Tyler Scott Alioto - Publications

Affiliations: 
2010-2015 CNAG-CRG (Barcelona, Spain) 
Area:
genetics, computational biology

46/59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Marcet-Houben M, Cruz F, Gómez-Garrido J, Alioto TS, Nunez-Rodriguez JC, Mesanza N, Gut M, Iturritxa E, Gabaldon T. Genomics of the expanding pine pathogen reveals patterns of ongoing genetic admixture. Msystems. e0092823. PMID 38364101 DOI: 10.1128/msystems.00928-23  0.467
2023 Alioto TS, Gut M, Rodiño-Janeiro BK, Cruz F, Gómez-Garrido J, Vázquez-Ucha JC, Mata C, Antoni R, Briansó F, Dabad M, Casals E, Ingham M, Álvarez-Tejado M, Bou G, Gut IG. Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales. Microbial Genomics. 9. PMID 38010338 DOI: 10.1099/mgen.0.001132  0.476
2023 Destanovik D, Schultz DT, Styfhals R, Cruz F, Gómez-Garrido J, Gut M, Gut I, Fiorito G, Simakov O, Alioto TS, Ponte G, Seuntjens E. A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797). G3 (Bethesda, Md.). PMID 37850903 DOI: 10.1093/g3journal/jkad220  0.448
2023 Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Pons J, Alós J, Barcelo-Serra M. Chromosome-level assembly and annotation of the Xyrichtys novacula (Linnaeus, 1758) genome. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 30. PMID 37797305 DOI: 10.1093/dnares/dsad021  0.529
2023 Cobo-Simón I, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Maloof JN, Méndez-Cea B, Seco JI, Linares JC, Gallego FJ. transcriptome sequencing and gene co-expression reveal a genomic basis for drought sensitivity and evidence of a rapid local adaptation on Atlas cedar (). Frontiers in Plant Science. 14: 1116863. PMID 37152146 DOI: 10.3389/fpls.2023.1116863  0.442
2023 Gomez-Garrido J, Cruz F, Alioto TS, Feiner N, Uller T, Gut M, Sanchez Escudero I, Tavecchia G, Rotger A, Otalora Acevedo KE, Baldo L. Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain). Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 37137526 DOI: 10.1093/dnares/dsad008  0.597
2023 de la Herrán R, Hermida M, Rubiolo J, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, ... ... Alioto T, et al. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex determining gene in the flatfish Solea senegalensis. Molecular Ecology Resources. PMID 36587276 DOI: 10.1111/1755-0998.13750  0.402
2022 Cobo-Simón I, Maloof JN, Li R, Amini H, Méndez-Cea B, García-García I, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Wegrzyn JL, Seco J, Linares JC, Gallego FJ. Contrasting transcriptomic patterns reveal a genomic basis for drought resilience in the relict fir Abies pinsapo Boiss. Tree Physiology. PMID 36210755 DOI: 10.1093/treephys/tpac115  0.374
2022 Liedtke HC, Cruz F, Gómez-Garrido J, Fuentes Palacios D, Marcet-Houben M, Gut M, Alioto T, Gabaldón T, Gomez-Mestre I. Chromosome-level assembly, annotation and phylome of Pelobates cultripes, the western spadefoot toad. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 29. PMID 35583263 DOI: 10.1093/dnares/dsac013  0.592
2021 Guerrero-Cózar I, Gomez-Garrido J, Berbel C, Martinez-Blanch JF, Alioto T, Claros MG, Gagnaire PA, Manchado M. Chromosome anchoring in Senegalese sole (Solea senegalensis) reveals sex-associated markers and genome rearrangements in flatfish. Scientific Reports. 11: 13460. PMID 34188074 DOI: 10.1038/s41598-021-92601-5  0.373
2021 Thomy J, Sanchez F, Gut M, Cruz F, Alioto T, Piganeau G, Grimsley N, Yau S. Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in . Cells. 10. PMID 33802698 DOI: 10.3390/cells10030664  0.456
2020 Gerdol M, Moreira R, Cruz F, Gómez-Garrido J, Vlasova A, Rosani U, Venier P, Naranjo-Ortiz MA, Murgarella M, Greco S, Balseiro P, Corvelo A, Frias L, Gut M, Gabaldón T, ... ... Alioto TS, et al. Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel. Genome Biology. 21: 275. PMID 33168033 DOI: 10.1186/s13059-020-02180-3  0.688
2020 Julca I, Marcet-Houben M, Cruz F, Gómez-Garrido J, Gaut BS, Díez CM, Gut IG, Alioto TS, Vargas P, Gabaldón T. Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.). Bmc Biology. 18: 148. PMID 33100219 DOI: 10.1186/s12915-020-00881-6  0.454
2020 Ledoux JB, Cruz F, Gómez-Garrido J, Antoni R, Blanc J, Gómez-Gras D, Kipson S, López-Sendino P, Antunes A, Linares C, Gut M, Alioto TS, Garrabou J. The Genome Sequence of the Octocoral - A Key Resource To Study the Impact of Climate Change in the Mediterranean. G3 (Bethesda, Md.). PMID 32660973 DOI: 10.1534/G3.120.401371  0.57
2020 Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, et al. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications. 11: 2631. PMID 32457347 DOI: 10.1038/S41467-020-16284-8  0.574
2019 Julca I, Marcet-Houben M, Cruz F, Vargas-Chavez C, Johnston JS, Gómez-Garrido J, Frias L, Corvelo A, Loska D, Cámara F, Gut M, Alioto T, Latorre A, Gabaldón T. Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha. Molecular Biology and Evolution. PMID 31702774 DOI: 10.1093/Molbev/Msz261  0.753
2019 Alioto TS, Cruz F, Gómez-Garrido J, Triyatni M, Gut M, Frias L, Esteve-Codina A, Menne S, Kiialainen A, Kumpesa N, Birzele F, Schmucki R, Gut IG, Spleiss O. The Genome Sequence of the Eastern Woodchuck () : A Preclinical Animal Model for Chronic Hepatitis B. G3 (Bethesda, Md.). PMID 31645421 DOI: 10.1534/G3.119.400413  0.517
2019 Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández I Martí Á, Frias L, Galán B, Garcia JL, Howad W, Gómez-Garrido J, Gut M, et al. Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence. The Plant Journal : For Cell and Molecular Biology. PMID 31529539 DOI: 10.1111/Tpj.14538  0.642
2019 Liedtke HC, Garrido JG, Esteve-Codina A, Gut M, Alioto T, Gomez-Mestre I. De Novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate G3: Genes, Genomes, Genetics. 9: 2647-2655. PMID 31217263 DOI: 10.1534/G3.119.400389  0.439
2019 Mosca E, Cruz F, Gómez-Garrido J, Bianco L, Rellstab C, Brodbeck S, Csilléry K, Fady B, Fladung M, Fussi B, Gömöry D, González-Martínez SC, Grivet D, Gut M, Hansen OK, ... ... Alioto T, et al. A Reference Genome Sequence for the European Silver Fir ( Mill.): A Community-Generated Genomic Resource. G3 (Bethesda, Md.). PMID 31217262 DOI: 10.1534/G3.119.400083  0.624
2019 Kuderna LFK, Lizano E, Julià E, Gomez-Garrido J, Serres-Armero A, Kuhlwilm M, Alandes RA, Alvarez-Estape M, Juan D, Simon H, Alioto T, Gut M, Gut I, Schierup MH, Fornas O, et al. Selective single molecule sequencing and assembly of a human Y chromosome of African origin. Nature Communications. 10: 4. PMID 30602775 DOI: 10.1038/S41467-018-07885-5  0.478
2018 Hernandez I, Dhiman H, Klanert G, Jadhav V, Auer N, Hanscho M, Baumann M, Esteve-Codina A, Dabad M, Gómez J, Alioto T, Merkel A, Raineri E, Heath S, Rico D, et al. Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture. Biotechnology and Bioengineering. PMID 30512195 DOI: 10.1002/Bit.26891  0.353
2018 Alioto T, Blanco E, Parra G, Guigó R. Using geneid to Identify Genes. Current Protocols in Bioinformatics. e56. PMID 30332532 DOI: 10.1002/cpbi.56  0.383
2018 Puerma E, Orengo DJ, Cruz F, Gómez-Garrido J, Librado P, Salguero D, Papaceit M, Gut M, Segarra C, Alioto TS, Aguadé M. The high-quality genome sequence of the oceanic island endemic species Drosophila guanche reveals signals of adaptive evolution in genes related to flight and genome stability. Genome Biology and Evolution. PMID 29947749 DOI: 10.1093/Gbe/Evy135  0.519
2017 Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes I, Armstrong J, Laayouni H, Gordon D, Huddleston J, Perez RG, Povolotskaya I, Armero AS, Garrido JG, Ho D, Ribeca P, ... Alioto T, et al. A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0). Gigascience. PMID 29092041 DOI: 10.1093/Gigascience/Gix098  0.604
2016 Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, ... ... Alioto T, et al. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology. 17: 251. PMID 27964752 DOI: 10.1186/S13059-016-1090-1  0.737
2016 Cruz F, Julca I, Gómez-Garrido J, Loska D, Marcet-Houben M, Cano E, Galán B, Frias L, Ribeca P, Derdak S, Gut M, Sánchez-Fernández M, García JL, Gut IG, Vargas P, ... Alioto TS, et al. Genome sequence of the olive tree, Olea europaea. Gigascience. 5: 29. PMID 27346392 DOI: 10.1186/S13742-016-0134-5  0.413
2016 Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, ... ... Alioto T, et al. Whole Genome Sequencing of Turbot (Scophthalmus maximus; Pleuronectiformes): A Fish Adapted to Demersal Life. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 26951068 DOI: 10.1093/Dnares/Dsw007  0.751
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  0.737
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  0.451
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  0.557
2013 Piqué N, Aquilini E, Alioto T, Miñana-Galbis D, Tomás JM. Genome sequence of Plesiomonas shigelloides strain 302-73 (serotype O1) Genome Announcements. 1: 525-531. PMID 23814109 DOI: 10.1128/Genomea.00404-13  0.434
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  0.425
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  0.648
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  0.635
2012 Alioto T. Gene prediction Methods in Molecular Biology. 855: 175-201. PMID 22407709 DOI: 10.1007/978-1-61779-582-4_6  0.568
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  0.442
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  0.509
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  0.617
2009 Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, ... ... Alioto T, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, N.Y.). 324: 522-8. PMID 19390049 DOI: 10.1126/Science.1169588  0.655
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 DOI: 10.1186/Gb-2009-10-1-201  0.545
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Alioto T, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.54
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  0.516
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  0.567
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  0.503
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  0.605
Low-probability matches (unlikely to be authored by this person)
2019 Chaves-Pozo E, Bandín I, Olveira JG, Esteve-Codina A, Gómez-Garrido J, Dabad M, Alioto T, Esteban MÁ, Cuesta A. European sea bass brain DLB-1 cell line is susceptible to nodavirus: A transcriptomic study Fish & Shellfish Immunology. 86: 14-24. PMID 30428392 DOI: 10.1016/J.Fsi.2018.11.024  0.299
2017 Chaves-Pozo E, Valero Y, Esteve-Codina A, Gómez-Garrido J, Dabad M, Alioto T, Meseguer J, Esteban MÁ, Cuesta A. Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study. Scientific Reports. 7: 15396. PMID 29133947 DOI: 10.1038/S41598-017-15629-6  0.291
2022 Guirado P, Miró E, Iglesias-Torrens Y, Navarro F, Campoy S, Alioto TS, Gómez-Garrido J, Madrid C, Balsalobre C. A New Variant of the Gene Cluster Found in a Conjugative Plasmid from a MDR Isolate. Antibiotics (Basel, Switzerland). 11. PMID 35453217 DOI: 10.3390/antibiotics11040466  0.215
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.  0.213
2021 Arca-Suárez J, Rodiño-Janeiro BK, Pérez A, Guijarro-Sánchez P, Vázquez-Ucha JC, Cruz F, Gómez-Garrido J, Alioto TS, Álvarez-Tejado M, Gut M, Gut I, Oviaño M, Beceiro A, Bou G. Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by WGS. International Journal of Antimicrobial Agents. 106456. PMID 34688835 DOI: 10.1016/j.ijantimicag.2021.106456  0.212
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  0.211
2022 Castro-Arnau J, Chauvigné F, Gómez-Garrido J, Esteve-Codina A, Dabad M, Alioto T, Finn RN, Cerdà J. Developmental RNA-Seq transcriptomics of haploid germ cells and spermatozoa uncovers novel pathways associated with teleost spermiogenesis. Scientific Reports. 12: 14162. PMID 35986060 DOI: 10.1038/s41598-022-18422-2  0.202
2020 Weil T, Ometto L, Esteve-Codina A, Gómez-Garrido J, Oppedisano T, Lotti C, Dabad M, Alioto T, Vrhovsek U, Hogenhout S, Anfora G. Linking omics and ecology to dissect interactions between the apple proliferation phytoplasma and its psyllid vector Cacopsylla melanoneura. Insect Biochemistry and Molecular Biology. 127: 103474. PMID 33007407 DOI: 10.1016/j.ibmb.2020.103474  0.168
2020 Núñez AI, Esteve-Codina A, Gómez-Garrido J, Brustolin M, Talavera S, Berdugo M, Dabad M, Alioto T, Bensaid A, Busquets N. Alteration in the Culex pipiens transcriptome reveals diverse mechanisms of the mosquito immune system implicated upon Rift Valley fever phlebovirus exposure. Plos Neglected Tropical Diseases. 14: e0008870. PMID 33301456 DOI: 10.1371/journal.pntd.0008870  0.162
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  0.155
2021 Gato E, Constanso IP, Rodiño-Janeiro BK, Guijarro-Sánchez P, Alioto T, Arroyo MJ, Méndez G, Mancera L, Gut M, Gut I, Álvarez-Tejado M, Bou G, Oviaño M. Occurrence of the gene in the -harbouring plasmids: adverse clinical impact for direct tracking of KPC-producing by MALDI-TOF MS. Journal of Clinical Microbiology. PMID 33980650 DOI: 10.1128/JCM.00238-21  0.153
2020 Cuevas-Ferrando E, Guirado P, Miró E, Iglesias-Torrens Y, Navarro F, Alioto TS, Gómez-Garrido J, Madrid C, Balsalobre C. Tetracycline resistance transmission in Campylobacter is promoted at temperatures resembling the avian reservoir. Veterinary Microbiology. 244: 108652. PMID 32402330 DOI: 10.1016/j.vetmic.2020.108652  0.132
2021 Gato E, Constanso IP, Candela A, Galán F, Rodiño-Janeiro BK, Arroyo MJ, Méndez G, Mancera L, Alioto T, Gut M, Gut I, Álvarez-Tejado M, Rodríguez-Sánchez B, Bou G, Oviaño M. An improved MALDI-TOF MS data analysis pipeline for the identification of carbapenemase-producing . Journal of Clinical Microbiology. PMID 33952594 DOI: 10.1128/JCM.00800-21  0.035
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