Ricardo Lebron; Cristina Gomez-Martin; Pedro Carpena; Pedro Bernaola-Galvan; Guillermo Barturen; Michael Hackenberg; Jose L. Oliver. NGSmethDB 2017: enhanced methylomes and differential methylation; Nucleic Acids Research 2016; doi: 10.1093/nar/gkw996; Full text

Ricardo Lebrón, Guillermo Barturen, Cristina Gómez-Martín, José L Oliver, Michael Hackenberg (2016) MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data. BioRxiv: doi:

Rueda A, Barturen G, Lebrón R, Gómez-Martín C, Alganza A, Oliver JL and Hackenberg M (2015) sRNAtoolbox: an integrated collection of small RNA research tools. Nucleic Acid Research 2015. Advance access.

Dios F., G. Barturen, R. Lebrón, A. Rueda, M. Hackenberg and J.L. Oliver. 2014. DNA clustering and genome complexity. Computational Biology and Chemistry:
DOI: 10.1016/j.compbiolchem.2014.08.011
GitHub repository

Editorial: Complexity in Genomes, Computational Biology and Chemistry, Special issue

Stefanie Geisen, Guillermo Barturen, Ángel M. Alganza, Michael Hackenberg and José L. Oliver. 2014. NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.
Nucl. Acids Res. (1 January 2014) 42 (D1): D53-D59 first published online November 22, 2013 doi:10.1093/nar/gkt1202
AbstractFree Full Text (HTML)Free Full Text (PDF)Free Screen PDF

Barturen G, Rueda A, Oliver JL and Hackenberg M (2014) MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.F1000Research 2014, 2:217
GitHub repository

Guillermo Barturen, Stefanie Geisen, Francisco Dios, E. J. Maarten Hamberg, Michael Hackenberg, and José L. Oliver. 2013. CpGislandEVO: A Database and Genome Browser for Comparative Evolutionary Genomics of CpG Islands.
BioMed Research International, vol. 2013, Article ID 709042, 6 pages, 2013. [PDF].

Pedro Bernaola-Galván, José L. Oliver, Michael Hackenberg, Ana V. Coronado, Plamen Ch. Ivanov, and Pedro Carpena. 2012. Segmentation of time series with long-range fractal correlations
The European Physical Journal B 85: 211 [PDF]

Michael Hackenberg, Antonio Rueda, Pedro Carpena, Pedro Bernaola Galván, Guillermo Barturen and José L. Oliver. 2012.
Clustering of DNA words and biological function: a proof of principle
Journal of Theoretical Biology 297: 127-136 [PDF]

Michael Hackenberg, Guillermo Barturen and José L. Oliver. 2012.
DNA Methylation Profiling from High-Throughput Sequencing Data
In: DNA Methylation – From Genomics to Technology
Dr. Tatiana Tatarinova (Ed.), ISBN: 978-953-51-0320-2, InTech

Pedro Carpena, José L. Oliver, Michael Hackenberg, Ana V. Coronado, Guillermo Barturen and Pedro Bernaola-Galván. 2011.
High-level organization of isochores into gigantic superstructures in the human genome
Physical Review E 83: 031908 (1-7)

Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, Ángel M. Alganza and José L. Oliver. 2011.
WordCluster: detecting clusters of DNA words and genomic elements
Algorithms for Molecular Biology 6:2

Michael Hackenberg, Guillermo Barturen and José L. Oliver. 2010.
NGSmethDB: A database for next-generation sequencing single-cytosine-resolution DNA methylation data
Nucleic Acids Research, 2010, 1–5 [PDF]

Michael Hackenberg, Guillermo Barturen, Pedro Carpena, Pedro L. Luque Escamilla, Christopher Previti, José L. Oliver. 2010.
Prediction of CpG-island function: CpG clustering vs. sliding-window methods
BMC Genomics 2010, 11:327

Carpena P, Bernaola-Galván P, Hackenberg M, Coronado AV, Oliver JL. 2009.
Level statistics of words: finding keywords in literary texts and symbolic sequences
Physical Review E 79: 035102(R) (1-4) [PDF]
Ver la noticia en New Scientist: Could quantum mathematics shake up Google?

Oliver JL, Bernaola-Galván P, Hackenberg M, Carpena P. 2008.
Phylogenetic distribution of large-scale genome patchiness.
BMC Evolutionary Biology 8: 107

Bernaola-Galván P, Carpena P, Oliver JL. 2008.
A standalone version of IsoFinder for the computational prediction of isochores in genome sequences.
arXiv:0806.1292v1 [q-bio.GN] [PDF]

Carpena P, Bernaola-Galván P, Coronado AV, Hackenberg M, Oliver JL. 2007.
Identifying characteristic scales in the human genome.
Physical Review E 75: 032903 [PDF]

Oliver JL. 2006.
Genes de humanidad.
Andalucia Investiga 28: 32 [PDF]

Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Martínez-Aroza J, Oliver JL. 2006.
CpGcluster: A distance-based algorithm for CpG-island detection.
BMC Bioinformatics 7: 446

Oliver JL. 2005.
BioAndalucia 4: 5-7 [PDF]

Luque-Escamilla PL, Martínez-Aroza J, Oliver JL, Gómez-Lopera JF, Román-Roldán R. 2005.
Compositional searching of CpG islands in the human genome.
Physical Review E 71: 6 [PDF]

Hackenberg M, Bernaola-Galván P, Carpena P, Oliver JL. 2005.
The biased distribution of Alus in human isochores might be driven by recombination.
Journal of Molecular Evolution 60: 365-377 [PDF]

Oliver JL, Carpena P, Hackenberg M, Bernaola-Galván P. 2004.
IsoFinder: computational prediction of isochores in genome sequences.
Nucleic Acids Research 32: W287-W292 [PDF]

Hackenberg M, Oliver JL. 2004.
Alu Clustering in the Human Genome: Origins and Consequences.
RECOMB 2004: Eight Annual International Conference on Research in Computational Molecular Biology, San Diego, California (USA) [PDF]

Cabrero J, López León MD, Martínez-Camacho JP, Oliver JL, Perfecti F, Viseras E. 2004.
Plan de Accion Tutorial del Dpto. de Genetica.
Universidad de Granada, Granada ISBN: 84-338-3241-7 [PDF]

Bernaola-Galván P, Oliver JL, Carpena P, Clay O, Bernardi G. 2004.
Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes.
Gene 333: 121-133 [PDF]

Marín A, Oliver JL. 2003.
GC-biased mutation pressure and ORF lengthening.
Journal of Molecular Evolution 56: 371-372 [PDF]

Li W, Bernaola-Galván P, Carpena P, Oliver JL. 2003.
Isochores merit the prefix ‘iso’.
Computational Biology and Chemistry 27: 5-10 [PDF]

Hackenberg M, Oliver JL. 2003.
Alu Evolution and Mutation Pressure.
RECOMB 2003: The Seventh Annual International Conference in Computational Molecular Biology, Berlin. [PDF]

Oliver JL, Carpena P, Román-Roldán R, Mata-Balaguer T, Mejías-Romero A, Hackenberg M, Bernaola-Galván P. 2002.
Isochore chromosome maps of the human genome.
Gene 300: 117-127 [PDF]

Grosse I, Bernaola-Galván P, Carpena P, Román-Roldán R, Oliver J, Stanley HE. 2002.
Analysis of symbolic sequences using the Jensen-Shannon divergence.
Physical Review E 65: 041905 [PDF]

Carpena P, Bernaola-Galván P, Román-Roldán R, Oliver JL. 2002.
A simple and species-independent coding measure.
Gene 300: 97-104 [PDF]

Bernaola-Galván P, Carpena P, Román-Roldán R, Oliver JL. 2002.
Study of statistical correlations in DNA sequences.
Gene 300: 105-115 [PDF]

Oliver JL, Bernaola-Galván P, Carpena P, Román-Roldán R. 2001.
Isochore chromosome maps of eukaryotic genomes.
Gene 276: 47-56 [PDF]

Bernaola-Galván P, Carpena P, Román-Roldán R, Oliver JL. 2001.
Mapping isochores by entropic segmentation of long genome sequences.
RECOMB Proceedings of the Fifth Annual International Conference on Computational Biology, Montreal, Canada. [PDF]

Bernaola-Galván P, Grosse I, Carpena P, Oliver JL, Román-Roldán R, Stanley HE. 2000.
Finding borders between coding and noncoding DNA regions by an entropic segmentation method.
Physical Review Letters 85: 1342-1345 [PDF]

Román Roldán R, Bernaola Galván P, Oliver JL. 1999.
Complejidad de secuencias simbólicas. Aplicación a secuencias de ADN.
Revista Española de Fisica 13: 33-37 [PDF]

Oliver JL, Román-Roldán R, Pérez J, Bernaola-Galván P. 1999.
SEGMENT: identifying compositional domains in DNA sequences.
Bioinformatics 15: 974-979 [PDF]

Marín A, Gutiérrez G, Oliver JL. 1999.
Compositional correlation between open reading frames with opposite transcriptional orientations in Escherichia coli.
Journal of Molecular Evolution 48: 712-716 [PDF]

Bernaola-Galván P, Oliver JL, Román-Roldán R. 1999.
Decomposition of DNA sequence complexity.
Physical Review Letters 83: 3336-3339 [PDF]

Bernaola-Galván P, Carpena P, Román-Roldán R, Oliver JL. 1999.
Compositional complexity of DNA sequence models.
Computer Physics Communications 122: 136-138 [PDF]

Román-Roldán R, Bernaola-Galván P, Oliver JL. 1998.
Sequence compositional complexity of DNA through an entropic segmentation method.
Physical Review Letters 80: 1344-1347 [PDF]

Oliver JL, Li W. 1998.
Quantitative analysis of compositional heterogeneity in long DNA sequences: the two-level segmentation test.
Genome Mapping, Sequencing & Biology, Cold Spring Harbor. [PDF]

Marín A, González F, Gutiérrez G, Oliver JL. 1998.
Gene lengths and GC content.
Nucleic Acids Research 26: 4540-4540 [PDF]

Li W, Stolovitzky G, Bernaola-Galván P, Oliver JL. 1998.
Compositional heterogeneity within, and uniformity between, DNA sequences of yeast chromosomes.
Genome Research 8: 916-928 [PDF]

García E, Jamilena M, Álvarez JI, Arnedo T, Oliver JL, Lozano R. 1998.
Genetic relationships among melon breeding lines revealed by RAPID markers and agronomic traits.
Theoretical and Applied Genetics 96: 878-885 [PDF]

Román-Roldán R, Bernaola-Galván P, Oliver JL. 1996.
Application of information theory to DNA sequence analysis: A review.
Pattern Recognition 29: 1187-1194 [PDF]

Oliver JL, Marín A. 1996.
A relationship between GC content and coding-sequence length.
Journal of Molecular Evolution 43: 216-223 [PDF]

Gutiérrez G, Casadesús J, Oliver JL, Marín A. 1996.
A possible relationship between VSP mismatch repair and gene expression level.
Journal of Molecular Evolution 43: 161-163 [PDF]

Bernaola-Galván P, Román-Roldán R, Oliver JL. 1996.
Compositional segmentation and long-range fractal correlations in DNA sequences.
Physical Review E 53: 5181-5189 [PDF]

Román-Roldán R, Bernaola-Galván P, Oliver JL. 1994.
Entropic Feature for Sequence Pattern through Iterated Function Systems.
Pattern Recognition Letters 15: 567-573 [PDF]

Oliver JL, Román-Roldán R. 1994.
Perfiles entrópicos de secuencias de DNA a través de imágenes caóticas asociadas.
Biología Computacional, A. Moya (ed), pp. 213-235, Universitat de Valéncia (Estudi General), Valencia. [PDF]

Oliver JL, Marín A, Martínez-Zapater JM. 1994.
Maize chloroplast gene transfer to nucleus.
Biotechnology in Agriculture and Forestry, Vol. 25, pp. 431-444. Y. P. S. Bajaj (ed) Springer-Verlag, New York. [PDF]

Marín A, Oliver JL, Medina JR. 1994.
El llenguatge dels gens: ús de codons en gens de vertebrats.
Treballs de la Societat Catalana de Biologia 45: 55-67 [PDF]

Marín A, Gutiérrez G, Oliver JL. 1994.
Uso de codones y preferencias de dinucleótidos: un estudio de las diferencias de composición dentro del genomio humano.
Biología Computacional, A. Moya (ed), pp. 185-197, Universitat de Valéncia (Estudi General), Valencia. [PDF]

Gutiérrez G, Oliver JL, Marín A. 1994.
On the Origin of the Periodicity of 3 in Protein-Coding DNA-Sequences.
Journal of Theoretical Biology 167: 413-414 [PDF]

Gutiérrez G, Casadesús J, Oliver JL, Marín A. 1994.
Compositional Heterogeneity of the Escherichia coli Genome – a Role for Vsp Repair.
Journal of Molecular Evolution 39: 340-346 [PDF]

García-Salcedo JA, Oliver JL, Stock RP, González A. 1994.
Molecular Characterization and Transcription of the Histone H2b Gene from the Protozoan Parasite Trypanosoma cruzi.
Molecular Microbiology 13: 1033-1043 [PDF]

Oliver, JL. 1993.
IX Seminario de Genética de Poblaciones y Evolución, Bubión, Granada. Comentario.
Boletín de la Sociedad Española de Genética, 4: 10-11 [PDF]

Oliver JL, Bernaola-Galván P, Guerrero-García J, Román-Roldán R. 1993.
Entropic Profiles of DNA-Sequences through Chaos-Game-Derived Images.
Journal of Theoretical Biology 160: 457-470 [PDF]

Martínez-Zapater JM, Marín A, Oliver JL. 1993.
Evolution of Base Composition in T-DNA Genes from Agrobacterium.
Molecular Biology and Evolution 10: 437-448 [PDF]

Gutiérrez G, Oliver JL, Marín A. 1993.
Dinucleotides and G+C Content in Human Genes – Opposite Behavior of GpG, GpC, and TpC at II-III Codon Positions and in Introns.
Journal of Molecular Evolution 37: 131-136 [PDF]

Rodríguez F, Oliver JL, Marín A, Medina JR. 1990.
The General Stochastic-Model of Nucleotide Substitution.
Journal of Theoretical Biology 142: 485-501 [PDF]

Oliver JL, Marín A, Martínez-Zapater JM. 1990.
Chloroplast Genes Transferred to the Nuclear-Plant Genome Have Adjusted to Nuclear-Base Composition and Codon Usage.
Nucleic Acids Research 18: 65-73 [PDF]

Oliver JL, Martín-Cuenca E. 1990.
Drift: Simulación de deriva genética.
Prácticas de Genética, A. Jiménez y otros (ed), pp. 329-330, Promociones y Publicaciones Universitarias, Barcelona. [PDF]

Oliver JL. 1990.
La ingeniería genética en plantas.
La Genética en el centenario de Mendel, J. A. Lupiañez and M. Ruiz-Rejón (ed), pp. 203-218, ICE, Universidad de Granada, Granada. [PDF]

Oliver JL, Visedo G, Martínez-Zapater JM. 1989.
Expresión de genes de isoenzimas en tumores provocados por Agrobacterium.
Genética, J. Fdez. Piqueras y. otros (ed), pp. 17-23, Fundación Ramón Areces, Madrid. [PDF]

Oliver JL, Ruiz Rejón M. 1989.
Perspectivas en Genética, Editorial Rueda, Madrid. [PDF]

Oliver JL, Marín A, Medina JR. 1989.
SDSE – a Software Package to Simulate the Evolution of a Pair of DNA-Sequences.
Computer Applications in the Biosciences (actualmente Bioinformatics) 5: 47-50 [PDF]

Oliver JL. 1989.
Manipulación genética en plantas.
Perspectivas en Genética, J. L. Oliver and M. Ruiz Rejón (ed), pp. 205-234, Ed. Rueda, Madrid. [PDF]

Marín A, Bertranpetit J, Oliver JL, Medina JR. 1989.
Variation in G+C-Content and Codon Choice – Differences among Synonymous Codon Groups in Vertebrate Genes.
Nucleic Acids Research 17: 6181-6189 [PDF]

Lop AF, Oliver JL. 1989.
Isozyme Differentiation among Sibling Species and among Populations of the Echinogammarus Berilloni-Group (Crustacea, Amphipoda).
Zeitschrift Fur Zoologische Systematik Und Evolutionsforschung (actualmente Journal of Zoological Systematics and Evolutionary Research) 27: 282-296 [PDF]

Oliver JL, Martínez-Zapater JM. 1988.
Evolución de genes cloroplásticos emigrados al nucleo en trigo y guisante.
Anales de la Estación Experimental de Aula Dei 19: 115-124 [PDF]

Ruiz Rejón M, C. Ruiz Rejón & J.L. Oliver. 1987.
Evolución de los cromosomas B.
Investigación y Ciencia 133: 92-101 [PDF]

Oliver JL, Sanz JL, Amils R, Marín A. 1987.
Inferring the Phylogeny of Archaebacteria – the Use of Ribosomal Sensitivity to Protein-Synthesis Inhibitors.
Journal of Molecular Evolution 24: 281-288 [PDF]

Ruiz Rejón, C, Cabello J, Lozano R, Oliver JL, Ruiz Rejón M. 1987
Electrophoretic detection of two biological species in the polyploid complex Muscari neglectum Guss ex Ten. (Liliaceae)
Isozyme Bulletin 20: 31 [PDF]

Oliver JL. 1986.
Isozyme Gene-Expression in Potato Tumors Incited by Agrobacterium.
Theoretical and Applied Genetics 72: 373-376 [PDF]

Martínez-Zapater JM, Oliver JL. 1986.
Identification of Potato Varieties: An Isozyme Approach.
Solanaceae: Biology and Systematics, W. G. Arcy (ed), pp. 457-467, Columbia University Press, New York. [PDF]

Visedo G, Oliver JL. 1985.
Semilla híbrida de tomate: Determinación de su grado de pureza mediante electroforesis.
TRIA 413: 102-103 [PDF]

Ruiz Rejón M, Pascual L, Ruiz Rejón C, Valdés B, Oliver JL. 1985.
A New Species of Muscari Subgenus Leopoldia from the Iberian Peninsula.
Biochemical Systematics and Ecology 13: 239-250 [PDF]

Oliver JL, Martínez Zapater JM. 1985.
A Genetic Classification of Potato Cultivars Based on Allozyme Patterns.
Theoretical and Applied Genetics 69: 305-311 [PDF]

Oliver JL. 1985.
Isozyme gene expression in callus tissues and crown gall tumors of potato.
Isozyme Bulletin 18: 67 [PDF]

Martínez Zapater JM, Oliver JL. 1985.
Isozyme Gene Duplication in Diploid and Tetraploid Potatoes.
Theoretical and Applied Genetics 70: 172-177 [PDF]

Oliver JL, Martínez Zapater JM. 1984.
Allozyme Variability and Phylogenetic-Relationships in the Cultivated Potato (Solanum tuberosum) and Related Species.
Plant Systematics and Evolution 148: 1-18 [PDF]

Oliver JL, Martínez-Zapater JM. 1984.
Phylogenetic relationships in the cultivated potato (Solanum tuberosum) and related species.
Isozyme Bulletin 17: 67 [PDF]

Martínez-Zapater JM, Oliver JL. 1984.
Tetrasomic inheritance at isozyme loci in the common potato (Solanum tuberosum).
Isozyme Bulletin 17: 68 [PDF]

Martínez Zapater JM, Oliver JL. 1984.
Genetic-Analysis of Isozyme Loci in Tetraploid Potatoes (Solanum tuberosum L.).
Genetics 108: 669-679 [PDF]

Oliver JL, Martínez-Zapater JM, Pascual L, Enríquez AM, Ruiz-Rejón C, Ruiz-Rejón M. 1983.
Different Genome Amplification Mechanisms and Duplicate Gene-Expression in Liliaceae.
Isozymes-Current Topics in Biological and Medical Research 10: 341-363 [PDF]

Ruiz Rejón M, Pérez L, Pascual L, Ruiz Rejón C, López D, Oliver JL. 1982.
An estimate of the outcrossing rate in natural populations of Muscari comosum (Liliaceae).
Isozyme Bulletin 15: 136 [PDF]

Oliver JL, Posse F, Martínez-Zapater JM, Enríquez AM, Ruiz-Rejón M. 1982.
B-Chromosomes and E-1 Isoenzyme Activity in Mosaic Bulbs of Scilla autumnalis (Liliaceae).
Chromosoma 85: 399-403 [PDF]

Ruiz-Rejón M, Oliver JL. 1981.
Genetic-Variability in Muscari comosum (Liliaceae) .1. A Comparative-Analysis of Chromosome Polymorphisms in Spanish and Aegean Populations.
Heredity 47: 403-408 [PDF]

Ruiz Rejón M, Pascual L, Ruiz Rejón C, Oliver JL. 1981.
Asphodelus fistulosus, Asphodelus tenuifolius, Asphodelus ramosus, Asphodelus aestivus, Muscari comosum.
Lagascalia (Números cromosómicos para la Flora española) 10: 247-252 [PDF]

Pascual L, Ruiz Rejón M, Oliver JL, Ruiz Rejón C. 1981.
Existence of gene duplication in ADH-2 of Dipcadi serotinum.
Isozyme Bulletin 14: 56 [PDF]

Ruiz-Rejón M, Posse F, Oliver JL. 1980.
The B-Chromosome System of Scilla autumnalis (Liliaceae) – Effects at the Isoenzyme Level.
Chromosoma 79: 341-348 [PDF]

Ruiz Rejón M, Oliver JL, Ruiz Rejón C, Pascual L, Soto J, Tejero E. 1980.
Scilla autumnalis, Scilla verna, Dipcadi serotinum, Endymion hispanicus, Allium pallens, Crocus nudiflorus.
Lagascalia (Números cromosómicos para la Flora española) 9: 249-254 [PDF]

Ruiz Rejón M, Oliver JL, Ruiz Rejón C. 1980.
Variabilidad cromosomica en Scilla autumnalis L. (Liliaceae) de la Peninsula Iberica.
Boletim da Sociedade Broteriana 53: 555-562 [PDF]

Ruiz Rejón M, Oliver JL. 1980.
Cytogenetic and Electrophoretic Evidence for a Polyploid Origin of the Basic Chromosome-Number X=14 in the Genus Asphodelus (Liliaceae).
Plant Systematics and Evolution 136: 259-265 [PDF]

Posse F, Ruiz Rejón M, Oliver JL. 1980.
Variability of esterase isozymes in Scilla autumnalis (Liliaceae).
Isozyme Bulletin 13: 91 [PDF]

Pascual L, Ruiz Rejón M, Oliver JL, Ruiz Rejón C. 1980.
Existence of ADH gene duplication in the diploid level of Dipcadi serotinum (L.) Medic.
Isozyme Bulletin 13: 63 [PDF]

Oliver JL, Ruiz Rejón M. 1980.
Differential Heat-Sensitivity of Esterase Electromorphs in Natural Polyploid Populations of Urginea maritima (Liliaceae).
Experientia (actualmente Cellular and Molecular Life Sciences) 36: 648-649 [PDF]

Oliver JL, Ruiz Rejón M. 1980.
Relation between Isozymes and Ploidy Level – Its Application to Biogeographical Studies of Muscari atlanticum (Liliaceae).
Taxon 29: 27-32 [PDF]

Ruiz Rejón M, Oliver JL, Posse F. 1978.
Asphodelus ramosus.
Lagascalia (Números cromosómicos para la Flora española) 8: 117-118 [PDF]

Ruiz Rejón M, Oliver JL. 1978.
Scilla autumnalis, Muscari atlanticum.
Lagascalia (Números cromosómicos para la Flora española) 8: 113-117 [PDF]

Ruiz Rejón M, Fernández Piqueras J, Oliver JL. 1978.
Urginea maritima.
Lagascalia (Numeros cromosomicos para la Flora española) 8: 118-120 [PDF]

Oliver JL, Ruiz Rejón M. 1978.
Variability of gene expression in natural populations.
Isozyme Bulletin 11: 63 [PDF]