Miguel Reboiro-jato - Academia.edu (original) (raw)
Papers by Miguel Reboiro-jato
The variables affecting the direct matrix assisted laser desorption ionization mass spectrometry-... more The variables affecting the direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine for classification purposes have been studied. The type of matrix, the number of bottles of wine, the number of technical replicates and the number of spots used for the sample analysis have been carefully assessed to obtain the best classification possible. Ten different algorithms have been assessed as classification tools using the experimental data collected after the analysis of fourteen types of wine. The best matrix was found to be ␣-Cyano with a sample to matrix ratio of 1:0.75. To correctly classify the wines, profiling a minimum of five bottles per type of wine is suggested, with a minimum of three MALDI spot replicates for each bottle. The best algorithm to classify the wines was found to be Bayes Net.
Journal of integrative bioinformatics, 2011
In this paper we present two case studies of Proteomics applications development using the AIBenc... more In this paper we present two case studies of Proteomics applications development using the AIBench framework, a Java desktop application framework mainly focused in scientific software development. The applications presented in this work are Decision Peptide-Driven, for rapid and accurate protein quantification, and Bacterial Identification, for Tuberculosis biomarker search and diagnosis. Both tools work with mass spectrometry data, specifically with MALDI-TOF spectra, minimizing the time required to process and analyze the experimental data.
Journal of integrative bioinformatics, 2010
Biological pathways are crucial to much of the scientific research today including the study of s... more Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.
Journal of integrative bioinformatics, 2012
Maximum-likelihood methods based on models of codon substitution have been widely used to infer p... more Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely a...
Advances in Intelligent and Soft Computing, 2010
Nowadays, integration of biological information coming from multiple sources is a common task for... more Nowadays, integration of biological information coming from multiple sources is a common task for the functional interpretation of experimental results during high-throughput data analysis. In concrete, metabolic pathways information is one of the most widely used genome annotation, during post-hoc analyses of differential gene expression experiments. This paper presents a multi-agent system able to retrieve and integrate metabolic functional annotations
International Journal of Data Mining and Bioinformatics, 2014
Matrix-Assisted Laser Desorption Ionisation Time-of-Flight (MALDI-TOF) is one of the high-through... more Matrix-Assisted Laser Desorption Ionisation Time-of-Flight (MALDI-TOF) is one of the high-throughput mass spectrometry technologies able to produce data requiring an extensive preprocessing before subsequent analyses. In this context, several low-level preprocessing techniques have been successfully developed for different tasks, including baseline correction, smoothing, normalisation, peak detection and peak alignment. In this work, we present a systematic comparison of different software packages aiding in the compulsory preprocessing of MALDI-TOF data. In order to guarantee the validity of our study, we test multiple configurations of each preprocessing technique that are subsequently used to train a set of classifiers whose performance (kappa and accuracy) provide us accurate information for the final comparison. Results from experiments show the real impact of preprocessing techniques on classification, evidencing that MassSpecWavelet provides the best performance and Support Vector Machines (SVM) are one of the most accurate classifiers.
Advances in Intelligent and Soft Computing, 2011
AIBench is a successful Java application framework focused in the biomedical field. In this paper... more AIBench is a successful Java application framework focused in the biomedical field. In this paper, we demonstrate the suitability of this framework in aiding the development of proteomics applications working with mass spectrometry data. We present two case ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 337344. spri... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 337344. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 Assessing the Suitability of MeSH Ontology for Classifying Medline Documents ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 345353. spri... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 345353. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 Assessing the Impact of Class-Imbalanced Data for Classifying Relevant/Irrelevant Medline Documents ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 8386. spring... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 8386. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 An Intuitive Workflow to Retrieve Somatic Mutations in Next Generation Sequencing Studies ...
An important emerging medical application domain for microarray technology is clinical decision s... more An important emerging medical application domain for microarray technology is clinical decision support in the form of diagnosis of diseases. For this task, several computational methods ranging from statistical alternatives to more complex hybrid systems have been previously proposed in the literature. In this work we study the utilisation of several ensemble alternatives for the task of classifying microarray data by using prior knowledge known to be biologically relevant to the target disease. The experimental results using different datasets and several gene sets show that the proposal is able to outperform previous approaches by introducing diversity as different gene sets.
Advances in Intelligent Systems and Computing, 2013
Biclustering techniques have been successfully applied to analyze microarray data and they begin ... more Biclustering techniques have been successfully applied to analyze microarray data and they begin to be applied to the analysis of mass spectrometry data, a high-throughput technology for proteomic data analysis which has been an active research area during the last years. In this work, we propose a novel workflow to the application of biclustering to MALDI-TOF mass spectrometry data, supported by a software desktop application which covering all of its stages. We evaluate the adequacy of applying biclustering to analyze mass spectrometry by comparing between biclustering and hierarchical clustering over two real datasets. Results are promising since they revealed the ability of these techniques to extract useful information, opening a door to further works.
Advances in Intelligent and Soft Computing, 2010
... Multi-agent System for Mass Spectrometry Analysis Miguel Reboiro-Jato, DanielGlez-Peña, Hugo ... more ... Multi-agent System for Mass Spectrometry Analysis Miguel Reboiro-Jato, DanielGlez-Peña, Hugo M. Santos, Mário S. Diniz, Carlos Lodeiro, José L. Capelo, and Florentino Fdez-Riverola* Abstract. ... Miguel Reboiro-Jato . Daniel Glez-Peña . ...
PROTEOMICS, 2011
The use of ultrasonic Q1 probe, in conjunction with immobilized trypsin, has been explored in thi... more The use of ultrasonic Q1 probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished after ultrasonication. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins -bovine serum albumin, a-lactalbumin, carbonic anhydrase and ovalbumin -were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18-O quantification. The digestion yields found were 90-117% for the ultrasonic and 5-21% for the vortex when those methods were compared with the classical overnight digestion.
Advances in Intelligent and Soft Computing, 2010
Advances in Intelligent and Soft Computing, 2010
2010 13th International Conference on Information Fusion, 2010
Journal of Integrated OMICS, 2011
Abstract Within a gene expression matrix, there are usually several particular macroscopic phenot... more Abstract Within a gene expression matrix, there are usually several particular macroscopic phenotypes of samples related to some diseases or drug effects, such as diseased samples, normal samples or drug treated samples. The goal of sample-based clustering is to find ...
Efficient Decision Support Systems - Practice and Challenges From Current to Future, 2011
PLoS ONE, 2013
The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described... more The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general. Citation: Araú jo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, et al. (2013) The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions. PLoS ONE 8(5): e63747.
The variables affecting the direct matrix assisted laser desorption ionization mass spectrometry-... more The variables affecting the direct matrix assisted laser desorption ionization mass spectrometry-based analysis of wine for classification purposes have been studied. The type of matrix, the number of bottles of wine, the number of technical replicates and the number of spots used for the sample analysis have been carefully assessed to obtain the best classification possible. Ten different algorithms have been assessed as classification tools using the experimental data collected after the analysis of fourteen types of wine. The best matrix was found to be ␣-Cyano with a sample to matrix ratio of 1:0.75. To correctly classify the wines, profiling a minimum of five bottles per type of wine is suggested, with a minimum of three MALDI spot replicates for each bottle. The best algorithm to classify the wines was found to be Bayes Net.
Journal of integrative bioinformatics, 2011
In this paper we present two case studies of Proteomics applications development using the AIBenc... more In this paper we present two case studies of Proteomics applications development using the AIBench framework, a Java desktop application framework mainly focused in scientific software development. The applications presented in this work are Decision Peptide-Driven, for rapid and accurate protein quantification, and Bacterial Identification, for Tuberculosis biomarker search and diagnosis. Both tools work with mass spectrometry data, specifically with MALDI-TOF spectra, minimizing the time required to process and analyze the experimental data.
Journal of integrative bioinformatics, 2010
Biological pathways are crucial to much of the scientific research today including the study of s... more Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.
Journal of integrative bioinformatics, 2012
Maximum-likelihood methods based on models of codon substitution have been widely used to infer p... more Maximum-likelihood methods based on models of codon substitution have been widely used to infer positively selected amino acid sites that are responsible for adaptive changes. Nevertheless, in order to use such an approach, software applications are required to align protein and DNA sequences, infer a phylogenetic tree and run the maximum-likelihood models. Therefore, a significant effort is made in order to prepare input files for the different software applications and in the analysis of the output of every analysis. In this paper we present the ADOPS (Automatic Detection Of Positively Selected Sites) software. It was developed with the goal of providing an automatic and flexible tool for detecting positively selected sites given a set of unaligned nucleotide sequence data. An example of the usefulness of such a pipeline is given by showing, under different conditions, positively selected amino acid sites in a set of 54 Coffea putative S-RNase sequences. ADOPS software is freely a...
Advances in Intelligent and Soft Computing, 2010
Nowadays, integration of biological information coming from multiple sources is a common task for... more Nowadays, integration of biological information coming from multiple sources is a common task for the functional interpretation of experimental results during high-throughput data analysis. In concrete, metabolic pathways information is one of the most widely used genome annotation, during post-hoc analyses of differential gene expression experiments. This paper presents a multi-agent system able to retrieve and integrate metabolic functional annotations
International Journal of Data Mining and Bioinformatics, 2014
Matrix-Assisted Laser Desorption Ionisation Time-of-Flight (MALDI-TOF) is one of the high-through... more Matrix-Assisted Laser Desorption Ionisation Time-of-Flight (MALDI-TOF) is one of the high-throughput mass spectrometry technologies able to produce data requiring an extensive preprocessing before subsequent analyses. In this context, several low-level preprocessing techniques have been successfully developed for different tasks, including baseline correction, smoothing, normalisation, peak detection and peak alignment. In this work, we present a systematic comparison of different software packages aiding in the compulsory preprocessing of MALDI-TOF data. In order to guarantee the validity of our study, we test multiple configurations of each preprocessing technique that are subsequently used to train a set of classifiers whose performance (kappa and accuracy) provide us accurate information for the final comparison. Results from experiments show the real impact of preprocessing techniques on classification, evidencing that MassSpecWavelet provides the best performance and Support Vector Machines (SVM) are one of the most accurate classifiers.
Advances in Intelligent and Soft Computing, 2011
AIBench is a successful Java application framework focused in the biomedical field. In this paper... more AIBench is a successful Java application framework focused in the biomedical field. In this paper, we demonstrate the suitability of this framework in aiding the development of proteomics applications working with mass spectrometry data. We present two case ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 337344. spri... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 337344. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 Assessing the Suitability of MeSH Ontology for Classifying Medline Documents ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 345353. spri... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 345353. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 Assessing the Impact of Class-Imbalanced Data for Classifying Relevant/Irrelevant Medline Documents ...
Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 8386. spring... more Page 1. MP Rocha et al. (Eds.): 5th International Conference on PACBB, AISC 93, pp. 8386. springerlink.com © Springer-Verlag Berlin Heidelberg 2011 An Intuitive Workflow to Retrieve Somatic Mutations in Next Generation Sequencing Studies ...
An important emerging medical application domain for microarray technology is clinical decision s... more An important emerging medical application domain for microarray technology is clinical decision support in the form of diagnosis of diseases. For this task, several computational methods ranging from statistical alternatives to more complex hybrid systems have been previously proposed in the literature. In this work we study the utilisation of several ensemble alternatives for the task of classifying microarray data by using prior knowledge known to be biologically relevant to the target disease. The experimental results using different datasets and several gene sets show that the proposal is able to outperform previous approaches by introducing diversity as different gene sets.
Advances in Intelligent Systems and Computing, 2013
Biclustering techniques have been successfully applied to analyze microarray data and they begin ... more Biclustering techniques have been successfully applied to analyze microarray data and they begin to be applied to the analysis of mass spectrometry data, a high-throughput technology for proteomic data analysis which has been an active research area during the last years. In this work, we propose a novel workflow to the application of biclustering to MALDI-TOF mass spectrometry data, supported by a software desktop application which covering all of its stages. We evaluate the adequacy of applying biclustering to analyze mass spectrometry by comparing between biclustering and hierarchical clustering over two real datasets. Results are promising since they revealed the ability of these techniques to extract useful information, opening a door to further works.
Advances in Intelligent and Soft Computing, 2010
... Multi-agent System for Mass Spectrometry Analysis Miguel Reboiro-Jato, DanielGlez-Peña, Hugo ... more ... Multi-agent System for Mass Spectrometry Analysis Miguel Reboiro-Jato, DanielGlez-Peña, Hugo M. Santos, Mário S. Diniz, Carlos Lodeiro, José L. Capelo, and Florentino Fdez-Riverola* Abstract. ... Miguel Reboiro-Jato . Daniel Glez-Peña . ...
PROTEOMICS, 2011
The use of ultrasonic Q1 probe, in conjunction with immobilized trypsin, has been explored in thi... more The use of ultrasonic Q1 probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished after ultrasonication. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins -bovine serum albumin, a-lactalbumin, carbonic anhydrase and ovalbumin -were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18-O quantification. The digestion yields found were 90-117% for the ultrasonic and 5-21% for the vortex when those methods were compared with the classical overnight digestion.
Advances in Intelligent and Soft Computing, 2010
Advances in Intelligent and Soft Computing, 2010
2010 13th International Conference on Information Fusion, 2010
Journal of Integrated OMICS, 2011
Abstract Within a gene expression matrix, there are usually several particular macroscopic phenot... more Abstract Within a gene expression matrix, there are usually several particular macroscopic phenotypes of samples related to some diseases or drug effects, such as diseased samples, normal samples or drug treated samples. The goal of sample-based clustering is to find ...
Efficient Decision Support Systems - Practice and Challenges From Current to Future, 2011
PLoS ONE, 2013
The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described... more The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth), has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila), a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general. Citation: Araú jo AR, Reis M, Rocha H, Aguiar B, Morales-Hojas R, et al. (2013) The Drosophila melanogaster methuselah Gene: A Novel Gene with Ancient Functions. PLoS ONE 8(5): e63747.