Coral del Val

• Associate Professor
• University of Granada

Burkitt lymphoma (BL) is an aggressive germinal center B‐cell‐derived malignancy. Historically, sporadic, endemic, and immunodeficiency‐associated variants were distinguished, which differ in the frequency of Epstein–Barr virus (EBV) positivity. Aiming to identify subgroups based on DNA methylation patterns, we here profiled 96 BL cases, 17 BL cell...

Mature aggressive B‐cell lymphomas, such as Burkitt lymphoma (BL) and Diffuse large B‐cell lymphoma (DLBCL), show variations in microRNA (miRNA) expression. The entity of High‐grade B‐cell lymphoma with 11q aberration (HGBCL‐11q) shares several biological features with both BL and DLBCL but data on its miRNA expression profile are yet scarce. Hence...

In oncology, there is a critical need for robust biomarkers that can be easily translated into the clinic. We introduce a novel approach using paired differential gene expression analysis for biological feature selection in machine learning models, enhancing robustness and interpretability while accounting for patient variability. This method compa...

Genome-wide association studies of human personality have been carried out, but transcription of the whole genome has not been studied in relation to personality in humans. We collected genome-wide expression profiles of adults to characterize the regulation of expression and function in genes related to human personality. We devised an innovative...

High-grade B-cell lymphoma with 11q aberrations (HGBL-11q) is a type of aggressive B-cell lymphoma that shares morphological, immunophenotypic and gene expression features with Burkitt lymphoma (BL). HGBL-11q and BL differ in terms of the MYC translocation and typical landscapes of structural and small nucleotide variants. HGBL-11q harbours the nam...

Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR is a transcription factor involved in polyhydroxyalkanoate (PHA) metabolism but also plays a role in the microaerobic network of this b...

Background: Malignant melanoma (MM) is a highly aggressive form of skin cancer whose incidence continues to rise worldwide. If diagnosed at an early stage of disease, it has an excellent prognosis, but the mortality increases significantly at advanced stages after distant spread. Unfortunately, early detection of aggressive melanoma remains a chal...

The human brain's resting-state functional connectivity (rsFC) provides stable trait-like measures of differences in the perceptual, cognitive, emotional, and social functioning of individuals. The rsFC of the prefrontal cortex is hypothesized to mediate a person's rational self-government, as is also measured by personality, so we tested whether i...

Genetic architecture of plasma lipidome provides insights into regulation of lipid metabolism and related diseases. We applied an unsupervised machine learning method, PGMRA, to discover phenotype-genotype many-to-many relations between genotype and plasma lipidome (phenotype) in order to identify the genetic architecture of plasma lipidome profile...

Pistachio is a nut crop domesticated in the Fertile crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of P. vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromo...

Reactive oxygen species (ROS) act as secondary messengers that can be sensed by specific redox-sensitive proteins responsible for the activation of signal transduction culminating in altered gene expression. The subcellular site, in which modifications in the ROS/oxidation state occur, can also act as a specific cellular redox network signal. The c...

Prostate cancer (PCa) is a tumor with a great heterogeneity, both at a molecular and clinical level. Despite its global good prognosis, cases can vary from indolent to lethal metastatic and scientific efforts are aimed to discern those with worse outcomes. Current prognostic markers, as Gleason score, fall short when it comes to distinguishing thes...

Phylogenetic, developmental, and brain-imaging studies suggest that human personality is the integrated expression of three major systems of learning and memory that regulate (1) associative conditioning, (2) intentionality, and (3) self-awareness. We have uncovered largely disjoint sets of genes regulating these dissociable learning processes in d...

The genetic basis for the emergence of creativity in modern humans remains a mystery despite sequencing the genomes of chimpanzees and Neanderthals, our closest hominid relatives. Data-driven methods allowed us to uncover networks of genes distinguishing the three major systems of modern human personality and adaptability: emotional reactivity, sel...

Experimental studies of learning suggest that human temperament may depend on the molecular mechanisms for associative conditioning, which are highly conserved in animals. The main genetic pathways for associative conditioning are known in experimental animals, but have not been identified in prior genome-wide association studies (GWAS) of human te...

Human personality is 30-60% heritable according to twin and adoption studies. Hundreds of genetic variants are expected to influence its complex development, but few have been identified. We used a machine learning method for genome-wide association studies (GWAS) to uncover complex genotypic-phenotypic networks and environmental interactions. The...

Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into...

Corona virus spike protein S is a large homo-trimeric protein embedded in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into...

SecA is an essential component of the Sec protein secretion pathway in bacteria. Secretory proteins targeted to the Sec pathway by their N-terminal signal peptide bind to SecA, which couples binding and hydrolysis of adenosine triphosphate with movement of the secretory protein across the membrane-embedded SecYEG protein translocon. The phylogeneti...

Colorectal cancer treatment has advanced over the past decade. The drug 5-fluorouracil is still used with a wide percentage of patients who do not respond. Therefore, a challenge is the identification of predictive biomarkers. The protein kinase R (PKR also called EIF2AK2) and its regulator, the non-coding pre-mir-nc886, have multiple effects on ce...

In breast cancer (BC), the presence of cancer stem cells (CSCs) has been related to relapse, metastasis, and radioresistance. Radiotherapy (RT) is an extended BC treatment, but is not always effective. CSCs have several mechanisms of radioresistance in place, and some miRNAs are involved in the cellular response to ionizing radiation (IR). Here, we...

The rise of omics techniques has resulted in an explosion of molecular data in modern biomedical research. Together with information from medical images and clinical data, the field of omics has driven the implementation of per-sonalized medicine. Biomedical and omics datasets are complex and heteroge-neous, and extracting meaningful knowledge from...

Cadmium (Cd), which is a toxic non-essential heavy metal capable of entering plants and thus the food chain, constitutes a major environmental and health concern worldwide. An understanding of the tools used by plants to overcome Cd stress could lead to the production of food crops with lower Cd uptake capacity and of plants with greater Cd uptake...

Anthropogenic activities, such as industrial processes, mining, and agriculture, lead to an increase in heavy metal concentrations in soil, water, and air. Given their stability in the environment, heavy metals are difficult to eliminate and can constitute a human health risk by entering the food chain through uptake by crop plants. An excess of he...

Bioinformatics is an interdisciplinary area that has raised a high interest for both academia and corporations in recent years. This rising area combines knowledge and skills from bio and Science, Technology, Engineering and Mathematics (STEM) areas. One of the advantages of the synergy between these two work areas is that it offers an opportunity...

PsbO is an extrinsic subunit of photosystem II engaged in complex binding interactions within photosystem II. At the interface between PsbO, D1 and D2 subunits of photosystem II, a cluster of charged and polar groups of PsbO is part of an extended hydrogen-bond network thought to participate in proton transfer. The precise role of specific amino ac...

Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requi...

Trypanosomes are early-branched eukaryotes that show an unusual dependence on post-transcriptional mechanisms to regulate gene expression. RNA-binding proteins are crucial in controlling mRNA fate in these organisms, but their RNA substrates remain largely unknown. Here we have analyzed on a global scale the mRNAs associated with the Trypanosoma br...

Objective: The authors sought to demonstrate that schizophrenia is a heterogeneous group of heritable disorders caused by different genotypic networks that cause distinct clinical syndromes. Method: In a large genome-wide association study of cases with schizophrenia and controls, the authors first identified sets of interacting single-nucleotid...

Motivation: Small non-coding RNAs (sRNAs) have major roles in the post-transcriptional regulation in prokaryotes. The experimental validation of a relatively small number of sRNAs in few species requires developing computational algorithms capable of robustly encoding the available knowledge and using this knowledge to predict sRNAs within and acr...

Long-distance proton transfers by proton pumps occurs in discrete steps that may involve the direct participation of protein sidechains and water molecules, and coupling of protonation changes to structural rearrangements of the protein matrix. Here we explore the role of inter-helical hydrogen bonding in long-distance protein conformational coupli...

Channelrhodopsins are microbial rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs the structure, dynamics, and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications....

It has been proposed that single nucleotide polymorphisms (SNPs) discovered by genome-wide association studies (GWAS) account for only a small fraction of the genetic variation of complex traits in human population. The remaining unexplained variance or missing heritability is thought to be due to marginal effects of many loci with small effects an...

We combined systematic bioinformatics analyses and molecular dynamics simulations to assess the conservation patterns of Ser and Thr motifs in membrane proteins, and the effect of such motifs on the structure and dynamics of α-helical transmembrane (TM) segments. We find that Ser/Thr motifs are often present in β-barrel TM proteins. At least one Se...

Electrophysiological experiments showed that the light-activated cation channel channelrhodopsin-2 (ChR2) pumps protons in the absence of a membrane potential. We determined here the kinetics of transient pH change using a water-soluble pH-indicator. It is shown that ChR2 released protons prior to uptake with a stoichiometry of 0.3 protons per ChR2...

We have performed a computational comparative analysis of six small non-coding RNA (sRNA) families in α-proteobacteria. Members of these families were first identified in the intergenic regions of the nitrogen-fixing endosymbiont S. meliloti by a combined bioinformatics screen followed by experimental verification. Consensus secondary structures in...

Gene expression regulation is an intricate, dynamic phenomenon essential for all biological functions. The necessary instructions for gene expression are encoded in cis-regulatory elements that work together and interact with the RNA polymerase to confer spatial and temporal patterns of transcription. Therefore, the identification of these elements...

Genetic and genomic approaches have been successfully employed to assign genes to distinct regulatory networks. The strength of the connections in these networks must be specified to define the kinetics of a group of genes, but the uncertainty concerning the connections between genes, the ambiguity inherent to the biological processes, and the impo...

The SecY/Sec61 translocon complex, located in the endoplasmic reticulum membrane of eukaryotes (Sec61) or the plasma membrane of prokaryotes (SecY), mediates the transmembrane secretion or insertion of nascent proteins. Mutations that permit the secretion of nascent proteins with defective signal sequences (Prl-phenotype), or interfere with the tra...

There are many tools available for the prediction of potential promoter regions and the transcription factor binding sites (TFBS) harboured by them. Unfortunately, these tools cannot really avoid the prediction of vast amounts of false positives, the greatest problem in promoter analysis. The combination of different methods and algorithms has show...

Tissue-distribution profiles are crucial for understanding the characteristics of cells and tissues in terms of their differential expression of genes. Most of the currently available resources for tissue-distribution profiles are either specialized for a few particular organisms, tissue types and disease stages or do not consider the “tissue ontol...

Supplementary material 2: In “Tissue Slim Library” the first column denotes the “standard tissue-type term” while second, third, fourth and fifth columns corresponds to the tissue-type terms at “Tissue Slim” Level-2, Level-3, Level-4 and Level-5. In each of the columns all the tissue-type terms corresponding to each level are separated by “,”.

Supplementary material 1: In “Tissue Synonym Library” each row corresponds to the standard tissue-type term and a list of the ESTs source tissue-type terms. The “;;” delimiter is used as a separator between the uncurated tissue-type terms. On the index page, a list of organisms is available to navigate across the Tissue Synonym Library.

An increasing amount of expressed sequence tag (EST) and genomic data, predominantly for the cnidarians Acropora, Hydra and Nematostella, reveals that cnidarians have a high genomic complexity, despite being one of the morphologically simplest multicellular animals. Considering the diversity of cnidarians, we performed an EST project on the hydroid...

The computational prediction of DNA methylation has become an important topic in the recent years due to its role in the epigenetic control of normal and cancer-related processes. While previous prediction approaches focused merely on differences between methylated and unmethylated DNA sequences, recent experimental results have shown the presence...

Supplemental tables. Table S1 provide the features describing PhoP regulated promoters and raw data used to build them. Table S2 details the bacterial strains and plasmids used in this study, and Table S3 the primers used to construct the promoters in GFP reporter plasmids.

Decision tree. This Figure shows the decision tree used to predict the four CGI methylation classes.

CGI dataset. This Excel table contains the CGI dataset that formed the foundation for our data-mining approach, as well as the classification of each CGI in the binary and tissue-specific methylation classes.

Results of the Principle Component Analysis. This Excel table contains the Eigenvector plots of the PCA that were used to measure the contribution of each attribute to the principal components as well as the principle components themselves.

Table of significant cluster intersections. This table shows the significant cluster intersections, ordered by size (#CGIs) and significance of each intersecting cluster (PI). Each cluster is identified by the data used in the clustering (Attribute or Methylation data) followed by the overall number of clusters, the clustering method (Hierarchical...

Distribution of HCNE-overlapping PBCs over the gene association classes. Absolute number and percentage of CGIs in each PBC and gene-association class that overlap with a HCNE. A total of 3 conflicting CGIs that were determined to contain CDS but were part of a HCNE were excluded. Significant enrichment (p-value < 0.05) of methylation classes with...

Table of variable correlation. Correlation analysis of all attributes shows that each relevant attribute was not replaceable by any other.

Intramembrane proteases, which cleave transmembrane (TM) helices, participate in numerous biological processes encompassing all branches of life. Several crystallographic structures of Escherichia coli GlpG rhomboid protease have been determined. In order to understand GlpG dynamics and lipid interactions in a native-like environment, we have exami...

Genomes of many organisms have been sequenced over the last few years. However, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed to address part of this problem: the location of genes along a genome and their expression. We propose a multi-objective methodology to comb...

A large amount of computational and experimental work has been devoted to uncovering network motifs in gene regulatory networks. The leading hypothesis is that evolutionary processes independently selected recurrent architectural relationships among regulators and target genes (motifs) to produce characteristic expression patterns of its members. H...

The aim of this study was to characterize soils contaminated by different levels of heavy metals and hydrocarbons (Madonna Dell'Acqua, Pisa, Italy). The soils were chemically and biochemically analysed by measuring the standard chemical properties and some enzyme activities related to microbial activity (dehydrogenase activity) and the soil carbon...

The Gene Ontology (GO) vocabulary has been extensively explored to analyze the functions of coexpressed genes. However, despite its extended use in Biology and Medical Sciences, there are still high levels of uncertainty about which ontology (i.e. Molecular Process, Cellular Component or Molecular Function) should be used, and at which level of spe...

Bacterial small non-coding RNAs (sRNAs) are being recognized as novel widespread regulators of gene expression in response to environmental signals. Here, we present the first search for sRNA-encoding genes in the nitrogen-fixing endosymbiont Sinorhizobium meliloti, performed by a genome-wide computational analysis of its intergenic regions. Compar...

The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can...

A DNA sequence can be described as a string composed of four symbols: A, T, C and G. Each symbol represents a chemically distinct nucleotide molecule. Combinations of two nucleotides are called dinucleotides and CpG islands represent regions of a DNA sequence, certain substrings, which are enriched in CpG dinucleotides (C followed by G). CpG island...

The influence of the mycorrhizal infection by G. mosseae (Nicol. et Gerd.) Gerd et Trappe on the growth of Medicago sativa L. plants under different level of soil pollution with heavy metals (Zn, Pb, Cd, Cu) and arsenicum was studied. It was established the strongly increase of the growth and shoot biomass of mycorrhizal plants. The positive effect...

A DNA sequence can be described as a string composed of four symbols: A, T, C and G, each representing a chemically distinct nucleotide molecule. Combinations of two nucleotides are called dinucleotides and CpG islands represent regions of a DNA sequence, certain substrings, which are enriched in CpG dinucleotides (C followed by G). CpG islands rep...

CPAN distribution of the CAFTAN software

Hand annotation of the DKFZ cDNAs sequences

polyasignal acd file for EMBOSS

Table of DKFZ annotated sequences

polyasignal executable for EMBOSS

Recent observations of insertional mutagenesis in preclinical and clinical settings emphasize the relevance of investigating comprehensively the spectrum of integration sites targeted by specific vectors. We followed the engraftment of lentivirally transduced human cord blood (CB) progenitor cells after transplantation into NOD/SCID mice using a se...

The rapid development of methods that select over/under expressed genes from RNA microarray experiments have not yet satisfied the need for tools that identify differential profiles that distinguish between experimental conditions such as time, treatment and phenotype. We evaluate several microar- ray analysis methods and study their performance, f...

Graft-versus-host disease (GvHD) is a severe complication in the context of allogeneic stem cell transplantation and adoptive immunotherapy. The transfer of a suicide gene into donor T-lymphocytes (TLCs) allows selective elimination of GvHD-causing cells. As retroviral gene transfer into hematopoietic stem cells can induce leukaemia, there is an ur...

Molecular Therapy (2006) 13, S297|[ndash]|S298; doi: 10.1016/j.ymthe.2006.08.854 769. Genes Encoding Receptors, Signal Transducers and Transcription Regulators are Preferred Targets of Retroviral Vector Integration in T-Lymphocytes In Vitro and In Vivo Frank A. Giordano1, Boris Fehse2, Agnes Hotz-Wagenblatt3, Sunitha Jonnakuty3, Coral Del Val3, Je...

Table S2. Comparison of GOPET with the annotation of 100 random selected protein sequences of Dictyostelium discoideum

Table S2. Comparison of GOTcha with the annotation of 100 random selected sequences of Dictyostelium discoideum

The increased availability of biological databases containing representations of complex objects permits access to vast amounts of data. In spite of the recent renewed interest in knowledge-discovery techniques (or data mining), there is a dearth of data analysis methods intended to facilitate understanding of the represented objects and related sy...

The rapid development of methods that select over/under expressed genes from microarray experiments have not yet matched the need for tools that identify informational profiles that differentiate between experimental conditions such as time, treatment and phenotype. Uncertainty arises when methods devoted to identify significantly expressed genes a...

The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To...

Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for their predictions. We recently established...

LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an updated user interface with enhanced query capabilities, (ii) a configurable output table and the option to download search results in XM...

AIM was to test the new molecular classification of MM based on changes in global gene expression attributable to cytogenetic aberrations detected by interphase FISH (iFISH) in order to (i) predict EFS in a group of 100 MM-patients treated by high dose chemotherapy, and (ii) to investigate whether the classification represents an independent progno...

Background: In multiple myeloma (MM), deletion of chromosome (chr.) 13q and hypodiploidy are adverse prognostic factors. Prognostic evaluation is frequently based on interphase-fluorescence in-situ hybridization (FISH) with a single probe for chr. 13q14. Patients and methods: CD138-positive bone marrow cells from 97 patients with newly diagnosed MM...

The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. W...