Relevant bibliographies by topics / Genomic techniques

Academic literature on the topic 'Genomic techniques'

Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Genomic techniques"

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Ramzan, Fahad, Adnan Younis, and Ki-Byung Lim. "Application of Genomic In Situ Hybridization in Horticultural Science." International Journal of Genomics 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/7561909.

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Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example,Diospyroshybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such asClivia,Rhododendron, andLycorisornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants.
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Xin-Yun Zhang, Fei Chen, Yuan-Ting Zhang, S. C. Agner, M. Akay, Zu-Hong Lu, M. M. Y. Waye, and S. K. W. Tsui. "Signal processing techniques in genomic engineering." Proceedings of the IEEE 90, no. 12 (December 2002): 1822–33. http://dx.doi.org/10.1109/jproc.2002.805308.

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Damaj, Mona B., Phillip D. Beremand, Marco T. Buenrostro-Nava, John Ivy, Siva P. Kumpatla, John Jifon, Getu Beyene, Qingyi Yu, Terry L. Thomas, and T. Erik Mirkov. "Isolating promoters of multigene family members from the polyploid sugarcane genome by PCR-based walking in BAC DNA." Genome 53, no. 10 (October 2010): 840–47. http://dx.doi.org/10.1139/g10-064.

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The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5′ flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.
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Morrison, Carl. "Fluorescent In Situ Hybridization and Array Comparative Genomic Hybridization: Complementary Techniques for Genomic Evaluation." Archives of Pathology & Laboratory Medicine 130, no. 7 (July 1, 2006): 967–74. http://dx.doi.org/10.5858/2006-130-967-fishaa.

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Abstract During the past few years a new high-throughput molecular technology, array comparative genomic hybridization, has received a great deal of attention. As a DNA-based tool, this technique is presumably more reproducible than expression arrays. In this review, I discuss how array comparative genomic hybridization is remarkably similar with regard to genome analysis to fluorescent in situ hybridization, a technique that is generally regarded as one of the more accurate and reproducible molecular techniques in diagnostic surgical pathology. A thorough understanding of this technology will be useful for all surgical pathologists in the near future, as this technology will no doubt have some influence on our daily practice.
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van Oppen, Madeleine J. H., and Melinda A. Coleman. "Advancing the protection of marine life through genomics." PLOS Biology 20, no. 10 (October 17, 2022): e3001801. http://dx.doi.org/10.1371/journal.pbio.3001801.

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The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.
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Upadhyay, Tejal, and Samir Patel. "Identifying Subtypes of Cancer Using Genomic Data by Applying Data Mining Techniques." International Journal of Natural Computing Research 8, no. 3 (July 2019): 55–64. http://dx.doi.org/10.4018/ijncr.2019070104.

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This article is about the study of genomics structures and identifying cancer types from it. It divides into six parts. The first part is about the introduction of cancer, types of cancers, how cancer arises, etc. The second part is about the genomic study and how cancer is related to that, which features are used for the study. The third part is about the software which the authors have used to study these genomic structures, which data sets are used, and what is the final output for this study. The fourth part shows the proposed algorithm for the study. The fifth part shows the data preprocessing and clustering. Different preprocessing and clustering algorithms are used. The sixth part shows the results and conclusion with a future scope. The genomics data which is used by this article is taken from the Cancer Genome Atlas data portal which is freely available. Some applied imputation techniques fill up for the missing values and important features are extracted. Different clustering algorithms are applied on genome dataset and results are generated.
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Kyselová, Jitka, Ladislav Tichý, and Kateřina Jochová. "The role of molecular genetics in animal breeding: A minireview." Czech Journal of Animal Science 66, No. 4 (March 26, 2021): 107–11. http://dx.doi.org/10.17221/251/2020-cjas.

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Current animal breeding approaches are strongly associated with the development of sophisticated molecular genetics methods and techniques. Worldwide expansion of genomic selection can be achieved by the identification of genetic DNA markers and implementation of the microarray (“chip”) technology. Further advancement was associated with next-generation sequencing methods, high-throughput genotyping platforms, targeted genome editing techniques, and studies of epigenetic mechanisms. The remarkable development of “omics” technologies, such as genomics, epigenomics, transcriptomics, proteomics and metabolomics, has enabled individual genomic prediction of animal performance, identification of disease-causing genes and biomarkers for the prevention and treatment and overall qualitative progress in animal production.
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Tramontano, Anna. "Comparative Modelling Techniques: Where are we?" Comparative and Functional Genomics 4, no. 4 (2003): 402–5. http://dx.doi.org/10.1002/cfg.306.

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The enormous increase in data availability brought about by genomic projects is paralleled by an equally unprecedented increase in the expectations for new medical, pharmacological, environmental and biotechnological discoveries. Whether or not we will be able to meet (at least partially) these expectations will depend on how well we will be able to interpret the data and translate the mono-dimensional information encrypted in genomes into a detailed understanding of its biological meaning at the phenotypic level. The process is far from being trivial, and the obstacles along the road are formidable: even the problem of identifying coding regions in eukaryotic genomes is not completely solved. Far more complex is identification of the function of the encoded proteins, and this will probably represent the most challenging problem for the next generations of scientists.
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Aziz, Md Momin Al, Md Nazmus Sadat, Dima Alhadidi, Shuang Wang, Xiaoqian Jiang, Cheryl L. Brown, and Noman Mohammed. "Privacy-preserving techniques of genomic data—a survey." Briefings in Bioinformatics 20, no. 3 (November 7, 2017): 887–95. http://dx.doi.org/10.1093/bib/bbx139.

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Nusrat, S., T. Harbig, and N. Gehlenborg. "Tasks, Techniques, and Tools for Genomic Data Visualization." Computer Graphics Forum 38, no. 3 (June 2019): 781–805. http://dx.doi.org/10.1111/cgf.13727.

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Dissertations / Theses on the topic "Genomic techniques"

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Haghighi, Maryam. "Application of Combinatorial Optimization Techniques in Genomic Median Problems." Thèse, Université d'Ottawa / University of Ottawa, 2011. http://hdl.handle.net/10393/20484.

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Constructing the genomic median of several given genomes is crucial in developing evolutionary trees, since the genomic median provides an estimate for the ordering of the genes in a common ancestor of the given genomes. This is due to the fact that the content of DNA molecules is often similar, but the difference is mainly in the order in which the genes appear in various genomes. The mutations that affect this ordering are called genome rearrangements, and many structural differences between genomes can be studied using genome rearrangements. In this thesis our main focus is on applying combinatorial optimization techniques to genomic median problems, with particular emphasis on the breakpoint distance as a measure of the difference between two genomes. We will study different variations of the breakpoint median problem from signed to unsigned, unichromosomal to multichromosomal, and linear to circular to mixed. We show how these median problems can be formulated in terms of problems in combinatorial optimization, and take advantage of well-known combinatorial optimization techniques and apply these powerful methods to study various median problems. Some of these median problems are polynomial and many are NP-hard. We find efficient algorithms and approximation methods for median problems based on well-known combinatorial optimization structures. The focus is on algorithmic and combinatorial aspects of genomic medians, and how they can be utilized to obtain optimal median solutions.
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Khanam, Taslima. "Sex determination and genetic management in Nile tilapia using genomic techniques." Thesis, University of Stirling, 2017. http://hdl.handle.net/1893/25285.

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The PhD research studied two aspects in tilapia, firstly the analysis of sex determination in Nile tilapia (evidence of complex sex-determining systems) and secondly the genetic management of the tilapia species, using different genomic analysis approaches. This research started with the development of two techniques: minimally invasive DNA sampling from fish mucus, which was found to be suitable for standard genotyping and double-digest restriction-site associated DNA sequencing – ddRADseq; and pre-extraction pooling of tissue samples for ddRADseq (BSA-ddRADseq), which was found to be suitable for identifying a locus linked to a trait of interest (sex in this case). The first molecular evidence concerning the sex determination in genetically improved farmed tilapia (GIFT) was described using BSA-ddRADseq. Given the multiple stock origin of GIFT, surprisingly only a single locus (in linkage group 23) was found to be associated with the phenotypic sex across the population. The first evidence of LG23 influence on phenotypic sex in the Stirling population of Nile tilapia was also found. Different combinations of estrogen hormones and high temperature were tested for feminising Nile tilapia: a combined treatment of estrogen hormone and high temperature was found to be more efficient in feminising Nile tilapia than the estrogen alone. A set of species-diagnostic SNP markers were tested which were found to be suitable to distinguish pure species (O. niloticus, O. mossambicus and O. aureus), and these were used to analyse species contribution to GIFT and a selected tilapia hybrid strain. The results of the current research added novel information to our understanding of sex determination in Nile tilapia, which will be helpful in the development of marker-assisted selection in GIFT and other Nile tilapia strains towards the production of all male offspring. The methods developed also have broader applicability in genetic and genomics research.
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Raiford, Douglas W. III. "Algorithmic Techniques Employed in the Isolation of Codon Usage Biases in Prokaryotic Genomes." Wright State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=wright1211902424.

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Brown, Margaret M. "Application of genomic techniques to development of biomarkers for the aquatic environment." Thesis, Glasgow Caledonian University, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443169.

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Sharma, Jason P. (Jason Poonam) 1979. "Classification performance of support vector machines on genomic data utilizing feature space selection techniques." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/87830.

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Renard, Meseguer Joan. "Identification of genes related to seed longevity in Arabidopsis thaliana using genomic molecular techniques." Doctoral thesis, Universitat Politècnica de València, 2021. http://hdl.handle.net/10251/170554.

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Tesis por compendio
[ES] La longevidad de las semillas, o el tiempo durante el cual permanecen las semillas viables, es de gran importancia para la conservación de la biodiversidad, la agricultura y la economía. Además, el estudio de este parámetro puede contribuir a conocer mejor los mecanismos moleculares comunes a todos los organismos para prevenir el envejecimiento. Una de las principales estrategias de las semillas para ralentizar su envejecimiento consiste en detener su metabolismo, a través de su deshidratación. Otros mecanismos moleculares para evitar daños son el aislamiento frente al entorno a través de la cubierta de la semilla, y la producción de antioxidantes y otras moléculas para evitar el daño oxidativo, uno de los principales causantes del envejecimiento de las semillas. Los mecanismos de reparación mitigan parte del daño acumulado. El organismo modelo de plantas Arabidopsis thaliana brinda la oportunidad de la realización de estudios genómicos para el estudio de, en este caso, la longevidad de las semillas para descubrir nuevos factores genéticos y mecanismos moleculares determinantes. Este conocimiento servirá para entender mejor los procesos de deterioro de las semillas y que también será clave para aumentar la longevidad de estas. Mediante el uso de variedades naturales genotipadas de Arabidopsis thaliana y un estudio de asociación del genoma conocido como GWAS, seguido de estudios de genética reversa, se han identificado 12 nuevos genes relacionados con la longevidad de las semillas, relacionados con la protección del embrión, el control del daño oxidativo, y la permeabilidad de la cubierta de la semilla. El desarrollo de la cubierta de la semilla está determinado por factores de transcripción. Plantas mutantes en diversos factores de transcripción involucrados en el desarrollo de la cubierta de la semilla presentan una longevidad alterada. La sobreexpresión de los factores de transcripción AtHB25 y COG1 provoca que las semillas presenten una mayor longevidad debido a una incrementada deposición de poliésteres lipídicos. Estas barreras de poliésteres lipídicos son la cutícula, formada por cutina, y la suberina. Ambas participan positivamente en la protección del embrión frente al ambiente exterior. Estudios genómicos de ambos factores de transcripción han demostrado que AtHB25 regula directamente a enzimas biosintéticos de los monómeros de suberina y cutina, y COG1 regula la expresión de enzimas relacionados con la polimerización de poliésteres lipídicos y lignina. La regulación en la que participa AtHB25 es muy importante debido a la alta conservación de las secuencias genómicas y funciones de AtHB25 en angiospermas, y parece involucrado en la respuesta a bajas temperaturas. Por otra parte, COG1, que está involucrado en la percepción de luz, regula parte del desarrollo del tegumento externo a través de la regulación de AP2, un factor clave en el establecimiento de la identidad de tejido de este tegumento de la cubierta de la semilla, donde se localiza la suberina. AtHB25 y COG1 están involucrados en la adaptación de la longevidad de la semilla a través de señales ambientales como la temperatura y la luz, respectivamente, regulando la deposición de poliésteres lipídicos.
[CAT] La longevitat de les llavors, o el temps que romanen les llavors viables, es de gran importància per la conservació de la biodiversitat, l'agricultura i l'economia. A més a més, l'estudi d'aquest paràmetre pot contribuir a conèixer millor els mecanismes moleculars comuns a tots els organismes per prevenir l'envelliment. Una de les principals estratègies de les llavor per retardar el seu envelliment consisteix detenir el seu metabolisme, mitjançant la seua deshidratació. Altres mecanismes moleculars per evitar danys son el seu aïllament de l'entorn per mitjan de la coberta de la llavor, i la producció d'antioxidants i altres molècules per evitar el dany oxidatiu, un dels principal causants del envelliment de les llavors. Els mecanismes de reparació mitiguen part del dany acumulat. L'organisme model Arabidopsis thaliana brinda la oportunitat de la realització d'estudis genòmics per a l'estudi de, en aquest cas, la longevitat de les llavors per descobrir nous factors genètics y mecanismes moleculars determinants. Aquest coneixement servirà per entendre millor els processos de deteriorament de les llavor i serà clau per augmentar la longevitat d'aquestes. Mitjançant l'ús de varietats naturals genotipades d'Arabidopsis thaliana i un estudi d'associació del genoma conegut com GWAS, seguits d'estudis de genètica inversa, s'han identificat 12 nous gens relacionats amb la longevitat de les llavors, relacionats amb la protecció de l'embrió, el control del dany oxidatiu, y la permeabilitat de la coberta de la llavor. El desenvolupament de la coberta de la llavor està determinada per factors de transcripció. Plantes mutants a diversos factors de transcripció involucrats al desenvolupament de la coberta de les llavors presenten una longevitat alterada. La sobreexpressió dels factors de transcripció AtHB25 i COG1 provoca que les llavors presenten una major longevitat degut a una deposició de polièsters lipídics incrementada. Aquestes barreres de polièsters lipídics son la cutícula, formada per cutina, i la suberina. Ambdues participen positivament la protecció de l'embrió enfront de l'entorn exterior. Estudis genòmics d'ambdós factors de transcripció han demostrat que AtHB25 directament regula a enzims biosintètics dels monòmers de suberina i cutina i COG1 regula enzims relacionats amb la polimerització de polièsters lipídics i lignines. La regulació en la que participa AtHB25 es molt important degut a l'alta conservació de les seqüències genòmiques i funcions de AtHB25 en angiospermes, i parteix estar involucrat en la resposta a baixes temperatures. Per altra banda, COG1, que està involucrat en la percepció de la llum, regula part del desenvolupament del integument extern mitjançant la regulació de AP2, un factor clau en l'establiment de la identitat de teixit de aquest integument de la coberta de la llavor, on es localitza la suberina. AtHB25 i COG1 estan involucrats en l'adaptació de la longevitat de la llavor per mitjan de senyals ambientals com la temperatura i la llum, respectivament, regulant la deposició de polièsters lipídics.
[EN] Seed longevity, or period that seeds remain viable, is important for biodiversity conservation, agriculture and economy. In addition, the study of this parameter could ease the knowledge about molecular mechanisms common to all organisms to prevent aging. One of the main strategies of seeds to reduce their aging consists to stop their metabolism, through drying. Other molecular mechanisms to avoid damages are the isolation from the environment with the seed coat, and the production of antioxidants and other molecules to avoid oxidative damage, one of the main seed aging causes. Repair mechanisms relieve part of the accumulated damage. The model plant Arabidopsis thaliana provides the opportunity to carry out genomic studies for the research of, in this case, seed longevity to discover determinant genetic factors and molecular mechanisms. This will serve to better understand seed deterioration processes and it will be key to increase seed longevity. Using natural genotyped varieties of Arabidopsis thaliana and a genome-wide association study (GWAS) followed by reverse genetic studies, 12 new genes related to seed longevity have been identified. They are related to embryo protection, oxidative damage control, and seed coat permeability. Seed coat development is determined by transcription factors. Mutant plants in some transcription factors involved in the seed coat development present altered seed longevity. The over-expression of the transcription factors AtHB25 and COG1 resulted in seeds with increased longevity due to an increased lipid polyester deposition. These lipid polyesters barriers are the cuticle, formed by cutin, and the suberin layer. Both participate positively in the embryo protection from the external environment. Genomic studies of both transcription factors have revealed that AtHB25 directly regulates biosynthetic enzymes of suberin and cutin monomers, and COG1 regulates the expression of enzymes related to the polymerization of lipid polyesters and lignin. The regulation involving AtHB25 is crucial due to the high conservation of genomic sequences and functions of AtHB25 in angiosperms, and it seems to be involved in the response to low temperatures. On the other hand, COG1, which is involved in light perception, regulates part of the development of the external integument through its regulation by AP2, a key factor in establishing the tissue identity of this seed coat integument, where suberin is located. AtHB25 and COG1 are involved in seed longevity adaptation through environmental signals such as temperature and light, respectively, regulating lipid polyesters deposition.
Agradezco a las instituciones públicas la inversión en investigación. Gracias a ella, los laboratorios, el personal y los distintos equipos se han podido financiar. Gaetano fue quien me ayudó enormemente conseguir la beca FPI del Ministerio de Economía y Competitividad BES-2015-072096, asociada al proyecto de investigación nacional BIO2014-52621-R-AR
Renard Meseguer, J. (2021). Identification of genes related to seed longevity in Arabidopsis thaliana using genomic molecular techniques [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/170554
TESIS
Compendio
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Hinojosa, Galisteo Joan Carles 1993. "Exploring the butterfly speciation continuum : A study on butterfly speciation in the transition to genomic techniques." Doctoral thesis, Universitat Pompeu Fabra, 2021. http://hdl.handle.net/10803/672348.

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Butterflies are among the best studied animals, but despite the research efforts carried out during centuries, our knowledge on their diversity and on the mechanisms generating it is still incomplete. In order to understand how butterflies diversify, the speciation continuum of six study cases was examined using morphometrics and several genetic techniques (from sequencing specific markers to genomics). The analysis of phenotypic and genetic variation combined with gene flow evidence allowed to identify the states of the speciation continuum, i.e. to study the relationships between populations. This approach was used as a framework (1) to make grounded taxonomic hypotheses and (2) to extract clues about the mechanisms that drive speciation. As a result, we described and proposed several cases of overlooked and oversplit taxa. We documented the existence of three types of mechanisms producing diversification in butterflies: drift, selection and hybridisation. Selection acted through adaptation to biotic environmental factors, which caused reproductive character displacement, host plant shift and allochrony mediated by adaptation to host plant flowering period. Additionally, the genetic techniques employed were evaluated and their advantages and limitations discussed
Les papallones són un dels animals més ben estudiats però, malgrat els esforços dedicats a la seva recerca, el coneixement que tenim sobre la seva diversitat i sobre els mecanismes que la generen és encara incomplet. Per tal d'entendre com les papallones diversifiquen, s'ha examinat el continu de l'especiació en sis casos mitjançant l'ús de la morfometria i de diverses tècniques genètiques (des de la seqüenciació de marcadors específics fins a la genòmica). L'anàlisi de la variació fenotípica i genètica combinada amb evidències sobre el flux genètic ha permès identificar els estats del continu de l'especiació, i.e. l'estudi de les relacions entre poblacions. Aquesta aproximació s'ha usat com a marc (1) per fer hipòtesis taxonòmiques fonamentades i (2) per extreure pistes sobre els mecanismes que dirigeixen l'especiació. Com a resultat, hem descrit i proposat diversos casos de tàxons que havien passat desapercebuts o que s'havien dividit excessivament. Documentem l'existència de tres tipus de mecanismes productors de diversitat en papallones: deriva, selecció i hibridació. La selecció actuà mitjançant l'adaptació a factors ambientals biòtics, que causaren desplaçament de caràcters reproductius, canvi de planta nutrícia i a\ll ocronia produïda per l'adaptació al període de floració de la planta nutrícia. Addicionalment, les tècniques genètiques emprades són avaluades i els seus avantatges i inconvenients discutits.
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Padmanabhan, Babu roshan. "Taxano-genomics, a strategy incorporating genomic data into the taxonomic description of human bacteria." Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5056.

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Mon projet de doctorat était de créer un pipeline pour taxono-génomique pour la comparaison de plusieurs génomes bactériens. Deuxièmement, je automatisé le processus d'assemblage (NGS) et annotation à l'aide de divers logiciels open source ainsi que la création de scripts de maison pour le laboratoire. Enfin, nous avons intégré le pipeline dans la description de plusieurs espèces bactériennes de laboratoire sur. Cette thèse est divisée principalement en Taxono- génomique et Microbiogenomics. Les avis de la section taxono-génomique, décrit sur les avancées technologiques en génomique et métagénomique pertinentes dans le domaine de la microbiologie médicale et décrit la stratégie taxono-génomique en détail et comment la stratégie polyphasique avec des approches génomiques sont reformatage de la définition de la taxonomie bactérienne. Les articles décrivent les bactéries cliniquement importantes, leur séquençage complet du génome et les études génomiques comparatives, génomiques et taxono-génomique de ces bactéries. Dans cette thèse, j'ai inclus les articles décrivant ces organismes: Megasphaera massiliensis, Corynebacterium ihumii, Collinsella massiliensis, Clostridium dakarense. Bacillus dielmoensis, jeddahense, Occidentia Massiliensis, Necropsobacter rosorum et Pantoea septica. Oceanobacillus
My PhD project was to create a pipeline for taxono-genomics for the comparison of multiple bacterial genomes. Secondly I automated the process of assembly (NGS) and annotation using various open source softwares as well as creating in house scripts for the lab. Finally we incorporated the pipeline in describing several bacterial species from out lab. This thesis is subdivided mainly into Taxono-genomics and Microbiogenomics. The reviews in taxono-genomics section, describes about the technological advances in genomics and metagenomics relevant to the field of medical microbiology and describes the strategy taxono-genomics in detail and how polyphasic strategy along with genomic approaches are reformatting the definition of bacterial taxonomy. The articles describes clinically important bacteria, their whole genome sequencing and the genomic, comparative genomic and taxono-genomic studies of these bacteria
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Tanov, Emil Pavlov. "The identification of biologically important secondary structures in disease-causing RNA viruses." University of the Western Cape, 2012. http://hdl.handle.net/11394/4562.

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Magister Scientiae - MSc
Viral genomes consist of either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The viral RNA molecules are responsible for two functions, firstly, their sequences contain the genetic code, which encodes the viral proteins, and secondly, they may form structural elements important in the regulation of the viral life-cycle. Using a host of computational and bioinformatics techniques we investigated how predicted secondary structure may influence the evolutionary dynamics of a group of single-stranded RNA viruses from the Picornaviridae family. We detected significant and marginally significant correlations between regions predicted to be structured and synonymous substitution constraints in these regions, suggesting that selection may be acting on those sites to maintain the integrity of certain structures. Additionally, coevolution analysis showed that nucleotides predicted to be base paired, tended to co-evolve with one another in a complimentary fashion in four out of the eleven species examined. Our analyses were then focused on individual structural elements within the genome-wide predicted structures. We ranked the predicted secondary structural elements according to their degree of evolutionary conservation, their associated synonymous substitution rates and the degree to which nucleotides predicted to be base paired coevolved with one another. Top ranking structures coincided with well characterized secondary structures that have been previously described in the literature. We also assessed the impact that genomic secondary structures had on the recombinational dynamics of picornavirus genomes, observing a strong tendency for recombination breakpoints to occur in non-coding regions. However, convincing evidence for the association between the distribution of predicted RNA structural elements and breakpoint clustering was not detected.
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Visser, Johan Christiaan. "A study of genomic variation in and the development of detection techniques for potato virus Y in South Africa." Thesis, Stellenbosch : Stellenbosch University, 2008. http://hdl.handle.net/10019.1/21878.

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Thesis (MSc)--University of Stellenbosch, 2008.
ENGLISH ABSTRACT: Potato virus Y (PVY) is responsible for considerable yield losses in the South African potato industry. The incidence of this virus has greatly increased over the past few years. Even more worrying is the variation of symptoms observed during PVY infection and the recent appearance of the more virulent PVYNTN strain in local fields. This project aimed to investigate the possible genetic variation within the viral genome and to establish the origin of strains. The project also aimed to establish a dependable, area specific enzyme-linked immunosorbent assay (ELISA) to replace the currently used ELISAs. Currently seed potato certification is done using ELISA kits imported from Europe. These kits were developed for the detection of overseas variants of PVY and the use thereof in South Africa has in the past lead to false negatives. Finally, this project set out to develop, optimize and establish a sensitive and reliable real-time reverse transcriptase polymerase chain reaction (qRT-PCR) detection protocol for PVY. In the first part of the study the coat protein (CP) gene of PVY isolates from plant material obtained from various parts of South Africa was amplified using RT-PCR. The resulting cDNA was then sequenced directly or cloned into a vector and then sequenced. The resulting sequences were aligned in a data matrix with international reference sequences, analyzed and grouped according to strain. Examination of the CP gene within this matrix as well as phylogenetic analysis revealed six main groups of PVY. These six groups included the traditional PVYN and PVYO groups and a recombinant group. Furthermore it also revealed variants of PVYN and PVYO. These mutants and recombinants pose a threat as they may lead to South African strains of PVY expressing coat proteins which vary from those found overseas. This may render the currently used European ELISA method of detection less effective and subsequently result in an increase in viral prevalence. This reinforced the need for a detection method based on local viral strains. Phylogenetic and Simplot analysis also confirmed that a recombinant strain between PVYN and PVYO had evolved and that PVYNTN was such a recombinant. The second part of the study aimed to develop and establish detection methods based on local variants of PVY. This included the development of ELISA and qRT-PCR detection methods of PVY. Previously amplified cDNA of the PVY CP gene was cloned into an expression vector and successfully expressed. Antibodies produced against the recombinant protein, when used in ELISA, however, failed to achieve the required levels of sensitivity. This prompted the development of qRT-PCR detection methods for PVY. Primer combinations for PVY were designed using the previously established CP gene data matrix. A reliable and sensitive SYBR® Green I based qRT-PCR assay was developed for the detection of PVY. The assay effectively detected all known South African variants of PVY. Furthermore, a Taqman® assay was developed for the detection of all variants of PVY. The Taqman® assay was 10 fold less sensitive and does not allow for amplicon verification through melting curve analysis, but it does add more specificity due to the addition of the probe. Although these qRT-PCR detection methods are still too expensive to replace the routine diagnostics done with ELISA, they do offer the opportunity to screen valuable mother material and confirm borderline cases in seed certification.
AFRIKAANSE OPSOMMING: Aartappel virus Y (PVY) is verantwoordelik vir aansienlike opbrengsverliese in die Suid-Afrikaanse aartappelindustrie. Die insidensie van infeksie deur die virus het drasties toegeneem oor die afgelope jare. Wat egter meer kommerwekkend is, is die groter variasie in simptome van PVY infeksie en die onlangse voorkoms ‘n meer virulente ras, PVYNTN. Hierdie projek poog om moontlike genetiese variasie van PVY te ondersoek en om die oorsprong van rasse op te spoor. Die projek het ook gepoog ook om ‘n bruikbare, betroubare en area spesifieke “enzyme-linked immunosorbent assay” (ELISA) toets te ontwikkel om die huidige ingevoerde ELISA te vervang. Hierdie toetse is ontwikkel om oorsese variante van PVY op te spoor en die gebruik daarvan het in die verlede gelei tot vals negatiewes. Verder is daar ook ondersoek ingestel na die ontwikkeling van ‘n sensitiewe en betroubare “real-time reverse transcriptase polymerase chain reaction” (qRT-PCR) protokol vir die opsporing van PVY. In die eerste deel van die studie is die mantelproteïen geen van PVY isolate vanuit plant materiaal geamplifiseer deur die gebruik van RT-PCR. Hierdie materiaal is vanaf verskeie streke in Suid-Afrika ontvang. ‘n Volgordebepalingsreaksie is uitgevoer op gekloneerde of ongekloneerde cDNA verkry uit die RT-PCR. DNA volgordes is in ‘n data matriks geplaas en vergelyk met internationale volgordes om die plaaslike isolate te analiseer en te groepeer. Deur vergelyking en filogenetiese ontleding kon ses hoofgroepe van PVY geïdentifiseer word, wat tradisionele PVYN en PVYO, sowel as ‘n rekombinante ras en variante binne die tradisionele PVYN en PVYO groepe ingesluit het. Rekombinante en mutante kan veroorsaak dat Suid-Afrikanse rasse van PVY mantelproteïene uitdruk wat afwyk van die oorsese rasse wat tot gevolg mag hê dat die ELISAs van oorsee minder effektief kan wees en kan lei tot verhoogde virus voorkoms. Die realiteit en gevaar versterk die gedagte dat ‘n deteksie metode gebaseer op plaaslike virusse absoluut krities is. Filogenetiese sowel as Simplot analise het bevestig dat ’n mutante ras tussen PVYN en PVYO ontstaan het en dat PVYNTN ’n rekombinante ras is. Die tweede deel van die studie was daarop gemik om deteksie metodes te ontwikkel wat gebaseer was op plaaslike variante van PVY. Dit sluit die ontwikkeling van ELISA sowel as qRT-PCR deteksie van PVY in. Voorheen geamplifiseerde cDNA is in ‘n ekspressievektor gekloneer en suksesvol uitgedruk. Teenliggaampies teen die rekombinante proteïen, indien in ELISA aangewend, kon egter nie die nodige sensitiwiteit oplewer nie. Dit het aanleiding gegee tot ontwikkeling van qRT-PCR deteksie metodes. Inleier kombinasies vir PVY was ontwikkel deur die gebruik van die bestaande mantelproteïen geen data matrikse. ‘n Betroubare en sensitiewe SYBR® Green I qRT-PCR deteksie protokol was ontwikkel vir die effektiewe deteksie van alle bekende Suid-Afrikanse rasse van PVY. Verder is ‘n sogenaamde “Taqman®” protokol ook ontwikkel vir deteksie van alle rasse. Die “Taqman®” protokol was 10 voudiglik minder gevoelig and laat nie bevestiging deur smeltkurwe analise toe nie, maar verleen meer spesifisiteit deur die toevoeging van die “Taqman® probe”. Hierdie qRT-PCR deteksie metodes is tans te duur om as roetine diagnostiese toetse te gebruik en kan dus nie ELISA vervang nie, maar hulle bied wel die geleentheid om waardevolle moeder materiaal te toets en grensgevalle in aartappelsaad sertifisering te bevestig.
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Books on the topic "Genomic techniques"

1

Dassanayake, Ranil S. Genomic and proteomic techniques: In post genomics era. Oxford: Alpha Science International, 2011.

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Genomic structural variants: Methods and protocols. New York: Humana Press, 2012.

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M, Hernandez Lyla, Institute of Medicine (U.S.). Roundtable on Translating Genomic-Based Research for Health., Institute of Medicine (U.S.). Board on Health Sciences Policy., and National Academies Press (U.S.), eds. Diffusion and use of genomic innovations in health and medicine: Workshop summary. Washington, D.C: National Academies Press, 2008.

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Sabourin, Marc. Evaluation of DNA extraction techniques for use in plasmid localization and a genomic library for Ophiostoma ulmi (Buisman) Nannf. Ottawa: National Library of Canada = Bibliothèque nationale du Canada, 1993.

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H, Bergman Nicholas, ed. Comparative genomics. Totowa, NJ: Humana Press, 2007.

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Deutsche Forschungsgemeinschaft. Senatskommission für Grundsatzfragen der Genforschung., ed. Humangenomforschung: Perspektiven und Konsequenzen. Weinheim: Wiley-VCH, 2000.

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Dictionary of DNA and genome technology. 3rd ed. Chichester, West Sussex: John Wiley & Sons, 2012.

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Sensen, C. W. Handbook of genome research: Genomics, proteomics, metabolomics, bioinformatics, ethical, and legal issues. Weinheim: Wiley-VCH, 2005.

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Muppalaneni, Naresh Babu, and Vinit Kumar Gunjan, eds. Computational Intelligence Techniques for Comparative Genomics. Singapore: Springer Singapore, 2015. http://dx.doi.org/10.1007/978-981-287-338-5.

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Genetics: Analysis of genes and genomes. 8th ed. Sudbury, Mass: Jones & Bartlett Learning, 2012.

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Book chapters on the topic "Genomic techniques"

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Onuchic, Luiz F., and Gregory G. Germino. "Genomic Libraries." In Techniques in Molecular Medicine, 261–72. Berlin, Heidelberg: Springer Berlin Heidelberg, 1999. http://dx.doi.org/10.1007/978-3-642-59811-1_17.

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Hamlet, Stephen, Eugen Petcu, and Saso Ivanovski. "Genomic Microarray Analysis." In Handbook of Vascular Biology Techniques, 391–405. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9716-0_30.

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Pal, Aruna. "Conventional and Basic Genomic Techniques." In Springer Protocols Handbooks, 1–29. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1818-9_1.

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Surzycki, Stefan. "Preparation of Genomic DNA from Bacteria." In Basic Techniques in Molecular Biology, 79–100. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-56968-5_4.

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Marlowe, Elizabeth M., and Donna M. Wolk. "Pathogen Detection in the Genomic Era." In Advanced Techniques in Diagnostic Microbiology, 505–23. Boston, MA: Springer US, 2006. http://dx.doi.org/10.1007/0-387-32892-0_28.

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Budhlakoti, Neeraj, Sayanti Guha Majumdar, Amar Kant Kushwaha, Chirag Maheshwari, Muzaffar Hasan, D. C. Mishra, Anuj Kumar, Jyotika Bhati, and Anil Rai. "Tools and Techniques for Genomic Imprinting." In Springer Protocols Handbooks, 335–46. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2533-0_18.

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Surzycki, Stefan. "Preparation of Genomic DNA from Animal Cells." In Basic Techniques in Molecular Biology, 33–56. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-56968-5_2.

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Surzycki, Stefan. "Preparation of Genomic DNA from Plant Cells." In Basic Techniques in Molecular Biology, 57–78. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-56968-5_3.

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Sobti, RC, Apurav Sharma, and Sanjeev Kumar Soni. "Applications of Biotechnological Techniques in Mitigating Environmental Concerns." In Genomic, Proteomics, and Biotechnology, 249–312. Boca Raton: CRC Press, 2022. http://dx.doi.org/10.1201/9781003220831-17.

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Jankowicz-Cieslak, Joanna, Ivan L. Ingelbrecht, and Bradley J. Till. "Mutation Detection in Gamma-Irradiated Banana Using Low Coverage Copy Number Variation." In Efficient Screening Techniques to Identify Mutants with TR4 Resistance in Banana, 113–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-64915-2_8.

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AbstractMutagenesis of in vitro propagated bananas is an efficient method to introduce novel alleles and broaden genetic diversity. The FAO/IAEA Plant Breeding and Genetics Laboratory previously established efficient methods for mutation induction of in vitro shoot tips in banana using physical and chemical mutagens as well as methods for the efficient discovery of ethyl methanesulphonate (EMS) induced single nucleotide mutations in targeted genes. Officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic changes such as insertions and deletions (InDels). Such dosage mutations may be particularly important for generating observable phenotypes in polyploids such as banana. Here, we describe a Next Generation Sequencing (NGS) approach in Cavendish (AAA) bananas to identify large genomic InDels. The method is based on low coverage whole genome sequencing (LC-WGS) using an Illumina short-read sequencing platform. We provide details for sonication-mediated library preparation and the installation and use of freely available computer software to identify copy number variation in Cavendish banana. Alternative DNA library construction procedures and bioinformatics tools are briefly described. Example data is provided for the mutant variety Novaria and cv Grande Naine (AAA), but the methodology can be equally applied for triploid bananas with mixed genomes (A and B) and is useful for the characterization of putative Fusarium Wilt TR4 resistant mutant lines described elsewhere in this protocol book.
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Conference papers on the topic "Genomic techniques"

1

Phogat, Manu, and Dharmender Kumar. "Feature Selection Techniques for Genomic Data." In 2022 International Conference on Machine Learning, Big Data, Cloud and Parallel Computing (COM-IT-CON). IEEE, 2022. http://dx.doi.org/10.1109/com-it-con54601.2022.9850466.

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Galdi, Paola, Angela Serra, Dario Greco, and Roberto Tagliaferri. "Effectiveness of projection techniques in genomic data analysis." In 2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI). IEEE, 2016. http://dx.doi.org/10.1109/rtsi.2016.7740567.

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Bhonde, Swati B., and Jayashree R. Prasad. "Deep Learning Techniques in Cancer Prediction Using Genomic Profiles." In 2021 6th International Conference for Convergence in Technology (I2CT). IEEE, 2021. http://dx.doi.org/10.1109/i2ct51068.2021.9417985.

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Maheeshanake, S. D. L. H., M. W. A. C. R. Wijesinghe, A. R. Weerasinghe, and M. A. I. Perera. "Unsupervised Techniques for Meta-Analysis of Cancer Genomic Data." In 2020 20th International Conference on Advances in ICT for Emerging Regions (ICTer). IEEE, 2020. http://dx.doi.org/10.1109/icter51097.2020.9325475.

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Hammad, Muhammed S., Vidan F. Ghoneim, and Mai S. Mabrouk. "Detection of COVID-19 Using Genomic Image Processing Techniques." In 2021 3rd Novel Intelligent and Leading Emerging Sciences Conference (NILES). IEEE, 2021. http://dx.doi.org/10.1109/niles53778.2021.9600525.

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Pandey, Gaurav, Gowtham Atluri, Gang Fang, Rohit Gupta, Michael Steinbach, and Vipin Kumar. "Association analysis techniques for analyzing complex biological data sets." In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS). IEEE, 2009. http://dx.doi.org/10.1109/gensips.2009.5174378.

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Kaplan, Roman, Leonid Yavits, and Ran Ginosar. "POSTER: BioSEAL: In-Memory Biological Sequence Alignment Accelerator for Large-Scale Genomic Data." In 2019 28th International Conference on Parallel Architectures and Compilation Techniques (PACT). IEEE, 2019. http://dx.doi.org/10.1109/pact.2019.00044.

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Kaur, Amandeep, Ajay Pal Singh Chauhan, and Ashwani Kumar Aggarwal. "Machine Learning Based Comparative Analysis of Methods for Enhancer Prediction in Genomic Data." In 2019 2nd International Conference on Intelligent Communication and Computational Techniques (ICCT). IEEE, 2019. http://dx.doi.org/10.1109/icct46177.2019.8969054.

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Zokaee, Farzaneh, Mingzhe Zhang, and Lei Jiang. "FindeR: Accelerating FM-Index-Based Exact Pattern Matching in Genomic Sequences through ReRAM Technology." In 2019 28th International Conference on Parallel Architectures and Compilation Techniques (PACT). IEEE, 2019. http://dx.doi.org/10.1109/pact.2019.00030.

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Occhipinti, Annalisa, and Claudio Angione. "A Computational Model of Cancer Metabolism for Personalised Medicine." In Building Bridges in Medical Science 2021. Cambridge Medicine Journal, 2021. http://dx.doi.org/10.7244/cmj.2021.03.001.3.

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Cancer cells must rewrite their ‘‘internal code’’ to satisfy the demand for growth and proliferation. Such changes are driven by a combination of genetic (e.g., genes’ mutations) and non-genetic factors (e.g., tumour microenvironment) that result in an alteration of cellular metabolism. For this reason, understanding the metabolic and genomic changes of a cancer cell can provide useful insight on cancer progression and survival outcomes. In our work, we present a computational framework that uses patient-specific data to investigate cancer metabolism and provide personalised survival predictions and cancer development outcomes. The proposed model integrates patient-specific multi-omics data (i.e., genomic, metabolomic and clinical data) into a metabolic model of cancer to produce a list of metabolic reactions affecting cancer progression. Quantitative and predictive analysis, through survival analysis and machine learning techniques, is then performed on the list of selected reactions. Since our model performs an analysis of patient-specific data, the outcome of our pipeline provides a personalised prediction of survival outcome and cancer development based on a subset of identified multi-omics features (genomic, metabolomic and clinical data). In particular, our work aims to develop a computational pipeline for clinicians that relates the omic profile of each patient to their survival probability, based on a combination of machine learning and metabolic modelling techniques. The model provides patient-specific predictions on cancer development and survival outcomes towards the development of personalised medicine.
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Reports on the topic "Genomic techniques"

1

Abbott, Albert G., Doron Holland, Douglas Bielenberg, and Gregory Reighard. Structural and Functional Genomic Approaches for Marking and Identifying Genes that Control Chilling Requirement in Apricot and Peach Trees. United States Department of Agriculture, September 2009. http://dx.doi.org/10.32747/2009.7591742.bard.

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Structural and functional genomic approaches for marking and identifying genes that control chilling requirement in apricot and peach trees. Specific aims: 1) Identify and characterize the genetic nature of chilling requirement for flowering and dormancy break of vegetative shoots in Prunusgermplasm through the utilization of existing apricot (NeweYa'ar Research Center, ARO) and peach (Clemson University) genetic mapping populations; 2) Use molecular genetic mapping techniques to identify markers flanking genomic regions controlling chilling; 3) Comparatively map the regions controlling chilling requirement in apricot and peach and locate important genomic regions influencing chilling requirement on the Prunus functional genomic database as an initial step for identification of candidate genes; 4) Develop from the functional genomics database a set of markers facilitating the development of cultivars with optimized chilling requirements for improved and sustained fruit production in warm-winter environments. Dormant apricot (prunus armeniaca L.) and peach [Prunus persica (L.) Batsch] trees require sustained exposure to low, near freezing, temperatures before vigorous floral and vegetative bud break is possible after the resumption of warm temperatures in the spring. The duration of chilling required (the chilling requirement, CR) is determined by the climatic adaptation of the particular cultivar, thus limiting its geographic distribution. This limitation is particularly evident when attempting to introduce superior cultivars to regions with very warm winter temperatures, such as Israel and the coastal southern United States. The physiological mechanism of CR is not understood and although breeding programs deliberately manipulate CR in apricot and peach crosses, robust closely associated markers to the trait are currently not available. We used segregating populations of apricot (100 Fl individuals, NeweYa'ar Research Center, ARO) and peach (378 F2 individuals, Clemson University) to discover several discreet genomic loci that regulate CR and blooming date. We used the extensive genomic/genetic resources available for Prunus to successfully combine our apricot and peach genetic data and identify five QTL with strong effects that are conserved between species as well as several QTL that are unique to each species. We have identified markers in the key major QTL regions for testing in breeding programs which we are carrying out currently; we have identified an initial set of candidate genes using the peach physical/transcriptome map and whole peach genome sequences and we are testing these currently to identify key target genes for manipulation in breeding programs. Our collaborative work to date has demonstrated the following: 1) CR in peach and apricot is predominantly controlled by a limited number ofQTL loci, seven detected in a peach F2 derived map comprising 65% of the character and 12 in an apricot Fl map comprising 71.6% and 55.6% of the trait in the Perfection and A. 1740 parental maps, respectively and that peach and apricot appear in our initial maps to share five genomic intervals containing potentially common QTL. 2) Application of common anchor markers of the Prunus/peach, physical/genetic map resources has allowed us not only to identify the shared intervals but also to have immediately available some putative candidate gene information from these intervals, the EVG region on LG1 in peach the TALY 1 region in apricot on LG2 in peach; and several others involved in vernalization pathways (LGI and LG7). 3) Mapped BACcontigs are easily defined from the complete physical map resources in peach through the common SSR markers that anchor our CR maps in the two species, 4) Sequences of BACs in these regions can be easily mined for additional polymorphic markers to use in MAS applications.
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Fluhr, Robert, and Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7696517.bard.

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Our original objectives were to assess the unexplored dimension of alternative splicing as a source of genetic variation. In particular, we sought to initially establish an alternative splicing database for Arabidopsis, the only plant for which a near-complete genome has been assembled. Our goal was to then use the database, in part, to advance plant gene prediction programs that are currently a limiting factor in annotating genomic sequence data and thus will facilitate the exploitation of the ever increasing quantity of raw genomic data accumulating for plants. Additionally, the database was to be used to generate probes for establishing high-throughput alternative transcriptome analysis in the form of a splicing-specific oligonucleotide microarray. We achieved the first goal and established a database and web site termed Alternative Splicing In Plants (ASIP, http://www.plantgdb.org/ASIP/). We also thoroughly reviewed the extent of alternative splicing in plants (Arabidopsis and rice) and proposed mechanisms for transcript processing. We noted that the repertoire of plant alternative splicing differs from that encountered in animals. For example, intron retention turned out to be the major type. This surprising development was proven by direct RNA isolation techniques. We further analyzed EST databases available from many plants and developed a process to assess their alternative splicing rate. Our results show that the lager genome-sized plant species have enhanced rates of alternative splicing. We did advance gene prediction accuracy in plants by incorporating scoring for non-canonical introns. Our data and programs are now being used in the continuing annotation of plant genomes of agronomic importance, including corn, soybean, and tomato. Based on the gene annotation data developed in the early part of the project, it turned out that specific probes for different exons could not be scaled up to a large array because no uniform hybridization conditions could be found. Therefore, we modified our original objective to design and produce an oligonucleotide microarray for probing alternative splicing and realized that it may be reasonable to investigate the extent of alternative splicing using novel commercial whole genome arrays. This possibility was directly examined by establishing algorithms for the analysis of such arrays. The predictive value of the algorithms was then shown by isolation and verification of alternative splicing predictions from the published whole genome array databases. The BARD-funded work provides a significant advance in understanding the extent and possible roles of alternative splicing in plants as well as a foundation for advances in computational gene prediction.
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Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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Heifetz, Yael, and Michael Bender. Success and failure in insect fertilization and reproduction - the role of the female accessory glands. United States Department of Agriculture, December 2006. http://dx.doi.org/10.32747/2006.7695586.bard.

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The research problem. Understanding of insect reproduction has been critical to the design of insect pest control strategies including disruptions of mate-finding, courtship and sperm transfer by male insects. It is well known that males transfer proteins to females during mating that profoundly affect female reproductive physiology, but little is known about the molecular basis of female mating response and no attempts have yet been made to interfere with female post-mating responses that directly bear on the efficacy of fertilization. The female reproductive tract provides a crucial environment for the events of fertilization yet thus far those events and the role of the female tract in influencing them are poorly understood. For this project, we have chosen to focus on the lower reproductive tract because it is the site of two processes critical to reproduction: sperm management (storage, maintenance, and release from storage) and fertilization. E,fforts during this project period centered on the elucidation of mating responses in the female lower reproductive tract The central goals of this project were: 1. To identify mating-responsive genes in the female lower reproductive tract using DNA microarray technology. 2. In parallel, to identify mating-responsive genes in these tissues using proteomic assays (2D gels and LC-MS/MS techniques). 3. To integrate proteomic and genomic analyses of reproductive tract gene expression to identify significant genes for functional analysis. Our main achievements were: 1. Identification of mating-responsive genes in the female lower reproductive tract. We identified 539 mating-responsive genes using genomic and proteomic approaches. This analysis revealed a shift from gene silencing to gene activation soon after mating and a peak in differential gene expression at 6 hours post-mating. In addition, comparison of the two datasets revealed an expression pattern consistent with the model that important reproductive proteins are pre-programmed for synthesis prior to mating. This work was published in Mack et al. (2006). Validation experiments using real-time PCR techniques suggest that microarray assays provide a conservativestimate of the true transcriptional activity in reproductive tissues. 2.lntegration of proteomics and genomics data sets. We compared the expression profiles from DNA microarray data with the proteins identified in our proteomic experiments. Although comparing the two data sets poses analyical challenges, it provides a more complete view of gene expression as well as insights into how specific genes may be regulated. This work was published in Mack et al. (2006). 3. Development of primary reproductive tract cell cultures. We developed primary cell cultures of dispersed reproductive tract cell types and determined conditions for organ culture of the entire reproductive tract. This work will allow us to rapidly screen mating-responsive genes for a variety of reproductive-tract specifi c functions. Scientific and agricultural significance. Together, these studies have defined the genetic response to mating in a part of the female reproductive tract that is critical for successful fertllization and have identified alarge set of mating-responsive genes. This work is the first to combine both genomic and proteomic approaches in determining female mating response in these tissues and has provided important insights into insect reproductive behavior.
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Wentworth, Jonathan, and David Rapley. Genome edited animals. Parliamentary Office of Science and Technology, November 2022. http://dx.doi.org/10.58248/pb50.

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Genome editing, also known as gene editing, encompasses a broad range of techniques that allows targeted changes in the DNA of animals (and plants). The Genetic Technology (Precision Breeding) Bill 2022 -2023, due for Second Reading in the House of Lords on 21 November 2022, intends to change the regulatory definition of certain genome-edited animals.
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Ovcharenko, I. FY06 LDRD Final Report "Development of Computational Techniques For Decoding The Language of Genomes". Office of Scientific and Technical Information (OSTI), January 2007. http://dx.doi.org/10.2172/899447.

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Ehrlich, Marcelo, John S. Parker, and Terence S. Dermody. Development of a Plasmid-Based Reverse Genetics System for the Bluetongue and Epizootic Hemorrhagic Disease Viruses to Allow a Comparative Characterization of the Function of the NS3 Viroporin in Viral Egress. United States Department of Agriculture, September 2013. http://dx.doi.org/10.32747/2013.7699840.bard.

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Project Title: "Development of a plasmid-based reverse genetics system for the Bluetongue and Epizootic Hemorrhagic Disease viruses to allow comparative characterization of the function of the NS3 viroporin in viral egress". Project details: No - IS-4192-09; Participants – Ehrlich M. (Tel Aviv University), Parker J.S. (Cornell University), DermodyT.S. (Vanderbilt University); Period - 2009-2013. Orbiviruses are insect-borne infectious agents of ruminants that cause diseases with considerable economical impact in Israel and the United States. The recent outbreaks of BTV in Europe and of Epizootic Hemorrhagic Disease Virus (EHDV) in Israel, underscore the need for: (i) a better comprehension of the infection process of orbiviruses, (ii) the identification of unique vs. common traits among different orbiviruses, (iii) the development of novel diagnosis and treatment techniques and approaches; all aimed at the achievement of more effective control and treatment measures. It is the context of these broad goals that the present project was carried out. To fulfill our long-term goal of identifying specific viral determinants of virulence, growth, and transmission of the orbiviruses, we proposed to: (i) develop reverse genetics systems for BTV and EHDV2-Ibaraki; and (ii) identify the molecular determinants of the NS3 nonstructural protein related to viroporin/viral egress activities. The first objective was pursued with a two-pronged approach: (i) development of a plasmid-based reverse genetics system for BTV-17, and (ii) development of an "in-vitro" transcription-based reverse genetics system for EHDV2-Ibaraki. Both approaches encountered technical problems that hampered their achievement. However, dissection of the possible causes of the failure to achieve viral spread of EHDV2-Ibaraki, following the transfection of in-vitro transcribed genomic segments of the virus, revealed a novel characteristic of EHDV2-Ibaraki infection: an uncharacteristically low fold increase in titer upon infection of different cell models. To address the function and regulation of NS3 we employed the following approaches: (i) development (together with Anima Cell Metrology) of a novel technique (based on the transfection of fluorescently-labeledtRNAs) that allows for the detection of the levels of synthesis of individual viral proteins (i.e. NS3) in single cells; (ii) development of a siRNA-mediated knockdown approach for the reduction in levels of expression of NS3 in EHDV2-Ibaraki infected cells; (iii) biochemical and microscopy-based analysis of the localization, levels and post-translational modifications of NS3 in infected cells. In addition, we identified the altered regulation and spatial compartmentalization of protein synthesis in cells infected with EHDV2-Ibaraki or the mammalian reovirus. In EHDV2-Ibaraki-infected cells such altered regulation in protein synthesis occurs in the context of a cell stress reponse that includes the induction of apoptosis, autophagy and activation of the stressrelated kinase c-Jun N-terminal Kinase (JNK). Interestingly, inhibition of such stress-related cellular processes diminishes the production of infectious virions, suggesting that EHDV usurps these responses for the benefit of efficient infection. Taken together, while the present project fell short of the generation of novel reverse genetics systems for orbiviruses, the development of novel experimental approaches and techniques, and their employment in the analysis of EHDV-infected cells, yielded novel insights in the interactions of orbiviruses with mammalian cells.
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Mishra, Bishnu P., and James M. Reecy. Generation of Bovine Genetic Markers by Representational Difference Analysis: a genome subtraction technique. Ames (Iowa): Iowa State University, January 2004. http://dx.doi.org/10.31274/ans_air-180814-457.

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9

Kent, Stephen. Use of Modern Chemical Protein Synthesis and Advanced Fluorescent Assay Techniques to Experimentally Validate the Functional Annotation of Microbial Genomes. Office of Scientific and Technical Information (OSTI), July 2012. http://dx.doi.org/10.2172/1087659.

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10

Weller, Joel, Harris Lewin, Micha Ron, George Wiggans, and Paul VanRaden. A Systematic Genome Search for Genes Affecting Economic Traits Dairy Cattle with the Aid of Genetic Markers. United States Department of Agriculture, April 1999. http://dx.doi.org/10.32747/1999.7695836.bard.

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The objectives were to continue collection of semen for the US dairy bull DNA repository, to conduct a systematic search of the Holstein genome for economically significant economic trait loci (ETL), to develop and refine statistical techniques for the analysis of the data generated, and to confirm significant effects by genotyping daughters i Israel and additional US sons. One-thousand-seventy-six sons of eight US grandsires were genotyped for 174 microsatellites located on all 29 autosomes. ETL were detected for milk production traits on seven chromosomes. ETL for milk and fat yield and fat and protein percentage on BTA3 was mapped to between the markers BL41 and TGLA263. The 95% confidence interval for the ETL affecting fat percentage on BTA14 localized this ETL between the contromere and chromosome position 11 cM. This ETL was verified in the Israeli cattle population by genotyping an independent sample of cows from seven families. The radiation hybrid data for the centromeric region of BTA14 is defined by a single linkage group. Order of Type I genes within this region, CYC-FADK-TG-SQLE, is conserved between human and cattle. Thus, HSA8, the human homologue of BTA14, can be used to identify candidate genes for the ETL.
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