Publications | CNAG Assembly and Annotation Team

Marcet-Houben, Marina et al. “Genomics Of The Expanding Pine Pathogen Lecanosticta Acicola Reveals Patterns Of Ongoing Genetic Admixture.”. mSystems (2024): n. pag.

Corominas, Montserrat et al. “The Catalan Initiative For The Earth Biogenome Project: Contributing Local Data To Global Biodiversity Genomics.”. NAR Genomics and Bioinformatics 6.3 (2024): n. pag.

Cartney, Ann M Mc et al. “The European Reference Genome Atlas: Piloting A Decentralised Approach To Equitable Biodiversity Genomics.”. npj Biodiversity 3.1 (2024): 28+.

Brown, Tom et al. “Genome Annotation And Other Post-Assembly Workflows For The Tree Of Life”. BioHackrXiv (2024): n. pag.

Destanovik, Dalila et al. “A Chromosome-Level Reference Genome For The Common Octopus, Octopus Vulgaris (Cuvier, 1797)”. G3 Genes|Genomes|Genetics (2023): n. pag.

Gómez-Garrido, Jèssica et al. “Chromosome-Level Genome Assembly Of Lilford's Wall Lizard, Podarcis Lilfordi (Günther, 1874) From The Balearic Islands (Spain).”. DNA Research (2023): n. pag.

de la Herrán, Roberto 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 23.4 (2023): 886-904, .

Theissinger, Kathrin et al. “How Genomics Can Help Biodiversity Conservation.”. Trends in Genetics 39.7 (2023): 545-559, .

Cruz, Fernando et al. “Chromosome-Level Assembly And Annotation Of The Xyrichtys Novacula (Linnaeus, 1758) Genome.”. DNA Research (2023): n. pag.

Theissinger, Kathrin et al. “How Genomics Can Help Biodiversity Conservation.”. Trends in Genetics 39.7 (2023): 545-559, .

Alioto, Tyler S et al. “Development Of A Novel Streamlined Workflow (Aacre) And Database (Incredble) For Genomic Analysis Of Carbapenem-Resistant Enterobacterales.”. Microbial genomics 9.11 (2023): n. pag.

Cobo-Simón, Irene et al. “De Novo Transcriptome Sequencing And Gene Co-Expression Reveal A Genomic Basis For Drought Sensitivity And Evidence Of A Rapid Local Adaptation On Atlas Cedar (Cedrus Atlantica)”. Frontiers in Plant Science 14 (2023): n. pag.

Abelenda, José A. et al. “High Ambient Temperature Impacts On Flowering Time In Brassica Napus Through Both H2A.z-Dependent And Independent Mechanisms”. Plant, Cell \& Environment n/a (2022): n. pag.

Cobo-Simón, Irene et al. “"Contrasting Transcriptomic Patterns Reveal A Genomic Basis For Drought Resilience In The Relict Fir Abies Pinsapo Boiss"”. Tree Physiology (2022): n. pag.

Formenti, Giulio et al. “The Era Of Reference Genomes In Conservation Genomics”. Trends in Ecology & Evolution (2022): n. pag.

Arca-Suárez, Jorge et al. “Emergence Of 16S Rrna Methyltransferases Among Carbapenemase-Producing Enterobacterales In Spain Studied By Whole-Genome Sequencing.”. International Journal of Antimicrobial Agents 59.1 (2022): 106456+.

Guirado, Pedro et al. “A New Variant Of The Aade-Sat4-Apha-3 Gene Cluster Found In A Conjugative Plasmid From A Mdr Campylobacter Jejuni Isolate.”. Antibiotics (Basel, Switzerland) 11.4 (2022): n. pag.

Liedtke, Christoph et al. “Chromosome-Level Assembly, Annotation And Phylome Of Pelobates Cultripes , The Western Spadefoot Toad”. DNA Research (2022): n. pag.

Castro-Arnau, Júlia et al. “Developmental Rna-Seq Transcriptomics Of Haploid Germ Cells And Spermatozoa Uncovers Novel Pathways Associated With Teleost Spermiogenesis.”. Scientific Reports 12.1 (2022): 14162+.

Gómez-Garrido, Jèssica et al. “Assemblatge De Genomes A Escala Cromosòmica Per Redescobrir I Conservar La Biodiversitat Catalana”. 72 (2022): n. pag.

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.

Guerrero-Cózar, Israel et al. “Chromosome Anchoring In Senegalese Sole (Solea Senegalensis) Reveals Sex-Associated Markers And Genome Rearrangements In Flatfish.”. Scientific Reports 11.1 (2021): 13460+.

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.