{"id":12,"date":"2013-05-17T22:38:00","date_gmt":"2013-05-17T20:38:00","guid":{"rendered":"http:\/\/jloliverlab.wordpress.com\/?page_id=7"},"modified":"2023-11-24T18:45:32","modified_gmt":"2023-11-24T16:45:32","slug":"publications","status":"publish","type":"page","link":"https:\/\/bioinfo2.ugr.es\/ceUGR\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

van Eijndhoven MAJ, Scheepbouwer C, Aparicio-Puerta E, Hackenberg M, Pegtel DM. IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution. STAR protocols<\/em>, 2023<\/strong>. https:\/\/doi.org\/10.1016\/j.xpro.2023.102645<\/a><\/p>\n

Scheepbouwer C, Hackenberg M, van Eijndhoven MAJ, Gerber A, Pegtel DM, G\u00f3mez-Mart\u00edn C. NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods. Nucleic Acids Research<\/em>, 2023<\/strong>. https:\/\/doi.org\/10.1093\/nar\/gkad429<\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Aparicio-Puerta E, van Eijndhoven MAJ, Medina JM, Hackenberg M, Pegtel DM. Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing. Cell Reports Methods<\/em>, 2023<\/strong>. https:\/\/doi.org\/10.1016\/j.crmeth.2023.100480<\/a><\/p>\n

Bernaola-Galv\u00e1n, P, Carpena P, G\u00f3mez-Mart\u00edn C, Oliver JL. Compositional Structure of the Genome: A review”.\u00a0Biology,\u00a0<\/em>2023<\/strong>. https:\/\/doi.org\/10.3390\/biology12060849<\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Zhou H, Medina JM, Aparicio-Puerta E, Hackenberg M, Shi B. Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits. Functional & Integrative Genomics, 2023. <\/strong>https:\/\/doi.org\/10.1007\/s10142-022-00920-1<\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Zhou H, Medina JM, Aparicio-Puerta E, Shi B, Hackenberg M. Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions. Biomolecules<\/em>, 2023<\/strong>. https:\/\/doi.org\/10.3390\/biom13030440<\/a><\/p>\n

Medina JM, Abbas MN, Bensaoud C, Hackenberg M, Kotsyfakis M. Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs. International Journal of Molecular Sciences,\u00a0<\/em>2022.\u00a0<\/strong>https:\/\/doi.org\/10.3390\/ijms23179761<\/a><\/p>\n

Medina JM, Jmel MA, Cuveele B, G\u00f3mez-Mart\u00edn C, Aparicio-Puerta E, Mekki I, Kot\u00e1l J, Almeida Martins L, Hackenberg M, Bensaoud C, Kotsyfakis M. Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host. Frontiers in Cellular and Infection Microbiology,<\/em> 2022. <\/strong>https:\/\/doi.org\/10.3389\/fcimb.2022.919786<\/a><\/p>\n

Bensaoud C, Tenzer S, Poplawski A, Medina JM, Jmel MA, Voet H, Mekki I, Aparicio\u2010Puerta E, Cuveele B, Distler U, Marini F, Hackenberg M, Kotsyfakis M.\u00a0Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick\u2010vertebrate host interface. Molecular Ecology,\u00a0<\/em>2022. <\/strong>https:\/\/doi.org\/10.1111\/mec.16561<\/a><\/p>\n

Aparicio-Puerta E, G\u00f3mez-Mart\u00edn C, Giannoukakos S, Medina JM, Scheepbouwer C, Garc\u00eda-Moreno A, Carmona-Saez P, Fromm B, Pegtel DM, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms.\u00a0Nucleic Acids Research, <\/em>2022. <\/strong>https:\/\/doi.org\/10.1093\/nar\/gkac363<\/a><\/p>\n

Fromm B, Zhong X, Tarbier M, Friedl\u00e4nder MR, Hackenberg M. The limits of human microRNA annotation have been met. RNA<\/em>, 2022.<\/strong> https:\/\/10.1261\/rna.079098.122<\/a><\/p>\n

Cristina G\u00f3mez Mart\u00edn, 2021<\/strong>. Variaci\u00f3n gen\u00e9tica asociada a la metilaci\u00f3n diferencial del ADN. Tesis Doctoral, Universidad de Granada<\/p>\n

G\u00f3mez-Mart\u00edn C, Aparicio-Puerta E, Medina JM, Barturen G, Oliver JL, Hackenberg M. geno5<\/sup>mC:a database to explore the association between genetic variation (SNPs) and CpG methylation in the human genome. Journal of Molecular Biology<\/em> 2020. <\/strong>\u00a0https:\/\/doi.org\/10.1016\/j.jmb.2020.11.008<\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Capel, C, Gonz\u00e1lez AM, Lebr\u00f3n R, Yuste-Lisbona FJ, Hackenberg M, Oliver JL, Santalla M, Lozano R. Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris<\/i> L.). Plants<\/em> 2020<\/b>, 9<\/em>, 545. https:\/\/doi.org\/10.3390\/plants9040545<\/a><\/p>\n

Moya A, Oliver JL, Verd\u00fa M, Delaye L, Arnau V, Bernaola-Galv\u00e1n P, de la Fuente R, D\u00edaz W, G\u00f3mez-Mart\u00edn C, Gonz\u00e1lez FM, Latorre A, Lebr\u00f3n R, Rom\u00e1n-Rold\u00e1n R. Driven progressive evolution of genome sequence complexity in Cyanobacteria. Scientific Reports<\/em> 2020, <\/strong>10,\u00a019073. <\/strong>https:\/\/doi.org\/10.1038\/s41598-020-76014-4<\/a><\/p>\n

Ricardo Lebr\u00f3n, 2019<\/strong>. Metilaci\u00f3n diferencial en el genoma humano y su asociaci\u00f3n con la transcripci\u00f3n. Tesis Doctoral, Universidad de Granada. [Tesis<\/a>]\u00a0[Presentaci\u00f3n<\/a>]<\/p>\n

G\u00f3mez-Mart\u00edn C, Lebr\u00f3n R, Oliver JL, Hackenberg M. Prediction of CpG Islands as an Intrinsic Clustering Property Found in Many Eukaryotic DNA Sequences and Its Relation to DNA Methylation. 2018<\/strong> In: Vavouri T., Peinado M. (eds) CpG Islands. Methods in Molecular Biology, vol 1766. Humana Press, New York, NY.\u00a0 DOI:\u00a0<\/abbr><\/span>https:\/\/doi.org\/10.1007\/978-1-4939-7768-0_3<\/span><\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Gonz\u00e1lez AM, Lebr\u00f3n R, Capel C, Yuste-Lisbona FJ, Hackenberg M, Oliver JL, Santalla M, Lozano R. RNA-seq analysis uncovers common bean genes involved in pod maturation and dehiscence. 8th International Conference on Legume Genetics and Genomics (ICLGG). Sept. 18-22, 2017<\/strong>. Si\u00f3fok, Hungary. http:\/\/iclgg2017.hu\/wp-content\/uploads\/2017\/03\/ICLGG2017-Book-of-abstracts.pdf<\/a><\/p>\n

G\u00f3mez-Mart\u00edn C, Lebr\u00f3n R, Rueda A, et al (2017) sRNAtoolboxVM: Small RNA Analysis in a Virtual Machine. In: MicroRNA Detect. Target Identif. Springer, Dalmay T (ed) pp 149\u2013174. Springer. http:\/\/link.springer.com\/protocol\/10.1007%2F978-1-4939-6866-4_12<\/a><\/p>\n

Guillermo Barturen, Jos\u00e9 L. Oliver, Michael Hackenberg (2017). Error Correction in Methylation Profiling From NGS Bisulfite Protocols. In: Algorithms for next-generation sequencing data: techniques, approaches and applications. Mourad Elloumi (editor). Springer.\u00a0https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-59826-0_8<\/a><\/p>\n

Ricardo Lebr\u00f3n, Cristina G\u00f3mez-Mart\u00edn, Pedro Carpena, Pedro Bernaola-Galv\u00e1n, Guillermo Barturen, Michael Hackenberg, Jos\u00e9 L. Oliver. NGSmethDB 2017: enhanced methylomes and differential methylation. Nucleic Acids Res<\/em> 2017; 45 (D1): D97-D103. doi: 10.1093\/nar\/gkw996 Free Full Text<\/a><\/p>\n

Ricardo Lebr\u00f3n, Guillermo Barturen, Cristina G\u00f3mez-Mart\u00edn, Jos\u00e9 L Oliver, Michael Hackenberg (2016) MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data. BioRxiv: http:\/\/biorxiv.org\/content\/early\/2016\/07\/31\/066795<\/a>. doi: http:\/\/dx.doi.org\/10.1101\/066795<\/a><\/p>\n

Cristina G\u00f3mez-Mart\u00edn. 2015. Metilaci\u00f3n diferencial y regiones libres de nucleosomas (NDRs) en el genoma humano. Trabajo Fin de M\u00e1ster, Universidad de Granada.<\/p>\n

Rueda A,\u00a0Barturen G, Lebr\u00f3n R, G\u00f3mez-Mart\u00edn C, Alganza A, Oliver JL and Hackenberg M (2015) sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acid Research<\/strong><\/em> 43 (W1): W467-W473. doi:10.1093\/nar\/gkv555<\/a><\/p>\n

Ricardo Lebr\u00f3n. 2014. Metilaci\u00f3n diferencial en el genoma humano. Trabajo Fin de M\u00e1ster, Universidad de Granada. [Memoria<\/a>]\u00a0[Presentaci\u00f3n<\/a>]<\/p>\n

Dios F., G. Barturen, R. Lebr\u00f3n, A. Rueda, M. Hackenberg and J.L. Oliver. 2014. DNA clustering and genome complexity. <\/span>Computational Biology and Chemistry: <\/strong>http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1476927114000905. <\/a>DOI: 10.1016\/j.compbiolchem.2014.08.011<\/span><\/a>. GitHub repository<\/a>
\nEditorial: Complexity in Genomes, Computational Biology and Chemistry, Special issue<\/a><\/p>\n

Guillermo Barturen. 2014. Regiones gen\u00f3micas implicadas en la metilaci\u00f3n diferencial del ADN.
\nTesis Doctoral, Universidad de Granada. [Tesis<\/a>]\u00a0[Presentaci\u00f3n<\/a>]<\/p>\n

Barturen G, Rueda A, Oliver JL and Hackenberg M (2014)\u00a0MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.F1000Research<\/i>\u00a0<\/strong>2014,\u00a02:217
\ndoi:10.12688\/f1000research.2-217.v2<\/a>
\nGitHub repository<\/a><\/p>\n

Stefanie Geisen, Guillermo Barturen, \u00c1ngel M. Alganza, Michael Hackenberg and Jos\u00e9 L. Oliver. 2014. NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.
\nNucl. Acids Res.<\/strong> (1 January 2014) 42 (D1): D53-D59 first published online November 22, 2013 doi:10.1093\/nar\/gkt1202
\nAbstract<\/a> – Free Full Text (HTML)<\/a> – Free Full Text (PDF)<\/a> – Free Screen PDF<\/a><\/p>\n

Guillermo Barturen, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, and Jos\u00e9 L. Oliver. 2013. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands.
\nBioMed Research International<\/strong>, vol. 2013, Article ID 709042, 6 pages, 2013. [PDF<\/a>].
\nhttp:\/\/dx.doi.org\/10.1155\/2013\/709042<\/a><\/p>\n

Pedro Bernaola-Galv\u00e1n, Jos\u00e9 L. Oliver, Michael Hackenberg, Ana V. Coronado, Plamen Ch. Ivanov, and Pedro Carpena. 2012. Segmentation of time series with long-range fractal correlations
\nThe European Physical Journal B<\/strong> 85: 211 [PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1140\/epjb\/e2012-20969-5<\/a><\/p>\n

Michael Hackenberg, Antonio Rueda, Pedro Carpena, Pedro Bernaola Galv\u00e1n, Guillermo Barturen and Jos\u00e9 L. Oliver. 2012.
\nClustering of DNA words and biological function: a proof of principle
\nJournal of Theoretical Biology<\/strong> 297: 127-136 [PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1016\/j.jtbi.2011.12.024<\/a><\/p>\n

Michael Hackenberg, Guillermo Barturen and Jos\u00e9 L. Oliver. 2012.
\nDNA Methylation Profiling from High-Throughput Sequencing Data
\nIn: DNA Methylation – From Genomics to Technology<\/strong>
\nDr. Tatiana Tatarinova (Ed.), ISBN: 978-953-51-0320-2, InTech
\n[PDF<\/a>]<\/p>\n

Hackenberg, M., Rodriguez-Ezpeleta, N. and Aransay, A.M. (2011) miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments, Nucleic acids research<\/strong>, 39, W132-138.\u00a0PDF<\/a>\u00a0PubMed<\/a><\/p>\n

Pedro Carpena, Jos\u00e9 L. Oliver, Michael Hackenberg, Ana V. Coronado, Guillermo Barturen and Pedro Bernaola-Galv\u00e1n. 2011.
\nHigh-level organization of isochores into gigantic superstructures in the human genome
\nPhysical Review E 83: 031908 (1-7)<\/strong> [PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1103\/PhysRevE.83.031908<\/a><\/p>\n

Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galv\u00e1n, Guillermo Barturen, \u00c1ngel M. Alganza and Jos\u00e9 L. Oliver. 2011.
\nWordCluster: detecting clusters of DNA words and genomic elements
\nAlgorithms for Molecular Biology<\/strong> 6<\/strong>:<\/strong>2
\nhttp:\/\/dx.doi.org\/10.1186\/1748-7188-6-2<\/a><\/p>\n

Michael Hackenberg, Guillermo Barturen and Jos\u00e9 L. Oliver. 2010.
\nNGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data
\nNucleic Acids Research<\/strong>, 2010, 1\u20135 [<\/a>PDF<\/a>]<\/a>
\nhttp:\/\/dx.doi.org\/10.1093\/nar\/gkq942<\/a><\/p>\n

Michael Hackenberg, Guillermo Barturen, Pedro Carpena, Pedro L. Luque Escamilla, Christopher Previti, Jos\u00e9 L. Oliver. 2010.
\nPrediction of CpG-island function: CpG clustering vs. sliding-window methods
\nBMC Genomics 2010, 11:<\/strong>327<\/strong>
\n<\/strong>http:\/\/dx.doi.org\/10.1186\/1471-2164-11-327<\/a><\/p>\n

Hackenberg, M., Sturm, M., Langenberger, D., Falcon-Perez, J.M. and Aransay, A.M. (2009) miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments, Nucleic acids research<\/strong>, 37, W68-76.\u00a0PDF<\/a>\u00a0PubMed<\/a><\/p>\n

Carpena P, Bernaola-Galv\u00e1n P, Hackenberg M, Coronado AV, Oliver JL. 2009.
\nLevel statistics of words: finding keywords in literary texts and symbolic sequences
\nPhysical Review E 79: 035102(R) (1-4) <\/strong>[PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1103\/PhysRevE.79.035102<\/a>
\nVer la noticia en New Scientist<\/strong>: Could quantum mathematics shake up Google?<\/a><\/p>\n

Oliver JL, Bernaola-Galv\u00e1n P, Hackenberg M, Carpena P. 2008.
\nPhylogenetic distribution of large-scale genome patchiness.
\nBMC Evolutionary Biology 8: 107<\/strong>
\nhttp:\/\/dx.doi.org\/10.1186\/1471-2148-8-107<\/a><\/p>\n

Bernaola-Galv\u00e1n P, Carpena P, Oliver JL. 2008.
\nA standalone version of IsoFinder for the computational prediction of isochores in genome sequences.
\narXiv:0806.1292v1<\/a> [q-bio.GN] <\/strong>[PDF<\/a>]<\/p>\n

Carpena P, Bernaola-Galv\u00e1n P, Coronado AV, Hackenberg M, Oliver JL. 2007.
\nIdentifying characteristic scales in the human genome.
\nPhysical Review E 75: 032903 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL. 2006.
\nGenes de humanidad.
\nAndalucia Investiga 28: 32 <\/strong>[PDF<\/a>]<\/p>\n

Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Mart\u00ednez-Aroza J, Oliver JL. 2006.
\nCpGcluster: A distance-based algorithm for CpG-island detection.
\nBMC Bioinformatics 7: 446<\/strong>
\nhttp:\/\/dx.doi.org\/10.1186\/1471-2105-7-446<\/a><\/p>\n

Oliver JL. 2005.
\nBioinform\u00e1tica.
\nBioAndalucia 4: 5-7 <\/strong>[PDF<\/a>]<\/p>\n

Luque-Escamilla PL, Mart\u00ednez-Aroza J, Oliver JL, G\u00f3mez-Lopera JF, Rom\u00e1n-Rold\u00e1n R. 2005.
\nCompositional searching of CpG islands in the human genome.
\nPhysical Review E 71: 6<\/strong> [PDF<\/a>]<\/p>\n

Hackenberg M, Bernaola-Galv\u00e1n P, Carpena P, Oliver JL. 2005.
\nThe biased distribution of Alus in human isochores might be driven by recombination.
\nJournal of Molecular Evolution 60: 365-377<\/strong> [PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1007\/s00239-004-0197-2<\/a><\/p>\n

Hackenberg, M. 2005.
\nDin\u00e1mica evolutiva de los retrotransposones Alu en el genoma humano.
\nTesis Doctoral, Universidad de Granada.
\nhttp:\/\/bioinfo2.ugr.es\/Publicaciones\/tesis_MH.pdf<\/a><\/p>\n

Oliver JL, Carpena P, Hackenberg M, Bernaola-Galv\u00e1n P. 2004.
\nIsoFinder: computational prediction of isochores in genome sequences.
\nNucleic Acids Research 32: W287-W292<\/strong> [PDF<\/a>]
\nhttp:\/\/dx.doi.org\/10.1093\/nar\/gkh399<\/a><\/p>\n

Hackenberg M, Oliver JL. 2004.
\nAlu Clustering in the Human Genome: Origins and Consequences.
\nRECOMB 2004: Eight Annual International Conference on Research in Computational Molecular Biology, San Diego, California (USA)<\/strong> [PDF<\/a>]<\/p>\n

Cabrero J, L\u00f3pez Le\u00f3n MD, Mart\u00ednez-Camacho JP, Oliver JL, Perfecti F, Viseras E. 2004.
\nPlan de Accion Tutorial del Dpto. de Genetica.
\nUniversidad de Granada, Granada ISBN: 84-338-3241-7 <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Oliver JL, Carpena P, Clay O, Bernardi G. 2004.
\nQuantifying intrachromosomal GC heterogeneity in prokaryotic genomes.
\nGene 333: 121-133 <\/strong>[PDF<\/a>]<\/p>\n

Mar\u00edn A, Oliver JL. 2003.
\nGC-biased mutation pressure and ORF lengthening.
\nJournal of Molecular Evolution 56: 371-372 <\/strong>[PDF<\/a>]<\/p>\n

Li W, Bernaola-Galv\u00e1n P, Carpena P, Oliver JL. 2003.
\nIsochores merit the prefix ‘iso’.
\nComputational Biology and Chemistry 27: 5-10<\/strong> [PDF<\/a>]<\/p>\n

Hackenberg M, Oliver JL. 2003.
\nAlu Evolution and Mutation Pressure.
\nRECOMB 2003: The Seventh Annual International Conference in Computational Molecular Biology, Berlin.<\/strong> [PDF<\/a>]<\/p>\n

Oliver JL, Carpena P, Rom\u00e1n-Rold\u00e1n R, Mata-Balaguer T, Mej\u00edas-Romero A, Hackenberg M, Bernaola-Galv\u00e1n P. 2002.
\nIsochore chromosome maps of the human genome.
\nGene 300: 117-127<\/strong> [PDF<\/a>]<\/p>\n

Grosse I, Bernaola-Galv\u00e1n P, Carpena P, Rom\u00e1n-Rold\u00e1n R, Oliver J, Stanley HE. 2002.
\nAnalysis of symbolic sequences using the Jensen-Shannon divergence.
\nPhysical Review E 65: 041905<\/strong> [PDF<\/a>]<\/p>\n

Carpena P, Bernaola-Galv\u00e1n P, Rom\u00e1n-Rold\u00e1n R, Oliver JL. 2002.
\nA simple and species-independent coding measure.
\nGene 300: 97-104<\/strong> [PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Carpena P, Rom\u00e1n-Rold\u00e1n R, Oliver JL. 2002.
\nStudy of statistical correlations in DNA sequences.
\nGene 300: 105-115 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Bernaola-Galv\u00e1n P, Carpena P, Rom\u00e1n-Rold\u00e1n R. 2001.
\nIsochore chromosome maps of eukaryotic genomes.
\nGene 276: 47-56 <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Carpena P, Rom\u00e1n-Rold\u00e1n R, Oliver JL. 2001.
\nMapping isochores by entropic segmentation of long genome sequences.
\nRECOMB Proceedings of the Fifth Annual International Conference on Computational Biology, Montreal, Canada. <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Grosse I, Carpena P, Oliver JL, Rom\u00e1n-Rold\u00e1n R, Stanley HE. 2000.
\nFinding borders between coding and noncoding DNA regions by an entropic segmentation method.
\nPhysical Review Letters 85: 1342-1345 <\/strong>[PDF<\/a>]<\/p>\n

Rom\u00e1n Rold\u00e1n R, Bernaola Galv\u00e1n P, Oliver JL. 1999.
\nComplejidad de secuencias simb\u00f3licas. Aplicaci\u00f3n a secuencias de ADN.
\nRevista Espa\u00f1ola de Fisica 13: 33-37 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Rom\u00e1n-Rold\u00e1n R, P\u00e9rez J, Bernaola-Galv\u00e1n P. 1999.
\nSEGMENT: identifying compositional domains in DNA sequences.
\nBioinformatics 15: 974-979 <\/strong><\/a>[PDF<\/a>]<\/p>\n

Mar\u00edn A, Guti\u00e9rrez G, Oliver JL. 1999.
\nCompositional correlation between open reading frames with opposite transcriptional orientations in Escherichia coli<\/em>.
\nJournal of Molecular Evolution 48: 712-716 <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Oliver JL, Rom\u00e1n-Rold\u00e1n R. 1999.
\nDecomposition of DNA sequence complexity.
\nPhysical Review Letters 83: 3336-3339 <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Carpena P, Rom\u00e1n-Rold\u00e1n R, Oliver JL. 1999.
\nCompositional complexity of DNA sequence models.
\nComputer Physics Communications 122: 136-138 <\/strong>[PDF<\/a>]<\/p>\n

Rom\u00e1n-Rold\u00e1n R, Bernaola-Galv\u00e1n P, Oliver JL. 1998.
\nSequence compositional complexity of DNA through an entropic segmentation method.
\nPhysical Review Letters 80: 1344-1347 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Li W. 1998.
\nQuantitative analysis of compositional heterogeneity in long DNA sequences: the two-level segmentation test.
\nGenome Mapping, Sequencing & Biology, Cold Spring Harbor. <\/strong>[PDF<\/a>]<\/p>\n

Mar\u00edn A, Gonz\u00e1lez F, Guti\u00e9rrez G, Oliver JL. 1998.
\nGene lengths and GC content.
\nNucleic Acids Research 26: 4540-4540<\/strong> [PDF<\/a>]<\/p>\n

Li W, Stolovitzky G, Bernaola-Galv\u00e1n P, Oliver JL. 1998.
\nCompositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes.
\nGenome Research 8: 916-928 <\/strong>[PDF<\/a>]<\/p>\n

Garc\u00eda E, Jamilena M, \u00c1lvarez JI, Arnedo T, Oliver JL, Lozano R. 1998.
\nGenetic relationships among melon breeding lines revealed by RAPID markers and agronomic traits.
\nTheoretical and Applied Genetics 96: 878-885 <\/strong>[PDF<\/a>]<\/p>\n

Rom\u00e1n-Rold\u00e1n R, Bernaola-Galv\u00e1n P, Oliver JL. 1996.
\nApplication of information theory to DNA sequence analysis: A review.
\nPattern Recognition 29: 1187-1194 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mar\u00edn A. 1996.
\nA relationship between GC content and coding-sequence length.
\nJournal of Molecular Evolution 43: 216-223 <\/strong>[PDF<\/a>]<\/p>\n

Guti\u00e9rrez G, Casades\u00fas J, Oliver JL, Mar\u00edn A. 1996.
\nA possible relationship between VSP mismatch repair and gene expression level.
\nJournal of Molecular Evolution 43: 161-163 <\/strong>[PDF<\/a>]<\/p>\n

Bernaola-Galv\u00e1n P, Rom\u00e1n-Rold\u00e1n R, Oliver JL. 1996.
\nCompositional segmentation and long-range fractal correlations in DNA sequences.
\nPhysical Review E 53: 5181-5189 <\/strong>[PDF<\/a>]<\/p>\n

Rom\u00e1n-Rold\u00e1n R, Bernaola-Galv\u00e1n P, Oliver JL. 1994.
\nEntropic Feature for Sequence Pattern through Iterated Function Systems.
\nPattern Recognition Letters 15: 567-573 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Rom\u00e1n-Rold\u00e1n R. 1994.
\nPerfiles entr\u00f3picos de secuencias de DNA a trav\u00e9s de im\u00e1genes ca\u00f3ticas asociadas.
\nBiolog\u00eda Computacional, A. Moya (ed), pp. 213-235, Universitat de Val\u00e9ncia (Estudi General), Valencia. <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mar\u00edn A, Mart\u00ednez-Zapater JM. 1994.
\nMaize chloroplast gene transfer to nucleus.
\nBiotechnology in Agriculture and Forestry, Vol. 25, pp. 431-444. Y. P. S. Bajaj (ed) Springer-Verlag, New York.<\/strong> [PDF<\/a>]<\/p>\n

Mar\u00edn A, Oliver JL, Medina JR. 1994.
\nEl llenguatge dels gens: \u00fas de codons en gens de vertebrats.
\nTreballs de la Societat Catalana de Biologia 45: 55-67 <\/strong>[PDF<\/a>]<\/p>\n

Mar\u00edn A, Guti\u00e9rrez G, Oliver JL. 1994.
\nUso de codones y preferencias de dinucle\u00f3tidos: un estudio de las diferencias de composici\u00f3n dentro del genomio humano.
\nBiolog\u00eda Computacional, A. Moya (ed), pp. 185-197, Universitat de Val\u00e9ncia (Estudi General), Valencia. <\/strong>[PDF<\/a>]<\/p>\n

Guti\u00e9rrez G, Oliver JL, Mar\u00edn A. 1994.
\nOn the Origin of the Periodicity of 3 in Protein-Coding DNA-Sequences.
\nJournal of Theoretical Biology 167: 413-414 <\/strong>[PDF<\/a>]<\/p>\n

Guti\u00e9rrez G, Casades\u00fas J, Oliver JL, Mar\u00edn A. 1994.
\nCompositional Heterogeneity of the Escherichia coli<\/em> Genome – a Role for Vsp Repair.
\nJournal of Molecular Evolution 39: 340-346 <\/strong>[PDF<\/a>]<\/p>\n

Garc\u00eda-Salcedo JA, Oliver JL, Stock RP, Gonz\u00e1lez A. 1994.
\nMolecular Characterization and Transcription of the Histone H2b Gene from the Protozoan Parasite Trypanosoma cruzi.<\/em>
\nMolecular Microbiology 13: 1033-1043 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Bernaola-Galv\u00e1n P, Guerrero-Garc\u00eda J, Rom\u00e1n-Rold\u00e1n R. 1993.
\nEntropic Profiles of DNA-Sequences through Chaos-Game-Derived Images.
\nJournal of Theoretical Biology 160: 457-470 <\/strong>[PDF<\/a>]<\/p>\n

Mart\u00ednez-Zapater JM, Mar\u00edn A, Oliver JL. 1993.
\nEvolution of Base Composition in T-DNA Genes from Agrobacterium<\/em>.
\nMolecular Biology and Evolution 10: 437-448 <\/strong>[PDF<\/a>]<\/p>\n

Guti\u00e9rrez G, Oliver JL, Mar\u00edn A. 1993.
\nDinucleotides and G+C Content in Human Genes – Opposite Behavior of GpG, GpC, and TpC at II-III Codon Positions and in Introns.
\nJournal of Molecular Evolution 37: 131-136 <\/strong>[PDF<\/a>]<\/p>\n

Rodr\u00edguez F, Oliver JL, Mar\u00edn A, Medina JR. 1990.
\nThe General Stochastic-Model of Nucleotide Substitution.
\nJournal of Theoretical Biology 142: 485-501 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mar\u00edn A, Mart\u00ednez-Zapater JM. 1990.
\nChloroplast Genes Transferred to the Nuclear-Plant Genome Have Adjusted to Nuclear-Base Composition and Codon Usage.
\nNucleic Acids Research 18: 65-73 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00edn-Cuenca E. 1990.
\nDrift: Simulaci\u00f3n de deriva gen\u00e9tica.
\nPr\u00e1cticas de Gen\u00e9tica, A. Jim\u00e9nez y otros (ed), pp. 329-330, Promociones y Publicaciones Universitarias, Barcelona. <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL. 1990.
\nLa ingenier\u00eda gen\u00e9tica en plantas.
\nLa Gen\u00e9tica en el centenario de Mendel, J. A. Lupia\u00f1ez and M. Ruiz-Rej\u00f3n (ed), pp. 203-218, ICE, Universidad de Granada, Granada. <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Visedo G, Mart\u00ednez-Zapater JM. 1989.
\nExpresi\u00f3n de genes de isoenzimas en tumores provocados por Agrobacterium<\/em>.
\nGen\u00e9tica, J. Fdez. Piqueras y. otros (ed), pp. 17-23, Fundaci\u00f3n Ram\u00f3n Areces, Madrid. <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Ruiz Rej\u00f3n M. 1989.
\nPerspectivas en Gen\u00e9tica, Editorial Rueda, Madrid. <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mar\u00edn A, Medina JR. 1989.
\nSDSE – a Software Package to Simulate the Evolution of a Pair of DNA-Sequences.
\nComputer Applications in the Biosciences (actualmente Bioinformatics) 5: 47-50 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL. 1989.
\nManipulaci\u00f3n gen\u00e9tica en plantas.
\nPerspectivas en Gen\u00e9tica, J. L. Oliver and M. Ruiz Rej\u00f3n (ed), pp. 205-234, Ed. Rueda, Madrid. <\/strong>[PDF<\/a>]<\/p>\n

Mar\u00edn A, Bertranpetit J, Oliver JL, Medina JR. 1989.
\nVariation in G+C-Content and Codon Choice – Differences among Synonymous Codon Groups in Vertebrate Genes.
\nNucleic Acids Research 17: 6181-6189 <\/strong>[PDF<\/a>]<\/p>\n

Lop AF, Oliver JL. 1989.
\nIsozyme Differentiation among Sibling Species and among Populations of the Echinogammarus Berilloni<\/em>-Group (Crustacea, Amphipoda).
\nZeitschrift Fur Zoologische Systematik Und Evolutionsforschung (actualmente Journal of Zoological Systematics and Evolutionary Research) 27: 282-296 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00ednez-Zapater JM. 1988.
\nEvoluci\u00f3n de genes cloropl\u00e1sticos emigrados al nucleo en trigo y guisante.
\nAnales de la Estaci\u00f3n Experimental de Aula Dei 19: 115-124 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, C. Ruiz Rej\u00f3n & J.L. Oliver. 1987.
\nEvoluci\u00f3n de los cromosomas B.
\nInvestigaci\u00f3n y Ciencia 133: 92-101 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Sanz JL, Amils R, Mar\u00edn A. 1987.
\nInferring the Phylogeny of Archaebacteria – the Use of Ribosomal Sensitivity to Protein-Synthesis Inhibitors.
\nJournal of Molecular Evolution 24: 281-288<\/strong> [PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n, C, Cabello J, Lozano R, Oliver JL, Ruiz Rej\u00f3n M. 1987
\nElectrophoretic detection of two biological species in the polyploid complex Muscari neglectum<\/em> Guss ex Ten. (Liliaceae)
\nIsozyme Bulletin 20: 31 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL. 1986.
\nIsozyme Gene-Expression in Potato Tumors Incited by Agrobacterium<\/em>.
\nTheoretical and Applied Genetics 72: 373-376 <\/strong>[PDF<\/a>]<\/p>\n

Mart\u00ednez-Zapater JM, Oliver JL. 1986.
\nIdentification of Potato Varieties: An Isozyme Approach.
\nSolanaceae: Biology and Systematics, W. G. Arcy (ed), pp. 457-467, Columbia University Press, New York. <\/strong>[PDF<\/a>]<\/p>\n

Visedo G, Oliver JL. 1985.
\nSemilla h\u00edbrida de tomate: Determinaci\u00f3n de su grado de pureza mediante electroforesis.
\nTRIA 413: 102-103 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Pascual L, Ruiz Rej\u00f3n C, Vald\u00e9s B, Oliver JL. 1985.
\nA New Species of Muscari<\/em> Subgenus Leopoldia<\/em> from the Iberian Peninsula.
\nBiochemical Systematics and Ecology 13: 239-250 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00ednez Zapater JM. 1985.
\nA Genetic Classification of Potato Cultivars Based on Allozyme Patterns.
\nTheoretical and Applied Genetics 69: 305-311<\/strong> [PDF<\/a>]<\/p>\n

Oliver JL. 1985.
\nIsozyme gene expression in callus tissues and crown gall tumors of potato.
\nIsozyme Bulletin 18: 67 <\/strong>[PDF<\/a>]<\/p>\n

Mart\u00ednez Zapater JM, Oliver JL. 1985.
\nIsozyme Gene Duplication in Diploid and Tetraploid Potatoes.
\nTheoretical and Applied Genetics 70: 172-177 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00ednez Zapater JM. 1984.
\nAllozyme Variability and Phylogenetic-Relationships in the Cultivated Potato (Solanum tuberosum<\/em>) and Related Species.
\nPlant Systematics and Evolution 148: 1-18 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00ednez-Zapater JM. 1984.
\nPhylogenetic relationships in the cultivated potato (Solanum tuberosum<\/em>) and related species.
\nIsozyme Bulletin 17: 67 <\/strong>[PDF<\/a>]<\/p>\n

Mart\u00ednez-Zapater JM, Oliver JL. 1984.
\nTetrasomic inheritance at isozyme loci in the common potato (Solanum tuberosum<\/em>).
\nIsozyme Bulletin 17: 68 <\/strong>[PDF<\/a>]<\/p>\n

Mart\u00ednez Zapater JM, Oliver JL. 1984.
\nGenetic-Analysis of Isozyme Loci in Tetraploid Potatoes (Solanum tuberosum<\/em> L.).
\nGenetics 108: 669-679 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Mart\u00ednez-Zapater JM, Pascual L, Enr\u00edquez AM, Ruiz-Rej\u00f3n C, Ruiz-Rej\u00f3n M. 1983.
\nDifferent Genome Amplification Mechanisms and Duplicate Gene-Expression in Liliaceae.
\nIsozymes-Current Topics in Biological and Medical Research 10: 341-363 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, P\u00e9rez L, Pascual L, Ruiz Rej\u00f3n C, L\u00f3pez D, Oliver JL. 1982.
\nAn estimate of the outcrossing rate in natural populations of Muscari comosum<\/em> (Liliaceae).
\nIsozyme Bulletin 15: 136<\/strong> [PDF<\/a>]<\/p>\n

Oliver JL, Posse F, Mart\u00ednez-Zapater JM, Enr\u00edquez AM, Ruiz-Rej\u00f3n M. 1982.
\nB-Chromosomes and E-1 Isoenzyme Activity in Mosaic Bulbs of Scilla autumnalis<\/em> (Liliaceae).
\nChromosoma 85: 399-403 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz-Rej\u00f3n M, Oliver JL. 1981.
\nGenetic-Variability in Muscari comosum<\/em> (Liliaceae) .1. A Comparative-Analysis of Chromosome Polymorphisms in Spanish and Aegean Populations.
\nHeredity 47: 403-408 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Pascual L, Ruiz Rej\u00f3n C, Oliver JL. 1981.
\nAsphodelus fistulosus, Asphodelus tenuifolius, Asphodelus ramosus, Asphodelus aestivus, Muscari comosum. <\/em>
\nLagascalia (N\u00fameros cromos\u00f3micos para la Flora espa\u00f1ola) 10: 247-252 <\/strong>[PDF<\/a>]<\/p>\n

Pascual L, Ruiz Rej\u00f3n M, Oliver JL, Ruiz Rej\u00f3n C. 1981.
\nExistence of gene duplication in ADH-2 of Dipcadi serotinum<\/em>.
\nIsozyme Bulletin 14: 56 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz-Rej\u00f3n M, Posse F, Oliver JL. 1980.
\nThe B-Chromosome System of Scilla autumnalis<\/em> (Liliaceae) – Effects at the Isoenzyme Level.
\nChromosoma 79: 341-348 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Oliver JL, Ruiz Rej\u00f3n C, Pascual L, Soto J, Tejero E. 1980.
\nScilla autumnalis, Scilla verna, Dipcadi serotinum, Endymion hispanicus, Allium pallens, Crocus nudiflorus. <\/em>
\nLagascalia (N\u00fameros cromos\u00f3micos para la Flora espa\u00f1ola) 9: 249-254<\/strong> [PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Oliver JL, Ruiz Rej\u00f3n C. 1980.
\nVariabilidad cromosomica en Scilla autumnalis<\/em> L. (Liliaceae) de la Peninsula Iberica.
\nBoletim da Sociedade Broteriana 53: 555-562 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Oliver JL. 1980.
\nCytogenetic and Electrophoretic Evidence for a Polyploid Origin of the Basic Chromosome-Number X=14 in the Genus Asphodelus<\/em> (Liliaceae).
\nPlant Systematics and Evolution 136: 259-265<\/strong> [PDF<\/a>]<\/p>\n

Posse F, Ruiz Rej\u00f3n M, Oliver JL. 1980.
\nVariability of esterase isozymes in Scilla autumnalis<\/em> (Liliaceae).
\nIsozyme Bulletin 13: 91 <\/strong>[PDF<\/a>]<\/p>\n

Pascual L, Ruiz Rej\u00f3n M, Oliver JL, Ruiz Rej\u00f3n C. 1980.
\nExistence of ADH gene duplication in the diploid level of Dipcadi serotinum<\/em> (L.) Medic.
\nIsozyme Bulletin 13: 63 <\/strong>[PDF<\/a>]<\/p>\n

Oliver JL, Ruiz Rej\u00f3n M. 1980.
\nDifferential Heat-Sensitivity of Esterase Electromorphs in Natural Polyploid Populations of Urginea maritima<\/em> (Liliaceae).
\nExperientia (actualmente Cellular and Molecular Life Sciences) 36: 648-649<\/strong> [PDF<\/a>]<\/p>\n

Oliver JL, Ruiz Rej\u00f3n M. 1980.
\nRelation between Isozymes and Ploidy Level – Its Application to Biogeographical Studies of Muscari atlanticum<\/em> (Liliaceae).
\nTaxon 29: 27-32 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Oliver JL, Posse F. 1978.
\nAsphodelus ramosus. <\/em>
\nLagascalia (N\u00fameros cromos\u00f3micos para la Flora espa\u00f1ola) 8: 117-118 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Oliver JL. 1978.
\nScilla autumnalis, Muscari atlanticum. <\/em>
\nLagascalia (N\u00fameros cromos\u00f3micos para la Flora espa\u00f1ola) 8: 113-117 <\/strong>[PDF<\/a>]<\/p>\n

Ruiz Rej\u00f3n M, Fern\u00e1ndez Piqueras J, Oliver JL. 1978.
\nUrginea maritima. <\/em>
\nLagascalia (Numeros cromosomicos para la Flora espa\u00f1ola) 8: 118-120<\/strong> [PDF<\/a>]<\/p>\n

Oliver JL, Ruiz Rej\u00f3n M. 1978.
\nVariability of gene expression in natural populations.
\nIsozyme Bulletin 11: 63 <\/strong>[PDF<\/a>]<\/p>\n","protected":false},"excerpt":{"rendered":"

van Eijndhoven MAJ, Scheepbouwer C, Aparicio-Puerta E, Hackenberg M, Pegtel DM. IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution. STAR protocols, 2023. https:\/\/doi.org\/10.1016\/j.xpro.2023.102645 Scheepbouwer C, Hackenberg M, van Eijndhoven MAJ, Gerber A, Pegtel …<\/p>\n

Publications<\/span> Read More »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":18,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/12"}],"collection":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/comments?post=12"}],"version-history":[{"count":11,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/12\/revisions"}],"predecessor-version":[{"id":1465,"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/pages\/12\/revisions\/1465"}],"wp:attachment":[{"href":"https:\/\/bioinfo2.ugr.es\/ceUGR\/wp-json\/wp\/v2\/media?parent=12"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}