I have a degree in Physical Sciences. Associate Professor of Computer Science of the Informatics Department of the School of Engineering (University of Valencia, Spain) and member of the new I2SysBio research institute. For about 15 years my main line of research is Bioinformatics. Director of the Official Master in Bioinformatics of the UV since its creation in 2012. Analyzing and visualizing bioinformatic data, designing new algorithms and web visualization tools is my main dedication in the UV.
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the c... more The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user’s PC under any operating system or on remote servers, as a cloud solution. “RNASeq” and “VariantSeq” are both available ...
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence ... more The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program a...
SummaryLike in other animals, the gut microbiome of fishes contains thousands of microbial specie... more SummaryLike in other animals, the gut microbiome of fishes contains thousands of microbial species that establish a complex network of relationships among each other and with the host. These interrelationships are shaped by biotic and abiotic factors, but little is known about how they evolved and how they are regulated by the environment, farmers and breeders. Herein, we introduce SAMBA (Structure-Learning ofAquacultureMicrobiomes Using aBayesian-NetworkApproach), the software implementation of a Bayesian network model for investigating how fish pan-microbiomes and all other variables of a given aquaculture system are related each to other. SAMBA is powered by a Bayesian network trainable model that learns the network structure of an aquaculture system using information from distinct biotic and abiotic variables of importance in fish farming, with special focus on microbial data provided from 16S amplicon sequencing. SAMBA accepts both qualitative and quantitative variables and con...
Abstract Melon is a worldwide extended cucurbit. Spain is the 5 world melon producer and leader i... more Abstract Melon is a worldwide extended cucurbit. Spain is the 5 world melon producer and leader in Europe. The melon genome is relatively small and its genetic map has an estimated size of 1,021 cM, which represents approximately 440 kb per cM. These data ...
What is siimplehub:Genetic data have the potential to be highly sensitive, so security and privac... more What is siimplehub:Genetic data have the potential to be highly sensitive, so security and privacy are extremely important in web applications that manage, collect and share these type of data.<br>As part of MGviz and siimple, and with the collaboration of the "Unidad de Genómica y Diagnóstico Genético" of INCLIVA, the TBC Group of the i2Sysbio and Seqplexing, a company dedicated to the development of technology for genetic analysis, we have created a web application focused on offering services for centralized user authentication and project management for gathering information between applications from the same organization.
<b>Copyright information:</b>Taken from "UVPAR: fast detection of functional shi... more <b>Copyright information:</b>Taken from "UVPAR: fast detection of functional shifts in duplicate genes"BMC Bioinformatics 2006;7():174-174.Published online 28 Mar 2006PMCID:PMC1570150. Grey: significant positive values (the duplicates of the first named species are the most conserved), Black: significant negative values (the second species has the most conserved duplicates). : window size.
<b>Copyright information:</b>Taken from "Global patterns of sequence evolution i... more <b>Copyright information:</b>Taken from "Global patterns of sequence evolution in "http://www.biomedcentral.com/1471-2164/8/408BMC Genomics 2007;8():408-408.Published online 9 Nov 2007PMCID:PMC2180185. Again, the y-axis reflects the relative frequency of the words in the pairs of chromosomes.
<b>Copyright information:</b>Taken from "Global patterns of sequence evolution i... more <b>Copyright information:</b>Taken from "Global patterns of sequence evolution in "http://www.biomedcentral.com/1471-2164/8/408BMC Genomics 2007;8():408-408.Published online 9 Nov 2007PMCID:PMC2180185. Details as in Figure 6.
Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels... more Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of tran-scription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at
The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brie... more The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brief time in the middle secretory phase, called the window of implantation (WOI). Despite its importance, regulation of the menstrual cycle remains incompletely understood. The aim of this study was to characterize the gene cooperation and regulation of menstrual cycle progression, to dissect the molecular complexity underlying acquisition of endometrial receptivity for a successful pregnancy, and to provide the scientific community with detailed gene co-expression information throughout the menstrual cycle on a user-friendly web-tool database. A retrospective gene co-expression analysis was performed based on the endometrial receptivity array (ERarray) gene signature from 523 human endometrial samples collected across the menstrual cycle, including during the WOI. Gene co-expression analysis revealed the WOI as having the significantly smallest proportion of negative correlations for trans...
The olive tree is of particular economic interest in the Mediterranean basin. Researchers have co... more The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz, 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consortium in the attack to the host plant. This community includes both biotrophic and necrotrophic organisms that alternate and live together during the infection. Our results not only describe how the microbial community progresses along these processes, but also explain the high complexity of these systems, that i...
ResumenEn este trabajo presentamos la paralelización de dos aplicaciones bioinformáticas utiliza... more ResumenEn este trabajo presentamos la paralelización de dos aplicaciones bioinformáticas utilizadas el análisis de largas secuencias de ADN. Está basada en un trabajo previo que transforma una secuencia de ADN en una secuencia binaria y se proponen diversas optimizaciones ...
Medical Genomics Visualization Group (MGviz), Siimple OSS, Seqplexing and Kanteron Systems have j... more Medical Genomics Visualization Group (MGviz), Siimple OSS, Seqplexing and Kanteron Systems have jointly developed NGS data analysis workflows that create automatic technical reports for precision medicine with fully integrated QC and LIMS procedures. Our genetic and pharmacogenetic data can be easily integrated in HIS systems and use HL7 standard protocols.We have developed a full suit of open source tools in Python, R and MERN stack for clinical bioinformatics as a service. These tools include serving variant annotation, interactive selection tools, reannotation and automatic clinical reports generation.We are doing trials to deploy this service in a cloud platform for creating a service for analyzing customized NGS gene panels and exomes in a clinical context for diabetes, cancer and mental disabilities.
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the c... more The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Server-Side requires a Linux operating system, PHP, SQL, Python, bash scripting, and third-party software. The GPRO Server-Side can be installed, via a Docker container, in the user’s PC under any operating system or on remote servers, as a cloud solution. “RNASeq” and “VariantSeq” are both available ...
The generation of different types of defective viral genomes (DVG) is an unavoidable consequence ... more The generation of different types of defective viral genomes (DVG) is an unavoidable consequence of the error-prone replication of RNA viruses. In recent years, a particular class of DVGs, those containing long deletions or genome rearrangements, has gain interest due to their potential therapeutic and biotechnological applications. Identifying such DVGs in high-throughput sequencing (HTS) data has become an interesting computational problem. Several algorithms have been proposed to accomplish this goal, though all incur false positives, a problem of practical interest if such DVGs have to be synthetized and tested in the laboratory. We present a metasearch tool, DVGfinder, that wraps the two most commonly used DVG search algorithms in a single workflow for the identification of the DVGs in HTS data. DVGfinder processes the results of ViReMa-a and DI-tector and uses a gradient boosting classifier machine learning algorithm to reduce the number of false-positive events. The program a...
SummaryLike in other animals, the gut microbiome of fishes contains thousands of microbial specie... more SummaryLike in other animals, the gut microbiome of fishes contains thousands of microbial species that establish a complex network of relationships among each other and with the host. These interrelationships are shaped by biotic and abiotic factors, but little is known about how they evolved and how they are regulated by the environment, farmers and breeders. Herein, we introduce SAMBA (Structure-Learning ofAquacultureMicrobiomes Using aBayesian-NetworkApproach), the software implementation of a Bayesian network model for investigating how fish pan-microbiomes and all other variables of a given aquaculture system are related each to other. SAMBA is powered by a Bayesian network trainable model that learns the network structure of an aquaculture system using information from distinct biotic and abiotic variables of importance in fish farming, with special focus on microbial data provided from 16S amplicon sequencing. SAMBA accepts both qualitative and quantitative variables and con...
Abstract Melon is a worldwide extended cucurbit. Spain is the 5 world melon producer and leader i... more Abstract Melon is a worldwide extended cucurbit. Spain is the 5 world melon producer and leader in Europe. The melon genome is relatively small and its genetic map has an estimated size of 1,021 cM, which represents approximately 440 kb per cM. These data ...
What is siimplehub:Genetic data have the potential to be highly sensitive, so security and privac... more What is siimplehub:Genetic data have the potential to be highly sensitive, so security and privacy are extremely important in web applications that manage, collect and share these type of data.<br>As part of MGviz and siimple, and with the collaboration of the "Unidad de Genómica y Diagnóstico Genético" of INCLIVA, the TBC Group of the i2Sysbio and Seqplexing, a company dedicated to the development of technology for genetic analysis, we have created a web application focused on offering services for centralized user authentication and project management for gathering information between applications from the same organization.
<b>Copyright information:</b>Taken from "UVPAR: fast detection of functional shi... more <b>Copyright information:</b>Taken from "UVPAR: fast detection of functional shifts in duplicate genes"BMC Bioinformatics 2006;7():174-174.Published online 28 Mar 2006PMCID:PMC1570150. Grey: significant positive values (the duplicates of the first named species are the most conserved), Black: significant negative values (the second species has the most conserved duplicates). : window size.
<b>Copyright information:</b>Taken from "Global patterns of sequence evolution i... more <b>Copyright information:</b>Taken from "Global patterns of sequence evolution in "http://www.biomedcentral.com/1471-2164/8/408BMC Genomics 2007;8():408-408.Published online 9 Nov 2007PMCID:PMC2180185. Again, the y-axis reflects the relative frequency of the words in the pairs of chromosomes.
<b>Copyright information:</b>Taken from "Global patterns of sequence evolution i... more <b>Copyright information:</b>Taken from "Global patterns of sequence evolution in "http://www.biomedcentral.com/1471-2164/8/408BMC Genomics 2007;8():408-408.Published online 9 Nov 2007PMCID:PMC2180185. Details as in Figure 6.
Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels... more Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of tran-scription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at
The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brie... more The human endometrium is a dynamic tissue that only is receptive to host the embryo during a brief time in the middle secretory phase, called the window of implantation (WOI). Despite its importance, regulation of the menstrual cycle remains incompletely understood. The aim of this study was to characterize the gene cooperation and regulation of menstrual cycle progression, to dissect the molecular complexity underlying acquisition of endometrial receptivity for a successful pregnancy, and to provide the scientific community with detailed gene co-expression information throughout the menstrual cycle on a user-friendly web-tool database. A retrospective gene co-expression analysis was performed based on the endometrial receptivity array (ERarray) gene signature from 523 human endometrial samples collected across the menstrual cycle, including during the WOI. Gene co-expression analysis revealed the WOI as having the significantly smallest proportion of negative correlations for trans...
The olive tree is of particular economic interest in the Mediterranean basin. Researchers have co... more The olive tree is of particular economic interest in the Mediterranean basin. Researchers have conducted several studies on one of the most devastating disorders affecting this tree, the Verticillium wilt of olive, which causes significant economic damage in numerous areas of this crop. We have analyzed the temporal metagenomic samples of a transcriptomic study in Olea europaea roots and leaves after root-damage and after a root Verticillium dahliae infection (Jimenez-Ruiz, 2017). Our results indicate that this infection, although led by Verticillium, is driven not by a single species but by a polymicrobial community, including their natural endophytes, which acts as a consortium in the attack to the host plant. This community includes both biotrophic and necrotrophic organisms that alternate and live together during the infection. Our results not only describe how the microbial community progresses along these processes, but also explain the high complexity of these systems, that i...
ResumenEn este trabajo presentamos la paralelización de dos aplicaciones bioinformáticas utiliza... more ResumenEn este trabajo presentamos la paralelización de dos aplicaciones bioinformáticas utilizadas el análisis de largas secuencias de ADN. Está basada en un trabajo previo que transforma una secuencia de ADN en una secuencia binaria y se proponen diversas optimizaciones ...
Medical Genomics Visualization Group (MGviz), Siimple OSS, Seqplexing and Kanteron Systems have j... more Medical Genomics Visualization Group (MGviz), Siimple OSS, Seqplexing and Kanteron Systems have jointly developed NGS data analysis workflows that create automatic technical reports for precision medicine with fully integrated QC and LIMS procedures. Our genetic and pharmacogenetic data can be easily integrated in HIS systems and use HL7 standard protocols.We have developed a full suit of open source tools in Python, R and MERN stack for clinical bioinformatics as a service. These tools include serving variant annotation, interactive selection tools, reannotation and automatic clinical reports generation.We are doing trials to deploy this service in a cloud platform for creating a service for analyzing customized NGS gene panels and exomes in a clinical context for diabetes, cancer and mental disabilities.
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Papers by Vicente Arnau