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Items: 45

1.

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules.

Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V, Aury JM.

Sci Rep. 2019 Oct 17;9(1):14908. doi: 10.1038/s41598-019-51470-9.

2.

Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma.

Prouteau A, Chocteau F, de Brito C, Cadieu E, Primot A, Botherel N, Degorce F, Cornevin L, Lagadic MA, Cabillic F, de Fornel-Thibaud P, Devauchelle P, Derrien T, Abadie J, André C, Hédan B.

Vet Comp Oncol. 2019 Aug 28. doi: 10.1111/vco.12536. [Epub ahead of print]

PMID:
31461207
3.

Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas.

Hitte C, Le Béguec C, Cadieu E, Wucher V, Primot A, Prouteau A, Botherel N, Hédan B, Lindblad-Toh K, André C, Derrien T.

Genes (Basel). 2019 Jun 23;10(6). pii: E477. doi: 10.3390/genes10060477.

4.

Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs.

Hédan B, Cadieu E, Botherel N, Dufaure de Citres C, Letko A, Rimbault M, Drögemüller C, Jagannathan V, Derrien T, Schmutz S, Leeb T, André C.

Genes (Basel). 2019 May 21;10(5). pii: E386. doi: 10.3390/genes10050386.

5.

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment.

Jochum C, AdŽić N, Stiakakis E, Derrien TL, Luo D, Kahl G, Likos CN.

Nanoscale. 2019 Jan 23;11(4):1604-1617. doi: 10.1039/c8nr05814h.

PMID:
30311616
6.

Characterisation and functional predictions of canine long non-coding RNAs.

Le Béguec C, Wucher V, Lagoutte L, Cadieu E, Botherel N, Hédan B, De Brito C, Guillory AS, André C, Derrien T, Hitte C.

Sci Rep. 2018 Sep 7;8(1):13444. doi: 10.1038/s41598-018-31770-2.

7.

Femtosecond Laser-Induced Periodic Surface Structures on Fused Silica: The Impact of the Initial Substrate Temperature.

Gräf S, Kunz C, Engel S, Derrien TJ, Müller FA.

Materials (Basel). 2018 Aug 2;11(8). pii: E1340. doi: 10.3390/ma11081340.

8.

Assembly Dynamics of Plasmonic DNA-Capped Gold Nanoparticle Monolayers.

Derrien TL, Zhang M, Dorion PO, Smilgies DM, Luo D.

Langmuir. 2018 Dec 11;34(49):14711-14720. doi: 10.1021/acs.langmuir.8b00484. Epub 2018 Jun 7.

PMID:
29782172
9.

An exome sequencing based approach for genome-wide association studies in the dog.

Broeckx BJG, Derrien T, Mottier S, Wucher V, Cadieu E, Hédan B, Le Béguec C, Botherel N, Lindblad-Toh K, Saunders JH, Deforce D, André C, Peelman L, Hitte C.

Sci Rep. 2017 Nov 15;7(1):15680. doi: 10.1038/s41598-017-15947-9.

10.

Discovery of Human-Similar Gene Fusions in Canine Cancers.

Ulvé R, Rault M, Bahin M, Lagoutte L, Abadie J, De Brito C, Coindre JM, Botherel N, Rousseau A, Wucher V, Cadieu E, Thieblemont C, Hitte C, Cornevin L, Cabillic F, Bachelot L, Gilot D, Hennuy B, Guillaudeux T, Le Goff A, Derrien T, Hédan B, André C.

Cancer Res. 2017 Nov 1;77(21):5721-5727. doi: 10.1158/0008-5472.CAN-16-2691. Epub 2017 Sep 7.

11.

High-speed manufacturing of highly regular femtosecond laser-induced periodic surface structures: physical origin of regularity.

Gnilitskyi I, Derrien TJ, Levy Y, Bulgakova NM, Mocek T, Orazi L.

Sci Rep. 2017 Aug 16;7(1):8485. doi: 10.1038/s41598-017-08788-z.

12.

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Apr 4;18(1):63. doi: 10.1186/s13059-017-1202-6. No abstract available.

13.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3. Erratum in: Genome Biol. 2017 Apr 4;18(1):63.

14.

Long noncoding RNA repertoire in chicken liver and adipose tissue.

Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S.

Genet Sel Evol. 2017 Jan 10;49(1):6. doi: 10.1186/s12711-016-0275-0.

15.

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.

Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PAJ, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T.

Nucleic Acids Res. 2017 May 5;45(8):e57. doi: 10.1093/nar/gkw1306.

16.

A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies.

Plassais J, Lagoutte L, Correard S, Paradis M, Guaguère E, Hédan B, Pommier A, Botherel N, Cadiergues MC, Pilorge P, Silversides D, Bizot M, Samuels M, Arnan C, Johnson R, Hitte C, Salbert G, Méreau A, Quignon P, Derrien T, André C.

PLoS Genet. 2016 Dec 29;12(12):e1006482. doi: 10.1371/journal.pgen.1006482. eCollection 2016 Dec.

17.

Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Djebali S, Wucher V, Foissac S, Hitte C, Corre E, Derrien T.

Methods Mol Biol. 2017;1468:E1. No abstract available.

PMID:
27943167
18.

Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus.

Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, Monsoor M, Godfroy O, Lipinska A, Perrineau MM, Van De Peer Y, Hitte C, Corre E, Coelho SM, Cock JM.

New Phytol. 2017 Apr;214(1):219-232. doi: 10.1111/nph.14321. Epub 2016 Nov 21.

19.

Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

Djebali S, Wucher V, Foissac S, Hitte C, Corre E, Derrien T.

Methods Mol Biol. 2017;1468:201-19. doi: 10.1007/978-1-4939-4035-6_14. Erratum in: Methods Mol Biol. 2017;1468:E1.

PMID:
27662878
20.

DNA Microgels as a Platform for Cell-Free Protein Expression and Display.

Kahn JS, Ruiz RC, Sureka S, Peng S, Derrien TL, An D, Luo D.

Biomacromolecules. 2016 Jun 13;17(6):2019-26. doi: 10.1021/acs.biomac.6b00183. Epub 2016 May 17.

PMID:
27112709
21.

Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.

22.

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.

Broeckx BJ, Hitte C, Coopman F, Verhoeven GE, De Keulenaer S, De Meester E, Derrien T, Alfoldi J, Lindblad-Toh K, Bosmans T, Gielen I, Van Bree H, Van Ryssen B, Saunders JH, Van Nieuwerburgh F, Deforce D.

Sci Rep. 2015 Aug 3;5:12810. doi: 10.1038/srep12810.

23.

DNA materials: bridging nanotechnology and biotechnology.

Yang D, Hartman MR, Derrien TL, Hamada S, An D, Yancey KG, Cheng R, Ma M, Luo D.

Acc Chem Res. 2014 Jun 17;47(6):1902-11. doi: 10.1021/ar5001082. Epub 2014 Jun 2.

PMID:
24884022
24.

Rippled area formed by surface plasmon polaritons upon femtosecond laser double-pulse irradiation of silicon.

Derrien TJ, Krüger J, Itina TE, Höhm S, Rosenfeld A, Bonse J.

Opt Express. 2013 Dec 2;21(24):29643-55. doi: 10.1364/OE.21.029643.

PMID:
24514516
25.

Crystallization of DNA-capped gold nanoparticles in high-concentration, divalent salt environments.

Tan SJ, Kahn JS, Derrien TL, Campolongo MJ, Zhao M, Smilgies DM, Luo D.

Angew Chem Int Ed Engl. 2014 Jan 27;53(5):1316-9. doi: 10.1002/anie.201307113. Epub 2013 Dec 20.

PMID:
24459055
26.

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R.

Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.

27.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res. 2012 Sep;22(9):1760-74. doi: 10.1101/gr.135350.111.

28.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.

29.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

30.

The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter".

Derrien T, Guigó R, Johnson R.

Front Genet. 2012 Jan 9;2:107. doi: 10.3389/fgene.2011.00107. eCollection 2011.

31.

Fast computation and applications of genome mappability.

Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, Ribeca P.

PLoS One. 2012;7(1):e30377. doi: 10.1371/journal.pone.0030377. Epub 2012 Jan 19.

32.

Annotation of the domestic dog genome sequence: finding the missing genes.

Derrien T, Vaysse A, André C, Hitte C.

Mamm Genome. 2012 Feb;23(1-2):124-31. doi: 10.1007/s00335-011-9372-0. Epub 2011 Nov 11.

PMID:
22076420
33.

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

Vaysse A, Ratnakumar A, Derrien T, Axelsson E, Rosengren Pielberg G, Sigurdsson S, Fall T, Seppälä EH, Hansen MS, Lawley CT, Karlsson EK; LUPA Consortium, Bannasch D, Vilà C, Lohi H, Galibert F, Fredholm M, Häggström J, Hedhammar A, André C, Lindblad-Toh K, Hitte C, Webster MT.

PLoS Genet. 2011 Oct;7(10):e1002316. doi: 10.1371/journal.pgen.1002316. Epub 2011 Oct 13.

34.

The origins, evolution, and functional potential of alternative splicing in vertebrates.

Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J.

Mol Biol Evol. 2011 Oct;28(10):2949-59. doi: 10.1093/molbev/msr127. Epub 2011 May 6.

35.

[Long non-coding RNAs with enhancer-like function in human cells].

Derrien T, Guigó R.

Med Sci (Paris). 2011 Apr;27(4):359-61. doi: 10.1051/medsci/2011274009. Epub 2011 Apr 28. French. No abstract available.

36.

Long noncoding RNAs as enhancers of gene expression.

Ørom UA, Derrien T, Guigo R, Shiekhattar R.

Cold Spring Harb Symp Quant Biol. 2010;75:325-31. doi: 10.1101/sqb.2010.75.058. Epub 2011 Apr 18.

37.

Long noncoding RNAs with enhancer-like function in human cells.

Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

Cell. 2010 Oct 1;143(1):46-58. doi: 10.1016/j.cell.2010.09.001.

38.

Revisiting the missing protein-coding gene catalog of the domestic dog.

Derrien T, Thézé J, Vaysse A, André C, Ostrander EA, Galibert F, Hitte C.

BMC Genomics. 2009 Feb 4;10:62. doi: 10.1186/1471-2164-10-62.

39.
40.

A comparative genome approach to marker ordering.

Faraut T, de Givry S, Chabrier P, Derrien T, Galibert F, Hitte C, Schiex T.

Bioinformatics. 2007 Jan 15;23(2):e50-6.

PMID:
17237105
41.

AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.

Derrien T, André C, Galibert F, Hitte C.

Bioinformatics. 2007 Feb 15;23(4):498-9. Epub 2006 Dec 4.

PMID:
17145741
42.

Coat colour in dogs: identification of the merle locus in the Australian shepherd breed.

Hédan B, Corre S, Hitte C, Dréano S, Vilboux T, Derrien T, Denis B, Galibert F, Galibert MD, André C.

BMC Vet Res. 2006 Feb 27;2:9.

43.

Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping.

Hitte C, Madeoy J, Kirkness EF, Priat C, Lorentzen TD, Senger F, Thomas D, Derrien T, Ramirez C, Scott C, Evanno G, Pullar B, Cadieu E, Oza V, Lourgant K, Jaffe DB, Tacher S, Dréano S, Berkova N, André C, Deloukas P, Fraser C, Lindblad-Toh K, Ostrander EA, Galibert F.

Nat Rev Genet. 2005 Aug;6(8):643-8. doi: 10.1038/nrg1658. Review.

PMID:
16012527
44.

Building comparative maps using 1.5x sequence coverage: human chromosome 1p and the canine genome.

Guyon R, Kirkness EF, Lorentzen TD, Hitte C, Comstock KE, Quignon P, Derrien T, André C, Fraser CM, Galibert F, Ostrander EA.

Cold Spring Harb Symp Quant Biol. 2003;68:171-7. No abstract available.

PMID:
15338615
45.

CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome.

Hitte C, Derrien T, André C, Ostrander EA, Galibert F.

Bioinformatics. 2004 Dec 12;20(18):3665-7. Epub 2004 Jul 15.

PMID:
15256409

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