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Items: 29

1.

Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis.

Chatron N, Cassinari K, Quenez O, Baert-Desurmont S, Bardel C, Buisine MP, Calpena E, Capri Y, Corominas Galbany J, Diguet F, Edery P, Isidor B, Labalme A, Le Caignec C, Lévy J, Lecoquierre F, Lindenbaum P, Pichon O, Rollat-Farnier PA, Simonet T, Saugier-Veber P, Tabet AC, Toutain A, Wilkie AOM, Lesca G, Sanlaville D, Nicolas G, Schluth-Bolard C.

Hum Mutat. 2019 Jun 23. doi: 10.1002/humu.23845. [Epub ahead of print]

PMID:
31230393
2.

Identification of a new VHL exon and complex splicing alterations in familial erythrocytosis or von Hippel-Lindau disease.

Lenglet M, Robriquet F, Schwarz K, Camps C, Couturier A, Hoogewijs D, Buffet A, Knight SJL, Gad S, Couvé S, Chesnel F, Pacault M, Lindenbaum P, Job S, Dumont S, Besnard T, Cornec M, Dreau H, Pentony M, Kvikstad E, Deveaux S, Burnichon N, Ferlicot S, Vilaine M, Mazzella JM, Airaud F, Garrec C, Heidet L, Irtan S, Mantadakis E, Bouchireb K, Debatin KM, Redon R, Bezieau S, Bressac-de Paillerets B, Teh BT, Girodon F, Randi ML, Putti MC, Bours V, Van Wijk R, Göthert JR, Kattamis A, Janin N, Bento C, Taylor JC, Arlot-Bonnemains Y, Richard S, Gimenez-Roqueplo AP, Cario H, Gardie B.

Blood. 2018 Aug 2;132(5):469-483. doi: 10.1182/blood-2018-03-838235. Epub 2018 Jun 11.

3.

Rare Coding Variants in ANGPTL6 Are Associated with Familial Forms of Intracranial Aneurysm.

Bourcier R, Le Scouarnec S, Bonnaud S, Karakachoff M, Bourcereau E, Heurtebise-Chrétien S, Menguy C, Dina C, Simonet F, Moles A, Lenoble C, Lindenbaum P, Chatel S, Isidor B, Génin E, Deleuze JF, Schott JJ, Le Marec H; ICAN Study Group, Loirand G, Desal H, Redon R.

Am J Hum Genet. 2018 Jan 4;102(1):133-141. doi: 10.1016/j.ajhg.2017.12.006.

4.

bioalcidae, samjs and vcffilterjs: object-oriented formatters and filters for bioinformatics files.

Lindenbaum P, Redon R.

Bioinformatics. 2018 Apr 1;34(7):1224-1225. doi: 10.1093/bioinformatics/btx734.

PMID:
29186339
5.

De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability.

Küry S, van Woerden GM, Besnard T, Proietti Onori M, Latypova X, Towne MC, Cho MT, Prescott TE, Ploeg MA, Sanders S, Stessman HAF, Pujol A, Distel B, Robak LA, Bernstein JA, Denommé-Pichon AS, Lesca G, Sellars EA, Berg J, Carré W, Busk ØL, van Bon BWM, Waugh JL, Deardorff M, Hoganson GE, Bosanko KB, Johnson DS, Dabir T, Holla ØL, Sarkar A, Tveten K, de Bellescize J, Braathen GJ, Terhal PA, Grange DK, van Haeringen A, Lam C, Mirzaa G, Burton J, Bhoj EJ, Douglas J, Santani AB, Nesbitt AI, Helbig KL, Andrews MV, Begtrup A, Tang S, van Gassen KLI, Juusola J, Foss K, Enns GM, Moog U, Hinderhofer K, Paramasivam N, Lincoln S, Kusako BH, Lindenbaum P, Charpentier E, Nowak CB, Cherot E, Simonet T, Ruivenkamp CAL, Hahn S, Brownstein CA, Xia F, Schmitt S, Deb W, Bonneau D, Nizon M, Quinquis D, Chelly J, Rudolf G, Sanlaville D, Parent P, Gilbert-Dussardier B, Toutain A, Sutton VR, Thies J, Peart-Vissers LELM, Boisseau P, Vincent M, Grabrucker AM, Dubourg C; Undiagnosed Diseases Network, Tan WH, Verbeek NE, Granzow M, Santen GWE, Shendure J, Isidor B, Pasquier L, Redon R, Yang Y, State MW, Kleefstra T, Cogné B; GEM HUGO; Deciphering Developmental Disorders Study, Petrovski S, Retterer K, Eichler EE, Rosenfeld JA, Agrawal PB, Bézieau S, Odent S, Elgersma Y, Mercier S.

Am J Hum Genet. 2017 Nov 2;101(5):768-788. doi: 10.1016/j.ajhg.2017.10.003.

6.

Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.

Penaud-Budloo M, Lecomte E, Guy-Duché A, Saleun S, Roulet A, Lopez-Roques C, Tournaire B, Cogné B, Léger A, Blouin V, Lindenbaum P, Moullier P, Ayuso E.

Hum Gene Ther Methods. 2017 Jun;28(3):148-162. doi: 10.1089/hgtb.2016.185. Epub 2017 Apr 21.

PMID:
28463571
7.

Dysfunction of the Voltage-Gated K+ Channel β2 Subunit in a Familial Case of Brugada Syndrome.

Portero V, Le Scouarnec S, Es-Salah-Lamoureux Z, Burel S, Gourraud JB, Bonnaud S, Lindenbaum P, Simonet F, Violleau J, Baron E, Moreau E, Scott C, Chatel S, Loussouarn G, O'Hara T, Mabo P, Dina C, Le Marec H, Schott JJ, Probst V, Baró I, Marionneau C, Charpentier F, Redon R.

J Am Heart Assoc. 2016 Jun 10;5(6). pii: e003122. doi: 10.1161/JAHA.115.003122.

8.

Targeted resequencing identifies TRPM4 as a major gene predisposing to progressive familial heart block type I.

Daumy X, Amarouch MY, Lindenbaum P, Bonnaud S, Charpentier E, Bianchi B, Nafzger S, Baron E, Fouchard S, Thollet A, Kyndt F, Barc J, Le Scouarnec S, Makita N, Le Marec H, Dina C, Gourraud JB, Probst V, Abriel H, Redon R, Schott JJ.

Int J Cardiol. 2016 Mar 15;207:349-58. doi: 10.1016/j.ijcard.2016.01.052. Epub 2016 Jan 11.

PMID:
26820365
9.

De Novo Truncating Mutations in the Kinetochore-Microtubules Attachment Gene CHAMP1 Cause Syndromic Intellectual Disability.

Isidor B, Küry S, Rosenfeld JA, Besnard T, Schmitt S, Joss S, Davies SJ, Lebel RR, Henderson A, Schaaf CP, Streff HE, Yang Y, Jain V, Chida N, Latypova X, Le Caignec C, Cogné B, Mercier S, Vincent M, Colin E, Bonneau D, Denommé AS, Parent P, Gilbert-Dussardier B, Odent S, Toutain A, Piton A, Dina C, Donnart A, Lindenbaum P, Charpentier E, Redon R, Iemura K, Ikeda M, Tanaka K, Bézieau S.

Hum Mutat. 2016 Apr;37(4):354-8. doi: 10.1002/humu.22952. Epub 2016 Feb 4.

10.

Search for Rare Copy-Number Variants in Congenital Heart Defects Identifies Novel Candidate Genes and a Potential Role for FOXC1 in Patients With Coarctation of the Aorta.

Sanchez-Castro M, Eldjouzi H, Charpentier E, Busson PF, Hauet Q, Lindenbaum P, Delasalle-Guyomarch B, Baudry A, Pichon O, Pascal C, Lefort B, Bajolle F, Pezard P, Schott JJ, Dina C, Redon R, Gournay V, Bonnet D, Le Caignec C.

Circ Cardiovasc Genet. 2016 Feb;9(1):86-94. doi: 10.1161/CIRCGENETICS.115.001213. Epub 2015 Dec 7.

PMID:
26643481
11.

Advanced Characterization of DNA Molecules in rAAV Vector Preparations by Single-stranded Virus Next-generation Sequencing.

Lecomte E, Tournaire B, Cogné B, Dupont JB, Lindenbaum P, Martin-Fontaine M, Broucque F, Robin C, Hebben M, Merten OW, Blouin V, François A, Redon R, Moullier P, Léger A.

Mol Ther Nucleic Acids. 2015 Oct 27;4:e260. doi: 10.1038/mtna.2015.32.

12.

Short-lived recombinant adeno-associated virus transgene expression in dystrophic muscle is associated with oxidative damage to transgene mRNA.

Dupont JB, Tournaire B, Georger C, Marolleau B, Jeanson-Leh L, Ledevin M, Lindenbaum P, Lecomte E, Cogné B, Dubreil L, Larcher T, Gjata B, Van Wittenberghe L, Le Guiner C, Penaud-Budloo M, Snyder RO, Moullier P, Léger A.

Mol Ther Methods Clin Dev. 2015 Apr 8;2:15010. doi: 10.1038/mtm.2015.10. eCollection 2015.

13.

Testing the burden of rare variation in arrhythmia-susceptibility genes provides new insights into molecular diagnosis for Brugada syndrome.

Le Scouarnec S, Karakachoff M, Gourraud JB, Lindenbaum P, Bonnaud S, Portero V, Duboscq-Bidot L, Daumy X, Simonet F, Teusan R, Baron E, Violleau J, Persyn E, Bellanger L, Barc J, Chatel S, Martins R, Mabo P, Sacher F, Haïssaguerre M, Kyndt F, Schmitt S, Bézieau S, Le Marec H, Dina C, Schott JJ, Probst V, Redon R.

Hum Mol Genet. 2015 May 15;24(10):2757-63. doi: 10.1093/hmg/ddv036. Epub 2015 Feb 3.

PMID:
25650408
14.

mod_bio: Apache modules for Next-Generation sequencing data.

Lindenbaum P, Redon R.

Bioinformatics. 2015 Jan 1;31(1):112-3. doi: 10.1093/bioinformatics/btu547. Epub 2014 Sep 4.

PMID:
25192739
15.

NGS library preparation may generate artifactual integration sites of AAV vectors.

Cogné B, Snyder R, Lindenbaum P, Dupont JB, Redon R, Moullier P, Leger A.

Nat Med. 2014 Jun;20(6):577-8. doi: 10.1038/nm.3578. No abstract available.

PMID:
24901560
16.

Mutations in FAM111B cause hereditary fibrosing poikiloderma with tendon contracture, myopathy, and pulmonary fibrosis.

Mercier S, Küry S, Shaboodien G, Houniet DT, Khumalo NP, Bou-Hanna C, Bodak N, Cormier-Daire V, David A, Faivre L, Figarella-Branger D, Gherardi RK, Glen E, Hamel A, Laboisse C, Le Caignec C, Lindenbaum P, Magot A, Munnich A, Mussini JM, Pillay K, Rahman T, Redon R, Salort-Campana E, Santibanez-Koref M, Thauvin C, Barbarot S, Keavney B, Bézieau S, Mayosi BM.

Am J Hum Genet. 2013 Dec 5;93(6):1100-7. doi: 10.1016/j.ajhg.2013.10.013. Epub 2013 Nov 21.

17.

Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death.

Bezzina CR, Barc J, Mizusawa Y, Remme CA, Gourraud JB, Simonet F, Verkerk AO, Schwartz PJ, Crotti L, Dagradi F, Guicheney P, Fressart V, Leenhardt A, Antzelevitch C, Bartkowiak S, Borggrefe M, Schimpf R, Schulze-Bahr E, Zumhagen S, Behr ER, Bastiaenen R, Tfelt-Hansen J, Olesen MS, Kääb S, Beckmann BM, Weeke P, Watanabe H, Endo N, Minamino T, Horie M, Ohno S, Hasegawa K, Makita N, Nogami A, Shimizu W, Aiba T, Froguel P, Balkau B, Lantieri O, Torchio M, Wiese C, Weber D, Wolswinkel R, Coronel R, Boukens BJ, Bézieau S, Charpentier E, Chatel S, Despres A, Gros F, Kyndt F, Lecointe S, Lindenbaum P, Portero V, Violleau J, Gessler M, Tan HL, Roden DM, Christoffels VM, Le Marec H, Wilde AA, Probst V, Schott JJ, Dina C, Redon R.

Nat Genet. 2013 Sep;45(9):1044-9. doi: 10.1038/ng.2712. Epub 2013 Jul 21. Erratum in: Nat Genet. 2013 Nov;45(11):1409. Borggrefe, Martin [added]; Schimpf, Rainer [added].

18.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJ, Chapman B, Cock PJ, Eriksson T, Gordon PM, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T.

J Biomed Semantics. 2013 Feb 11;4(1):6. doi: 10.1186/2041-1480-4-6.

19.

Mass spectrometry-based identification of native cardiac Nav1.5 channel α subunit phosphorylation sites.

Marionneau C, Lichti CF, Lindenbaum P, Charpentier F, Nerbonne JM, Townsend RR, Mérot J.

J Proteome Res. 2012 Dec 7;11(12):5994-6007. doi: 10.1021/pr300702c. Epub 2012 Nov 9.

20.

BioStar: an online question & answer resource for the bioinformatics community.

Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I.

PLoS Comput Biol. 2011 Oct;7(10):e1002216. doi: 10.1371/journal.pcbi.1002216. Epub 2011 Oct 27. No abstract available.

21.

Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME.

Lindenbaum P, Le Scouarnec S, Portero V, Redon R.

Bioinformatics. 2011 Nov 15;27(22):3200-1. doi: 10.1093/bioinformatics/btr554. Epub 2011 Oct 7.

22.

Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis.

Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C.

Nat Genet. 2011 Mar 6;43(4):306-8. doi: 10.1038/ng.778.

PMID:
21378989
23.

The Gene Wiki: community intelligence applied to human gene annotation.

Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI.

Nucleic Acids Res. 2010 Jan;38(Database issue):D633-9. doi: 10.1093/nar/gkp760. Epub 2009 Sep 15.

24.

Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta.

Brooks P, Marcaillou C, Vanpeene M, Saraiva JP, Stockholm D, Francke S, Favis R, Cohen N, Rousseau F, Tores F, Lindenbaum P, Hager J, Philippi A.

BMC Genet. 2009 Mar 30;10:16. doi: 10.1186/1471-2156-10-16.

25.

Association of autism with polymorphisms in the paired-like homeodomain transcription factor 1 (PITX1) on chromosome 5q31: a candidate gene analysis.

Philippi A, Tores F, Carayol J, Rousseau F, Letexier M, Roschmann E, Lindenbaum P, Benajjou A, Fontaine K, Vazart C, Gesnouin P, Brooks P, Hager J.

BMC Med Genet. 2007 Dec 6;8:74.

26.

Haplotypes in the gene encoding protein kinase c-beta (PRKCB1) on chromosome 16 are associated with autism.

Philippi A, Roschmann E, Tores F, Lindenbaum P, Benajou A, Germain-Leclerc L, Marcaillou C, Fontaine K, Vanpeene M, Roy S, Maillard S, Decaulne V, Saraiva JP, Brooks P, Rousseau F, Hager J.

Mol Psychiatry. 2005 Oct;10(10):950-60.

PMID:
16027742
28.

CloneIt: finding cloning strategies, in-frame deletions and frameshifts.

Lindenbaum P.

Bioinformatics. 1998 Jun;14(5):465-6.

PMID:
9682060
29.

In vivo and in vitro phosphorylation of rotavirus NSP5 correlates with its localization in viroplasms.

Poncet D, Lindenbaum P, L'Haridon R, Cohen J.

J Virol. 1997 Jan;71(1):34-41.

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