012 Aug 31;13:438. doi: 10.1186/1471-2164-13-438.

35.

Structural and dynamical analysis of biological networks.

Klein C, Marino A, Sagot MF, Vieira Milreu P, Brilli M.

Brief Funct Genomics. 2012 Nov;11(6):420-33. doi: 10.1093/bfgp/els030. Epub 2012 Aug 20.

PMID:
22908211
36.

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Acuña V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF.

Bioinformatics. 2012 Oct 1;28(19):2474-83. Epub 2012 Jul 10.

PMID:
22782547
37.

Sampling solution traces for the problem of sorting permutations by signed reversals.

Baudet C, Dias Z, Sagot MF.

Algorithms Mol Biol. 2012 Jun 15;7(1):18. doi: 10.1186/1748-7188-7-18.

38.

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.

39.

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.

Sacomoto GA, Kielbassa J, Chikhi R, Uricaru R, Antoniou P, Sagot MF, Peterlongo P, Lacroix V.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5. doi: 10.1186/1471-2105-13-S6-S5.

40.

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny.

Véron AS, Lemaitre C, Gautier C, Lacroix V, Sagot MF.

BMC Genomics. 2011 Jun 10;12:303. doi: 10.1186/1471-2164-12-303.

41.

Bacterial syntenies: an exact approach with gene quorum.

Deniélou YP, Sagot MF, Boyer F, Viari A.

BMC Bioinformatics. 2011 May 24;12:193. doi: 10.1186/1471-2105-12-193.

42.

Wolbachia detection: an assessment of standard PCR protocols.

Simões PM, Mialdea G, Reiss D, Sagot MF, Charlat S.

Mol Ecol Resour. 2011 May;11(3):567-72. doi: 10.1111/j.1755-0998.2010.02955.x. Epub 2011 Jan 18.

PMID:
21481216
43.

CycADS: an annotation database system to ease the development and update of BioCyc databases.

Vellozo AF, Véron AS, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldón T, Sagot MF, Charles H, Colella S.

Database (Oxford). 2011 Apr 7;2011:bar008. doi: 10.1093/database/bar008. Print 2011.

44.

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi.

Mendes ND, Freitas AT, Vasconcelos AT, Sagot MF.

BMC Genomics. 2010 Sep 29;11:529. doi: 10.1186/1471-2164-11-529.

45.

Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata.

Cottret L, Milreu PV, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot MF.

PLoS Comput Biol. 2010 Sep 2;6(9). pii: e1000904. doi: 10.1371/journal.pcbi.1000904.

46.

Cassis: detection of genomic rearrangement breakpoints.

Baudet C, Lemaitre C, Dias Z, Gautier C, Tannier E, Sagot MF.

Bioinformatics. 2010 Aug 1;26(15):1897-8. doi: 10.1093/bioinformatics/btq301. Epub 2010 Jun 23.

47.

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W132-7. doi: 10.1093/nar/gkq312. Epub 2010 May 5.

48.

An asymmetric approach to preserve common intervals while sorting by reversals.

Braga MD, Gautier C, Sagot MF.

Algorithms Mol Biol. 2009 Dec 30;4:16. doi: 10.1186/1748-7188-4-16.

49.

A note on the complexity of finding and enumerating elementary modes.

Acuña V, Marchetti-Spaccamela A, Sagot MF, Stougie L.

Biosystems. 2010 Mar;99(3):210-4. doi: 10.1016/j.biosystems.2009.11.004. Epub 2009 Dec 3.

PMID:
19962421
50.

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

Brinza L, Viñuelas J, Cottret L, Calevro F, Rahbé Y, Febvay G, Duport G, Colella S, Rabatel A, Gautier C, Fayard JM, Sagot MF, Charles H.

C R Biol. 2009 Nov;332(11):1034-49. doi: 10.1016/j.crvi.2009.09.007. Epub 2009 Oct 14. Review.

PMID:
19909925

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