| Year |
Citation |
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| 2016 |
Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, ... ... Alioto T, et al. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biology. 17: 32. PMID 26911872 DOI: 10.1186/s13059-016-0883-6 |
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| 2015 |
Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon L, Sertier AS, Patch AM, Jäger N, Ginsbach P, Drews R, et al. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nature Communications. 6: 10001. PMID 26647970 DOI: 10.1038/ncomms10001 |
1 |
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| 2013 |
Alioto T, Picardi E, Guigó R, Pesole G. ASPic-GeneID: A lightweight pipeline for gene prediction and alternative isoforms detection Biomed Research International. 2013. PMID 24308000 DOI: 10.1155/2013/502827 |
1 |
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| 2013 |
Steijger T, Abril JF, Engström PG, Kokocinski F, Hubbard TJ, Guigó R, Harrow J, Bertone P. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 10: 1177-84. PMID 24185837 DOI: 10.1038/nmeth.2714 |
1 |
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| 2013 |
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P. Systematic evaluation of spliced alignment programs for RNA-seq data. Nature Methods. 10: 1185-91. PMID 24185836 DOI: 10.1038/nmeth.2722 |
1 |
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| 2012 |
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, ... ... Alioto T, et al. Landscape of transcription in human cells. Nature. 489: 101-8. PMID 22955620 DOI: 10.1038/nature11233 |
1 |
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| 2012 |
Garcia-Mas J, Benjak A, Sanseverino W, Bourgeois M, Mir G, González VM, Hénaff E, Câmara F, Cozzuto L, Lowy E, Alioto T, Capella-Gutiérrez S, Blanca J, Cañizares J, Ziarsolo P, et al. The genome of melon (Cucumis melo L.). Proceedings of the National Academy of Sciences of the United States of America. 109: 11872-7. PMID 22753475 DOI: 10.1073/pnas.1205415109 |
1 |
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| 2012 |
Sato S, Tabata S, Hirakawa H, Asamizu E, Shirasawa K, Isobe S, Kaneko T, Nakamura Y, Shibata D, Aoki K, Egholm M, Knight J, Bogden R, Li C, Shuang Y, ... ... Alioto T, et al. The tomato genome sequence provides insights into fleshy fruit evolution Nature. 485: 635-641. PMID 22660326 DOI: 10.1038/nature11119 |
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| 2012 |
Alioto T. Gene prediction Methods in Molecular Biology. 855: 175-201. PMID 22407709 DOI: 10.1007/978-1-61779-582-4_6 |
1 |
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| 2011 |
Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. The origins, evolution, and functional potential of alternative splicing in vertebrates Molecular Biology and Evolution. 28: 2949-2959. PMID 21551269 DOI: 10.1093/molbev/msr127 |
1 |
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| 2011 |
. A user's guide to the encyclopedia of DNA elements (ENCODE). Plos Biology. 9: e1001046. PMID 21526222 DOI: 10.1371/journal.pbio.1001046 |
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| 2010 |
Richards S, Gibbs RA, Gerardo NM, Moran N, Nakabachi A, Stern D, Tagu D, Wilson ACC, Muzny D, Kovar C, Cree A, Chacko J, Chandrabose MN, Dao MD, Dinh HH, ... ... Alioto T, et al. Genome sequence of the pea aphid Acyrthosiphon pisum Plos Biology. 8. DOI: 10.1371/journal.pbio.1000313 |
1 |
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| 2010 |
Ngai J, Alioto TS. Genomics of Odor Receptors in Zebrafish The Senses: a Comprehensive Reference. 4: 553-560. DOI: 10.1016/B978-012370880-9.00111-0 |
1 |
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| 2009 |
Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Identifying protein-coding genes in genomic sequences Genome Biology. 10: 201. PMID 19226436 |
1 |
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| 2008 |
Alioto T, Guigó R. State of the art in eukaryotic gene prediction Modern Genome Annotation: the Biosapiens Network. 7-39. DOI: 10.1007/978-3-211-75123-7_2 |
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| 2008 |
Alioto TS, Guigó R, Picardi E, Pesole G. GenePC and ASPIC integrate gene predictions with expressed sequence alignments to predict alternative transcripts Series On Advances in Bioinformatics and Computational Biology. 6: 363-372. |
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| 2007 |
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research. 17: 746-59. PMID 17567994 DOI: 10.1101/gr.5660607 |
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| 2007 |
Alioto TS. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Research. 35: D110-5. PMID 17082203 DOI: 10.1093/nar/gkl796 |
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| 2006 |
Alioto TS, Ngai J. The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids. Bmc Genomics. 7: 309. PMID 17156446 DOI: 10.1186/1471-2164-7-309 |
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| 2005 |
Alioto TS, Ngai J. The odorant receptor repertoire of teleost fish. Bmc Genomics. 6: 173. PMID 16332259 DOI: 10.1186/1471-2164-6-173 |
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| 2004 |
Takehashi M, Alioto T, Stedeford T, Persad AS, Banasik M, Masliah E, Tanaka S, Ueda K. Septin 3 gene polymorphism in Alzheimer's disease. Gene Expression. 11: 263-70. PMID 15200238 DOI: 10.3727/000000003783992243 |
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