Publications

Pearman, Peter B. et al. “Genotyping‐By‐Sequencing Resolves Relationships In Polygonaceae Tribe Eriogoneae”. Taxon (2021): n. pag.
Gato, Eva et al. “Occurrence Of The P019 Gene In The Blakpc-Harbouring Plasmids: Adverse Clinical Impact For Direct Tracking Of Kpc-Producing Klebsiella Pneumoniae By Maldi-Tof Ms.”. Journal of Clinical Microbiology (2021): n. pag.
Gato, Eva et al. “An Improved Matrix-Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry Data Analysis Pipeline For The Identification Of Carbapenemase-Producing Klebsiella Pneumoniae.”. Journal of Clinical Microbiology 59.7 (2021): n. pag.
Thomy, Julie et al. “Combining Nanopore And Illumina Sequencing Permits Detailed Analysis Of Insertion Mutations And Structural Variations Produced By Peg-Mediated Transformation In Ostreococcus Tauri.”. Cells 10.3 (2021): n. pag.
Almudi, Isabel et al. “Genomic Adaptations To Aquatic And Aerial Life In Mayflies And The Origin Of Insect Wings.”. Nature Communications 11.1 (2020): 2631+.
Julca, Irene et al. “Genomic Evidence For Recurrent Genetic Admixture During The Domestication Of Mediterranean Olive Trees (Olea Europaea L.)”. BMC Biology 18.1 (2020): 148+.
Cuevas-Ferrando, E et al. “Tetracycline Resistance Transmission In Campylobacter Is Promoted At Temperatures Resembling The Avian Reservoir.”. Veterinary Microbiology 244 (2020): 108652+.
Weil, Tobias et al. “Linking Omics And Ecology To Dissect Interactions Between The Apple Proliferation Phytoplasma And Its Psyllid Vector Cacopsylla Melanoneura.”. Insect Biochemistry and Molecular Biology 127 (2020): 103474+.
Ledoux, Jean-Baptiste et al. “The Genome Sequence Of The Octocoral Paramuricea Clavata - A Key Resource To Study The Impact Of Climate Change In The Mediterranean.”. G3 (Bethesda, Md.) 10.9 (2020): 2941-2952, .
Gerdol, Marco et al. “Massive Gene Presence-Absence Variation Shapes An Open Pan-Genome In The Mediterranean Mussel”. Genome Biology 21.1 (2020): 275+.
Núñez, Ana I et al. “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 14.12 (2020): n. pag.
Julca, Irene et al. “Phylogenomics Identifies An Ancestral Burst Of Gene Duplications Predating The Diversification Of Aphidomorpha”. Molecular Biology and Evolution (2019): n. pag.
Kuderna, Lukas F K et al. “Selective Single Molecule Sequencing And Assembly Of A Human Y Chromosome Of African Origin.”. Nature Communications 10.1 (2019): 4+.
Mosca, Elena et al. “A Reference Genome Sequence For The European Silver Fir (Abies Alba Mill.): A Community-Generated Genomic Resource”. G3: Genes, Genomes, Genetics (2019): n. pag.
Liedtke, Christoph et al. “De Novo Assembly And Annotation Of The Larval Transcriptome Of Two Spadefoot Toads Widely Divergent In Developmental Rate”. G3: Genes, Genomes, Genetics (2019): n. pag.
Montánchez, Itxaso et al. “Analysis Of Vibrio Harveyi Adaptation In Sea Water Microcosms At Elevated Temperature Provides Insights Into The Putative Mechanisms Of Its Persistence And Spread In The Time Of Global Warming”. 9.1 (2019): 289+.
Alioto, Tyler 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 (2019): n. pag.
Alioto, Tyler S. et al. “The Genome Sequence Of The Eastern Woodchuck (Marmota Monax) : A Preclinical Animal Model For Chronic Hepatitis B”. G3: Genes, Genomes, Genetics (2019): n. pag.
Puerma, Eva et al. “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 10.8 (2018): 1956-1969, .
Alioto, Tyler et al. “Using Geneid To Identify Genes.”. Current Protocols in Bioinformatics (2018): n. pag.
Chaves-Pozo, Elena et al. “European Sea Bass Brain Dlb-1 Cell Line Is Susceptible To Nodavirus: A Transcriptomic Study.”. Fish & Shellfish Immunology 86 (2018): 14-24, .
Hernandez, Inmaculada 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 (2018): n. pag.
Kuderna, Lukas F K et al. “A 3-Way Hybrid Approach To Generate A New High-Quality Chimpanzee Reference Genome (Pan_Tro_3.0).”. GigaScience 6.11 (2017): 1-6, .
Chaves-Pozo, Elena et al. “Innate Cell-Mediated Cytotoxic Activity Of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional And Rna-Seq Study.”. Scientific reports 7.1 (2017): 15396+.
Kleinman-Ruiz, Daniel et al. “Novel Efficient Genome-Wide Snp Panels For The Conservation Of The Highly Endangered Iberian Lynx.”. BMC Genomics 18.1 (2017): 556+.
Cruz, Fernando et al. “Genome Sequence Of The Olive Tree, Olea Europaea.”. GigaScience 5 (2016): 29+.
Abascal, Federico et al. “Extreme Genomic Erosion After Recurrent Demographic Bottlenecks In The Highly Endangered Iberian Lynx.”. Genome Biology 17.1 (2016): 251+.
Vlasova, Anna 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 (2016): 32+.
Figueras, Antonio et al. “Whole Genome Sequencing Of Turbot (Scophthalmus Maximus; Pleuronectiformes): A Fish Adapted To Demersal Life.”. DNA Research 23.3 (2016): 181-192, .
Gabaldón, Toni, and Tyler S. Alioto. “Whole-Genome Sequencing Recommendations”. Field Guidelines For Genetic Experimental Designs In High-Throughput Sequencing. Cham: Springer International Publishing, 2016. 13-41, .
Alioto, Tyler S et al. “A Comprehensive Assessment Of Somatic Mutation Detection In Cancer Using Whole-Genome Sequencing.”. Nature Communications 6 (2015): 10001+.
Alioto, Tyler. “The Genome Of The Iberian Lynx”. Plant And Animal Genome Xxiii Conference. Plant and Animal Genome, 2015. Print.
Alioto, Tyler et al. “Aspic-Geneid: A Lightweight Pipeline For Gene Prediction And Alternative Isoforms Detection.”. BioMed research international 2013 (2013): 502827+.
Piqué, Núria et al. “Genome Sequence Of Plesiomonas Shigelloides Strain 302-73 (Serotype O1).”. Genome announcements 1.4 (2013): n. pag.
Djebali, Sarah et al. “Landscape Of Transcription In Human Cells.”. Nature 489.7414 (2012): 101-108, .
Garcia-Mas, Jordi et al. “The Genome Of Melon (Cucumis Melo L.).”. Proceedings of the National Academy of Sciences of the United States of America 109.29 (2012): 11872-11877, .
Alioto, Tyler. “Gene Prediction.”. Methods in Molecular Biology 855 (2012): 175-201, .
Consortium, ENCODE Project. “An Integrated Encyclopedia Of Dna Elements In The Human Genome.”. Nature 489.7414 (2012): 57-74, .
Mudge, Jonathan M et al. “The Origins, Evolution, And Functional Potential Of Alternative Splicing In Vertebrates.”. Molecular Biology and Evolution 28.10 (2011): 2949-2959, .
Consortium, ENCODE Project. “A User's Guide To The Encyclopedia Of Dna Elements (Encode).”. PLoS Biology 9.4 (2011): n. pag.