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Items: 38

1.

Intestinal Inflammation in Children with Cystic Fibrosis Is Associated with Crohn's-Like Microbiota Disturbances.

Enaud R, Hooks KB, Barre A, Barnetche T, Hubert C, Massot M, Bazin T, Clouzeau H, Bui S, Fayon M, Berger P, Lehours P, Bébéar C, Nikolski M, Lamireau T, Delhaes L, Schaeverbeke T.

J Clin Med. 2019 May 10;8(5). pii: E645. doi: 10.3390/jcm8050645.

2.

Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures.

Soula A, Valere M, López-González MJ, Ury-Thiery V, Groppi A, Landry M, Nikolski M, Favereaux A.

Life Sci Alliance. 2018 Sep 30;1(5):e201800018. doi: 10.26508/lsa.201800018. eCollection 2018 Oct.

3.

Microbiota Composition May Predict Anti-Tnf Alpha Response in Spondyloarthritis Patients: an Exploratory Study.

Bazin T, Hooks KB, Barnetche T, Truchetet ME, Enaud R, Richez C, Dougados M, Hubert C, Barré A, Nikolski M, Schaeverbeke T.

Sci Rep. 2018 Apr 3;8(1):5446. doi: 10.1038/s41598-018-23571-4.

4.

A Peptide Targeting Inflammatory CNS Lesions in the EAE Rat Model of Multiple Sclerosis.

Boiziau C, Nikolski M, Mordelet E, Aussudre J, Vargas-Sanchez K, Petry KG.

Inflammation. 2018 Jun;41(3):932-947. doi: 10.1007/s10753-018-0748-0.

PMID:
29516383
5.

Diversity of HIV-1 in Aquitaine, Southwestern France, 2012-2016.

Tumiotto C, Bellecave P, Recordon-Pinson P, Groppi A, Nikolski M, Fleury H.

AIDS Res Hum Retroviruses. 2018 May;34(5):471-473. doi: 10.1089/AID.2017.0298. Epub 2018 Mar 22.

PMID:
29439582
6.

Argininosuccinate synthase 1 (ASS1): A marker of unclassified hepatocellular adenoma and high bleeding risk.

Henriet E, Abou Hammoud A, Dupuy JW, Dartigues B, Ezzoukry Z, Dugot-Senant N, Leste-Lasserre T, Pallares-Lupon N, Nikolski M, Le Bail B, Blanc JF, Balabaud C, Bioulac-Sage P, Raymond AA, Saltel F.

Hepatology. 2017 Dec;66(6):2016-2028. doi: 10.1002/hep.29336. Epub 2017 Oct 30.

PMID:
28646562
7.

MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method.

Rudewicz J, Soueidan H, Uricaru R, Bonnefoi H, Iggo R, Bergh J, Nikolski M.

Front Genet. 2016 Dec 8;7:214. doi: 10.3389/fgene.2016.00214. eCollection 2016.

8.

Towards an open grapevine information system.

Adam-Blondon AF, Alaux M, Pommier C, Cantu D, Cheng ZM, Cramer GR, Davies C, Delrot S, Deluc L, Di Gaspero G, Grimplet J, Fennell A, Londo JP, Kersey P, Mattivi F, Naithani S, Neveu P, Nikolski M, Pezzotti M, Reisch BI, Töpfer R, Vivier MA, Ware D, Quesneville H.

Hortic Res. 2016 Nov 23;3:16056. eCollection 2016. Review.

9.

Aptamer selection by direct microfluidic recovery and surface plasmon resonance evaluation.

Dausse E, Barré A, Aimé A, Groppi A, Rico A, Ainali C, Salgado G, Palau W, Daguerre E, Nikolski M, Toulmé JJ, Di Primo C.

Biosens Bioelectron. 2016 Jun 15;80:418-425. doi: 10.1016/j.bios.2016.02.003. Epub 2016 Feb 3.

PMID:
26874109
10.

Data standards can boost metabolomics research, and if there is a will, there is a way.

Rocca-Serra P, Salek RM, Arita M, Correa E, Dayalan S, Gonzalez-Beltran A, Ebbels T, Goodacre R, Hastings J, Haug K, Koulman A, Nikolski M, Oresic M, Sansone SA, Schober D, Smith J, Steinbeck C, Viant MR, Neumann S.

Metabolomics. 2016;12:14. doi: 10.1007/s11306-015-0879-3. Epub 2015 Nov 17. Review.

11.

COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access.

Salek RM, Neumann S, Schober D, Hummel J, Billiau K, Kopka J, Correa E, Reijmers T, Rosato A, Tenori L, Turano P, Marin S, Deborde C, Jacob D, Rolin D, Dartigues B, Conesa P, Haug K, Rocca-Serra P, O'Hagan S, Hao J, van Vliet M, Sysi-Aho M, Ludwig C, Bouwman J, Cascante M, Ebbels T, Griffin JL, Moing A, Nikolski M, Oresic M, Sansone SA, Viant MR, Goodacre R, Günther UL, Hankemeier T, Luchinat C, Walther D, Steinbeck C.

Metabolomics. 2015;11(6):1587-1597. Epub 2015 May 26.

12.

Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca).

Mariette S, Wong Jun Tai F, Roch G, Barre A, Chague A, Decroocq S, Groppi A, Laizet Y, Lambert P, Tricon D, Nikolski M, Audergon JM, Abbott AG, Decroocq V.

New Phytol. 2016 Jan;209(2):773-84. doi: 10.1111/nph.13627. Epub 2015 Sep 10.

13.

Proposal for a European Public Health Research Infrastructure for Sharing of health and Medical administrative data (PHRIMA).

Burgun A, Oksen DV, Kuchinke W, Prokosch HU, Ganslandt T, Buchan I, van Staa T, Cunningham J, Gjerstorff ML, Dufour JC, Gibrat JF, Nikolski M, Verger P, Cambon-Thomsen A, Masella C, Lettieri E, Bertele P, Salokannel M, Thiebaut R, Persoz C, Chêne G, Ohmann C.

Stud Health Technol Inform. 2015;216:1005.

PMID:
26262306
14.

Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated for large operable or locally advanced hormone-receptor-positive breast cancer.

Quenel-Tueux N, Debled M, Rudewicz J, MacGrogan G, Pulido M, Mauriac L, Dalenc F, Bachelot T, Lortal B, Breton-Callu C, Madranges N, de Lara CT, Fournier M, Bonnefoi H, Soueidan H, Nikolski M, Gros A, Daly C, Wood H, Rabbitts P, Iggo R.

Br J Cancer. 2015 Aug 11;113(4):585-94. doi: 10.1038/bjc.2015.247. Epub 2015 Jul 14.

15.

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.

Bioinformatics. 2015 Oct 1;31(19):3147-55. doi: 10.1093/bioinformatics/btv316. Epub 2015 May 27.

PMID:
26023104
16.

Finding and identifying the viral needle in the metagenomic haystack: trends and challenges.

Soueidan H, Schmitt LA, Candresse T, Nikolski M.

Front Microbiol. 2015 Jan 7;5:739. doi: 10.3389/fmicb.2014.00739. eCollection 2014.

17.

Finishing bacterial genome assemblies with Mix.

Soueidan H, Maurier F, Groppi A, Sirand-Pugnet P, Tardy F, Citti C, Dupuy V, Nikolski M.

BMC Bioinformatics. 2013;14 Suppl 15:S16. doi: 10.1186/1471-2105-14-S15-S16. Epub 2013 Oct 15.

18.

Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats.

Dupuy V, Sirand-Pugnet P, Baranowski E, Barré A, Breton M, Couture C, Dordet-Frisoni E, Gaurivaud P, Jacob D, Lemaitre C, Manso-Silván L, Nikolski M, Nouvel LX, Poumarat F, Tardy F, Thébault P, Theil S, Citti C, Blanchard A, Thiaucourt F.

Genome Announc. 2013 Jun 13;1(3). pii: e00354-13. doi: 10.1128/genomeA.00354-13.

19.

Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle.

Manso-Silván L, Tardy F, Baranowski E, Barré A, Blanchard A, Breton M, Couture C, Citti C, Dordet-Frisoni E, Dupuy V, Gaurivaud P, Jacob D, Lemaitre C, Nikolski M, Nouvel LX, Poumarat F, Thébault P, Theil S, Thiaucourt F, Sirand-Pugnet P.

Genome Announc. 2013 Jun 13;1(3). pii: e00348-13. doi: 10.1128/genomeA.00348-13.

20.

Draft Genome Sequences of Mycoplasma auris and Mycoplasma yeatsii, Two Species of the Ear Canal of Caprinae.

Dordet-Frisoni E, Baranowski E, Barré A, Blanchard A, Breton M, Couture C, Dupuy V, Gaurivaud P, Jacob D, Lemaitre C, Manso-Silván L, Nikolski M, Nouvel LX, Poumarat F, Sirand-Pugnet P, Thébault P, Theil S, Thiaucourt F, Citti C, Tardy F.

Genome Announc. 2013 Jun 13;1(3). pii: e00280-13. doi: 10.1128/genomeA.00280-13.

21.

Further steps in TANGO: improved taxonomic assignment in metagenomics.

Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.

PMID:
23645816
22.

The family based variability in protein family expansion.

Sarkar A, Nikolski M, Durrens P.

Int J Bioinform Res Appl. 2013;9(2):121-33. doi: 10.1504/IJBRA.2013.052473.

PMID:
23467059
23.

Identification of conserved gene clusters in multiple genomes based on synteny and homology.

Sarkar A, Soueidan H, Nikolski M.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S18. doi: 10.1186/1471-2105-12-S9-S18.

24.

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.

Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D.

BMC Plant Biol. 2011 Jun 13;11:104. doi: 10.1186/1471-2229-11-104.

25.

Minimum Information About a Simulation Experiment (MIASE).

Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N.

PLoS Comput Biol. 2011 Apr;7(4):e1001122. doi: 10.1371/journal.pcbi.1001122. Epub 2011 Apr 28. No abstract available.

26.

SyDiG: uncovering Synteny in Distant Genomes.

Jean G, Nikolski M.

Int J Bioinform Res Appl. 2011;7(1):43-62.

PMID:
21441096
27.

Mining the semantics of genome super-blocks to infer ancestral architectures.

Jean G, Sherman DJ, Nikolski M.

J Comput Biol. 2009 Sep;16(9):1267-84. doi: 10.1089/cmb.2008.0046.

PMID:
19772437
28.

Comparative genomics of protoploid Saccharomycetaceae.

Génolevures Consortium, Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E.

Genome Res. 2009 Oct;19(10):1696-709. doi: 10.1101/gr.091546.109. Epub 2009 Jun 12.

29.

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.

Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P; Génolevures Consortium.

Nucleic Acids Res. 2009 Jan;37(Database issue):D550-4. doi: 10.1093/nar/gkn859. Epub 2008 Nov 16.

30.

Fusion and fission of genes define a metric between fungal genomes.

Durrens P, Nikolski M, Sherman D.

PLoS Comput Biol. 2008 Oct;4(10):e1000200. doi: 10.1371/journal.pcbi.1000200. Epub 2008 Oct 24.

31.

Exploratory simulation of cell ageing using hierarchical models.

Cvijovic M, Soueidan H, Sherman DJ, Klipp E, Nikolski M.

Genome Inform. 2008;21:114-25.

PMID:
19425152
32.

Extrapolation of metabolic pathways as an aid to modelling completely sequenced nonSaccharomyces yeasts.

Iragne F, Nikolski M, Sherman D.

FEMS Yeast Res. 2008 Feb;8(1):132-9. Epub 2007 Aug 22.

33.

Family relationships: should consensus reign?--consensus clustering for protein families.

Nikolski M, Sherman DJ.

Bioinformatics. 2007 Jan 15;23(2):e71-6. Erratum in: Bioinformatics. 2009 Sep 1;25(17):2294.

PMID:
17237108
34.

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts.

Sherman D, Durrens P, Iragne F, Beyne E, Nikolski M, Souciet JL.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D432-5.

35.

ProViz: protein interaction visualization and exploration.

Iragne F, Nikolski M, Mathieu B, Auber D, Sherman D.

Bioinformatics. 2005 Jan 15;21(2):272-4. Epub 2004 Sep 3.

PMID:
15347570
36.

Genome evolution in yeasts.

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL.

Nature. 2004 Jul 1;430(6995):35-44.

PMID:
15229592
37.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol. 2004 Feb;22(2):177-83.

PMID:
14755292
38.

Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts.

Sherman D, Durrens P, Beyne E, Nikolski M, Souciet JL; Génolevures Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D315-8.

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