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FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome.
Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PAJ, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. Wucher V, et al. Among authors: alfoldi j. Nucleic Acids Res. 2017 May 5;45(8):e57. doi: 10.1093/nar/gkw1306. Nucleic Acids Res. 2017. PMID: 28053114 Free PMC article.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F, Lindblad-Toh K. Grabherr MG, et al. Among authors: alfoldi j. Bioinformatics. 2010 May 1;26(9):1145-51. doi: 10.1093/bioinformatics/btq102. Epub 2010 Mar 5. Bioinformatics. 2010. PMID: 20208069 Free PMC article.
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
Hoeppner MP, Lundquist A, Pirun M, Meadows JR, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald MG, Swofford R, Mauceli E, Moghadam BT, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald JP, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander ES, di Palma F, Lindblad-Toh K, Grabherr MG. Hoeppner MP, et al. Among authors: alfoldi j. PLoS One. 2014 Mar 13;9(3):e91172. doi: 10.1371/journal.pone.0091172. eCollection 2014. PLoS One. 2014. PMID: 24625832 Free PMC article.
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Carneiro M, et al. Among authors: alfoldi j. Science. 2014 Aug 29;345(6200):1074-1079. doi: 10.1126/science.1253714. Science. 2014. PMID: 25170157 Free PMC article.
The genomic substrate for adaptive radiation in African cichlid fish.
Brawand D, Wagner CE, Li YI, Malinsky M, Keller I, Fan S, Simakov O, Ng AY, Lim ZW, Bezault E, Turner-Maier J, Johnson J, Alcazar R, Noh HJ, Russell P, Aken B, Alföldi J, Amemiya C, Azzouzi N, Baroiller JF, Barloy-Hubler F, Berlin A, Bloomquist R, Carleton KL, Conte MA, D'Cotta H, Eshel O, Gaffney L, Galibert F, Gante HF, Gnerre S, Greuter L, Guyon R, Haddad NS, Haerty W, Harris RM, Hofmann HA, Hourlier T, Hulata G, Jaffe DB, Lara M, Lee AP, MacCallum I, Mwaiko S, Nikaido M, Nishihara H, Ozouf-Costaz C, Penman DJ, Przybylski D, Rakotomanga M, Renn SCP, Ribeiro FJ, Ron M, Salzburger W, Sanchez-Pulido L, Santos ME, Searle S, Sharpe T, Swofford R, Tan FJ, Williams L, Young S, Yin S, Okada N, Kocher TD, Miska EA, Lander ES, Venkatesh B, Fernald RD, Meyer A, Ponting CP, Streelman JT, Lindblad-Toh K, Seehausen O, Di Palma F. Brawand D, et al. Among authors: alfoldi j. Nature. 2014 Sep 18;513(7518):375-381. doi: 10.1038/nature13726. Epub 2014 Sep 3. Nature. 2014. PMID: 25186727 Free PMC article.
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. Peng X, et al. Among authors: alfoldi j. Nat Biotechnol. 2014 Dec;32(12):1250-5. doi: 10.1038/nbt.3079. Epub 2014 Nov 17. Nat Biotechnol. 2014. PMID: 25402615 Free PMC article.
Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.
Broeckx BJ, Hitte C, Coopman F, Verhoeven GE, De Keulenaer S, De Meester E, Derrien T, Alfoldi J, Lindblad-Toh K, Bosmans T, Gielen I, Van Bree H, Van Ryssen B, Saunders JH, Van Nieuwerburgh F, Deforce D. Broeckx BJ, et al. Among authors: alfoldi j. Sci Rep. 2015 Aug 3;5:12810. doi: 10.1038/srep12810. Sci Rep. 2015. PMID: 26235384 Free PMC article.
59 results