A5009966967- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Fractal and DNA sequence analysis
- RNA modifications and cancer
- Environmental and Ecological Studies
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Genetic diversity and population structure
- Administrative Law and Governance
- Plant Virus Research Studies
- Regional Development and Innovation
- Plant Reproductive Biology
- CRISPR and Genetic Engineering
- Organizational Management and Innovation
- Energy Efficiency and Management
- Cancer-related gene regulation
- Quality and Management Systems
- Potato Plant Research
- Genomics and Chromatin Dynamics
- Plant Pathogens and Resistance
- Computational Drug Discovery Methods
- Photosynthetic Processes and Mechanisms
- Finance, Taxation, and Governance
Universidad de Granada
2016-2025
University of Alicante
2024
Parque Tecnológico de la Salud
2010-2022
Biotechnology Institute
2017
Centro de Investigación Biomédica en Red
2013-2014
Instituto de Biotecnología de León
2013
Museo Nacional de Ciencias Naturales
2009
Universidad de Jaén
2005
Rockefeller University
1998
Universidad de Málaga
1998
Small RNA research is a rapidly growing field. Apart from microRNAs, which are important regulators of gene expression, other types functional small molecules have been reported in animals and plants. MicroRNAs host-microbe interactions parasite microRNAs might modulate the innate immunity host. Furthermore, RNAs can be detected bodily fluids making them attractive non-invasive biomarker candidates. Given general broad interest RNAs, particular large number bioinformatics aided analysis...
Abstract Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances different directions. New protocols for sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or include internal controls spike-in sequences. microRNA reference databases were developed with foci, either prioritizing accuracy (low number false positives) completeness negatives). Additionally, other molecules well...
We study statistical properties of the Jensen-Shannon divergence D, which quantifies difference between probability distributions, and has been widely applied to analyses symbolic sequences. present three interpretations D in framework physics, information theory, mathematical statistics, obtain approximations mean, variance, distribution random, uncorrelated a segmentation method based on that is able segment nonstationary sequence into stationary subsequences, apply this DNA sequences, are...
A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose long-range correlated DNA sequences into statistically significant, compositionally homogeneous patches. By adequately setting significance level for segmenting sequence, underlying power-law distribution of patch lengths can be revealed. Some identified domains were uncorrelated, but most them continued display correlations even after several steps recursive segmentation, thus indicating a complex...
Abstract Background Despite their involvement in the regulation of gene expression and importance as genomic markers for promoter prediction, no objective standard exists defining CpG islands (CGIs), since all current approaches rely on a large parameter space formed by thresholds length, fraction G+C content. Results Given higher frequency dinucleotides at CGIs, compared to bulk DNA, distance distributions between neighboring CpGs should differ island CpGs. A new algorithm ( CpGcluster ) is...
We present a new computational approach to finding borders between coding and noncoding DNA. This has two features: (i) DNA sequences are described by 12-letter alphabet that captures the differential base composition at each codon position, (ii) search for is carried out means of an entropic segmentation method which uses only general statistical properties find this highly accurate in regions requires no "prior training" on known data sets. Our results appear be more than those obtained...
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 sequence level. We move a sliding pointer from left right along DNA sequence. At each position of pointer, compute mean G+C values and pointer. then determine for which difference between (as measured by t-statistic) reaches its maximum. Next, statistical significance this potential cutting point, after...
The relationship between G+C-content and codon usage in genes of human, mus, rat, bovine chicken nuclear genomes was investigated. Correlation lineal regression analyses were carried out on plots that related the frequency each within synonymous group to coding sequence as a whole. Under GC pressure, most quartet groups there is preferential choice C-ending codon, except leucine valine where G-ending preferred. Among duets, codons specifying phenylalanine glutamate shows strongest dependence...
Using a generalization of the level statistics analysis quantum disordered systems, we present an approach able to extract automatically keywords in literary texts. Our takes into account not only frequencies words text but also their spatial distribution along text, and is based on fact that relevant are significantly clustered (i.e., they self-attract each other), while irrelevant distributed randomly text. Since reference corpus needed, our especially suitable for single documents which...
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 DNA. To obtain value each individual cytosine, bisulfite-treated sequence reads are first aligned reference genome, and then levels done from alignments. A huge effort has been made quickly correctly align many different algorithms programs do this have created. However, second step just as crucial non-trivial, but...
A new complexity measure, based on the entropic segmentation of DNA sequences into compositionally homogeneous domains, is proposed. Sequence compositional (SCC) deals directly with complex heterogeneity in nonstationary sequences. The plot SCC as a function significance level provides profile sequence structure at different length scales. found to be higher long-range correlation than those without, and noncoding coding Furthermore, general agreement between sequence, one hand, biological...
Next-generation sequencing (NGS) together with bisulphite conversion allows the generation of whole genome methylation maps at single-cytosine resolution.This studying absence in a particular region over range tissues, differential tissue or changes occurring along pathological conditions.However, no database exists fully addressing such requirements.We propose here NGSmethDB (http://bioinfo2.ugr.es/NGSmethDB/gbrowse/) for storage and retrieval data derived from NGS.Two cytosine contexts...
Endosymbiosis can be considered a regressive or degenerative evolutionary process characterized at the genomic level by genome erosion and degeneration due to high mutational pressure towards AT. The biological complexity of endosymbionts must less than that free-living bacteria from which they evolved. In present work, we contrasted whether two proposed metrics for measuring in both types bacteria, Genomic Signature (GS) Biobit (BB), reflect their complexity, expecting higher values...
Endosymbiosis can be considered a regressive or degenerative evolutionary process characterized at the genomic level by genome erosion and degeneration due to high mutational pressure toward AT (adenine thymine) bases. The biological complexity of endosymbionts must lower than that free-living bacteria from which they evolved. In present work, we contrasted whether two proposed metrics for measuring in both types bacteria, GS BB, reflect their complexity, expecting higher values...
Abstract The rapid evolution of SARS-CoV-2 during the pandemic was characterized by fixation a plethora mutations, many which enable virus to evade host resistance, likely altering virus’ genome compositional structure (i.e., arrangement domains varying lengths and nucleotide frequencies within genome). To explore this hypothesis, we summarize evolutionary effects these mutations computing Sequence Compositional Complexity (SCC) in random stratified datasets fully sequenced genomes....
The heterogeneity within, and similarities between, yeast chromosomes are studied. For the former, we show by size distribution of domains, coding density, open reading frames, spatial power spectra, deviation from binomial for C + G% in large moving windows that there is a strong sequences random sequences. latter, not only do graphically illustrate similarity above mentioned statistics, but also carry out rigorous analysis variance (ANOVA) test. hypothesis all similar cannot be rejected...
Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property mammal genomes. Conventionally, these regions detected by sliding window approaches using %G + C, observed/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters a statistical the genome sequence. We compare sliding-window to (i.e. CpGcluster) predictions applying new ways putative functionality islands. Analyzing co-localization with several genomic...