95 results on '"Derrien T"'
Search Results
2. Large area laser surface micro/nanopatterning by contact microsphere lens arrays
- Author
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Sedao, X., Derrien, T. J.-Y., Romer, G. R. B. E., Pathiraj, B., and Huis in ‘t Veld, A. J.
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- 2013
- Full Text
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3. In Situ Observations of the Growth Mode of Vacuum-Deposited α-Sexithiophene
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Derrien, T. L., primary, Lauritzen, A. E., additional, Kaienburg, P., additional, Hardigree, J. F. M., additional, Nicklin, C., additional, and Riede, M., additional
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- 2020
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4. A comparative genome approach to marker ordering
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Faraut, T., de Givry, S., Chabrier, P., Derrien, T., Galibert, F., Hitte, C., and Schiex, T.
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- 2007
5. Multiplicity of Laser-Excited Electromagnetic Modes and their Roles in LIPSS Formation on Thin Metallic Films
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Dostovalov, A. V., primary, Derrien, T. J.-Y., additional, Korolkov, V. P., additional, Babin, S. A., additional, and Bulgakova, N. M., additional
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- 2019
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6. Plasmonic formation mechanism of periodic 100-nm-structures upon femtosecond laser irradiation of silicon in water.
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Derrien, T. J.-Y., Koter, R., Krüuger, J., Höhm, S., Rosenfeld, A., and Bonse, J.
- Subjects
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SILICON , *FEMTOSECOND lasers , *PLASMONICS , *IRRADIATION , *WATER - Abstract
The formation of laser-induced periodic surface structures (LIPSS) upon irradiation of silicon by multiple (N=100) linearly polarized Ti:sapphire femtosecond laser pulses (duration τ=30 fs, center wavelength λ0~790 nm) is studied experimentally in air and water environment. The LIPSS surface morphologies are characterized by scanning electron microscopy and their spatial periods are quantified by two-dimensional Fourier analyses. It is demonstrated that the irradiation environment significantly influences the periodicity of the LIPSS. In air, so-called low-spatial frequency LIPSS (LSFL) were found with periods somewhat smaller than the laser wavelength (⋀LSFL~0.7×k0) and an orientation perpendicular to the laser polarization. In contrast, for laser processing in water a reduced ablation threshold and LIPSS with approximately five times smaller periods ⋀LIPSS~0.15×λ0 were observed in the same direction as in air. The results are discussed within the frame of recent LIPSS theories and complemented by a thin film based surface plasmon polariton model, which successfully describes the tremendously reduced LIPSS periods in water. [ABSTRACT FROM AUTHOR]
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- 2014
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7. The evidence of the role of surface plasmon polaritons in formation of femtosecond highly-regular laser-induced periodic structures on Cr films
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Dostovalov, A. V., primary, Derrien, T. J.-Y., additional, Přeučil, F., additional, Mocek, T., additional, Korolkov, V. P., additional, Babin, S. A., additional, and Bulgakova, N. M., additional
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- 2018
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8. In SituObservations of the Growth Mode of Vacuum-Deposited α-Sexithiophene
- Author
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Derrien, T. L., Lauritzen, A. E., Kaienburg, P., Hardigree, J. F. M., Nicklin, C., and Riede, M.
- Abstract
The real-time morphological evolution of vacuum-deposited α-sexithiophene (α-6T) on a weakly interacting (glass) substrate at ambient temperature is reported. In situgrazing-incidence small-angle X-ray scattering (GISAXS) enabled the observation of nanoscale aggregates, while in situgrazing-incidence wide-angle scattering (GIWAXS) allowed the study of the molecular-scale morphology. The in situGISAXS measurements revealed that the α-6T growth proceeds via a Stranski–Krastanov mode, whereby 2–4 complete monolayers are deposited, followed by subsequent layers formed via island growth. In situGIWAXS also showed the evolution of the polymorph composition during the thin-film growth. Initially, the disordered β-phase and the low-temperature (LT)-phase are deposited in nearly equal proportion until a thickness of 8 nm, whereby the LT-phase begins to dominate until a final α-6T thickness of 50 nm where the scattering intensity of the LT-phase is more than double that of the β-phase. The change in the polymorph composition coincided with an increase in the LT-phase d-spacing, indicating a lattice strain relief as the thin film moves from surface to bulk-mediated growth. The GISAXS findings were confirmed through direct imaging using ex situatomic force microscopy (AFM) at various thicknesses, revealing the existence of both initial the initial and intermediate monolayers and final island morphologies. The findings reveal the real-time morphological evolution of α-6T across both the molecular scale and the nanoscale and highlight the role of strain in polymorph growth. Due to the importance of the thin-film microstructure in device performance, it is expected that these results will aid in the development of structure–property relationships necessary to realize the full potential of organic electronics.
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- 2020
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- View/download PDF
9. Assessment of transcript reconstruction methods for RNA-seq
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Steijger, T., Abril, J.F., Engström, P.G., Kokocinski, F., Akerman, M., Alioto, T., Ambrosini, G., Antonarakis, S.E., Behr, J., Bertone, P., Bohnert, R., Bucher, P., Cloonan, N., Derrien, T., Djebali, S., Du, J., Dudoit, S., Gerstein, M., Gingeras, T.R., Gonzalez, D., Grimmond, S.M., Guigó, R., Habegger, L., Harrow, J., Hubbard, T.J., Iseli, C., Jean, G., Kahles, A., Lagarde, J., Leng, J., Lefebvre, G., Lewis, S., Mortazavi, A., Niermann, P., Rätsch, G., Reymond, A., Ribeca, P., Richard, H., Rougemont, J., Rozowsky, J., Sammeth, M., Sboner, A., Schulz, M.H., Searle, S.M., Solorzano, N.D., Solovyev, V., Stanke, M., Stevenson, B.J., Stockinger, H., Valsesia, A., Weese, D., White, S., Wold, B.J., Wu, J., Wu, T.D., Zeller, G., Zerbino, D., Zhang, M.Q., RGASP Consortium, Head of Medical Sequencing, Institut de Génétique et Développement de Rennes (IGDR), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Department of Statistics [Berkeley], University of California [Berkeley], University of California-University of California, Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Sanger Institute, Wellcome Trust, Laboratoire d'Informatique de Nantes Atlantique (LINA), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière (CRICM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Protéines de défense des réponses immune et inflammatoire : identification, régulation et rôles physiopathologiques, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Lausanne (UNIL), Centre Georges Chevrier. Ordre et désordre dans l'histoire des sociétés (UMR5605) (CGC), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), School of Life Sciences [Lausanne], Ecole Polytechnique Fédérale de Lausanne (EPFL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Department of Computer Science [Royal Holloway], Royal Holloway [University of London] (RHUL), University of California [Santa Cruz] (UCSC), University of California, Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Institut de Génétique et Développement de Rennes ( IGDR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -IFR140-Centre National de la Recherche Scientifique ( CNRS ), Centro de Regulación Genómica ( CRG ), Universitat Pompeu Fabra [Barcelona], Department of Statistics, Laboratoire d'Informatique de Nantes Atlantique ( LINA ), Mines Nantes ( Mines Nantes ) -Université de Nantes ( UN ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de Recherche de l'Institut du Cerveau et de la Moelle épinière ( CRICM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Université de Rouen Normandie ( UNIROUEN ), Normandie Université ( NU ) -Normandie Université ( NU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Université de Lausanne ( UNIL ), Centre Georges Chevrier. Ordre et désordre dans l'histoire des sociétés (UMR5605) ( CGC ), Centre National de la Recherche Scientifique ( CNRS ) -Université de Bourgogne ( UB ), Ecole Polytechnique Fédérale de Lausanne ( EPFL ), Swiss Institute of Bioinformatics ( SIB ), Swiss Institute of Bioinformatics, Centro Nacional de Análisi Genómico ( CNAG ), Royal Holloway [University of London] ( RHUL ), University of California [Santa Cruz] ( UCSC ), Swiss Institute of Bioinformatics - Lausanne ( SIB ), Stony Brook University [The State University of New York] ( SBU ), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne = University of Lausanne (UNIL), University of California [Santa Cruz] (UC Santa Cruz), and University of California (UC)
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Technology ,Messenger ,RNA, Messenger/metabolism ,RNA-Seq ,RGASP Consortium ,Sequence Analysis, RNA/methods ,Biochemistry ,Genome ,Medical and Health Sciences ,Exon ,0302 clinical medicine ,Transcription (biology) ,2.1 Biological and endogenous factors ,ddc:576.5 ,Aetiology ,[ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Genetics ,0303 health sciences ,Genome project ,Exons ,Biological Sciences ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Drosophila melanogaster ,RNA splicing ,Sequence Analysis ,Algorithms ,Biotechnology ,RNA Splicing ,Computational biology ,Biology ,Biologia computacional ,03 medical and health sciences ,[ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM] ,Empalmament (Genètica) ,Animals ,Humans ,Caenorhabditis elegans ,Molecular Biology ,030304 developmental biology ,GENCODE ,Gene Expression Profiling ,Intron ,Computational Biology ,Cell Biology ,Computational Biology/methods ,Introns ,RNA Splice Sites ,Software ,RNA ,[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] ,030217 neurology & neurosurgery ,Developmental Biology - Abstract
We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data. This work was supported by grants BIO2011-26205 and CSD2007-00050 from the Ministerio de Educación y Ciencia
- Published
- 2013
10. Thermal response of semiconductor tip during femtosecond laser-assisted field evaporation
- Author
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Derrien, T. J.-Y., Silaeva, E., Arnoldi, L., Vella, Angela, Deconihout, B., Itina, Tatiana, Laboratoire Hubert Curien [Saint Etienne] (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS), Groupe de physique des matériaux (GPM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), ANR, cines, Laboratoire Hubert Curien (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), and Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
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laser-assisted field evaporation ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,thermal model ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2012
11. Femtosecond laser-induced surface structures of silicon: thermal and optical study of formation mechanism
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Derrien, T. J.-Y., Torres, R., Sentis, Marc, Colombier, Jean-Philippe, Itina, Tatiana, Laboratoire Hubert Curien [Saint Etienne] (LHC), Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS)-Institut d'Optique Graduate School (IOGS), Laboratoire Lasers, Plasmas et Procédés photoniques (LP3), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), CINES, Laboratoire Hubert Curien (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
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[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,ComputingMilieux_MISCELLANEOUS - Abstract
International audience
- Published
- 2012
12. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping
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Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Rosengren Pielberg, G., Sigurdsson, S., Fall, T., Seppälä, E.H., Hansen, M.S., Lawley, C.T., Karlsson, E.K., Bannasch, D.L., Vilà, C., Lohi, H., Galibert, F., Fredholm, M., Häggström, O., Hedhammar, A., André, C., Lindblad-Toh, K., Hitte, C., van Steenbeek, F.G., Fieten, H., Leegwater, P.A.J., LUPA Consortium, x, Webster, M.T., Advances in Veterinary Medicine, Tissue Repair, and Geneeskunde van gezelschapsdieren
- Abstract
The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.
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- 2011
13. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping
- Author
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Advances in Veterinary Medicine, Tissue Repair, Geneeskunde van gezelschapsdieren, Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Rosengren Pielberg, G., Sigurdsson, S., Fall, T., Seppälä, E.H., Hansen, M.S., Lawley, C.T., Karlsson, E.K., Bannasch, D.L., Vilà, C., Lohi, H., Galibert, F., Fredholm, M., Häggström, O., Hedhammar, A., André, C., Lindblad-Toh, K., Hitte, C., van Steenbeek, F.G., Fieten, H., Leegwater, P.A.J., LUPA Consortium, x, Webster, M.T., Advances in Veterinary Medicine, Tissue Repair, Geneeskunde van gezelschapsdieren, Vaysse, A., Ratnakumar, A., Derrien, T., Axelsson, E., Rosengren Pielberg, G., Sigurdsson, S., Fall, T., Seppälä, E.H., Hansen, M.S., Lawley, C.T., Karlsson, E.K., Bannasch, D.L., Vilà, C., Lohi, H., Galibert, F., Fredholm, M., Häggström, O., Hedhammar, A., André, C., Lindblad-Toh, K., Hitte, C., van Steenbeek, F.G., Fieten, H., Leegwater, P.A.J., LUPA Consortium, x, and Webster, M.T.
- Published
- 2011
14. The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates
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Mudge, J. M., primary, Frankish, A., additional, Fernandez-Banet, J., additional, Alioto, T., additional, Derrien, T., additional, Howald, C., additional, Reymond, A., additional, Guigo, R., additional, Hubbard, T., additional, and Harrow, J., additional
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- 2011
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15. Study On Laser-Induced Periodic Structures And Photovoltaic Application
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Torres, R., primary, Itina, T. E., additional, Vervisch, V., additional, Halbwax, M., additional, Derrien, T., additional, Sarnet, T., additional, Sentis, M., additional, Ferreira, J., additional, Torregrosa, F., additional, Roux, L., additional, and Phipps, Claude, additional
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- 2010
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16. The GENCODE human gene set
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Searle, S, primary, Frankish, A, additional, Bignell, A, additional, Aken, B, additional, Derrien, T, additional, Diekhans, M, additional, Harte, R, additional, Howald, C, additional, Kokocinski, F, additional, Lin, M, additional, Tress, M, additional, Van Baren, M, additional, Barnes, I, additional, Hunt, T, additional, Carvalho-Silva, D, additional, Davidson, C, additional, Donaldson, S, additional, Gilbert, J, additional, Kay, M, additional, Lloyd, D, additional, Loveland, J, additional, Mudge, J, additional, Snow, C, additional, Vamathevan, J, additional, Wilming, L, additional, Brent, M, additional, Gerstein, M, additional, Guigó, R, additional, Kellis, M, additional, Reymond, A, additional, Zadissa, A, additional, Valencia, A, additional, Harrow, J, additional, and Hubbard, T, additional
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- 2010
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17. Long Noncoding RNAs as Enhancers of Gene Expression
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Orom, U. A., primary, Derrien, T., additional, Guigo, R., additional, and Shiekhattar, R., additional
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- 2010
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18. Evaluation of luminosity reduction in the ilc head-on scheme from parasitic collisions
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Brossard, J., primary, Bambade, P., additional, Derrien, T., additional, Napoly, O., additional, Payet, J., additional, Alabau, M.C., additional, and Angal-Kalinin, D., additional
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- 2007
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19. Building Comparative Maps Using 1.5x Sequence Coverage: Human Chromosome 1p and the Canine Genome
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GUYON, R., primary, KIRKNESS, E.F., additional, LORENTZEN, T.D., additional, HITTE, C., additional, COMSTOCK, K.E., additional, QUIGNON, P., additional, DERRIEN, T., additional, ANDRE, C., additional, FRASER, C.M., additional, GALIBERT, F., additional, and OSTRANDER, E.A., additional
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- 2003
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20. The GENCODE human gene set
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Searle S, Adam Frankish, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, Davidson C, Donaldson S, Gilbert J, Kay M, and Lloyd D
21. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
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Tc, Mathers, Chen Y, Kaithakottil G, Legeai F, Sam Mugford, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Gj, Kettles, Kowitwanich K, Lavenier D, and Lenzi P
22. Building comparative maps using 1.5x sequence coverage: Human chromosome 1p and the canine genome
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Guyon, R., Kirkness, E. F., Lorentzen, T. D., Hitte, C., Comstock, K. E., Quignon, P., Derrien, T., André, C., Claire Fraser, Galibert, F., and Ostrander, E. A.
23. The GENCODE human gene set
- Author
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Searle S, Frankish A, alexandra Bignell, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, and Hubbard T
24. Periodic Surface Functional Group Density on Graphene Induced by Pulsed Laser Patterning of SiO2/Si Substrate
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Mirza, I., Drogowska, K. A., Rodriguez, A., Kovaricek, P., Sladek, J., Derrien, T. J. Y., Gedvilas, M., Gediminas Raciukaitis, Bulgakova, N., and Kalbac, M.
25. Application of a two-temperature model for the investigation of the periodic structure formation on Si surface in femtosecond laser interactions
- Author
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Derrien, T. Jy, Sarnet, T., Sentis, M., Tatiana ITINA, Laboratoire Lasers, Plasmas et Procédés photoniques (LP3), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Hubert Curien (LHC), Institut d'Optique Graduate School (IOGS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), ANR-07-BLAN-0301,Nanomorphing,Towards dielectric material nano-morphing with ultra-fast lasers(2007), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Laboratoire Hubert Curien [Saint Etienne] (LHC), and Institut d'Optique Graduate School (IOGS)-Université Jean Monnet [Saint-Étienne] (UJM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Plasma Physics (physics.plasm-ph) ,Femtosecond laser ,Condensed Matter - Materials Science ,LIPSS ,Black silicon ,Materials Science (cond-mat.mtrl-sci) ,FOS: Physical sciences ,Ripple ,[SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering ,Physics - Plasma Physics ,Optics (physics.optics) ,Physics - Optics - Abstract
International audience; We consider the case of surface irradiation by a small number of femtosecond laser shots leading to the formation of surface ripples. To explain this effect, we propose a numerical model that accounts for the following processes: (i) interference of the laser irradiation with an electromagnetic surface wave propagating on a silicon sample; (ii) free carrier formation and laser energy absorption; (iii) energy relaxation and electron-phonon coupling. We perform numerical calculations taking into account the interference of a surface wave with laser; and present the obtained simulation results in order to explain formation mechanisms of the experimentally observed patterns
26. Revisiting the missing protein-coding gene catalog of the domestic dog
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Galibert Francis, Ostrander Elaine A, André Catherine, Vaysse Amaury, Thézé Julien, Derrien Thomas, and Hitte Christophe
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog. Results Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (dN/dS), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates. Conclusion This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.
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- 2009
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27. Nanofabrication with pulsed lasers.
- Author
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Kabashin, A.V., Grojo, D., Sarnet, T., Delaporte, P., Blandin, P., Charmasson, L., Torres, R., Derrien, T., and Sentis, M.
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- 2011
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28. Coat colour in dogs: identification of the Merle locus in the Australian shepherd breed
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Denis Bernard, Galibert Francis, Derrien Thomas, Vilboux Thierry, Dréano Stéphane, Hitte Christophe, Corre Sébastien, Hédan Benoit, Galibert Marie-Dominique, and André Catherine
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Veterinary medicine ,SF600-1100 - Abstract
Abstract Background Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. Results Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction θ = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. Conclusion This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways.
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- 2006
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29. An integrated encyclopedia of DNA elements in the human genome
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Robert Altshuler, Laura Elnitski, Michael Anaya, Alec Victorsen, Deborah Winter, Javier Herrero, Katherine Varley, Andrea Sboner, Oscar Junhong Luo, Marco Mariotti, Cristina Sisu, Mike Kay, Timothy Dreszer, Jane Loveland, Alexandra Bignell, Ewan Birney, Tim @timjph Hubbard, Kuljeet Sandhu, Eric Haugen, Chris Gunter, Alexej Abyzov, Lucas Ward, Georgi Marinov, Michael Pazin, Thomas Gingeras, Alexander Dobin, Kimberly Foss, Xianjun Dong, Benoit Miotto, Piotr Mieczkowski, Cedric Notredame, Andrew Berry, Shawn Gillespie, Axel Visel, Shawn Levy, Richard Sandstrom, Jose M Gonzalez, Melissa Fullwood, Timo Lassmann, Michael Tress, Julien Lagarde, Kevin Yip, Leslie Adams, Sylvain Foissac, Bronwen Aken, Piero Carninci, Suganthi Balasubramanian, Andrea Tanzer, Sarah Djebali, Michael Hoffman, Gloria Despacio-Reyes, Peter Park, Felix Kokocinski, Katherine Fisher-Aylor, Juan M Vaquerizas, Peggy Farnham, Patrick Collins, Amonida Zadissa, Pedro Ferreira, Philippe Batut, Michael Snyder, Electra Tapanari, Adam Frankish, Paul Flicek, AMARTYA SANYAL, Tyler Alioto, Giovanni Bussotti, Laurence Meyer, Jingyi Jessica Li, Matthew Blow, Tristan FRUM, Roger Alexander, Rory Johnson, Charles Steward, Meizhen Zheng, Margus Lukk, Ross Hardison, Claire Davidson, Gary Saunders, Alan Boyle, Luiz Penalva, Rajinder Kaul, Lazaro Centanin, Florencia Pauli Behn, Thomas Derrien, Nathan Sheffield, Toby Hunt, Eric Nguyen, Jeff Vierstra, Konrad Karczewski, Kimberly Bell, Yanbao Yu, Hagen U Tilgner, James Taylor, Balázs Bánfai, Catherine Snow, Benjamin Vernot, Stephan Kirchmaier, Michael Sammeth, Steven Wilder, Angelika Merkel, Joanna Mieczkowska, Guoliang Li, Wei Lin, Jennifer Harrow, Thomas Oliver Auer, Daniel Barrell, Eddie Park, Alvis Brazma, Hazuki Takahashi, Nathan Johnson, Daniel Sobral, Terry Furey, Alexandre Reymond, Jonathan Mudge, Anshul Kundaje, Jose Rodriguez, Akshay Bhinge, James Gilbert, Jakub Karczewski, Venkat Malladi, Troy Whitfield, Orion Buske, Ian Dunham, Jennifer Moran, Joachim Wittbrodt, Charles B. Epstein, Laurens Wilming, Jason Gertz, Joshua Akey, Joel Rozowsky, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), National Human Genome Research Institute (NHGRI), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Antonarakis, Stylianos, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Altshuler, Robert Charles, Ernst, Jason, Kellis, Manolis, Kheradpour, Pouya, Ward, Lucas D., Eaton, Matthew Lucas, Hendrix, David A., Jungreis, Irwin, Lin, Michael F., Washietl, Stefan, Lists of participants and their affiliations appear at the end of the paper and in the 'Collaboration/Projet' field., The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein), U01HG004695 (E. Birney), U54HG004563 (G. E. Crawford), U54HG004557 (T. R. Gingeras), U54HG004555 (T. J. Hubbard), U41HG004568 (W. J. Kent), U54HG004576 (R. M. Myers), U54HG004558 (M. Snyder), U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker), RC2HG005591 and R01HG003700 (M. C. Giddings), R01HG004456-03 (Y. Ruan), U01HG004571 (S. A. Tenenbaum), U01HG004561 (Z. Weng), RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591, R01HG003541,U01HG004561,RC2HG005679andR01HG003988(L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323, E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California., Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F, Epstein CB, Frietze S, Harrow J, Kaul R, Khatun J, Lajoie BR, Landt SG, Lee BK, Pauli F, Rosenbloom KR, Sabo P, Safi A, Sanyal A, Shoresh N, Simon JM, Song L, Trinklein ND, Altshuler RC, Birney E, Brown JB, Cheng C, Djebali S, Dong X, Dunham I, Ernst J, Furey TS, Gerstein M, Giardine B, Greven M, Hardison RC, Harris RS, Herrero J, Hoffman MM, Iyer S, Kellis M, Khatun J, Kheradpour P, Kundaje A, Lassmann T, Li Q, Lin X, Marinov GK, Merkel A, Mortazavi A, Parker SC, Reddy TE, Rozowsky J, Schlesinger F, Thurman RE, Wang J, Ward LD, Whitfield TW, Wilder SP, Wu W, Xi HS, Yip KY, Zhuang J, Pazin MJ, Lowdon RF, Dillon LA, Adams LB, Kelly CJ, Zhang J, Wexler JR, Green ED, Good PJ, Feingold EA, Bernstein BE, Birney E, Crawford GE, Dekker J, Elnitski L, Farnham PJ, Gerstein M, Giddings MC, Gingeras TR, Green ED, Guigó R, Hardison RC, Hubbard TJ, Kellis M, Kent W, Lieb JD, Margulies EH, Myers RM, Snyder M, Stamatoyannopoulos JA, Tenenbaum SA, Weng Z, White KP, Wold B, Khatun J, Yu Y, Wrobel J, Risk BA, Gunawardena HP, Kuiper HC, Maier CW, Xie L, Chen X, Giddings MC, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Kheradpour P, Mikkelsen TS, Gillespie S, Goren A, Ram O, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Eaton ML, Kellis M, 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, Batut P, Bell I, Bell K, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena HP, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Li G, Luo OJ, Park E, Preall JB, Presaud K, Ribeca P, Risk BA, Robyr D, Ruan X, Sammeth M, Sandhu KS, Schaeffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Hayashizaki Y, Harrow J, Gerstein M, Hubbard TJ, Reymond A, Antonarakis SE, Hannon GJ, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR, Rosenbloom KR, Sloan CA, Learned K, Malladi VS, Wong MC, Barber GP, Cline MS, Dreszer TR, Heitner SG, Karolchik D, Kent W, Kirkup VM, Meyer LR, Long JC, Maddren M, Raney BJ, Furey TS, Song L, Grasfeder LL, Giresi PG, Lee BK, Battenhouse A, Sheffield NC, Simon JM, Showers KA, Safi A, London D, Bhinge AA, Shestak C, Schaner MR, Kim SK, Zhang ZZ, Mieczkowski PA, Mieczkowska JO, Liu Z, McDaniell RM, Ni Y, Rashid NU, Kim MJ, Adar S, Zhang Z, Wang T, Winter D, Keefe D, Birney E, Iyer VR, Lieb JD, Crawford GE, Li G, Sandhu KS, Zheng M, Wang P, Luo OJ, Shahab A, Fullwood MJ, Ruan X, Ruan Y, Myers RM, Pauli F, Williams BA, Gertz J, Marinov GK, Reddy TE, Vielmetter J, Partridge E, Trout D, Varley KE, Gasper C, Bansal A, Pepke S, Jain P, Amrhein H, Bowling KM, Anaya M, Cross MK, King B, Muratet MA, Antoshechkin I, Newberry KM, McCue K, Nesmith AS, Fisher-Aylor KI, Pusey B, DeSalvo G, Parker SL, Balasubramanian S, Davis NS, Meadows SK, Eggleston T, Gunter C, Newberry J, Levy SE, Absher DM, Mortazavi A, Wong WH, Wold B, Blow MJ, Visel A, Pennachio LA, Elnitski L, Margulies EH, Parker SC, Petrykowska HM, Abyzov A, Aken B, Barrell D, Barson G, Berry A, Bignell A, Boychenko V, Bussotti G, Chrast J, Davidson C, Derrien T, Despacio-Reyes G, Diekhans M, Ezkurdia I, Frankish A, Gilbert J, Gonzalez JM, Griffiths E, Harte R, Hendrix DA, Howald C, Hunt T, Jungreis I, Kay M, Khurana E, Kokocinski F, Leng J, Lin MF, Loveland J, Lu Z, Manthravadi D, Mariotti M, Mudge J, Mukherjee G, Notredame C, Pei B, Rodriguez JM, Saunders G, Sboner A, Searle S, Sisu C, Snow C, Steward C, Tanzer A, Tapanari E, Tress ML, van Baren MJ, Walters N, Washietl S, Wilming L, Zadissa A, Zhang Z, Brent M, Haussler D, Kellis M, Valencia A, Gerstein M, Reymond A, Guigó R, Harrow J, Hubbard TJ, Landt SG, Frietze S, Abyzov A, Addleman N, Alexander RP, Auerbach RK, Balasubramanian S, Bettinger K, Bhardwaj N, Boyle AP, Cao AR, Cayting P, Charos A, Cheng Y, Cheng C, Eastman C, Euskirchen G, Fleming JD, Grubert F, Habegger L, Hariharan M, Harmanci A, Iyengar S, Jin VX, Karczewski KJ, Kasowski M, Lacroute P, Lam H, Lamarre-Vincent N, Leng J, Lian J, Lindahl-Allen M, Min R, Miotto B, Monahan H, Moqtaderi Z, Mu XJ, O'Geen H, Ouyang Z, Patacsil D, Pei B, Raha D, Ramirez L, Reed B, Rozowsky J, Sboner A, Shi M, Sisu C, Slifer T, Witt H, Wu L, Xu X, Yan KK, Yang X, Yip KY, Zhang Z, Struhl K, Weissman SM, Gerstein M, Farnham PJ, Snyder M, Tenenbaum SA, Penalva LO, Doyle F, Karmakar S, Landt SG, Bhanvadia RR, Choudhury A, Domanus M, Ma L, Moran J, Patacsil D, Slifer T, Victorsen A, Yang X, Snyder M, Auer T, Centanin L, Eichenlaub M, Gruhl F, Heermann S, Hoeckendorf B, Inoue D, Kellner T, Kirchmaier S, Mueller C, Reinhardt R, Schertel L, Schneider S, Sinn R, Wittbrodt B, Wittbrodt J, Weng Z, Whitfield TW, Wang J, Collins PJ, Aldred SF, Trinklein ND, Partridge EC, Myers RM, Dekker J, Jain G, Lajoie BR, Sanyal A, Balasundaram G, Bates DL, Byron R, Canfield TK, Diegel MJ, Dunn D, Ebersol AK, Frum T, Garg K, Gist E, Hansen R, Boatman L, Haugen E, Humbert R, Jain G, Johnson AK, Johnson EM, Kutyavin TV, Lajoie BR, Lee K, Lotakis D, Maurano MT, Neph SJ, Neri FV, Nguyen ED, Qu H, Reynolds AP, Roach V, Rynes E, Sabo P, Sanchez ME, Sandstrom RS, Sanyal A, Shafer AO, Stergachis AB, Thomas S, Thurman RE, Vernot B, Vierstra J, Vong S, Wang H, Weaver MA, Yan Y, Zhang M, Akey JM, Bender M, Dorschner MO, Groudine M, MacCoss MJ, Navas P, Stamatoyannopoulos G, Kaul R, Dekker J, Stamatoyannopoulos JA, Dunham I, Beal K, Brazma A, Flicek P, Herrero J, Johnson N, Keefe D, Lukk M, Luscombe NM, Sobral D, Vaquerizas JM, Wilder SP, Batzoglou S, Sidow A, Hussami N, Kyriazopoulou-Panagiotopoulou S, Libbrecht MW, Schaub MA, Kundaje A, Hardison RC, Miller W, Giardine B, Harris RS, Wu W, Bickel PJ, Banfai B, Boley NP, Brown JB, Huang H, Li Q, Li JJ, Noble WS, Bilmes JA, Buske OJ, Hoffman MM, Sahu AD, Kharchenko PV, Park PJ, Baker D, Taylor J, Weng Z, Iyer S, Dong X, Greven M, Lin X, Wang J, Xi HS, Zhuang J, Gerstein M, Alexander RP, Balasubramanian S, Cheng C, Harmanci A, Lochovsky L, Min R, Mu XJ, Rozowsky J, Yan KK, Yip KY, Birney E., and Miotto, Benoit
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Encyclopedias as Topic ,[SDV]Life Sciences [q-bio] ,DNA Footprinting ,Genoma humà ,Binding Sites/genetics ,Histones/chemistry/metabolism ,0302 clinical medicine ,Exons/genetics ,ddc:576.5 ,0303 health sciences ,Multidisciplinary ,[SDV.MHEP] Life Sciences [q-bio]/Human health and pathology ,[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,DNA-Binding Proteins/metabolism ,region ,Chemistry ,Genetic Predisposition to Disease/genetics ,Genomics ,Polymorphism, Single Nucleotide/genetics ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,Neoplasms/genetics ,Chromatin ,Cell biology ,in vivo ,Genetic Variation/genetics ,030220 oncology & carcinogenesis ,Deoxyribonuclease I/metabolism ,Proteins/genetics ,transcription factor-binding ,chromosome conformation capture ,DNA Methylation/genetics ,Chromosomes, Human/genetics/metabolism ,Chromatin Immunoprecipitation ,Mammals/genetics ,DNA/genetics ,determinant ,Article ,03 medical and health sciences ,map ,Animals ,Humans ,Transcription Factors/metabolism ,Alleles ,mouse ,030304 developmental biology ,Transcription, Genetic/genetics ,Chromatin/genetics/metabolism ,Sequence Analysis, RNA ,human cell ,Molecular Sequence Annotation ,Regulatory Sequences, Nucleic Acid/genetics ,Promoter Regions, Genetic/genetics ,DNA binding site ,Genòmica ,Genome, Human/genetics ,chromatin ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology ,Genètica ,Genome-Wide Association Study - Abstract
The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. The Consortium is funded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568 /n(W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder);/nU54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan); U01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and/nReinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591,R01HG003541, U01HG004561, RC2HG005679andR01HG003988(L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research/nProgram of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341). Research in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute, Department of Energy Contract DE-AC02-05CH11231, University of California.
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- 2012
30. Building Comparative Maps Using 1.5x Sequence Coverage: Human Chromosome lp and the Canine Genome.
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Guyon, R., Kirkness, E. F., Lorentzen, T. D., Hitte, C., Comstock, K. E., Quignon, P., Derrien, T., André, C., Fraser, C. M., Galibert, F., and Ostrander, E. A.
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GENE mapping , *ANIMAL genome mapping , *HUMAN gene mapping , *EFFECT of radiation on human chromosomes , *GENOMICS , *RADIOGENETICS - Abstract
Describes a study on genome structure and evolutionary relationships between dogs and humans. Use of the 1x sequence to identify canine orthologs in the study; Number of genes from human chromosome 1p arm used in the study; Information on the radiation hybrid mapping implemented in the study.
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- 2003
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31. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
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Zhi Lu, Giltae Song, Troy W. Whitfield, Vishwanath R. Iyer, Teresa Vales, Angelika Merkel, Max Libbrecht, David Haussler, Ting Wang, Kristen Lee, Lingyun Song, Richard M. Myers, Alfonso Valencia, Rachel A. Harte, Xiaoqin Xu, Lucas D. Ward, Hazuki Takahashi, Nathan C. Sheffield, Thomas Derrien, Georgi K. Marinov, Eric D. Nguyen, Bernard B. Suh, Brian J. Raney, Richard Sandstrom, Thomas D. Tullius, Benoit Miotto, Alexander Dobin, Youhan Xu, Lukas Habegger, Ian Dunham, Brian A. Risk, Paul G. Giresi, Morgan C. Giddings, Hualin Xi, Anshul Kundaje, Robert S. Harris, Devin Absher, Peter J. Bickel, Yanbao Yu, Browen Aken, Colin Kingswood, Bryan R. Lajoie, Peter J. Good, Katrina Learned, Laura Elnitski, Shirley Pepke, Brandon King, Piero Carninci, Xinqiong Yang, Ghia Euskirchen, Kathryn Beal, Christelle Borel, Michael Muratet, Robert L. Grossman, David G. Knowles, Zarmik Moqtaderi, Veronika Boychenko, Steven P. Wilder, Michael L. Tress, Florencia Pauli, Alan P. Boyle, Andrea Tanzer, Philipp Kapranov, Serafim Batzoglou, Audra K. Johnson, Jun Neri, Nitin Bhardwaj, Elise A. Feingold, Venkat S. Malladi, Michael M. Hoffman, William Stafford Noble, Andrea Sboner, Mark Gerstein, Stephanie L. Parker, Jacqueline Dumais, Felix Schlesinger, Deborah R. Winter, Randall H. Brown, Thanh Truong, Rebecca F. Lowdon, Paolo Ribeca, Brooke Rhead, Peggy J. Farnham, Krista Thibeault, Terrence S. Furey, Donna Karolchik, Alec Victorsen, Xiaoan Ruan, Rehab F. Abdelhamid, Amy S. Nesmith, Jing Wang, Nicholas M. Luscombe, Alina R. Cao, Diane Trout, Teri Slifer, Peter E. Newburger, Cricket A. Sloan, Dimitra Lotakis, Stephen M. J. Searle, Ali Mortazavi, Alexandra Bignell, Alex Reynolds, Orion J. Buske, Chris Zaleski, Theresa K. Canfield, Ian Bell, Jin Lian, Vanessa K. Swing, Katalin Toth Fejes, Catherine Ucla, Robert E. Thurman, Jacqueline Chrast, Wei Lin, Tim Hubbard, Gary Saunders, Minyi Shi, Vihra Sotirova, Sherman M. Weissman, Jason D. Lieb, Richard Humbert, Kevin M. Bowling, Assaf Gordon, Tarjei S. Mikkelsen, Jing Leng, Thomas R. Gingeras, Fabian Grubert, Nader Jameel, Jost Vielmetter, Hannah Monahan, Preti Jain, Lindsay L. Waite, Tony Shafer, Joel Rozowsky, Michael Coyne, Brian Reed, M. Kay, Harsha P. Gunawardena, Ross C. Hardison, Gavin Sherlock, Alexandra Charos, Joseph D. Fleming, Ann S. Zweig, Jason Gertz, Rajinder Kaul, Xianjun Dong, Alexandre Reymond, Carrie A. Davis, Haiyan Huang, Chao Cheng, Marco Mariotti, Phil Lacroute, Jason A. Dilocker, Kenneth McCue, R. Robilotto, Stylianos E. Antonarakis, Sridar V. Chittur, Justin Jee, Barbara J. Wold, Sudipto K. Chakrabortty, Erica Dumais, Amartya Sanyal, Nathan Boley, Tianyuan Wang, Julien Lagarde, Anthony Kirilusha, Jonathan B. Preall, Kevin Roberts, Erika Giste, Hugo Y. K. Lam, Alvis Brazma, Gregory J. Hannon, Eric Rynes, Philippe Batut, Kevin Struhl, Margus Lukk, Manching Ku, Suganthi Balasubramanian, Sonali Jha, Jorg Drenkow, W. James Kent, Michael Snyder, Jie Wang, Anna Battenhouse, Charles B. Epstein, Rami Rauch, Christopher Shestak, John A. Stamatoyannopoulos, Gaurab Mukherjee, Cédric Howald, Tanya Kutyavin, Huaien Wang, Scott A. Tenenbaum, Wan Ting Poh, Kate R. Rosenbloom, Manolis Kellis, Pauline A. Fujita, Linfeng Wu, Anita Bansal, Molly Weaver, Linda L. Grasfeder, Peter J. Sabo, Qiang Li, Melissa S. Cline, Robert M. Kuhn, Darin London, Seth Frietze, Atif Shahab, Shane Neph, Damian Keefe, James B. Brown, Mark Diekhans, Webb Miller, Katherine Aylor Fisher, Jiang Du, Hadar H. Sheffer, Sarah Djebali, Frank Doyle, Nathan Lamarre-Vincent, Chia-Lin Wei, Laura A.L. Dillon, Jennifer Harrow, Robert C. Altshuler, Tyler Alioto, Raymond K. Auerbach, Adam Frankish, Rebekka O. Sprouse, Patrick J. Collins, E. Christopher Partridge, Zheng Liu, Yoichiro Shibata, Elliott H. Margulies, Abigail K. Ebersol, Kimberly A. Showers, Eric D. Green, Krishna M. Roskin, Job Dekker, Barbara N. Pusey, Ekta Khurana, Gilberto DeSalvo, Yijun Ruan, Hao Wang, Jainab Khatun, Henriette O'Geen, Alexej Abyzov, Brian Williams, Ryan M. McDaniell, Maya Kasowski, Manoj Hariharan, Felix Kokocinski, Gloria Despacio-Reyes, Zhancheng Zhang, Subhradip Karmakar, Ewan Birney, Koon-Kiu Yan, Xian Chen, Shinny Vong, Daniel Sobral, Nick Bild, Seul K.C. Kim, Timo Lassmann, Li Wang, Minerva E. Sanchez, Vaughan Roach, Theodore Gibson, Stephen C. J. Parker, Michael F. Lin, Patrick A. Navas, Laurence R. Meyer, Luiz O. F. Penalva, Bradley E. Bernstein, Kevin P. White, Emilie Aït Yahya Graison, Juan M. Vaquerizas, Sushma Iyengar, Kimberly M. Newberry, Akshay Bhinge, Xiaolan Zhang, Kim Bell, Yoshihide Hayashizaki, Lucas Lochovsky, Noam Shoresh, Hagen Tilgner, Philip Cayting, Dorrelyn Patacsil, Timothy E. Reddy, Eric Haugen, Katherine E. Varley, M. van Baren, Nathan D. Trinklein, Bum Kyu Lee, Tristan Frum, Marianne Lindahl-Allen, Timothy Durham, Roderic Guigó, Christopher W. Maier, Micha Sammeth, Debasish Raha, Timothy R. Dreszer, Benedict Paten, Robbyn Issner, Michael R. Brent, Kevin Y. Yip, Kim Blahnik, Jason Ernst, Zhiping Weng, Henry Amrhein, Arend Sidow, Javier Herrero, Hui Gao, Stephen G. Landt, Pouya Kheradpour, Galt P. Barber, Gregory E. Crawford, Toby Hunt, HudsonAlpha Institute for Biotechnology [Huntsville, AL], ENCODE Project Consortium : Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE, Bernstein BE, Epstein CB, Shoresh N, Ernst J, Mikkelsen TS, Kheradpour P, Zhang X, Wang L, Issner R, Coyne MJ, Durham T, Ku M, Truong T, Ward LD, Altshuler RC, Lin MF, Kellis M, Gingeras TR, Davis CA, Kapranov P, Dobin A, Zaleski C, Schlesinger F, Batut P, Chakrabortty S, Jha S, Lin W, Drenkow J, Wang H, Bell K, Gao H, Bell I, Dumais E, Dumais J, Antonarakis SE, Ucla C, Borel C, Guigo R, Djebali S, Lagarde J, Kingswood C, Ribeca P, Sammeth M, Alioto T, Merkel A, Tilgner H, Carninci P, Hayashizaki Y, Lassmann T, Takahashi H, Abdelhamid RF, Hannon G, Fejes-Toth K, Preall J, Gordon A, Sotirova V, Reymond A, Howald C, Graison E, Chrast J, Ruan Y, Ruan X, Shahab A, Ting Poh W, Wei CL, Crawford GE, Furey TS, Boyle AP, Sheffield NC, Song L, Shibata Y, Vales T, Winter D, Zhang Z, London D, Wang T, Birney E, Keefe D, Iyer VR, Lee BK, McDaniell RM, Liu Z, Battenhouse A, Bhinge AA, Lieb JD, Grasfeder LL, Showers KA, Giresi PG, Kim SK, Shestak C, Myers RM, Pauli F, Reddy TE, Gertz J, Partridge EC, Jain P, Sprouse RO, Bansal A, Pusey B, Muratet MA, Varley KE, Bowling KM, Newberry KM, Nesmith AS, Dilocker JA, Parker SL, Waite LL, Thibeault K, Roberts K, Absher DM, Wold B, Mortazavi A, Williams B, Marinov G, Trout D, Pepke S, King B, McCue K, Kirilusha A, DeSalvo G, Fisher-Aylor K, Amrhein H, Vielmetter J, Sherlock G, Sidow A, Batzoglou S, Rauch R, Kundaje A, Libbrecht M, Margulies EH, Parker SC, Elnitski L, Green ED, Hubbard T, Harrow J, Searle S, Kokocinski F, Aken B, Frankish A, Hunt T, Despacio-Reyes G, Kay M, Mukherjee G, Bignell A, Saunders G, Boychenko V, Van Baren M, Brown RH, Khurana E, Balasubramanian S, Zhang Z, Lam H, Cayting P, Robilotto R, Lu Z, Guigo R, Derrien T, Tanzer A, Knowles DG, Mariotti M, James Kent W, Haussler D, Harte R, Diekhans M, Kellis M, Lin M, Kheradpour P, Ernst J, Reymond A, Howald C, Graison EA, Chrast J, Tress M, Rodriguez JM, Snyder M, Landt SG, Raha D, Shi M, Euskirchen G, Grubert F, Kasowski M, Lian J, Cayting P, Lacroute P, Xu Y, Monahan H, Patacsil D, Slifer T, Yang X, Charos A, Reed B, Wu L, Auerbach RK, Habegger L, Hariharan M, Rozowsky J, Abyzov A, Weissman SM, Gerstein M, Struhl K, Lamarre-Vincent N, Lindahl-Allen M, Miotto B, Moqtaderi Z, Fleming JD, Newburger P, Farnham PJ, Frietze S, O'Geen H, Xu X, Blahnik KR, Cao AR, Iyengar S, Stamatoyannopoulos JA, Kaul R, Thurman RE, Wang H, Navas PA, Sandstrom R, Sabo PJ, Weaver M, Canfield T, Lee K, Neph S, Roach V, Reynolds A, Johnson A, Rynes E, Giste E, Vong S, Neri J, Frum T, Johnson EM, Nguyen ED, Ebersol AK, Sanchez ME, Sheffer HH, Lotakis D, Haugen E, Humbert R, Kutyavin T, Shafer T, Dekker J, Lajoie BR, Sanyal A, James Kent W, Rosenbloom KR, Dreszer TR, Raney BJ, Barber GP, Meyer LR, Sloan CA, Malladi VS, Cline MS, Learned K, Swing VK, Zweig AS, Rhead B, Fujita PA, Roskin K, Karolchik D, Kuhn RM, Haussler D, Birney E, Dunham I, Wilder SP, Keefe D, Sobral D, Herrero J, Beal K, Lukk M, Brazma A, Vaquerizas JM, Luscombe NM, Bickel PJ, Boley N, Brown JB, Li Q, Huang H, Gerstein M, Habegger L, Sboner A, Rozowsky J, Auerbach RK, Yip KY, Cheng C, Yan KK, Bhardwaj N, Wang J, Lochovsky L, Jee J, Gibson T, Leng J, Du J, Hardison RC, Harris RS, Song G, Miller W, Haussler D, Roskin K, Suh B, Wang T, Paten B, Noble WS, Hoffman MM, Buske OJ, Weng Z, Dong X, Wang J, Xi H, Tenenbaum SA, Doyle F, Penalva LO, Chittur S, Tullius TD, Parker SC, White KP, Karmakar S, Victorsen A, Jameel N, Bild N, Grossman RL, Snyder M, Landt SG, Yang X, Patacsil D, Slifer T, Dekker J, Lajoie BR, Sanyal A, Weng Z, Whitfield TW, Wang J, Collins PJ, Trinklein ND, Partridge EC, Myers RM, Giddings MC, Chen X, Khatun J, Maier C, Yu Y, Gunawardena H, Risk B, Feingold EA, Lowdon RF, Dillon LA, Good PJ, Harrow J, Searle S., Becker, Peter B, Broad Institute of MIT and Harvard, Lincoln Laboratory, Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Department of Physics, Kellis, Manolis, Epstein, Charles B., Bernstein, Bradley E., Shoresh, Noam, Ernst, Jason, Mikkelsen, Tarjei Sigurd, Kheradpour, Pouya, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Ward, Lucas D., Altshuler, Robert Charles, Lin, Michael F., ENCODE Project Consortium, Antonarakis, Stylianos, and Miotto, Benoit
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RNA, Messenger/genetics ,[SDV]Life Sciences [q-bio] ,Messenger ,Genoma humà ,Genome ,Medical and Health Sciences ,0302 clinical medicine ,Models ,ddc:576.5 ,Biology (General) ,Conserved Sequence ,Genetics ,0303 health sciences ,General Neuroscience ,RNA-Binding Proteins ,Genomics ,Biological Sciences ,Chromatin ,3. Good health ,[SDV] Life Sciences [q-bio] ,DNA-Binding Proteins ,Gene Components ,030220 oncology & carcinogenesis ,DNA methylation ,Encyclopedia ,HIV/AIDS ,Proteïnes de la sang -- Aspectes genètics ,General Agricultural and Biological Sciences ,Databases, Nucleic Acid ,Human ,Research Article ,Quality Control ,Process (engineering) ,QH301-705.5 ,1.1 Normal biological development and functioning ,Computational biology ,Biology ,ENCODE ,General Biochemistry, Genetics and Molecular Biology ,Chromatin/metabolism ,Vaccine Related ,03 medical and health sciences ,Databases ,Genetic ,Underpinning research ,Humans ,RNA, Messenger ,RNA-Binding Proteins/genetics/metabolism ,Vaccine Related (AIDS) ,Gene ,030304 developmental biology ,Internet ,General Immunology and Microbiology ,Nucleic Acid ,Agricultural and Veterinary Sciences ,Base Sequence ,Models, Genetic ,Genome, Human ,Prevention ,Human Genome ,Computational Biology ,DNA Methylation ,ENCODE Project Consortium ,Gene Expression Regulation ,DNA-Binding Proteins/genetics/metabolism ,RNA ,Human genome ,Immunization ,Generic health relevance ,Developmental Biology - Abstract
The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome., National Human Genome Research Institute (U.S.), National Institutes of Health (U.S.)
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- 2011
32. Limiting factors for charge generation in low-offset fullerene-based organic solar cells.
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Jungbluth A, Cho E, Privitera A, Yallum KM, Kaienburg P, Lauritzen AE, Derrien T, Kesava SV, Habib I, Pratik SM, Banerji N, Brédas JL, Coropceanu V, and Riede M
- Abstract
Free charge generation after photoexcitation of donor or acceptor molecules in organic solar cells generally proceeds via (1) formation of charge transfer states and (2) their dissociation into charge separated states. Research often either focuses on the first component or the combined effect of both processes. Here, we provide evidence that charge transfer state dissociation rather than formation presents a major bottleneck for free charge generation in fullerene-based blends with low energetic offsets between singlet and charge transfer states. We investigate devices based on dilute donor content blends of (fluorinated) ZnPc:C
60 and perform density functional theory calculations, device characterization, transient absorption spectroscopy and time-resolved electron paramagnetic resonance measurements. We draw a comprehensive picture of how energies and transitions between singlet, charge transfer, and charge separated states change upon ZnPc fluorination. We find that a significant reduction in photocurrent can be attributed to increasingly inefficient charge transfer state dissociation. With this, our work highlights potential reasons why low offset fullerene systems do not show the high performance of non-fullerene acceptors., (© 2024. The Author(s).)- Published
- 2024
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33. LncRNAs in domesticated animals: from dog to livestock species.
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, and Derrien T
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- Animals, Animals, Domestic genetics, Dogs, Genome, Livestock genetics, Mice, Phylogeny, Transcriptome, RNA, Long Noncoding genetics
- Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation., (© 2021. The Author(s).)
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- 2022
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34. Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.
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Plassais J, vonHoldt BM, Parker HG, Carmagnini A, Dubos N, Papa I, Bevant K, Derrien T, Hennelly LM, Whitaker DT, Harris AC, Hogan AN, Huson HJ, Zaibert VF, Linderholm A, Haile J, Fest T, Habib B, Sacks BN, Benecke N, Outram AK, Sablin MV, Germonpré M, Larson G, Frantz L, and Ostrander EA
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- Alleles, Animals, Body Size genetics, Breeding, Humans, Canidae genetics, Wolves genetics
- Abstract
Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.
1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6 , 10 , 11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs., Competing Interests: Declaration of interests The authors declare no competing interests., (Published by Elsevier Inc.)- Published
- 2022
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35. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets.
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Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, and Hedan B
- Abstract
Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT , was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4 , and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7 , GABPB1 , and SPPL2A , located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine.
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- 2022
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36. Author Correction: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.
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Jehl F, Muret K, Bernard M, Boutin M, Lagoutte L, Désert C, Dehais P, Esquerré D, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Pitel F, Zerjal T, Klopp C, and Lagarrigue S
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- 2021
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37. Identification of common predisposing loci to hematopoietic cancers in four dog breeds.
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Hédan B, Cadieu É, Rimbault M, Vaysse A, Dufaure de Citres C, Devauchelle P, Botherel N, Abadie J, Quignon P, Derrien T, and André C
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- Animals, Chromosome Mapping, Dog Diseases pathology, Dogs, Genome-Wide Association Study, Haplotypes genetics, Hematologic Neoplasms pathology, Hematologic Neoplasms veterinary, High-Throughput Nucleotide Sequencing, Histiocytic Sarcoma pathology, Humans, Cyclin-Dependent Kinase Inhibitor p16 genetics, Dog Diseases genetics, Genetic Predisposition to Disease, Hematologic Neoplasms genetics, Histiocytic Sarcoma genetics
- Abstract
Histiocytic sarcoma (HS) is a rare but aggressive cancer in both humans and dogs. The spontaneous canine model, which has clinical, epidemiological, and histological similarities with human HS and specific breed predispositions, provides a unique opportunity to unravel the genetic basis of this cancer. In this study, we aimed to identify germline risk factors associated with the development of HS in canine-predisposed breeds. We used a methodology that combined several genome-wide association studies in a multi-breed and multi-cancer approach as well as targeted next-generation sequencing, and imputation We combined several dog breeds (Bernese mountain dogs, Rottweilers, flat-coated retrievers, and golden retrievers), and three hematopoietic cancers (HS, lymphoma, and mast cell tumor). Results showed that we not only refined the previously identified HS risk CDKN2A locus, but also identified new loci on canine chromosomes 2, 5, 14, and 20. Capture and targeted sequencing of specific loci suggested the existence of regulatory variants in non-coding regions and methylation mechanisms linked to risk haplotypes, which lead to strong cancer predisposition in specific dog breeds. We also showed that these canine cancer predisposing loci appeared to be due to the additive effect of several risk haplotypes involved in other hematopoietic cancers such as lymphoma or mast cell tumors as well. This illustrates the pleiotropic nature of these canine cancer loci as observed in human oncology, thereby reinforcing the interest of predisposed dog breeds to study cancer initiation and progression., Competing Interests: The authors have declared that no competing interests exist.
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- 2021
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38. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes.
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, and Kidd JM
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- Animals, Dogs classification, Long Interspersed Nucleotide Elements, Short Interspersed Nucleotide Elements, Species Specificity, Dogs genetics, GC Rich Sequence, Genome, Interspersed Repetitive Sequences
- Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation., Competing Interests: Competing interest statement: J.V.M. is an inventor on patent US6150160, is a paid consultant for Gilead Sciences, serves on the scientific advisory board of Tessera Therapeutics Inc. (where he is paid as a consultant and has equity options), and currently serves on the American Society of Human Genetics Board of Directors. A.R.B. is the cofounder and Chief Science Officer of Embark Veterinary., (Copyright © 2021 the Author(s). Published by PNAS.)
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- 2021
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39. Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma.
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Prouteau A, Denis JA, De Fornel P, Cadieu E, Derrien T, Kergal C, Botherel N, Ulvé R, Rault M, Bouzidi A, François R, Dorso L, Lespagnol A, Devauchelle P, Abadie J, André C, and Hédan B
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- Animals, Biomarkers, Tumor blood, Biomarkers, Tumor genetics, Circulating Tumor DNA genetics, DNA Copy Number Variations, Dog Diseases diagnosis, Dogs, Female, Histiocytic Sarcoma blood, Histiocytic Sarcoma diagnosis, Histiocytic Sarcoma genetics, Lymphoma diagnosis, Lymphoma genetics, Lymphoma veterinary, Male, Melanoma diagnosis, Melanoma genetics, Mouth Neoplasms blood, Mouth Neoplasms diagnosis, Mouth Neoplasms genetics, Mutation, Protein Tyrosine Phosphatase, Non-Receptor Type 11 analysis, Protein Tyrosine Phosphatase, Non-Receptor Type 11 genetics, Sensitivity and Specificity, Circulating Tumor DNA blood, Dog Diseases blood, Dog Diseases genetics, Histiocytic Sarcoma veterinary, Melanoma veterinary, Mouth Neoplasms veterinary
- Abstract
Circulating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. Thus, we used droplet digital PCR or PCR for antigen receptor rearrangement, to explore tumor-specific point mutations, copy number alterations, and chromosomal rearrangements in the plasma of cancer-affected dogs. We detected ctDNA in 21/23 (91.3%) of histiocytic sarcoma (HS), 2/8 (25%) of oral melanoma, and 12/13 (92.3%) of lymphoma cases. The utility of ctDNA in diagnosing HS was explored in 133 dogs, including 49 with HS, and the screening of recurrent PTPN11 mutations in plasma had a specificity of 98.8% and a sensitivity between 42.8 and 77% according to the clinical presentation of HS. Sensitivity was greater in visceral forms and especially related to pulmonary location. Follow-up of four dogs by targeting lymphoma-specific antigen receptor rearrangement in plasma showed that minimal residual disease detection was concordant with clinical evaluation and treatment response. Thus, our study shows that ctDNA is detectable in the plasma of cancer-affected dogs and is a promising biomarker for diagnosis and clinical follow-up. ctDNA detection appears to be useful in comparative oncology research due to growing interest in the study of natural canine tumors and exploration of new therapies.
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- 2021
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40. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.
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Jehl F, Muret K, Bernard M, Boutin M, Lagoutte L, Désert C, Dehais P, Esquerré D, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Pitel F, Zerjal T, Klopp C, and Lagarrigue S
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- Animals, Atlases as Topic, Avian Proteins genetics, Gene Expression Profiling, Gene Expression Regulation, Gene Regulatory Networks, MicroRNAs genetics, Organ Specificity, Sequence Analysis, RNA, Tissue Distribution, Chickens genetics, Computational Biology methods, Molecular Sequence Annotation methods, RNA, Long Noncoding genetics
- Abstract
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC ( http://www.fragencode.org/ ), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.
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- 2020
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41. PTPN11 mutations in canine and human disseminated histiocytic sarcoma.
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Hédan B, Rault M, Abadie J, Ulvé R, Botherel N, Devauchelle P, Copie-Bergman C, Cadieu E, Parrens M, Alten J, Zalcman EL, Cario G, Damaj G, Mokhtari K, Le Loarer F, Coulomb-Lhermine A, Derrien T, Hitte C, Bachelot L, Breen M, Gilot D, Blay JY, Donadieu J, and André C
- Subjects
- Adult, Aged, Aged, 80 and over, Animals, Biopsy, Cell Line, Tumor, Cell Proliferation drug effects, Child, Child, Preschool, DNA Mutational Analysis, Disease Models, Animal, Dog Diseases blood, Dog Diseases pathology, Dogs, Drug Screening Assays, Antitumor methods, Female, Histiocytic Sarcoma drug therapy, Histiocytic Sarcoma pathology, Histiocytic Sarcoma veterinary, Humans, Infant, MAP Kinase Signaling System drug effects, MAP Kinase Signaling System genetics, Male, Middle Aged, Mitogen-Activated Protein Kinases antagonists & inhibitors, Mitogen-Activated Protein Kinases metabolism, Mutation, Protein Kinase Inhibitors therapeutic use, Protein Tyrosine Phosphatase, Non-Receptor Type 11 antagonists & inhibitors, Ribonucleases, Tumor Suppressor Proteins, Young Adult, Dog Diseases genetics, Histiocytes pathology, Histiocytic Sarcoma genetics, Protein Kinase Inhibitors pharmacology, Protein Tyrosine Phosphatase, Non-Receptor Type 11 genetics
- Abstract
In humans, histiocytic sarcoma (HS) is an aggressive cancer involving histiocytes. Its rarity and heterogeneity explain that treatment remains a challenge. Sharing high clinical and histopathological similarities with human HS, the canine HS is conversely frequent in specific breeds and thus constitutes a unique spontaneous model for human HS to decipher the genetic bases and to explore therapeutic options. We identified sequence alterations in the MAPK pathway in at least 63.9% (71/111) of HS cases with mutually exclusive BRAF (0.9%; 1/111), KRAS (7.2%; 8/111) and PTPN11 (56.75%; 63/111) mutations concentrated at hotspots common to human cancers. Recurrent PTPN11 mutations are associated to visceral disseminated HS subtype in dogs, the most aggressive clinical presentation. We then identified PTPN11 mutations in 3/19 (15.7%) human HS patients. Thus, we propose PTPN11 mutations as key events for a specific subset of human and canine HS: the visceral disseminated form. Finally, by testing drugs targeting the MAPK pathway in eight canine HS cell lines, we identified a better anti-proliferation activity of MEK inhibitors than PTPN11 inhibitors in canine HS neoplastic cells. In combination, these results illustrate the relevance of naturally affected dogs in deciphering genetic mechanisms and selecting efficient targeted therapies for such rare and aggressive cancers in humans., (© 2020 UICC.)
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- 2020
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42. Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma.
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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, and Hédan B
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- Animals, Dogs, Female, Genetic Predisposition to Disease, Male, Melanoma genetics, Mitotic Index, Mouth Neoplasms genetics, Prognosis, Chromosome Aberrations veterinary, Dog Diseases genetics, Melanoma veterinary, Mouth Neoplasms veterinary
- Abstract
Canine oral melanoma is the first malignancy of the oral cavity in dogs and is characterized by a local invasiveness and a high metastatic propensity. A better knowledge of genetic alterations is expected to improve management of this tumour. Copy number alterations are known characteristics of mucosal melanomas both in dogs and humans. The goal of this study was to explore the prognostic value of somatic focal amplifications on chromosomes (Canis Familiaris [CFA]) 10 and 30 in canine oral melanoma. The cohort included 73 dogs with oral melanoma confirmed by histology, removed surgically without adjuvant therapy and with a minimal follow-up of 6 months. Epidemiological, clinical and histological data were collected and quantitative-PCR were performed on formalin-fixed paraffin-embedded (FFPE) samples to identify specific focal amplifications. The 73 dogs included in the study had a median survival time of 220 days. Focal amplifications on CFA 10 and 30 were recurrent (49.3% and 50.7% of cases, respectively) and CFA 30 amplification was significantly associated with the amelanotic phenotype (P = .046) and high mitotic index (MI; P = .0039). CFA 30 amplification was also linked to poor prognosis (P = .0005). Other negative prognostic factors included gingiva location (P = .003), lymphadenomegaly (P = .026), tumour ulceration at diagnosis (P = .003), MI superior to 6 mitoses over 10 fields (P = .001) and amelanotic tumour (P = .029). In multivariate analyses using Cox proportional hazards regression, CFA 30 amplification (Hazard ratio [HR] = 2.08; P = .011), tumour location (HR = 2.20; P = .005) and histological pigmentation (HR = 1.87; P = .036) were significantly associated with shorter survival time. Focal amplification of CFA 30 is linked to an aggressive subset and constitutes a new prognostic factor., (© 2019 John Wiley & Sons Ltd.)
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- 2020
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43. Multi-species annotation of transcriptome and chromatin structure in domesticated animals.
- Author
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Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, Pinard-Van der Laan MH, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, and Giuffra E
- Subjects
- Animals, Cattle, Chickens, Goats, Phylogeny, Sus scrofa, Animals, Domestic genetics, Chromatin genetics, Molecular Sequence Annotation, Transcriptome
- Abstract
Background: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells)., Results: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species., Conclusions: We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
- Published
- 2019
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44. Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules.
- Author
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Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V, and Aury JM
- Subjects
- Animals, Brain, DNA, Complementary genetics, DNA, Complementary isolation & purification, Datasets as Topic, Gene Library, High-Throughput Nucleotide Sequencing instrumentation, Liver, Mice, Nanopore Sequencing instrumentation, RNA genetics, RNA isolation & purification, RNA-Seq instrumentation, Sequence Analysis, DNA instrumentation, High-Throughput Nucleotide Sequencing methods, Nanopore Sequencing methods, RNA-Seq methods, Sequence Analysis, DNA methods, Transcriptome genetics
- Abstract
Our vision of DNA transcription and splicing has changed dramatically with the introduction of short-read sequencing. These high-throughput sequencing technologies promised to unravel the complexity of any transcriptome. Generally gene expression levels are well-captured using these technologies, but there are still remaining caveats due to the limited read length and the fact that RNA molecules had to be reverse transcribed before sequencing. Oxford Nanopore Technologies has recently launched a portable sequencer which offers the possibility of sequencing long reads and most importantly RNA molecules. Here we generated a full mouse transcriptome from brain and liver using the Oxford Nanopore device. As a comparison, we sequenced RNA (RNA-Seq) and cDNA (cDNA-Seq) molecules using both long and short reads technologies and tested the TeloPrime preparation kit, dedicated to the enrichment of full-length transcripts. Using spike-in data, we confirmed that expression levels are efficiently captured by cDNA-Seq using short reads. More importantly, Oxford Nanopore RNA-Seq tends to be more efficient, while cDNA-Seq appears to be more biased. We further show that the cDNA library preparation of the Nanopore protocol induces read truncation for transcripts containing internal runs of T's. This bias is marked for runs of at least 15 T's, but is already detectable for runs of at least 9 T's and therefore concerns more than 20% of expressed transcripts in mouse brain and liver. Finally, we outline that bioinformatics challenges remain ahead for quantifying at the transcript level, especially when reads are not full-length. Accurate quantification of repeat-associated genes such as processed pseudogenes also remains difficult, and we show that current mapping protocols which map reads to the genome largely over-estimate their expression, at the expense of their parent gene.
- Published
- 2019
- Full Text
- View/download PDF
45. Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas.
- Author
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Hitte C, Le Béguec C, Cadieu E, Wucher V, Primot A, Prouteau A, Botherel N, Hédan B, Lindblad-Toh K, André C, and Derrien T
- Subjects
- Animals, Breeding, Dog Diseases pathology, Dogs, Gene Expression Profiling, Genome genetics, High-Throughput Nucleotide Sequencing, Humans, Melanoma pathology, Mouth Neoplasms pathology, Transcriptome genetics, Dog Diseases genetics, Melanoma genetics, Mouth Neoplasms genetics, RNA, Long Noncoding genetics
- Abstract
Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression, and more particularly, in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort ( n = 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers, and golden retrievers), and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog-human conserved DE lncRNAs, including SOX21-AS , ZEB2-AS , and CASC15 lncRNAs. Using unsupervised co-expression network analysis with coding genes, we inferred the potential functions of the DE lncRNAs, suggesting associations with cancer-related genes, cell cycle, and carbohydrate metabolism Gene Ontology (GO) terms. Finally, we exploited our multi-breed design to identify DE lncRNAs within breeds. This study provides a unique transcriptomic resource for studying oral melanoma in dogs, and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.
- Published
- 2019
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46. Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs.
- Author
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Hédan B, Cadieu E, Botherel N, Dufaure de Citres C, Letko A, Rimbault M, Drögemüller C, Jagannathan V, Derrien T, Schmutz S, Leeb T, and André C
- Subjects
- Animals, Dogs, Horses genetics, Mice, Mutation, Missense, Genome-Wide Association Study, Melanins genetics, Membrane Proteins genetics, Skin Pigmentation genetics
- Abstract
White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment in the hairs, was suggested to correspond to extreme dilution of the phaeomelanin, by both the expression of only phaeomelanin (locus E) and its extreme dilution (locus I). To go further, we performed genome-wide association studies (GWAS) using a multiple breed approach. The first GWAS, using 34 white dogs and 128 non-white dogs, including White Shepherds, Poodles, Cotons de Tulear and Bichons allowed us to identify two significantly associated loci on the locus E and a novel locus on chromosome 20. A second GWAS using 15 other breeds presenting extreme phaeomelanin dilution confirmed the position of locus I on the chromosome 20 (position 55 Mb p
corrected = 6 × 10-13 ). Using whole-genome sequencing, we identified a missense variant in the first exon of MFSD12 , a gene recently identified to be involved in human, mouse and horse pigmentation. We confirmed the role of this variant in phaeomelanin dilution of numerous canine breeds, and the conserved role of MFSD12 in mammalian pigmentation.- Published
- 2019
- Full Text
- View/download PDF
47. Characterisation and functional predictions of canine long non-coding RNAs.
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Le Béguec C, Wucher V, Lagoutte L, Cadieu E, Botherel N, Hédan B, De Brito C, Guillory AS, André C, Derrien T, and Hitte C
- Subjects
- Animals, Dogs, Humans, Organ Specificity, RNA, Long Noncoding genetics, Databases, Nucleic Acid, Gene Expression Regulation physiology, RNA, Long Noncoding biosynthesis, Transcriptome
- Abstract
Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.
- Published
- 2018
- Full Text
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48. An exome sequencing based approach for genome-wide association studies in the dog.
- Author
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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, and Hitte C
- Subjects
- Animals, Chromosome Mapping, Dogs, Exome genetics, Genotype, Polymorphism, Single Nucleotide genetics, Breeding, Genome-Wide Association Study statistics & numerical data, Quantitative Trait Loci genetics, Exome Sequencing
- Abstract
Genome-wide association studies (GWAS) are widely used to identify loci associated with phenotypic traits in the domestic dog that has emerged as a model for Mendelian and complex traits. However, a disadvantage of GWAS is that it always requires subsequent fine-mapping or sequencing to pinpoint causal mutations. Here, we performed whole exome sequencing (WES) and canine high-density (cHD) SNP genotyping of 28 dogs from 3 breeds to compare the SNP and linkage disequilibrium characteristics together with the power and mapping precision of exome-guided GWAS (EG-GWAS) versus cHD-based GWAS. Using simulated phenotypes, we showed that EG-GWAS has a higher power than cHD to detect associations within target regions and less power outside target regions, with power being influenced further by sample size and SNP density. We analyzed two real phenotypes (hair length and furnishing), that are fixed in certain breeds to characterize mapping precision of the known causal mutations. EG-GWAS identified the associated exonic and 3'UTR variants within the FGF5 and RSPO2 genes, respectively, with only a few samples per breed. In conclusion, we demonstrated that EG-GWAS can identify loci associated with Mendelian phenotypes both within and across breeds.
- Published
- 2017
- Full Text
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49. Discovery of Human-Similar Gene Fusions in Canine Cancers.
- Author
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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, and André C
- Subjects
- Animals, Base Sequence, Blotting, Western, Chromosome Breakpoints, Dog Diseases metabolism, Dogs, Gene Expression Regulation, Neoplastic, Glioma genetics, Glioma metabolism, Glioma veterinary, Humans, Lymphoma, B-Cell genetics, Lymphoma, B-Cell metabolism, Lymphoma, B-Cell veterinary, Neoplasms metabolism, Oncogene Fusion, Oncogene Proteins, Fusion metabolism, Reverse Transcriptase Polymerase Chain Reaction, Translocation, Genetic, Dog Diseases genetics, Neoplasms genetics, Neoplasms veterinary, Oncogene Proteins, Fusion genetics
- Abstract
Canine cancers represent a tremendous natural resource due to their incidence and striking similarities to human cancers, sharing similar clinical and pathologic features as well as oncogenic events, including identical somatic mutations. Considering the importance of gene fusions as driver alterations, we explored their relevance in canine cancers. We focused on three distinct human-comparable canine cancers representing different tissues and embryonic origins. Through RNA-Seq, we discovered similar gene fusions as those found in their human counterparts: IGK - CCND3 in B-cell lymphoma, MPB - BRAF in glioma, and COL3A1 - PDGFB in dermatofibrosarcoma protuberans-like. We showed not only similar partner genes but also identical breakpoints leading to oncogene overexpression. This study demonstrates similar gene fusion partners and mechanisms in human-dog corresponding tumors and allows for selection of targeted therapies in preclinical and clinical trials with pet dogs prior to human trials, within the framework of personalized medicine. Cancer Res; 77(21); 5721-7. ©2017 AACR ., (©2017 American Association for Cancer Research.)
- Published
- 2017
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50. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
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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, and Derrien T
- Subjects
- Animals, Benchmarking, Decision Trees, Dogs, Gene Expression Regulation, Humans, Mice, Molecular Sequence Annotation statistics & numerical data, Open Reading Frames, RNA, Long Noncoding classification, RNA, Long Noncoding metabolism, RNA, Messenger classification, RNA, Messenger genetics, RNA, Messenger metabolism, Sequence Analysis, RNA, Genome, Molecular Sequence Annotation methods, RNA, Long Noncoding genetics, Software, Transcriptome
- Abstract
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2017
- Full Text
- View/download PDF
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