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| Registros recuperados: 33 | |
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| Riaño Pachón, Diego Mauricio; González Estrada, Elizabeth; Alexa, Adrian; Ramírez, Fidel; Vischi Winck, Flavia; Gómez Merino, Fernando, Coord.; Silva Rojas, Hilda Victoria, Coord.; Pérez Rodríguez, Paulino, Coord.. |
| En esta publicación intitulada “Bioinformática: aplicaciones a la genómica y proteómica” se detallan algunos de los avances más sobresalientes de los temas de genómica y proteómica, derivados de un curso internacional sobre el tema, organizado por el Colegio de Postgraduados. Estos avances incluyen aspectos de las dos ciencias ómicas, incluyendo genómica y biología estructural, código R, análisis comparativo y evolución, agrupamiento y minería de datos en R, redes de interacciones entre proteínas y proteómica bioinformática. BIOINFORMATICS : APPLICATIONS TO GENOMICS AND PROTEOMICS. ABSTRACT : In this publication entitled "Bioinformatics: applications to genomics and proteomics" are some of the most salient issues of genomics and proteomics, derived from an... |
| Tipo: Libro |
Palavras-chave: Bioinformática; Proteómica; Genómica; ADN; Proteínas; Modelación; Simulación; Análisis de genómas; Biología estructural; Código R; Análisis comparativo; Minería de datos; Computación aplicada; Bioinformatics; Proteomics; DNA; Proteins; Models; Genomics; Simulation; R Code; Data mining; Computing; Genome analysis. |
| Ano: 2010 |
URL: http://hdl.handle.net/10521/313 |
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| Alvarenga,Samuel Mazzinghy; Caixeta,Eveline Teixeira; Hufnagel,Bárbara; Thiebaut,Flávia; Maciel-Zambolim,Eunize; Zambolimand,Laércio; Sakiyama,Ney Sussumu. |
| Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Coffea; Data mining; ESTs; Genomics; In silico; Bioinformatics. |
| Ano: 2010 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000400031 |
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| Haag,Karen Luisa. |
| Abstract Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Genomics; Metagenomics; Microbiota; Symbiosis; Holobiont. |
| Ano: 2018 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200189 |
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| Mehta,Angela; Silva,Marilia Santos; Guidetti-Gonzalez,Simone; Carrer,Helaine; Takita,Marco Aurélio; Martins,Natália F.. |
| Citrus spp. are economically important crops, which in Brazil are grown mainly in the State of São Paulo. Citrus cultures are attacked by several pathogens, causing severe yield losses. In order to better understand this culture, the Millenium Project (IAC Cordeirópolis) was launched in order to sequence Citrus ESTs (expressed sequence tags) from different tissues, including leaf, bark, fruit, root and flower. Plants were submitted to biotic and abiotic stresses and investigated under different development stages (adult vs. juvenile). Several cDNA libraries were constructed and the sequences obtained formed the Citrus ESTs database with almost 200,000 sequences. Searches were performed in the Citrus database to investigate the presence of different... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Citrus; Cell signaling; Genomics. |
| Ano: 2007 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500003 |
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| Kremer,Frederico Schmitt; McBride,Alan John Alexander; Pinto,Luciano da Silva. |
| Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Microbial genetics; Molecular microbiology; Genomics; Microbiology; Draft genomes. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000400553 |
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| RESENDE, R. M. S.; MARTINS, F. B.; VILELA, M. de M.; MORAES, A. C. L.; FERREIRA, R. C. U.; DÉO, T. G.; MOREIRA, F. A.; PASTINA, M. M.; NODA, R. W.; SOUZA, A. P.. |
| Although Brazil is the major producer and exporter of beef in the world, the rangelands are cultivated with varieties obtained by selection on germplasm and conventional breeding. Only lately genomic information started to be used in the tropical forage breeding programs mostly because of the genome complexity and costs. Urochloa ruziziensis is a sexual autotetraploid forage that has a significant role in integrated systems that are currently important in the agribusiness in certain regions of Brazil and is essential as female parent in other Urochloa spp. breeding programs. Thus, this work intends to use the Genotyping by Sequencing (GBS) approach to identify SNP markers to construct the first map of the species and estimate breeding values for Genomic... |
| Tipo: Fôlder / Folheto / Cartilha (INFOTECA-E) |
Palavras-chave: Genomics; Genetic markers; Pipelines; Breeding. |
| Ano: 2019 |
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1120361 |
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| Smith, Seth R.; Amish, Stephen J.; Bernatchez, Louis; Le Luyer, Jeremy; Wilson, Chris; Boeberitz, Olivia; Luikart, Gordon; Scribner, Kim T.. |
| Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal... |
| Tipo: Text |
Palavras-chave: Linkage map; Salvelinus; QTL; RAD; Genomics; Lake trout. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00634/74659/74565.pdf |
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| Hillen, J. E. J.; Coscia, I.; Vandeputte, Marc; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, Alain; Allal, Francois; Maes, G. E.; Volckaert, F. A. M.. |
| The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was... |
| Tipo: Text |
Palavras-chave: Artificial selection; DdRAD; Fish; Genetic diversity; Genomics; Inbreeding. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00392/50314/50993.pdf |
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| Kazantzidis, Ioannis; Florez-revuelta, Francisco; Dequidt, Mickael; Hill, Natasha; Nebel, Jean-christophe. |
| With the development of applications associated to ego-vision systems, smart-phones, and autonomous cars, automated analysis of videos generated by freely moving cameras has become a major challenge for the computer vision community. Current techniques are still not suitable to deal with real-life situations due to, in particular, wide scene variability and the large range of camera motions. Whereas most approaches attempt to control those parameters, this paper introduces a novel video analysis paradigm, ‘vide-omics’, inspired by the principles of genomics where variability is the expected norm. Validation of this new concept is performed by designing an implementation addressing foreground extraction from videos captured by freely moving cameras.... |
| Tipo: Text |
Palavras-chave: Computer vision; Freely moving camera; Genomics; Foreground detection; Segmentation; Scanlines. |
| Ano: 2018 |
URL: http://archimer.ifremer.fr/doc/00405/51643/52191.pdf |
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| Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loescher, Carolin R.; Kremp, Anke; Delorenzo, Marie E.; Ovreas, Lise; Tolman, Jennifer; Laroche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-lemeilleur, Florence; Leopoldina Aguirre-macedo, Ma; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-ezpeleta, Naiara; Berteaux-lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A. Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-lise; Martinez, Jonathan; Costello, Mark J.; Amaral-zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Gloeckner, Frank Oliver. |
| Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits. |
| Tipo: Text |
Palavras-chave: Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards. |
| Ano: 2015 |
URL: https://archimer.ifremer.fr/doc/00371/48262/48647.pdf |
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| Wenne, Roman; Boudry, Pierre; Hemmer-hansen, Jakob; Lubieniecki, Krzysztof P.; Was, Anna; Kause, Antti. |
| The development and application of genomics has been facilitated in a number of fields by the availability of new methodologies and tools, such as high throughput DNA sequencing and complementary DNA (cDNA) microarrays. Genomic tools are already used in research on commercially important fish and shellfish species. Thousands of expressed sequence tags (EST) are now available for some of these species, and the sequencing of complete genomes of tilapia, cod, salmonids, flatfishes, sea bass and Pacific oyster has been proposed. Microarray technology through simultaneous analysis of the expression of thousands of genes allows the identification of candidate genes involved in the function of multiple physiological, morphological and behavioural traits of... |
| Tipo: Text |
Palavras-chave: Oyster; Fish; Quantitative trait loci; Mariculture; Fisheries; Genetics; Genomics. |
| Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-2927.pdf |
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| Zarski, Daniel; Thaovi Nguyen,; Le Cam, Aurelie; Montfort, Jerome; Dutto, Gilbert; Vidal, Marie-odile; Fauvel, Christian; Bobe, Julien. |
| Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were... |
| Tipo: Text |
Palavras-chave: Microarray; Genomics; Transcriptomics; Aquaculture; Controlled reproduction. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00371/48220/48345.pdf |
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| Vandeputte, Marc; Baroiller, Jean-francois; Haffray, Pierrick; Quillet, Edwige. |
| Genetic improvement is a major contributing factor in developing efficient aquaculture, as it is in other forms of animal production. Moreover, as most fish species are only slightly domesticated, the potential gains are very large. Many of the current methods, developed during the XXth century, are classically used in livestock rearing (choice of breeds, crossbreeding, selective breeding). Others are much more specific to aquatic organisms (genetic control of sex, sterilization through triploidization). The spread of selected lines in aquaculture has been effective only since the 1990s, with lines selected essentially on growth and producing some impressive results. Transgenesis, although technically feasible on growth rate, is not used in practice and... |
| Tipo: Text |
Palavras-chave: Selection; Genomics; Fishes; Breeding; Aquaculture. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6564.pdf |
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| Meng, Arnaud; Corre, Erwan; Probert, Ian; Gutierrez-rodriguez, Andres; Siano, Raffaele; Annamale, Anita; Alberti, Adriana; Da Silva, Corinne; Wincker, Patrick; Le Crom, Stephane; Not, Fabrice; Bittner, Lucie. |
| Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional... |
| Tipo: Text |
Palavras-chave: Genomics; Proteomics; Microbial biology; Molecular evolution; Protists; Transcriptomics. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00444/55550/57209.pdf |
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| Renault, Tristan. |
| Global mollusc production is continuously increasing and reached 12.8 million tonnes in 2004 representing 28.2 percent of the total world production valued at US$ 9.4 billions. However, cultivated molluscs may suffer from severe mortality outbreaks. Among the possible causes is the occurrence of infectious diseases due to a variety of pathogens including protozoan parasites, bacteria and viruses. Preventing and controlling diseases has become a priority for aquaculture sustainability. However, molluscs are unique in terms of health management. Molluscs like other invertebrates, lack a true adaptative immune system. Vaccination can not be used to protect them against pathogens. Moreover, molluscs are usually reared in the open sea which strongly limits the... |
| Tipo: Text |
Palavras-chave: Diagnosis; Phylogeny; Genomics; Mollluscs; Pathogens. |
| Ano: 2008 |
URL: http://archimer.ifremer.fr/doc/2008/publication-4574.pdf |
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| Hedgecock, Dennis; Gaffney, Patrick M.; Goulletquer, Philippe; Guo, Ximing; Reece, Kimberly; Warr, Gregory. |
| An international community of biologists presents the Pacific oyster Crassostrea gigas as a candidate for genome sequencing. This oyster has global distribution and for the past several years the highest annual production of any freshwater or marine organism (4.2 million metric tons, worth $3.5 billion US). Economic and cultural importance of oysters motivates a great deal of biologic research, which provides a compelling rationale for sequencing an oyster genome. Strong rationales for sequencing the oyster genome also come from contrasts to other genomes: membership in the Lophotrochozoa, an understudied branch of the Eukaryotes and high fecundity, with concomitantly high DNA sequence polymorphism and a population biology that is more like plants than any... |
| Tipo: Text |
Palavras-chave: Genomics; Evolutionary and ecological; Nucleotide diversity; Lophotrochozoa; Crassostrea gigas genome sequence; Pacific oyster. |
| Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-2128.pdf |
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| Registros recuperados: 33 | |
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