11 results on '"John Robert Mendoza"'
Search Results
2. A Convolutional Neural Network Approach for Estimating Tropical Cyclone Intensity Using Satellite-based Infrared Images.
- Author
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Jay Samuel Combinido, John Robert Mendoza, and Jeffrey Aborot
- Published
- 2018
- Full Text
- View/download PDF
3. Efficient feature extraction for internet data analysis using AS2Vec.
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John Robert Mendoza, Roel Ocampo, Isabel Montes, and Cedric Angelo M. Festin
- Published
- 2018
- Full Text
- View/download PDF
4. Peering into peering: Building better tools for better peering decisions.
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John Robert Mendoza, Josuel Racca, Isabel Montes, Roel Ocampo, and Cedric Angelo M. Festin
- Published
- 2016
- Full Text
- View/download PDF
5. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication
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Eric Rondeau, John Robert Mendoza, Manu Kumar Gundappa, Daniel J. Macqueen, Lars Grønvold, Rori V. Rohlfs, Simen Rød Sandve, Torgeir R. Hvidsten, Ben F. Koop, Gareth Benjamin Gillard, Line Lieblein Røsæg, Øystein Monsen, and Matilde Mengkrog Holen
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Transposable element ,Genome evolution ,QH301-705.5 ,Gene Dosage ,Biology ,QH426-470 ,Gene dosage ,Genome ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Gene Duplication ,Genetics ,Selection, Genetic ,Biology (General) ,Gene ,Phylogeny ,Selection (genetic algorithm) ,030304 developmental biology ,0303 health sciences ,Genes, Essential ,Research ,Genomics ,Phenotype ,Human genetics ,Gene Expression Regulation ,Liver ,Organ Specificity ,Evolutionary biology ,030217 neurology & neurosurgery - Abstract
BackgroundWhole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80–100 million years ago.ResultsWe find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of “toxic mutations”. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression.ConclusionsOur results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
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- 2021
6. Comparative regulomics reveals pervasive selection on gene dosage following whole genome duplication
- Author
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Ben F. Koop, Gareth Benjamin Gillard, Simen Rød Sandve, Daniel J. Macqueen, Torgeir R. Hvidsten, Lars Groenvold, Oeystein Monsen, Rori V. Rohlfs, Manu Kumar Gundappa, Line L Roesaeg, Matilde Mengkrog Holen, John Robert Mendoza, and Eric Rondeau
- Subjects
Transposable element ,Genome evolution ,Phylogenetic tree ,Evolutionary biology ,Promoter ,Biology ,Gene ,Genome ,Gene dosage ,Phenotype - Abstract
Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Although ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards pseudogenization, strong evolutionary constraints have frequently also favoured symmetric shifts in gene dosage of both copies, likely to achieve gene dose reduction while avoiding accumulation of ‘toxic mutations’. Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one source of novel binding sites driving tissue-specific gains in expression. Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
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- 2020
7. Corrigendum to: Rice Galaxy: an open resource for plant science
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Joshua Dizon, Nickolai Alexandrov, Tobias Kretzschmar, Pierre Larmande, Venice Margarette Juanillas, Gabriel Zhou, Ramil Mauleon, John Robert Mendoza, Nicolas Beaume, Michael J. Thomson, Kunalan Ratharanjan, Jon Peter Perdon, Alexis Dereeper, Manuel Ruiz, Lindsay R. Triplett, Gaëtan Droc, Jillian M. Lang, Jason H. Haga, Beth Plale, Jan E. Leach, and Locedie Mansueto
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Resource (biology) ,business.industry ,Environmental resource management ,Oryza ,Health Informatics ,Genomics ,Galaxy ,Computer Science Applications ,Plant Breeding ,Geography ,Plant science ,Seed Bank ,Databases, Genetic ,Corrigendum ,business ,Software - Abstract
Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers.The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
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- 2019
8. Rice Galaxy: An open resource for plant science
- Author
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Gabriel Zhou, Pierre Larmande, Jan E. Leach, Ramil Mauleon, Tobias Kretzschmar, Venice Margarette Juanillas, Nicolas Beaume, Gaëtan Droc, Kunalan Ratharanjan, John Robert Mendoza, Joshua Dizon, Michael J. Thomson, Beth Plale, Locedie Mansueto, Manuel Ruiz, Jillian M. Lang, Jason H. Haga, Nickolai Alexandrov, Jon Peter Perdon, Alexis Dereeper, and Lindsay R. Triplett
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0106 biological sciences ,Germplasm ,Application des ordinateurs ,01 natural sciences ,Genome ,F30 - Génétique et amélioration des plantes ,chemistry.chemical_compound ,Molecular marker ,Technical Note ,riz ,2. Zero hunger ,0303 health sciences ,biology ,U10 - Informatique, mathématiques et statistiques ,high-density genotypes ,food and beverages ,single-nucleotide polymorphism ,Computer Science Applications ,C30 - Documentation et information ,Diffusion de l'information ,Banque de données ,Génotype ,workflow ,Health Informatics ,Computational biology ,Quantitative trait locus ,Oryza ,DNA sequencing ,03 medical and health sciences ,Genotyping ,reproducibility ,Genetic association ,030304 developmental biology ,Genetic diversity ,Génome ,rice ,15. Life on land ,biology.organism_classification ,chemistry ,breeding ,genome-wide association studies ,genomes ,Galaxy project ,010606 plant biology & botany - Abstract
BackgroundRice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci (QTL) discovery and molecular marker development. Comparative sequence analyses across QTL regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers.FindingsWe adopted the Galaxy framework to build the federated Rice Galaxy resource, with shared datasets, tools, and analysis workflows relevant to rice research. The shared datasets include high density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from nine published rice genomes. Rice Galaxy includes tools for designing single nucleotide polymorphism (SNP) assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented.ConclusionsRice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
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- 2019
9. Efficient feature extraction for internet data analysis using AS2Vec
- Author
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Roel Ocampo, Isabel Montes, John Robert Mendoza, and Cedric Angelo M. Festin
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Computer science ,business.industry ,Feature vector ,Feature extraction ,02 engineering and technology ,010501 environmental sciences ,Predictive analytics ,Complex network ,Machine learning ,computer.software_genre ,01 natural sciences ,Network operations center ,Subject-matter expert ,Management system ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,The Internet ,Artificial intelligence ,business ,computer ,0105 earth and related environmental sciences - Abstract
Predictive network analytics uses machine learning algorithms to empower network operators with greater ability to optimize exigent Internet engineering decisions and automate complex network management tasks. However, deriving relevant features that make these algorithms work is resource-intensive, requiring ready access to domain expertise and large amount of network data. We propose AS2Vec, an automated and efficient feature extraction method for constructing vector embeddings for representing autonomous systems (ASes) in Internet data analysis. AS2Vec can efficiently generate meaningful n-dimensional feature vectors that capture global connectivity properties of ASes using only a single resource for network data. We demonstrated, through machine learning tasks, that these feature vectors contain distinctive patterns which preserve structural equivalence and class separability among ASes, facilitating accurate predictions on an imbalanced AS classification problem. This may bring us one step closer towards realizing a "knowledge-defined network" as predictive analytics seamlessly integrates into network operations and management systems.
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- 2018
10. Peering into peering: Building better tools for better peering decisions
- Author
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Josuel Racca, John Robert Mendoza, Cedric Angelo M. Festin, Roel Ocampo, and Isabel Montes
- Subjects
Engineering ,business.industry ,Traffic engineering ,Peering ,Locality ,Internet backbone ,The Internet ,Routing (electronic design automation) ,Traffic flow ,business ,Tier 1 network ,Computer network - Abstract
Network operators need to assess the effects of routing policies and traffic engineering methods in order to guide planning and operational decisions related to peering. We propose a peering analysis framework based on the correlation of inferred AS paths and traffic flow information. We define the data sets needed and a four-step methodology designed to reduce network data dimensionality, determine traffic proximity, identify traffic propensity, and quantify the impact of traffic locality. We demonstrate how the correlation of traffic flow and AS paths, and the application of our four-step approach, uncovers rich information when applied to a real-world case study of a local Internet service provider.
- Published
- 2016
11. Genomic variation in 3,010 diverse accessions of Asian cultivated rice
- Author
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Min Li, Miaolin Chen, Kevin Palis, Rod A. Wing, Dario Copetti, Jinyuan Lu, Hei Leung, Jeffrey Detras, Xianchang He, Zhiqiang Hu, Yanhong Li, Zhen Yue, Jayson Talag, Jiayang Li, John Robert Mendoza, Jiabao Xu, Locedie Mansueto, Wensheng Wang, Victor Jun Ulat, Tianqing Zheng, Ye Yin, Ma. Elizabeth B. Naredo, Kenneth L. McNally, Nickolai Alexandrov, Jauhar Ali, Alexander Poliakov, Fei Shen, Roven Rommel Fuentes, Xiaodong Fang, Rui Li, Xiuqin Zhao, Jue Ruan, Yongming Gao, Yue Zhao, Zhikang Li, Chaochun Wei, Dmytro Chebotarov, Jing Li, Jianlong Xu, Jia Ben, Hong Yu, Dave Kudrna, Millicent D. Sanciangco, Hongliang Zhang, Shuaishuai Tai, Xueqiang Wang, Yongchao Niu, Wushu Hu, Fan Zhang, Chunchao Wang, Binying Fu, Zhichao Wu, Xinyuan Zhang, Inna Dubchak, Jianxin Shi, Qiang Gao, Xiao Cui, Frances Nikki Borja, Zhaotong Dong, Jianwei Zhang, Chen Sun, Ruaraidh Sackville Hamilton, Miao Wang, Jinjie Li, Jean-Christophe Glaszmann, Seunghee Lee, Dabing Zhang, Gengyun Zhang, Zichao Li, Ramil Mauleon, and Yongli Zhou
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0106 biological sciences ,0301 basic medicine ,Crops, Agricultural ,Agricultural genetics ,Asia ,Sélection ,Plant genetics ,Population ,Genomics ,Oryza ,Genes, Plant ,01 natural sciences ,Polymorphism, Single Nucleotide ,Article ,F30 - Génétique et amélioration des plantes ,Evolution, Molecular ,03 medical and health sciences ,Variation génétique ,INDEL Mutation ,Genetic variation ,Domestication ,education ,Phylogeny ,riz ,Genetic diversity ,education.field_of_study ,Multidisciplinary ,Oryza sativa ,biology ,food and beverages ,Genetic Variation ,biology.organism_classification ,Plant Breeding ,030104 developmental biology ,Genetics, Population ,Natural variation in plants ,Haplotypes ,Evolutionary biology ,Provenance ,Genome, Plant ,010606 plant biology & botany - Abstract
Here we analyse genetic variation, population structure and diversity among 3,010 diverse Asian cultivated rice (Oryza sativa L.) genomes from the 3,000 Rice Genomes Project. Our results are consistent with the five major groups previously recognized, but also suggest several unreported subpopulations that correlate with geographic location. We identified 29 million single nucleotide polymorphisms, 2.4 million small indels and over 90,000 structural variations that contribute to within- and between-population variation. Using pan-genome analyses, we identified more than 10,000 novel full-length protein-coding genes and a high number of presence–absence variations. The complex patterns of introgression observed in domestication genes are consistent with multiple independent rice domestication events. The public availability of data from the 3,000 Rice Genomes Project provides a resource for rice genomics research and breeding., Analyses of genetic variation and population structure based on over 3,000 cultivated rice (Oryza sativa) genomes reveal subpopulations that correlate with geographic location and patterns of introgression consistent with multiple rice domestication events.
- Published
- 2016
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