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	Provedor de dados Repositório Alice (30) Autor ZERLOTINI, A. (30) LOBO, F. P. (11) OLIVEIRA, G. (8) GIACHETTO, P. F. (7) SILVA, F. R. da (6) YAMAGISHI, M. E. B. (6) CINTRA, L. C. (5) ARAÚJO, F. (4) CARNEIRO, N. P. (4) CARVALHO, M. R. S. (4) CESAR, A. S. M. (4) COIMBRA, R. S. (4) DINIZ, W. J. S. (4) KUSER-FALCÃO, P. R. (4) LEITE, L. R. (4) MACHADO, M. A. (4) MUDADU, M. A. (4) NICIURA, S. C. M. (4) OLIVEIRA, P. S. N. (4) SILVA, M. V. G. B. (4) Mais... Palavra-chave Bioinformatics (13) Bioinformática (13) Genome (6) Polimorfismo de nucleotídeo único (5) Single nucleotide polymorphism (5) Genoma (4) Genomics (4) Gado de corte (3) Sequence analysis (3) Zebu (3) Alocação de carbono (2) Cattle (2) Computer software (2) Expressão gênica (2) Gene expression (2) Genômica (2) Schistosoma (2) Sequência de RNA (2) Allele (1) Animal breeding (1) Mais... Tipo do documento Anais e Proceedings de eventos (18) Artigo de periódico (7) Parte de livro (3) Separatas (2) Ano 2015 (6) 2014 (7) 2013 (6) 2012 (9) 2011 (2) País Brazil (30) Idioma Inglês (28) Português (2)		Ordenar por:  Relevância Autor Título Ano Registros recuperados: 30 Primeira ... 1 2 ... Última A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. Repositório Alice PROTASIO, A. V.; TSAI, I. J.; BABBAGE, A.; NICHOL, S.; HUNT, M.; ASLETT, M. A.; SILVA, N. de; VELARDE, G. S.; ANDERSON, T. J. C.; CLARK, R. C.; DAVIDSON, C.; DILLON, G. P.; HOLROYD, N. E.; LOVERDE, P. T.; LLOYD, C.; MCQUILLAN, J.; OLIVEIRA, G.; OTTO, T. D.; PARKER-MANUEL, S. J.; QUAIL, M. A.; WILSON, R. A.; ZERLOTINI, A.; DUNNE, D. W.; BERRIMAN, M.. Schistosomiasis is one of the most prevalent parasitic diseases, affecting millions of people in developing countries. Amongst the human-infective species, Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome. We used Sanger capillary and deep-coverage Illumina sequencing from clonal worms to upgrade the highly fragmented draft 380 Mb genome to one with only 885 scaffolds and more than 81% of the bases organised into chromosomes. We have also used transcriptome sequencing (RNA-seq) from four time points in the parasite?s life cycle to refine gene predictions and profile their expression. More than 45% of predicted genes have been extensively modified and the total number has... Tipo: Artigo de periódico Palavras-chave: Schistosoma. Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/940202 Allele specific expression analysis in bovine muscle tissue. Repositório Alice SOUZA, M. M.; MOKRY, F. C.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A.; CESAR, A. S. M.; MORÉ, D.; MOURÃO, G.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; COUTINHO, L. L.; ZERLOTINI, A.; REGITANO, L. C.. Imprinted genes have been target of many studies, mainly in human and mouse, and lately in bovines due to the interest of understanding the epigenetic mechanisms underlying important meat quality phenotypes and the possibility of applying it in animal breeding programs in the future. Genomic DNA from 146 steers was genotyped using the Illumina BovineHD BeadChip in order to identify heterozygous individuals with known allele origin. Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Expressão gênica; Genoma; Bioinformatics; Genome; Gene expression. Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1035029 Allele specific expression analysis in bovine muscle tissue. Repositório Alice SOUZA, M. M.; MOKRY, F. C.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A.; CESAR, A. S. M.; MORÉ, D.; MOURÃO, G.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; ZERLOTINI, A.; REGITANO, L. C.. Tipo: Separatas Palavras-chave: Allele; Specific expression analysis; Bovine muscle tissue. Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1029313 Chromatin structural changes around satellite repeats on the female sex chromosome in Schistosoma mansoni and their possible role in sex chromosome emergence. Repositório Alice LEPESANT, J. M. J.; COSSEAU, C.; BOISSIER, J.; FREITAG, M.; PORTELA, J.; CLIMENT, D.; PERRIN, C.; ZERLOTINI, A.; GRUNAU, C.. Background: In the leuphotrochozoan parasitic platyhelminth Schistosoma mansoni, male individuals are homogametic (ZZ) whereas females are heterogametic (ZW). To elucidate the mechanisms that led to the emergence of sex chromosomes, we compared the genomic sequence and the chromatin structure of male and female individuals. As for many eukaryotes, the lower estimate for the repeat content is 40%, with an unknown proportion of domesticated repeats. We used massive sequencing to de novo assemble all repeats, and identify unambiguously Z-specific, W-specific and pseudoautosomal regions of the S. mansoni sex chromosomes. Results: We show that 70 to 90% of S. mansoni W and Z are pseudoautosomal. No female-specific gene could be identified. Instead, the... Tipo: Artigo de periódico Palavras-chave: Schistosoma. Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/940197 Complex pattern of CAST allelic expression in bovine muscle tissue. Repositório Alice SOUZA, M. M.; ZERLOTINI, A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A. L.; MOKRY, F. B.; CESAR, A. S. M.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; COUTINHO, L. L.; REGITANO, L. C. A.. ISMB 2014. Pôster E13. Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Polimorfismo de nucleotídeo único; Bioinformatics; Single nucleotide polymorphism. Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1007540 Counting RNAseq reads: which way is better? Repositório Alice SILVA, F. R. da; NODA, R. W.; ZERLOTINI, A.; LOBO, F. P.; CARNEIRO, N. P.. In this work we show the variation of results we?ve found while working with ~1 billion Illumina reads from drought tolerant Sorghum bicolor genotype in the presence and absence of the stress and compared results found for key genes already characterized. Tipo: Parte de livro Palavras-chave: Bioinformática; Sequência de RNA; Sorghum.; Sorgo; Bioinformatics.. Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/981626 De novo assembly of a Nelore (Bos indicus) bull genome based on short read sequences. Repositório Alice CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P.; SILVA, F. R. da; GIACHETTO, P. F.; KUSER-FALCÃO, P. R. K.; SILVA, L. O. C. da; EGITO, A. A. do; SIQUEIRA, F.; SILVA, N. M. A. da; PAIVA, S. R.; YAMAGISHI, M. E. B.; CAETANO, A. R.. Zebu cattle breeds (Bos indicus) are widely used for milk and beef production in the tropics and show natural adaptations to biotic and abiotic stresses especially found in these regions. Advanced genomic tools will be essential to help unveil and explore the underlying genetic variations that distinguish taurine and indicine cattle and, at the same time, will facilitate the work of breeders striding towards incorporating genomic tools into breeding programs aiming to improve productivity and beef and milk quality. Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Gado de corte; Zebu; Cattle; Bioinformatics. Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1006398 Efficient gap-closure of eukaryotic genome sequence assemblies by third-generation sequencing. Repositório Alice CRUZ, I. R. da C.; GERALDO, J. A.; LEITE, L. R.; ZERLOTINI, A.; ARAÚJO, F.; SILVA, M. V. G. B.; COIMBRA, R. S.; CARVALHO, M. R. S.; OLIVEIRA, G.. Recently, we produced the first draft assemblies of Guzerá and Gir genomes. Two Zebu (Bos indicus) breeds adapted to tropical climate and under genetic evaluation to milk purposes in Brazil. Tipo: Anais e Proceedings de eventos Palavras-chave: Sequenciamento de genoma de zebu; Plataforma SOLiD; Genome; Zebu; Sequence analysis. Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946528 Embrapa Bioinformatic Multi-user laboratory. Repositório Alice CINTRA, L. C.; ZERLOTINI, A.; SILVA, F. R. da; LOBO, F. P.; YAMAGISHI, M. E. B.; KUSER-FALCÃO, P. R. K.; GIACHETTO, P. F.. Recently Brazilian Agricultural Research Corporation (Embrapa) implemented the Embrapa Bioinformatic Multi-user Laboratory(LMB) that provides a central point of convergency for related bioinformatics issues in the organization, a high performance computing (HPC) infrastructure to be used by employees and partners on solution of computational intensive problems in bioinformatics, and principally, provides specialized collaborators to realize training, assist the elaboration of projects with bioinformatics components and in specific cases contribute to execute them. The importance of LMB is best understood when one takes into account the way Embrapa research centers are geographically located. The research centers are distributed among the several regions of... Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Laboratório Multiusuário de Bioinformática.; Bioinformatics. Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/974773 Embrapa Bioinformatics Multi-Users Laboratory - LMB. Repositório Alice KUSER-FALCÃO, P. R.; YAMAGISHI, M. E. B.; GIACHETTO, P. F.; SILVA, F. R.; LOBO, F. P.; CINTRA, L. C.; ZERLOTINI, A.; HIGA, R.; VIEIRA, F.. The Bioinformatics Multi-Users Laboratory of Embrapa provides an array of shared research resources and infra-structure to the Embrapa community and research collaborators The primary mission of the LMB is to address the increasing need of Embrapa investigators for support and solutions in Bioinformatics in a collaborative environment. To fulfill this mission, the LMB collaborates on research projects that require expertise in genome assembly, meta-genomics analysis to unravel candidate genes, molecular markers, differential gene expression, and structural bioinformatics, and assists in the implementation of computational solutions . Tipo: Anais e Proceedings de eventos Palavras-chave: Pesquisa e desenvolvimento; Bioinformática; Research and development; Bioinformatics. Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946438 Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. Repositório Alice RUIZ, J. C.; D'AFONSECA, V.; SILVA, A.; ALI, A.; PINTO, A. C.; SANTOS, A. R.; ROCHA, A. A. M. C.; LOPES, D. O.; DORELLA, F. A.; PACHECO, L. G. C.; COSTA, M. P.; TURK, M. Z.; SEYFFERT, N.; MORAES, P. M. R. O.; SOARES, S. C.; ALMEIDA, S. S.; CASTRO, T. L. P.; ABREU, V. A. C.; TROST, E.; BAUMBACH, J.; TAUCH, A.; SCHNEIDER, M. P. C.; McCULLOCH, J.; CERDEIRA, L. T.; RAMOS, R. T. J.; ZERLOTINI, A.; DOMINITINI, A.; RESENDE, D. M.; COSER, E. M.; OLIVEIRA, L. M.; PEDROSA, A. L.; VIEIRA, C. U.; GUIMARÃES, C. T.; BARTHOLOMEU, D. C.; OLIVEIRA, D. M.; SANTOS, F. R.; RABELO, É. M.; LOBO, F. P.; FRANCO, G. R.; COSTA, A. F.; CASTRO, I. M.; DIAS, S. R. C.; FERRO, J. A.; ORTEGA, J. M.; PAIVA, L. V.; GOULART, L. R.; ALMEIDA, J. F.; FERRO, M. I. T.; CARNEIRO, N. P.; FALCÃO, P. R. K.; GRYNBERG, P.; TEIXEIRA, S. M. R.; BROMMONSCHENKEL, S.; OLIVEIRA, S. C.; MEYER, R.; MOORE, R. J.; MIYOSHI, A.; OLIVEIRA, G. C.; AZEVEDO, V.. Background: Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings: We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in... Tipo: Artigo de periódico Palavras-chave: Genoma de C pseudotuberculosis; Análise de genoma; Ilhas de patogenicidade; Corynebacterium Pseudotuberculosis; Caseous lymphadenitis; Pathogenicity. Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/914696 Evidence for reductive genome evolution and lateral acquisition of virulence functions in two Corynebacterium pseudotuberculosis strains. Repositório Alice RUIZ, J. C.; D'AFONSECA, V.; SILVA, A.; ALI, A.; PINTO, A. C.; SANTOS, A. R.; ROCHA, A. A. M. C.; LOPES, D. O.; DORELLA, F. A.; PACHECO, L. G. C.; COSTA, M. P.; TURK, M. Z.; SEYFFERT, N.; MORAES, P. M. R. O.; SOARES, S. C.; ALMEIDA, S. S.; CASTRO, T. L. P.; ABREU, V. A. C.; TROST, E.; BAUMBACH, J.; TAUCH, A.; SCHNEIDER, M. P. C.; McCULLOCH, J.; CERDEIRA, L. T.; RAMOS, R. T. J.; ZERLOTINI, A.; DOMINITINI, A.; RESENDE, D. M.; COSER, E. M.; OLIVEIRA, L. M.; PEDROSA, A. L.; VIEIRA, C. U.; GUIMARAES, C. T.; BARTHOLOMEU, D. C.; OLIVEIRA, D. M.; SANTOS, F. R.; RABELO, E. M.; LOBO, F. P.; FRANCO, G. R.; COSTA, A. F.; CASTRO, I. M.; DIAS, S. R. C.; FERRO, J. A.; ORTEGA, J. M.; PAIVA, L. V.; ALMEIDA, J. F.; GOULART, L. R.; FERRO, M. I. T.; CARNEIRO, N. P.; FALCÃO, P. R. K.; GRYNBERG, P.; TEIXEIRA, S. M. R.; BROMMONSCHENKEL, S.; OLIVEIRA, S. C.; MEYER, R.; MOORE, R. J.; MIYOSHI, A.; OLIVEIRA, G. C.; AZEVEDO, V.. Background: Corynebacterium pseudotuberculosis, a Gram-positive, facultative intracellular pathogen, is the etiologic agent of the disease known as caseous lymphadenitis (CL). CL mainly affects small ruminants, such as goats and sheep; it also causes infections in humans, though rarely. This species is distributed worldwide, but it has the most serious economic impact in Oceania, Africa and South America. Although C. pseudotuberculosis causes major health and productivity problems for livestock, little is known about the molecular basis of its pathogenicity. Methodology and Findings: We characterized two C. pseudotuberculosis genomes (Cp1002, isolated from goats; and CpC231, isolated from sheep). Analysis of the predicted genomes showed high similarity in... Tipo: Artigo de periódico Palavras-chave: Genética; Patógeno.; Genome. Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/906799 Genética da resistência de planta adulta à ferrugem da folha em trigo - cultivar Toropi. Repositório Alice CASASSOLA, A.; BRAMMER, S. P.; CHAVES, M. S.; NHANI JUNIOR, A.; MARTINELLI, J. A.; KUSER-FALCAO, P. R.; ZERLOTINI, A.; GRANDO, M. F.; STEFANATO, F.; BOYD, L.. Orientadora: Sandra Patussi Brammer. Tipo: Parte de livro Palavras-chave: Ferrugem da folha; RNA-Seq; Expressão diferencial. Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1018075 GO enrichment of microarray data from maize root under drough. Repositório Alice NODA, R. W.; LAAT, D. M. de; GUIMARÃES, C. T.; SOUZA, T. C. de; DIAS, L. L. C.; LOBO, F. P.; MAGALHÃES, J. V. de; COIMBRA, R. S.; MAGALHÃES, P. C.; ZERLOTINI, A.; FRANCO, G. M.; CARNEIRO, N. P.. In this study microarray data from roots of a drought tolerant inbred maize line (Embrapa?s breeding program) under two water regimes was analyzed. The analysis revealed that 746 genes were differentially expressed, of which 455 were up- and 291 were down-regulated. Tipo: Parte de livro Palavras-chave: Genômica; Milho; Microarray technology; Corn; Genomics. Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/981622 Monoallelic expression of NNAT gene in Nelore steers skeletal muscle. Repositório Alice SOUZA, M. M.; ZERLOTINI, A.; TIZIOTO, P. C.; OLIVEIRA, P. S. N.; SOMAVILLA, A. L.; MOKRY, F. B.; CESAR, A. S. M.; DINIZ, W. J. S.; MUDADU, M. A.; NICIURA, S. C. M.; COUTINHO, L. L.; REGITANO, L. C. A.. ABSTRACT: The NNAT gene plays a role on adipogenesis, brain development and insulin secretion. NNAT is described as paternal imprinted in bovine fetal tissue, but it is still underexplored in adult tissues. In order to improve the understanding of NNAT expression, muscle from Nellore was used to assess its allelic expression. Genomic DNA from 38 steers was genotyped for identification of heterozygous individuals with known allele origin. Total mRNA from muscle was extracted and sequenced by HiScanSQ, and afterwards the reads of each allele were counted for each animal. A total of 8 reciprocal heterozygous had more than 10 reads for the chosen SNP. All animals showed monoallelic expression, being 5 with paternal allele expressed, while 7 had the G allele... Tipo: Anais e Proceedings de eventos Palavras-chave: Neuronatin; Zebu; Genomic imprinting. Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1006155 New single sucleotide polymorphisms in Guzerá breed revealed by whole-genome re-sequencing. Repositório Alice CRUZ, I. R.; GERALDO, J. A.; OLIVEIRA, F. S. de; LEITE, L. R.; ARAÚJO, F.; ZERLOTINI, A.; LOPES, B. C.; ARBEX, W. A.; MACHADO, M. A.; PEIXOTO, M. G. C. D.; VERNEQUE, R. da S.; MARTINS, M. F.; SILVA, M. V. G. B.; COIMBAR, R. S.; CARVALHO, M. R. S.; OLIVEIRA, G.. The objective of our work was to sequence and assemble the Guzerá genome in order to identify race-­specific variations that might be used in breeding programs. Tipo: Anais e Proceedings de eventos Palavras-chave: Polimorfismo de nucleotídeo único; Criação de animais; Análise de sequência de genomas; Single nucleotide polymorphism; Animal breeding; Sequence analysis; Genomics. Ano: 2013 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/973157 Novel polymorphisms in genes associated with milk and meat production and disease resistance in the Guzerá breed identified by whole-genome sequencing. Repositório Alice ROSSE, I. C.; ASSIS, J. G.; OLIVEIRA, F. S.; LEITE, L. R.; ARAUJO, F.; ZERLOTINI, A.; LOPES, B. C.; ARBEX, W. A.; MACHADO, M. A.; PEIXOTO, M. G. C. D.; VERNEQUE, R. S.; GUIMARÃES, M. F. M.; SILVA, M. V. G. B.; COIMBRA, R. S.; OLIVEIRA, G.; CARVALHO, M. R. S.. In this context, the objective of this work was to sequence and assemble the genome of one Guzerá bull in order to identify breed-specific variations that might be included in the genotyping arrays and be useful in breeding programs. Tipo: Anais e Proceedings de eventos Palavras-chave: Polimorfismo de nucleotídeo único; Gado de corte; Single nucleotide polymorphism; Cattle. Ano: 2014 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1006143 POTION: a massive parallel program for identification of homologous genes under positive selection on genomic scale datasets. Repositório Alice HONGO, J.; CASTRO, G.; SILVA, F.; CINTRA, L.; ZERLOTINI, A.; LOBO, F.. The search for positive selection is also highly parallelizable, since each group of homologous can be analyzed independently. Here we describe POTION (POsitive selecTION), a massively parallel software to automatically detect positive selection on genomic scale data, ideal for analysis of large datasets in cluster infrastructures Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Genômica; Bioinformatics; Computer software; Genomics. Ano: 2012 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946632 POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. Repositório Alice HONGO, J. A.; CASTRO, G. M. de; CINTRA, L. C.; ZERLOTINI, A.; LOBO, F. P.. Abstract: Background: Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed... Tipo: Artigo de periódico Palavras-chave: Potion; Evolução Darwiniana; Comparative genomics; Positive selection; Gene; Fenótipo; Pesquisa; Genomics; Phylogeny; Genes; Genome. Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1027912 POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes. Repositório Alice HONGO, J. A.; CASTRO, G. de; CINTRA, L.; ZERLOTINI, A.; LOBO, F.. We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes. Tipo: Anais e Proceedings de eventos Palavras-chave: Bioinformática; Expressão gênica; Bioinformatics; Computer software; Gene expression. Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1035022 Registros recuperados: 30 Primeira ... 1 2 ... Última

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