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Items: 50

1.

Computational discovery of direct associations between GO terms and protein domains.

Alborzi SZ, Ritchie DW, Devignes MD.

BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):413. doi: 10.1186/s12859-018-2380-2.

2.

Low-Dose Alkylphenol Exposure Promotes Mammary Epithelium Alterations and Transgenerational Developmental Defects, But Does Not Enhance Tumorigenic Behavior of Breast Cancer Cells.

Chamard-Jovenin C, Thiebaut C, Chesnel A, Bresso E, Morel C, Smail-Tabbone M, Devignes MD, Boukhobza T, Dumond H.

Front Endocrinol (Lausanne). 2017 Oct 23;8:272. doi: 10.3389/fendo.2017.00272. eCollection 2017.

3.

Discovering associations between adverse drug events using pattern structures and ontologies.

Personeni G, Bresso E, Devignes MD, Dumontier M, Smaïl-Tabbone M, Coulet A.

J Biomed Semantics. 2017 Aug 22;8(1):29. doi: 10.1186/s13326-017-0137-x.

4.

A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins.

Coluzzi C, Guédon G, Devignes MD, Ambroset C, Loux V, Lacroix T, Payot S, Leblond-Bourget N.

Front Microbiol. 2017 Mar 20;8:443. doi: 10.3389/fmicb.2017.00443. eCollection 2017.

5.

ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains.

Alborzi SZ, Devignes MD, Ritchie DW.

BMC Bioinformatics. 2017 Feb 13;18(1):107. doi: 10.1186/s12859-017-1519-x.

6.

Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP-11 structural models.

El Houasli M, Maigret B, Devignes MD, Ghoorah AW, Grudinin S, Ritchie DW.

Proteins. 2017 Mar;85(3):463-469. doi: 10.1002/prot.25182. Epub 2016 Oct 24.

PMID:
27701764
7.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

8.

Classification and Exploration of 3D Protein Domain Interactions Using Kbdock.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Methods Mol Biol. 2016;1415:91-105. doi: 10.1007/978-1-4939-3572-7_5.

PMID:
27115629
9.

New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration.

Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N.

Front Microbiol. 2016 Jan 6;6:1483. doi: 10.3389/fmicb.2015.01483. eCollection 2015.

10.

A structure-based classification and analysis of protein domain family binding sites and their interactions.

Ghoorah AW, Devignes MD, Alborzi SZ, Smaïl-Tabbone M, Ritchie DW.

Biology (Basel). 2015 Apr 9;4(2):327-43. doi: 10.3390/biology4020327.

11.

ECCB 2014: The 13th European Conference on Computational Biology.

Devignes MD, Moreau Y.

Bioinformatics. 2014 Sep 1;30(17):i345-8. doi: 10.1093/bioinformatics/btu512. No abstract available.

12.

Prediction of monomer isomery in Florine: a workflow dedicated to nonribosomal peptide discovery.

Caradec T, Pupin M, Vanvlassenbroeck A, Devignes MD, Smaïl-Tabbone M, Jacques P, Leclère V.

PLoS One. 2014 Jan 21;9(1):e85667. doi: 10.1371/journal.pone.0085667. eCollection 2014.

13.

KBDOCK 2013: a spatial classification of 3D protein domain family interactions.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Nucleic Acids Res. 2014 Jan;42(Database issue):D389-95. doi: 10.1093/nar/gkt1199. Epub 2013 Nov 23.

14.

Protein docking using case-based reasoning.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Proteins. 2013 Dec;81(12):2150-8. doi: 10.1002/prot.24433.

PMID:
24123156
15.

Integrative relational machine-learning for understanding drug side-effect profiles.

Bresso E, Grisoni R, Marchetti G, Karaboga AS, Souchet M, Devignes MD, Smaïl-Tabbone M.

BMC Bioinformatics. 2013 Jun 26;14:207. doi: 10.1186/1471-2105-14-207.

16.

Extended spectrum of MBD5 mutations in neurodevelopmental disorders.

Bonnet C, Ali Khan A, Bresso E, Vigouroux C, Béri M, Lejczak S, Deemer B, Andrieux J, Philippe C, Moncla A, Giurgea I, Devignes MD, Leheup B, Jonveaux P.

Eur J Hum Genet. 2013 Dec;21(12):1457-61. doi: 10.1038/ejhg.2013.22. Epub 2013 Feb 20.

17.

Functional classification of genes using semantic distance and fuzzy clustering approach: evaluation with reference sets and overlap analysis.

Devignes MD, Benabderrahmane S, Smaïl-Tabbone M, Napoli A, Poch O.

Int J Comput Biol Drug Des. 2012;5(3-4):245-60. doi: 10.1504/IJCBDD.2012.049207. Epub 2012 Sep 24.

PMID:
23013652
18.

Spatial clustering of protein binding sites for template based protein docking.

Ghoorah AW, Devignes MD, Smaïl-Tabbone M, Ritchie DW.

Bioinformatics. 2011 Oct 15;27(20):2820-7. doi: 10.1093/bioinformatics/btr493. Epub 2011 Aug 27.

PMID:
21873637
19.

Ontology-based knowledge discovery in pharmacogenomics.

Coulet A, Smaïl-Tabbone M, Napoli A, Devignes MD.

Adv Exp Med Biol. 2011;696:357-66. doi: 10.1007/978-1-4419-7046-6_36.

PMID:
21431576
20.

IntelliGO: a new vector-based semantic similarity measure including annotation origin.

Benabderrahmane S, Smail-Tabbone M, Poch O, Napoli A, Devignes MD.

BMC Bioinformatics. 2010 Dec 1;11:588. doi: 10.1186/1471-2105-11-588.

21.

HexServer: an FFT-based protein docking server powered by graphics processors.

Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W445-9. doi: 10.1093/nar/gkq311. Epub 2010 May 5.

22.

Comparison of three preprocessing filters efficiency in virtual screening: identification of new putative LXRbeta regulators as a test case.

Ghemtio L, Devignes MD, Smaïl-Tabbone M, Souchet M, Leroux V, Maigret B.

J Chem Inf Model. 2010 May 24;50(5):701-15. doi: 10.1021/ci900356m.

PMID:
20420434
23.

Activation of peroxisome proliferator-activated receptor gamma by human cytomegalovirus for de novo replication impairs migration and invasiveness of cytotrophoblasts from early placentas.

Rauwel B, Mariamé B, Martin H, Nielsen R, Allart S, Pipy B, Mandrup S, Devignes MD, Evain-Brion D, Fournier T, Davrinche C.

J Virol. 2010 Mar;84(6):2946-54. doi: 10.1128/JVI.01779-09. Epub 2009 Dec 30.

24.

Gene-disease relationship discovery based on model-driven data integration and database view definition.

Yilmaz S, Jonveaux P, Bicep C, Pierron L, Smaïl-Tabbone M, Devignes MD.

Bioinformatics. 2009 Jan 15;25(2):230-6. doi: 10.1093/bioinformatics/btn612. Epub 2008 Nov 27.

25.

Ontology-guided data preparation for discovering genotype-phenotype relationships.

Coulet A, Smaïl-Tabbone M, Benlian P, Napoli A, Devignes MD.

BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S3. doi: 10.1186/1471-2105-9-S4-S3.

26.

Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment.

Beautrait A, Leroux V, Chavent M, Ghemtio L, Devignes MD, Smaïl-Tabbone M, Cai W, Shao X, Moreau G, Bladon P, Yao J, Maigret B.

J Mol Model. 2008 Feb;14(2):135-48. doi: 10.1007/s00894-007-0257-9. Epub 2008 Jan 3.

PMID:
18172702
27.

Screening of subtle copy number changes in Aicardi syndrome patients with a high resolution X chromosome array-CGH.

Yilmaz S, Fontaine H, Brochet K, Grégoire MJ, Devignes MD, Schaff JL, Philippe C, Nemos C, McGregor JL, Jonveaux P.

Eur J Med Genet. 2007 Sep-Oct;50(5):386-91. Epub 2007 Jun 7.

PMID:
17625997
28.

A transgenic mouse model engineered to investigate human brain-derived neurotrophic factor in vivo.

Guillemot F, Cerutti I, Auffray C, Devignes MD.

Transgenic Res. 2007 Apr;16(2):223-37. Epub 2007 Jan 16.

PMID:
17225071
29.

Immunoselection and characterization of a human genomic PPAR binding fragment located within POTE genes.

Murad H, Collet P, Brunner E, Schohn H, Bécuwe P, Devignes MD, Dauça M, Domenjoud L.

Biochimie. 2007 Mar;89(3):329-36. Epub 2006 Oct 18.

PMID:
17070643
30.

Effects of PPAR and RXR ligands in semaphorin 6B gene expression of human MCF-7 breast cancer cells.

Murad H, Collet P, Huin-Schohn C, Al-Makdissy N, Kerjan G, Chedotal A, Donner M, Devignes MD, Becuwe P, Schohn H, Domenjoud L, Dauça M.

Int J Oncol. 2006 Apr;28(4):977-84.

PMID:
16525649
31.

Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene.

Bertaux O, Toselli-Mollereau E, Auffray C, Devignes MD.

Gene. 2004 Jun 9;334:83-97.

PMID:
15256258
32.

The human semaphorin 6B gene is down regulated by PPARs.

Collet P, Domenjoud L, Devignes MD, Murad H, Schohn H, Dauça M.

Genomics. 2004 Jun;83(6):1141-50.

PMID:
15177567
33.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

34.
35.

Refined localization of twenty-one genes in subregion p13.1 of human chromosome 1.

Chelala C, Imbeaud S, Devignes MD, Zoorob R, Auffray C.

Cytogenet Cell Genet. 2001;92(3-4):209-12.

PMID:
11435689
36.

The genexpress IMAGE knowledge base of the human muscle transcriptome: a resource of structural, functional, and positional candidate genes for muscle physiology and pathologies.

Piétu G, Eveno E, Soury-Segurens B, Fayein NA, Mariage-Samson R, Matingou C, Leroy E, Dechesne C, Krieger S, Ansorge W, Reguigne-Arnould I, Cox D, Dehejia A, Polymeropoulos MH, Devignes MD, Auffray C.

Genome Res. 1999 Dec;9(12):1313-20.

37.

Report of the Sixth International Workshop on Human Chromosome 11 Mapping 1998. Nice, France, May 2-5, 1998.

Gaudray P, Carle GF, Gerhard DS, Gessler M, Mannens MM, Athanasiou M, Bliek J, Calender A, Debelenko LV, Devignes M, Evans GA, Favier R, Forbes S, Gaudray G, Gawin B, Gordon M, Grimmond S, Grossfeld P, Harris J, Hattori M, Hosoda F, Hummerich H, James M, Kalla J, Katsanis N, et al.

Cytogenet Cell Genet. 1999;86(3-4):167-86. No abstract available.

PMID:
10575203
38.

The complete cDNA sequence encoding dog gastric lipase.

Vaganay S, Joliff G, Bertaux O, Toselli E, Devignes MD, Bénicourt C.

DNA Seq. 1998 Mar;8(4):257-62.

PMID:
10520456
39.

Detailed transcript map of a 810-kb region at 11p14 involving identification of 10 novel human 3' exons.

Guillemot F, Auffray C, Devignes MD.

Eur J Hum Genet. 1999 May-Jun;7(4):487-95.

40.

The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics.

Piétu G, Mariage-Samson R, Fayein NA, Matingou C, Eveno E, Houlgatte R, Decraene C, Vandenbrouck Y, Tahi F, Devignes MD, Wirkner U, Ansorge W, Cox D, Nagase T, Nomura N, Auffray C.

Genome Res. 1999 Feb;9(2):195-209.

41.
42.

Report of the Fifth International Workshop on Human Chromosome 11 Mapping 1996.

Shows TB, Alders M, Bennett S, Burbee D, Cartwright P, Chandrasekharappa S, Cooper P, Courseaux A, Davies C, Devignes MD, Devilee P, Elliott R, Evans G, Fantes J, Garner H, Gaudray P, Gerhard DS, Gessler M, Higgins M, Hummerich H, James M, Lagercrantz J, Litt M, Little P, Zabel B, et al.

Cytogenet Cell Genet. 1996;74(1-2):1-56. No abstract available.

PMID:
8893803
43.

Integrated physical, genetic, and genic map covering 3 Mb around the human NGF gene (NGFB) at 1p13.

Carrier A, Rosier MF, Guillemot F, Goguel AF, Pulcini F, Bernheim A, Auffray C, Devignes MD.

Genomics. 1996 Jan 1;31(1):80-9.

PMID:
8808283
44.

Mapping of 22 YACs on human chromosomes by fish using yeast DNA Alu-PCR products for competition.

Goguel AF, Pulcini F, Danglot G, Fauvet D, Devignes MD, Bernheim A.

Ann Genet. 1996;39(2):64-8.

PMID:
8766135
45.

Regional assignment of 68 new human gene transcripts on chromosome 11.

Rosier MF, Reguigne-Arnould I, Couillin P, Devignes MD, Auffray C.

Genome Res. 1995 Aug;5(1):60-70. Erratum in: Genome Res 1995 Oct;5(3):318-9.

46.

Rapid and high efficiency site-directed mutagenesis by improvement of the homologous recombination technique.

Martin A, Toselli E, Rosier MF, Auffray C, Devignes MD.

Nucleic Acids Res. 1995 May 11;23(9):1642-3. No abstract available.

47.

[IMAGE: molecular integration of the analysis of the human genome and its expression].

Auffray C, Behar G, Bois F, Bouchier C, Da Silva C, Devignes MD, Duprat S, Houlgatte R, Jumeau MN, Lamy B, et al.

C R Acad Sci III. 1995 Feb;318(2):263-72. French.

PMID:
7757816
48.

A 1.7-Mb YAC contig around the human BDNF gene (11p13): integration of the physical, genetic, and cytogenetic maps in relation to WAGR syndrome.

Rosier MF, Goguel AF, Martin A, Le Paslier D, Couillin P, Houlgatte R, Bernheim A, Auffray C, Devignes MD.

Genomics. 1994 Nov 1;24(1):69-77.

PMID:
7896291
49.

Chicken tyrosine hydroxylase gene: isolation and functional characterization of the 5' flanking region.

Carrier A, Devignes MD, Renoir D, Auffray C.

J Neurochem. 1993 Dec;61(6):2215-24.

PMID:
7504087
50.

Cloning and mapping of 5' exons from the gene encoding chicken beta nerve growth factor.

Carrier A, Devignes MD, Rosier MF, Auffray C.

Gene. 1992 Jul 15;116(2):173-9.

PMID:
1634115

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