Jose L. Oliver

Jose L. Oliver
University of Granada | UGR · Department of Genetics

PhD

About

146
Publications
14,927
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5,869
Citations
Citations since 2017
11 Research Items
1180 Citations
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200
2017201820192020202120222023050100150200
Additional affiliations
January 1975 - February 1987
Universidad Autónoma de Madrid
October 1974 - present
Universidad de Granada

Publications

Publications (146)
Article
Full-text available
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyze...
Preprint
Full-text available
Disclaimer text The author has withdrawn this manuscript due to a duplicate posting of manuscript number BIORXIV/2021/467547. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Article
Full-text available
Trichomes are specialised epidermal cells developed in the aerial surface of almost every terrestrial plant. These structures form physical barriers, which combined with their capability of synthesis of complex molecules, prevent plagues from spreading and confer trichomes a key role in the defence against herbivores. In this work, the tomato gene...
Preprint
In the brief time since the outbreak of the COVID 19 pandemic, and despite its proofreading mechanism, the SARS-CoV-2 coronavirus has accumulated a significant amount of genetic variability through recombination and mutation events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize...
Article
Full-text available
Progressive evolution, or the tendency towards increasing complexity, is a controversial issue in biology, which resolution entails a proper measurement of complexity. Genomes are the best entities to address this challenge, as they encode the historical information of a species’ biotic and environmental interactions. As a case study, we have measu...
Article
Full-text available
Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in tw...
Preprint
Full-text available
Progressive evolution, the tendency towards increasing complexity, is a controversial issue in Biology, whose resolution requires a proper measurement of complexity. Genomes are the best entities to address this challenge, as they record the history and information gaining of organisms in their ongoing biotic and environmental interactions. Using s...
Article
Full-text available
Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA r...
Chapter
The promoter region of around 70% of all genes in the human genome is overlapped by a CpG island (CGI). CGIs have known functions in the transcription initiation and outstanding compositional features like high G+C content and CpG ratios when compared to the bulk DNA. We have shown before that CGIs manifest as clusters of CpGs in mammalian genomes...
Chapter
Whole genome bisulfite sequencing (WGBS) has emerged as the primary technique for DNA methylation studies, because of its great potential in terms of speed, specificity, and the capability of addressing new biological implications as non-CpG context methylation or hemimethylation. However, despite the improvement that has meant the appearance of WG...
Chapter
High-throughput sequencing (HTS) data for small RNAs (noncoding RNA molecules that are 20–250 nucleotides in length) can now be routinely generated by minimally equipped wet laboratories; however, the bottleneck in HTS-based research has shifted now to the analysis of such huge amount of data. One of the reasons is that many analysis types require...
Article
Full-text available
The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly mode...
Poster
Full-text available
In recent years, small RNA molecules have become one of the most interesting topics in genomics. This is due to its role in many vital processes such as cell differentiation [1]. More recently, microRNAs were shown to be useful as prognostic and diagnostic biomarkers, therapeutic agent in medicine [2], or as transgenes in plant science [3], among o...
Poster
Full-text available
Gene expression in eukaryotes is a regulated process that takes place both at the pre- and post-transcriptional level. Prior to transcription, the chromatin state needs to change mainly due to several epigenetic marks such as the addition of methyl-groups to either DNA or histone residues. Once the promoter and other regulatory regions such as enha...
Article
Full-text available
Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types of functional small RNA molecules have been reported in animals and plants. MicroRNAs are important in host-microbe interactions and parasite microRNAs might modulate the innate immunity of the host. Furthermore, small...
Article
Full-text available
Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling...
Article
Full-text available
The updated release of 'NGSmethDB' (http://bioinfo2.ugr.es/NGSmethDB) is a repository for single-base whole-genome methylome maps for the best-assembled eukaryotic genomes. Short-read data sets from NGS bisulfite-sequencing projects of cell lines, fresh and pathological tissues are first pre-processed and aligned to the corresponding reference geno...
Article
Full-text available
Whole genome methylation profiling at a single cytosine resolution is now feasible due to the advent of high-throughput sequencing techniques together with bisulfite treatment of the DNA. To obtain the methylation value of each individual cytosine, the bisulfite-treated sequence reads are first aligned to a reference genome, and then the profiling...
Article
Full-text available
Hypomethylated, CpG-rich DNA segments (CpG islands, CGIs) are epigenome markers involved in key biological processes. Aberrant methylation is implicated in the appearance of several disorders as cancer, immunodeficiency, or centromere instability. Furthermore, methylation differences at promoter regions between human and chimpanzee strongly associa...
Data
Full-text available
Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nons...
Article
Full-text available
Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nons...
Article
Relevant words in literary texts (key words) are known to be clustered, while common words are randomly distributed. Given the clustered distribution of many functional genome elements, we hypothesize that the biological text per excellence, the DNA sequence, might behave in the same way: k-length words (k-mers) with a clear function may be spatial...
Chapter
Full-text available
This work was supported by the Ministry of Innovation and Science of the Spanish Government [BIO2010-20219 (M.H.), BIO2008-01353 (J.L.O.)]; ‘Juan de la Cierva’ grant (to M.H.) and Basque Country ‘Programa de formacion de investigadores’ grant (to G.B.).
Data
Full-text available
Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nons...
Conference Paper
Full-text available
Background / Purpose: With the advent of high-throughput sequencing techniques, the generation of single base resolution methylation maps have become a feasible task. The detection of regions with homogenous methylation levels is an important goal as: 1) CpG islands should manifest as homogenously hypomethylated regions within these maps and 2) p...
Article
Full-text available
Human DNA shows a complex structure with compositional features at many scales; the isochores--long DNA segments (~10⁵ bp) of relatively homogeneous guanine-cytosine (G + C) content--are the largest well-documented and well-analyzed compositional structures. However, we report here on the existence of a high-level compositional organization of isoc...
Article
Full-text available
Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statistically comprehensible way. The detection of clustering often re...
Article
Full-text available
Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution. This allows studying the absence of methylation in a particular genome region over a range of tissues, the differential tissue methylation or the changes occurring along pathological conditions....
Article
Full-text available
Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistic...
Article
The sibling species of the Echinogammarus berilloni-group are endemic for the Iberian Peninsula and southern France. These species show wide morphological variability with some overlap in their dianostic characters making their distinction difficult. Reroductive isolation and enzmatic jivergence amon allopatric and sympatric populations of four spe...
Article
Full-text available
Using a generalization of the level statistics analysis of quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our approach takes into account not only the frequencies of the words present in the text but also their spatial distribution along the text, and is based on the fact that relevant w...
Article
Full-text available
Isochores are long genome segments relatively homogeneous in G+C. A heuristic algorithm based on entropic segmentation has been developed by our group, and a web server implementing all the required components is available. However, a researcher may want to perform batch processing of many sequences simultaneously in its local machine, instead of a...
Data
Numerical values for the α(ℓ) profiles. The numerical values to trace the α(ℓ) profiles for all the chromosomes with sequence contigs of sufficient lengths from the eleven species analyzed here are given (Excel file).
Article
Full-text available
The phylogenetic distribution of large-scale genome structure (i.e. mosaic compositional patchiness) has been explored mainly by analytical ultracentrifugation of bulk DNA. However, with the availability of large, good-quality chromosome sequences, and the recently developed computational methods to directly analyze patchiness on the genome sequenc...
Article
Full-text available
The scale-free, long-range correlations detected in DNA sequences contrast with characteristic lengths of genomic elements, being particularly incompatible with the isochores (long, homogeneous DNA segments). By computing the local behavior of the scaling exponent alpha of detrended fluctuation analysis (DFA), we discriminate between sequences with...
Data
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 19 to Y
Data
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 1 to 6
Data
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 7 to 12
Data
Comparison between analytical and experimental randomization. Length distribution of clusters with different numbers of CpGs. The analytical distribution (black line) is virtually identical to the experimental one obtained by a randomization that preserves the CpG frequency.
Data
Alignment with SERPINB5 promoter. Sequence alignment between the promoter of SERPINB5 (SPR, associated with a GC-rich region) and the CGI predicted by CpGcluster. None of the remaining CGI finders were able to detect any CGI in this region. The transcription start site (TSS), as given by the DBTSS data base [34], is shown in bold type.
Data
Distribution of distances between neighboring CpG dinucleotides in the human chromosomes 13 to 18
Article
Full-text available
Despite their involvement in the regulation of gene expression and their importance as genomic markers for promoter prediction, no objective standard exists for defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by the thresholds of length, CpG fraction and G+C content. Given the higher frequency of CpG...
Article
Full-text available
We report on an entropic edge detector based on the local calculation of the Jensen-Shannon divergence with application to the search for CpG islands. CpG islands are pieces of the genome related to gene expression and cell differentiation, and thus to cancer formation. Searching for these CpG islands is a major task in genetics and bioinformatics....
Article
Full-text available
Alu retrotransposons do not show a homogeneous distribution over the human genome but have a higher density in GC-rich (H) than in AT-rich (L) isochores. However, since they preferentially insert into the L isochores, the question arises: What is the evolutionary mechanism that shifts the Alu density maximum from L to H isochores? To disclose the r...
Article
La recerca en biologia no es pot entendre avui sense la computació. A causa, sobretot, del desenvolupament de les tecnologies genòmiques, la biologia ha passat en molt poc temps, de ser una ciència en la qual l'esforç humà s'orientava principalment envers l'obtenció d'unes poques dades, a ser una ciència que genera un volum enorme de dades sense pr...
Article
Full-text available
Isochores are long genome segments homogeneous in G+C. Here, we describe an algorithm (IsoFinder) running on the web (http://bioinfo2.ugr.es/IsoF/isofinder.html) able to predict isochores at the sequence level. We move a sliding pointer from left to right along the DNA sequence. At each position of the pointer, we compute the mean G+C values to the...
Article
The sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (GC) heterogeneity, largely in view of lateral transfers. We present here a brief overview of some methods for visualizing and quantifying GC variation in prokaryotes. We used these methods to examine heterogeneity le...
Article
The sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (GC) heterogeneity, largely in view of lateral transfers. We present here a brief overview of some methods for visualizing and quantifying GC variation in prokaryotes. We used these methods to examine heterogeneity le...
Article
The sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (GC) heterogeneity, largely in view of lateral transfers. We present here a brief overview of some methods for visualizing and quantifying GC variation in prokaryotes. We used these methods to examine heterogeneity le...
Article
The isochore concept in the human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in the IHGSC's analysis concerning the existence of isochores is misleading, because the homogeneity was not examined at a large enough length scale and consequently an inapp...
Article
We present a coding measure which is based on the statistical properties of the stop codons, and that is able to estimate accurately the variation of coding content along an anonymous sequence. As the stop codons play the same role in all the genomes (with very few exceptions) the measure turns out to be species-independent. We show results both fo...
Article
Here we present a study of statistical correlations among different positions in DNA sequences and their implications by directly using the autocorrelation function. Such an analysis is possible now because of the availability of large sequences or even complete genomes of many organisms. After describing the way in which the autocorrelation functi...
Article
The human genome is a mosaic of isochores, which are long DNA segments (z.Gt;300 kbp) relatively homogeneous in G+C. Human isochores were first identified by density-gradient ultracentrifugation of bulk DNA, and differ in important features, e.g. genes are found predominantly in the GC-richest isochores. Here, we use a reliable segmentation method...
Article
Full-text available
We study statistical properties of the Jensen-Shannon divergence D, which quantifies the difference between probability distributions, and which has been widely applied to analyses of symbolic sequences. We present three interpretations of D in the framework of statistical physics, information theory, and mathematical statistics, and obtain approxi...
Article
Cytogenetic and electrophoretic analyses on 2n = 28 strains of Asphodelus cerasiferus strongly suggest that the basic number x = 14 of the genus Asphodelus is of secondary polyploid origin from x = 7.
Article
Introduction The chloroplast genome of higher plants is a small circular chromosome, whose length generally varies between 120 and 160 kb among different species. Size differences are mainly due to variations in the length of a large inverted duplication (IO-76 kb) while the two single-copy regions are highly conserved in size and gene content. Chl...
Article
The electrophoretic patterns of esterase (E-l), alcohol dehydroge- nase (ADH), and glutamate oxaloacetate transaminase (GOT) isozymes were studied in two Spanish populations of the lily Scilla autumnalis with B- chromosome carrying individuals. The E-l isozyme activity appears only in those individuals with B-chromosomes. None of the bulbs free of...
Article
nstraints on DNA sequences. Introduction The information theory, developed primarily by Shannon & Weaver (1949), was mostly devoted to communication problems. Yet, it was being applied, often successfully, to many other fields where the information concept was essential, such as the interpretation of DNA sequences. Several authors (Gatlin, 1972; Gu...
Article
RAPD markers and agronomic traits were used to determine the genetic relationships among 32 breeding lines of melon belonging to seven varietal types. Most of the breeding lines were Galia and Piel de Sapo genotypes, which are currently being used in breeding programmes to develop new hybrid combinations. A total of 115 polymorphic reliable bands f...
Article
We have studied the behavior of the di- nucleotide preferences under G + C content variation in human genes. The doublet preferences for each dinucleotide were compared between two functionally distinct zones in genes, the II-III codon positions, and the introns. The 16 dinucleotides have been tentatively classified in three groups: served could be...
Article
Full-text available
Introduction Trypanosoma cruzi is a haemoflagellated protozoan belonging to the order Kinetoplastidae, and is the causa- tive agent of Chagas' disease, which afflicts millions of people in the American continent (World Health Organization 1989). Its life cycle Includes several developmental Received 28February,1994:revised6June,1994:accepted 8June,...
Article
Full-text available
otato varieties analyzed. This research was supported in part by a grant from Caja de Ahorros y Monte de Piedad de Madrid, Spain. Thanks are also due to A. Saudo and H. Stegemann for help with the manuscript and to M. Vlez for her technical assistance. 458 $. M. Mart[ne-Zapater and Sod L. Oliver laboratory manipulations (freezing of the whole tuber...
Article
Introduction Crown gall and hairy root disease are plant tumors resulting from a set of genes with morphogenic effects which alter normal cell development and differentiation being introduced into the nuclear plant genome. Both tumors are induced in many dicotyledonous plants by oncogenic strains of Agrobacterium faciens and A. rhizogenes, respecti...
Article
Introduction Gene duplication is a primary mechanism for the acquisition of new genes during evolution 1970; Markert et al. 1975). Isozymes have usually been produced by gene duplication (Markert et al. 1975) and therefore they are very useful tools for studying the evolution of duplicate genes. Many studies have been done on several groups of fish...
Article
This paper analyzes correlations in base composition between pairs of neighboring genes in Escherichia coli. TheG+Ccontents of nearby, but convergently or divergently transcribed, genes show weak but significant correlations, and this is attributed to compositional variation among genomic regions. The finding that the base composition varies among...
Article
Supernumerary (B) chromosomes have been studied in a Spanish population of Scilla autumnalis L. (Liliaceae). Out of the 140 individuals analysed, seven had 2n=14+lB, one 2n=l4+2B, one 2n=14+3B and one 2n= 14 + 9B. An analysis of esterase isozyme patterns shows that all 130 individuals with a standard karyotype (2n= 14) have two esterase loci, Est-2...
Article
Analytical DNA ultracentrifugation revealed that eukaryotic genomes are mosaics of isochores: long DNA segments (>300 kb on average) relatively homogeneous in G+C. Important genome features are dependent on this isochore structure, e.g. genes are found predominantly in the GC-richest isochore classes. However, no reliable method is available to rig...
Article
Full-text available
We present a new computational approach to finding borders between coding and noncoding DNA. This approach has two features: (i) DNA sequences are described by a 12-letter alphabet that captures the differential base composition at each codon position, and (ii) the search for the borders is carried out by means of an entropic segmentation method wh...