Littérature scientifique sur le sujet « Genomic analysi »
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Articles de revues sur le sujet "Genomic analysi"
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Barazandeh, A., M. R. Mohammadabadi, M. Ghaderi-Zefrehei et H. Nezamabadi-pour. « Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features ». Czech Journal of Animal Science 61, No. 11 (17 novembre 2016) : 487–95. http://dx.doi.org/10.17221/78/2015-cjas.
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Caulfield, Mark. « 6 Translating genomics for clinical benefit ». Postgraduate Medical Journal 95, no 1130 (21 novembre 2019) : 686.3–686. http://dx.doi.org/10.1136/postgradmedj-2019-fpm.6.
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The UK 100,000 Genomes Project has focussed on transforming genomic medicine in the National Health Service using whole genome sequencing in rare disease, cancer and infection. Genomics England partnering with the NHS established 13 Genomic Medicine Centres, the NHS whole genome sequencing centre and the Genomics England Clinical Interpretation Partnership (3337 researchers from 24 countries). We sequenced the 100,000th genome on the 5th December 2019 and completed an initial analysis for participants in July 2019. Alongside these genomes we have assembled a longitudinal life course dataset for research and diagnosis including 2.6 billion clinical data points for the 3000 plus researchers to work on to drive up the value of the genomes for direct healthcare. In parallel we have partnered the NHS to establish one of the world’s most advanced Genomic Medicine Service where we re-evaluated 300,000 genomic tests and upgraded 25% of tests to newer technologies with an annual review. The Department of Health have announced the ambition to undertake 5 million genome analyses over the next 5 years focused on new areas tractable to health gain.
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Surrey, Lea F., Minjie Luo, Fengqi Chang et Marilyn M. Li. « The Genomic Era of Clinical Oncology : Integrated Genomic Analysis for Precision Cancer Care ». Cytogenetic and Genome Research 150, no 3-4 (2016) : 162–75. http://dx.doi.org/10.1159/000454655.
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Genomic alterations are important biological markers for cancer diagnosis and prognosis, disease classification, risk stratification, and treatment selection. Chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) technologies are superb new tools for evaluating cancer genomes. These state-of-the-art technologies offer high-throughput, highly accurate, targeted and whole-genome evaluation of genomic alterations in tumor tissues. The application of CMA and NGS technologies in cancer research has generated a wealth of useful information about the landscape of genomic alterations in cancer and their implications in cancer care. As the knowledge base in cancer genomics and genome biology grows, the focus of research is now shifting toward the clinical applications of these technologies to improve patient care. Although not yet standard of care in cancer, there is an increasing interest among the cancer genomics communities in applying these new technologies to cancer diagnosis in the Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories. Many clinical laboratories have already started adopting these technologies for cancer genomic analysis. We anticipate that CMA and NGS will soon become the major diagnostic means for cancer genomic analysis to meet the increasing demands of precision cancer care.
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Bertelli, Claire, Keith E. Tilley et Fiona S. L. Brinkman. « Microbial genomic island discovery, visualization and analysis ». Briefings in Bioinformatics 20, no 5 (3 juin 2018) : 1685–98. http://dx.doi.org/10.1093/bib/bby042.
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Abstract Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.
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Kerdprasop, Nittaya, et Kittisak Kerdprasop. « Constraint-Based System for Genomic Analysis ». International Journal of Information and Education Technology 5, no 2 (2015) : 119–23. http://dx.doi.org/10.7763/ijiet.2015.v5.487.
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Barron-Montenegro, Rocío, Rodrigo García, Fernando Dueñas, Dácil Rivera, Andrés Opazo-Capurro, Stephen Erickson et Andrea I. Moreno-Switt. « Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis ». Antibiotics 10, no 7 (2 juillet 2021) : 806. http://dx.doi.org/10.3390/antibiotics10070806.
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Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.
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Blanca, Léo, Eugène Christo-Foroux, Sofia Rigou et Matthieu Legendre. « Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes ». Viruses 12, no 11 (7 novembre 2020) : 1270. http://dx.doi.org/10.3390/v12111270.
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Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.
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Dhanapal, Arun Prabhu, et Mahalingam Govindaraj. « Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era : The Road towards Fast-Track Crop Plant Improvement ». Genetics Research International 2015 (19 mars 2015) : 1–15. http://dx.doi.org/10.1155/2015/684321.
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The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.
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Vilen, Heikki, Juha-Matti Aalto, Anna Kassinen, Lars Paulin et Harri Savilahti. « A Direct Transposon Insertion Tool for Modification and Functional Analysis of Viral Genomes ». Journal of Virology 77, no 1 (1 janvier 2003) : 123–34. http://dx.doi.org/10.1128/jvi.77.1.123-134.2003.
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ABSTRACT Advances in DNA transposition technology have recently generated efficient tools for various types of functional genetic analyses. We demonstrate here the power of the bacteriophage Mu-derived in vitro DNA transposition system for modification and functional characterization of a complete bacterial virus genome. The linear double-stranded DNA genome of Escherichia coli bacteriophage PRD1 was studied by insertion mutagenesis with reporter mini-Mu transposons that were integrated in vitro into isolated genomic DNA. After introduction into bacterial cells by electroporation, recombinant transposon-containing virus clones were identified by autoradiography or visual blue-white screening employing α-complementation of E. coli β-galactosidase. Additionally, a modified transposon with engineered NotI sites at both ends was used to introduce novel restriction sites into the phage genome. Analysis of the transposon integration sites in the genomes of viable recombinant phage generated a functional map, collectively indicating genes and genomic regions essential and nonessential for virus propagation. Moreover, promoterless transposons defined the direction of transcription within several insert-tolerant genomic regions. These strategies for the analysis of viral genomes are of a general nature and therefore may be applied to functional genomics studies in all prokaryotic and eukaryotic cell viruses.
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Salamon, Hugh, Midori Kato-Maeda, Peter M. Small, Jorg Drenkow et Thomas R. Gingeras. « Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data ». Genome Research 10, no 12 (21 novembre 2000) : 2044–54. http://dx.doi.org/10.1101/gr.152900.
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Genomic diversity within and between populations is caused by single nucleotide mutations, changes in repetitive DNA systems, recombination mechanisms, and insertion and deletion events. The contribution of these sources to diversity, whether purely genetic or of phenotypic consequence, can only be investigated if we have the means to quantitate and characterize diversity in many samples. With the advent of complete sequence characterization of representative genomes of different species, the possibility of developing protocols to screen for genetic polymorphism across entire genomes is actively being pursued. The large numbers of measurements such approaches yield demand that we pay careful attention to the numerical analysis of data. In this paper we present a novel application of an Affymetrix GeneChip to perform genome-wide screens for deletion polymorphism. A high-density oligonucleotide array formatted for mRNA expression and targeted at a fully sequenced 4.4-million–base pair Mycobacterium tuberculosis standard strain genome was adapted to compare genomic DNA. Hybridization intensities to 111,000 probe pairs (perfect complement and mismatch complement) were measured for genomic DNA from a clinical strain and from a vaccine organism. Because individual probe-pair hybridization intensities exhibit limited sensitivity/specificity characteristics to detect deletions, data-analytical methodology to exploit measurements from multiple probes in tandem locations across the genome was developed. The TSTEP (Tandem Set Terminal Extreme Probability) algorithm designed specifically to analyze the tandem hybridization measurements data was applied and shown to discover genomic deletions with high sensitivity. The TSTEP algorithm provides a foundation for similar efforts to characterize deletions in many hybridization measures in similar-sized and larger genomes. Issues relating to the design of genome content screening experiments and the implications of these methods for studying population genomics and the evolution of genomes are discussed.
Thèses sur le sujet "Genomic analysi"
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DI, CANITO ALESSANDRA. « Genomic and functional analysis of Rhodococcus strains to identify genes and degradative functions for soil quality evaluation ». Doctoral thesis, Università degli Studi di Milano-Bicocca, 2019. http://hdl.handle.net/10281/241307.
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La qualità del suolo è una delle principali problematiche ambientali degli ultimi decenni a causa dell’aumento dell’inquinamento antropico. In condizioni di stress, i microrganismi del suolo subiscono alterazioni che attraverso tecnologie molecolari possono essere usate come parametro per il monitoraggio dei siti contaminati. I batteri appartenenti al genere Rhodococcus hanno un ruolo importante nella degradazione dei composti più recalcitranti. Sono versatili ed ampiamente distribuiti in natura; essi degradano diversi composti organici, tra cui idrocarburi alifatici ed aromatici, eterociclici, nitrili, sulfuri ed erbicidi. Inoltre, essi possono sopravvivere in presenza di composti tossici, carenza di carbonio, irradiazione UV e stress osmotico. Questa versatilità è correlata alla complessità dei loro genomi, i quali contengono molteplici geni catabolici, ridondanza genica e un sofisticato network regolatorio. L’obiettivo di questo progetto è ottenere nuovi tools molecolari da ceppi di Rhodococcus da usare come marcatori per valutare la qualità dei suoli, mediante analisi dei pathway metabolici e dei cluster genici coinvolti nella degradazione dei contaminanti ambientali. In questo lavoro, l’attenzione è stata rivolta verso i genomi dei ceppi: R. opacus R7, R. aetherivorans BCP1 e R. erythropolis MI2. Un’analisi fenotipica ha permesso di valutare il potenziale metabolico e la risposta allo stress dei ceppi R7 e BCP1; sono stati testati diversi contaminanti (idrocarburi alifatici e cicloalcani, aromatici, policiclici aromatici, acidi naftenici ed altri acidi carbossilici) e varie condizioni di stress (alta osmolarità, differenti valori di pH, composti tossici, antibiotici). Un approccio genomico ha permesso di correlare le abilità metaboliche a determinanti genici, coinvolti nei diversi metabolismi (naftalene, o-xilene, n-alcani, acidi naftenici, fenoli, ftalato) e nella persistenza ambientale. In particolare, sono stati esaminati i pathway degradativi dell’o-xilene e degli acidi naftenici di R. opacus R7. Analisi bioinformatiche e molecolari hanno permesso di valutare il coinvolgimento di diversi geni nei pathway degradativi. R7 è in grado di degradare l’o-xilene inducendo la trascrizione dei geni akb (sistema diossigenasico) formando il diidrodiolo. Tuttavia, la ridondanza di monossigenasi e idrossilasi (prmA and pheA1A2A3), ha suggerito l’attivazione di altri sistemi convergenti, strategia utilizzata dai rhodococci per degradare composti recalcitranti e persistere in ambienti contaminati. I pathway degradativi degli acidi naftenici (NAs) non sono ancora noti ma sono state proposte due possibili vie: i) aromatizzazione dell’anello del cicloesano ii) attivazione come CoA tioestere. I risultati delle RT e RT-qPCR hanno mostrato che R7 degrada l’acido cicloesanocarbossilico (CHCA), attraverso una cicloesano carbossilato-CoA ligasi (aliA). L’applicazione di questo lavoro è stata dimostrata in esperimenti di microcosmo simulando condizioni reali con sabbia bioaugmentata con R7. Le capacità dei batteri autoctoni e di R7 di degradare il CHCA sono state comparate e i risultati mostrano che R7 degrada il contaminante più velocemente rispetto alla comunità microbica e che il suo contributo aumenta la velocità di degradazione del CHCA, seguita monitorando l’espressione del gene aliA mediante esperimenti di RT e RT-qPCR. Un’applicazione biotecnologica di questo lavoro è stata valutata in R. erythropolis MI2, studiando il pathway di degradazione del 4,4’- acido disolfuro ditiobutirrico (DTDB), un promettente substrato per la sintesi dei politioesteri poiché il suo intermedio metabolico, acido 4-mercaptobutirrico ne è un precursore. L’obiettivo di questo studio è stato perseguito generando mutanti di delezione del ceppo MI2 per i geni coinvolti nelle reazioni finali del pathway di degradazione.Soil quality has been one of the major issues of the last decades, because of the increase of anthropogenic pollution. Soil contains organisms involved in vital functions (nutrient/hydrological cycles and degradation of toxic compounds). Under stress conditions, soil microorganisms undergo several alterations so molecular technologies use microbial communities as an ecological parameter in monitoring polluted sites. Bacteria belonging to Rhodococcus genus have an important role in recalcitrant compound degradations. It is a metabolically versatile genus, widely distributed in nature. Rhodococcus spp. can degrade a wide range of organic compounds (aliphatic/aromatic hydrocarbons, heterocyclic, nitriles, sulfuric, herbicides) and to survive in presence of toxic compounds, carbon starvation, UV irradiation and osmotic stress. In line with their catabolic diversity, they possess large and complex genomes, containing a multiplicity of catabolic genes, high genetic redundancy and a sophisticated regulatory network. The aim of this project is to obtain molecular tools to use as "marker" sequences for soil assessment, through analysis of metabolic pathways and catabolic gene clusters involved in the degradation of the most diffused environmental contaminants. In particular, this work focused the attention on three Rhodococcus strain genomes: R. opacus R7, R. aetherivorans BCP1 and R. erythropolis MI2. A Phenotype Microarray approach was used to evaluate R7 and BCP1 strains metabolic potential and their stress response. Also, the capability to utilize various contaminants (aliphatic hydrocarbons and cycloalkanes, aromatic compounds, polycyclic aromatic compounds, naphthenic acids and other carboxylic acids) and to persist under stress conditions (high osmolarity, pH stress, toxic compounds, antibiotics) was tested. A genome-based approach was used to relate their abilities to genetic determinants involved in the analysed metabolisms (naphthalene, o-xylene, n-alkanes, naphthenic acids, phenols, phthalate) and in their environmental persistence. In particular, o-xylene and naphthenic acids degradations were investigated in R. opacus R7. Computational and molecular analyses revealed the putative involvement of several genes in these degradation pathways. R7 can degrade o-xylene by the induction of the akb genes (deoxygenation) producing the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for monooxygenases/hydroxylases (prmA and pheA1A2A3), supports the involvement of other genes that induce the formation of phenols, converging to the phenol oxidation path. The activation of converging oxygenase systems represents a strategy in Rhodococcus genus to degrade recalcitrant compounds and to persist in contaminated environments. NAs degradation pathway is not fully clear but two main routes have been proposed: i) aromatization of the cyclohexane ring ii) activation as CoA thioester. RT and RT-qPCR results showed that R. opacus R7 degrade cyclohexanecarboxylic acid (CHCA) molecule (used as a model) by a cyclohexane carboxylate CoA ligase (aliA). An application of this work was demonstrated by a microcosm approach, simulating a bioaugmentation process with R7 strain. Autochthone bacteria and R7 capabilities to degrade CHCA were evaluated and compared; results indicated that R7 can degrade the contaminant faster than the microbial community and that its contribute increased CHCA degradation rate. The degradation rate was followed by RT and RT-qPCR, monitoring the expression of the aliA gene. Moreover, a biotechnological application was investigated in R. erythropolis MI2, studying the disulfide 4,4-dithiodibutyric acid (DTDB) degradation pathway. DTDB is a promising substrate for polythioester (PTE) synthesis; indeed, its degradation produces the PTE building block 4-mercaptobutyric acid. The aim was pursued generating R. erythropolis MI2 marker-free deletion mutants for genes involved in the final steps of the pathway.
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Wong, Chi-fat, et 黃志發. « Genome sequencing and comparative genomic analysis of Pseudomonas mendocina DLHK ». Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hdl.handle.net/10722/197162.
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Nitrogen oxides are targeted as important gas pollutants to be eliminated. Biological removal of nitrogen oxides, like the use of bio-trickling reactor, is gaining popularity over conventional methods. A bacterium isolated from a bio-trickling reactor showing high performance in removing nitrogen oxides was identified to be Pseudomonas mendocina. The genome of this isolate was sequenced using 454 pyrosequencing technology to a high level of completeness with 33 contigs and N50 contig length of 273 kbp. The genome was annotated by Prokaryotic Genome Automatic Annotaion Pipeline (PGAAP)and the strain was named P. mendocina DLHK. Examination of P. mendocina DLHK genome annotation found nitrate reductase but not nitrite reductase, nitric oxide reductase and nitrous oxide reductase. Novel genes or pathways might be available in P. mendocina DLHK contributingits denitrification function in the bio-trickling reactor.
To better understand the evolution of Pseudomonas, a comprehensive comparative study was performed. Genomes of the Pseudomonasgenus were reannotated. Core genes were extracted to construct a phylogenomic tree using supermatrix approach. Effectiveness of using single phylogenetic marker in constructing phylogeny of Pseudomonas was evaluated using rpoB gene marker. Both methods generated phylogenetic trees of very similar topology, suggesting that rpoB gene can be a very effective marker in the rapid construction of Pseudomonas phylogeny.It is surprising to note that Azotobacter vinelandii DJ was included in the large clade of Pseudomonas and have the closest relationship with P. stutzeri in both phylogenetic trees, providing evidence that this species should be reclassified into the genus Pseudomonas.
Cluster of Orthologous Groups (COG)category distribution of all pseudomonads were analysed for physiological significance. The large amount of gene categorised into the COG for amino acid metabolism and transcription may imply the importance for these 2 functions on the survival of pseudomonads. It is again surprising to note the COG distribution pattern of A. vinelandii DJ is different from other pseudomonads, especially to its closest phylogenetic neighbour P. stutzeri.
Horizontal gene transfer events inpseudomonads were investigated because of its importance in prokaryotic evolution. The high congruence of the phylogemonic tree to most core genes suggests that the phylogenomic tree is a good piece of evidence describing the evolution of pseudomonads. It is a bit surprising to observe that quite a number of core genes may have exhibited horizontal gene transfer which show incongruence of the gene tree to the core genes. The impact of horizontal gene transfer events on the functionality and evolution of pseudomonads remains to be investigated.published_or_final_version
Biological Sciences
Master
Master of Philosophy
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Bertoldi, Loris. « Bioinformatics for personal genomics : development and application of bioinformatic procedures for the analysis of genomic data ». Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421950.
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In the last decade, the huge decreasing of sequencing cost due to the development of high-throughput technologies completely changed the way for approaching the genetic problems. In particular, whole exome and whole genome sequencing are contributing to the extraordinary progress in the study of human variants opening up new perspectives in personalized medicine. Being a relatively new and fast developing field, appropriate tools and specialized knowledge are required for an efficient data production and analysis.
In line with the times, in 2014, the University of Padua funded the BioInfoGen Strategic Project with the goal of developing technology and expertise in bioinformatics and molecular biology applied to personal genomics. The aim of my PhD was to contribute to this challenge by implementing a series of innovative tools and by applying them for investigating and possibly solving the case studies included into the project.
I firstly developed an automated pipeline for dealing with Illumina data, able to sequentially perform each step necessary for passing from raw reads to somatic or germline variant detection. The system performance has been tested by means of internal controls and by its application on a cohort of patients affected by gastric cancer, obtaining interesting results.
Once variants are called, they have to be annotated in order to define their properties such as the position at transcript and protein level, the impact on protein sequence, the pathogenicity and more. As most of the publicly available annotators were affected by systematic errors causing a low consistency in the final annotation, I implemented VarPred, a new tool for variant annotation, which guarantees the best accuracy (>99%) compared to the state-of-the-art programs, showing also good processing times. To make easy the use of VarPred, I equipped it with an intuitive web interface, that allows not only a graphical result evaluation, but also a simple filtration strategy.
Furthermore, for a valuable user-driven prioritization of human genetic variations, I developed QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. The prioritization is achieved by a global positive selection process that promotes the emergence of the most reliable variants, rather than filtering out those not satisfying the applied criteria.
QueryOR has been used to analyze the two case studies framed within the BioInfoGen project. In particular, it allowed to detect causative variants in patients affected by lysosomal storage diseases, highlighting also the efficacy of the designed sequencing panel. On the other hand, QueryOR simplified the recognition of LRP2 gene as possible candidate to explain such subjects with a Dent disease-like phenotype, but with no mutation in the previously identified disease-associated genes, CLCN5 and OCRL.
As final corollary, an extensive analysis over recurrent exome variants was performed, showing that their origin can be mainly explained by inaccuracies in the reference genome, including misassembled regions and uncorrected bases, rather than by platform specific errors.Nell’ultimo decennio, l’enorme diminuzione del costo del sequenziamento dovuto allo sviluppo di tecnologie ad alto rendimento ha completamente rivoluzionato il modo di approcciare i problemi genetici. In particolare, il sequenziamento dell’intero esoma e dell’intero genoma stanno contribuendo ad un progresso straordinario nello studio delle varianti genetiche umane, aprendo nuove prospettive nella medicina personalizzata. Essendo un campo relativamente nuovo e in rapido sviluppo, strumenti appropriati e conoscenze specializzate sono richieste per un’efficiente produzione e analisi dei dati. Per rimanere al passo con i tempi, nel 2014, l’Università degli Studi di Padova ha finanziato il progetto strategico BioInfoGen con l’obiettivo di sviluppare tecnologie e competenze nella bioinformatica e nella biologia molecolare applicate alla genomica personalizzata. Lo scopo del mio dottorato è stato quello di contribuire a questa sfida, implementando una serie di strumenti innovativi, al fine di applicarli per investigare e possibilmente risolvere i casi studio inclusi all’interno del progetto. Inizialmente ho sviluppato una pipeline per analizzare i dati Illumina, capace di eseguire in sequenza tutti i processi necessari per passare dai dati grezzi alla scoperta delle varianti sia germinali che somatiche. Le prestazioni del sistema sono state testate mediante controlli interni e tramite la sua applicazione su un gruppo di pazienti affetti da tumore gastrico, ottenendo risultati interessanti. Dopo essere state chiamate, le varianti devono essere annotate al fine di definire alcune loro proprietà come la posizione a livello del trascritto e della proteina, l’impatto sulla sequenza proteica, la patogenicità, ecc. Poiché la maggior parte degli annotatori disponibili presentavano errori sistematici che causavano una bassa coerenza nell’annotazione finale, ho implementato VarPred, un nuovo strumento per l’annotazione delle varianti, che garantisce la migliore accuratezza (>99%) comparato con lo stato dell’arte, mostrando allo stesso tempo buoni tempi di esecuzione. Per facilitare l’utilizzo di VarPred, ho sviluppato un’interfaccia web molto intuitiva, che permette non solo la visualizzazione grafica dei risultati, ma anche una semplice strategia di filtraggio. Inoltre, per un’efficace prioritizzazione mediata dall’utente delle varianti umane, ho sviluppato QueryOR, una piattaforma web adatta alla ricerca all’interno dei geni causativi, ma utile anche per trovare nuove associazioni gene-malattia. QueryOR combina svariate caratteristiche innovative che lo rendono comprensivo, flessibile e facile da usare. La prioritizzazione è raggiunta tramite un processo di selezione positiva che fa emergere le varianti maggiormente significative, piuttosto che filtrare quelle che non soddisfano i criteri imposti. QueryOR è stato usato per analizzare i due casi studio inclusi all’interno del progetto BioInfoGen. In particolare, ha permesso di scoprire le varianti causative dei pazienti affetti da malattie da accumulo lisosomiale, evidenziando inoltre l’efficacia del pannello di sequenziamento sviluppato. Dall’altro lato invece QueryOR ha semplificato l’individuazione del gene LRP2 come possibile candidato per spiegare i soggetti con un fenotipo simile alla malattia di Dent, ma senza alcuna mutazione nei due geni precedentemente descritti come causativi, CLCN5 e OCRL. Come corollario finale, è stata effettuata un’analisi estensiva su varianti esomiche ricorrenti, mostrando come la loro origine possa essere principalmente spiegata da imprecisioni nel genoma di riferimento, tra cui regioni mal assemblate e basi non corrette, piuttosto che da errori piattaforma-specifici.
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Mungall, Christopher. « Next-generation information systems for genomics ». Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5020.
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The advent of next-generation sequencing technologies is transforming biology by enabling individual researchers to sequence the genomes of individual organisms or cells on a massive scale. In order to realize the translational potential of this technology we will need advanced information systems to integrate and interpret this deluge of data. These systems must be capable of extracting the location and function of genes and biological features from genomic data, requiring the coordinated parallel execution of multiple bioinformatics analyses and intelligent synthesis of the results. The resulting databases must be structured to allow complex biological knowledge to be recorded in a computable way, which requires the development of logic-based knowledge structures called ontologies. To visualise and manipulate the results, new graphical interfaces and knowledge acquisition tools are required. Finally, to help understand complex disease processes, these information systems must be equipped with the capability to integrate and make inferences over multiple data sets derived from numerous sources. RESULTS: Here I describe research, design and implementation of some of the components of such a next-generation information system. I first describe the automated pipeline system used for the annotation of the Drosophila genome, and the application of this system in genomic research. This was succeeded by the development of a flexible graphoriented database system called Chado, which relies on the use of ontologies for structuring data and knowledge. I also describe research to develop, restructure and enhance a number of biological ontologies, adding a layer of logical semantics that increases the computability of these key knowledge sources. The resulting database and ontology collection can be accessed through a suite of tools. Finally I describe how the combination of genome analysis, ontology-based database representation and powerful tools can be combined in order to make inferences about genotype-phenotype relationships within and across species. CONCLUSION: The large volumes of complex data generated by high-throughput genomic and systems biology technology threatens to overwhelm us, unless we can devise better computing tools to assist us with its analysis. Ontologies are key technologies, but many existing ontologies are not interoperable or lack features that make them computable. Here I have shown how concerted ontology, tool and database development can be applied to make inferences of value to translational research.
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Chen, Yuansha. « Comparative genomic analysis of Vibrio cholerae O31 capsule, O-antigen, pathogenesis and genome / ». College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/4112.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2006.Thesis research directed by: Marine-Estuarine-Environmental Sciences. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Danks, Jacob R. « Algorithm Optimizations in Genomic Analysis Using Entropic Dissection ». Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc804921/.
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In recent years, the collection of genomic data has skyrocketed and databases of genomic data are growing at a faster rate than ever before. Although many computational methods have been developed to interpret these data, they tend to struggle to process the ever increasing file sizes that are being produced and fail to take advantage of the advances in multi-core processors by using parallel processing. In some instances, loss of accuracy has been a necessary trade off to allow faster computation of the data. This thesis discusses one such algorithm that has been developed and how changes were made to allow larger input file sizes and reduce the time required to achieve a result without sacrificing accuracy. An information entropy based algorithm was used as a basis to demonstrate these techniques. The algorithm dissects the distinctive patterns underlying genomic data efficiently requiring no a priori knowledge, and thus is applicable in a variety of biological research applications. This research describes how parallel processing and object-oriented programming techniques were used to process larger files in less time and achieve a more accurate result from the algorithm. Through object oriented techniques, the maximum allowable input file size was significantly increased from 200 mb to 2000 mb. Using parallel processing techniques allowed the program to finish processing data in less than half the time of the sequential version. The accuracy of the algorithm was improved by reducing data loss throughout the algorithm. Finally, adding user-friendly options enabled the program to use requests more effectively and further customize the logic used within the algorithm.
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Sinha, Amit U. « Discovery and analysis of genomic patterns applications to transcription factor binding and genome rearrangement / ». Cincinnati, Ohio : University of Cincinnati, 2008. http://www.ohiolink.edu/etd/view.cgi?1204227723.
Texte intégralRésumé :
Thesis (Ph.D.)--University of Cincinnati, 2008.Advisor: Raj Bhatnagar. Title from electronic thesis title page (viewed April 24, 2008). Keywords: computational biology; bioinformatics; transcription factor; genome rearrangement. Includes abstract. Includes bibliographical references.
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Morlot, Jean-Baptiste. « Annotation of the human genome through the unsupervised analysis of high-dimensional genomic data ». Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066641/document.
Texte intégralRésumé :
Le corps humain compte plus de 200 types cellulaires différents possédant une copie identique du génome mais exprimant un ensemble différent de gènes. Le contrôle de l'expression des gènes est assuré par un ensemble de mécanismes de régulation agissant à différentes échelles de temps et d'espace. Plusieurs maladies ont pour cause un dérèglement de ce système, notablement les certains cancers, et de nombreuses applications thérapeutiques, comme la médecine régénérative, reposent sur la compréhension des mécanismes de la régulation géniques. Ce travail de thèse propose, dans une première partie, un algorithme d'annotation (GABI) pour identifier les motifs récurrents dans les données de séquençage haut-débit. La particularité de cet algorithme est de prendre en compte la variabilité observée dans les réplicats des expériences en optimisant le taux de faux positif et de faux négatif, augmentant significativement la fiabilité de l'annotation par rapport à l'état de l'art. L'annotation fournit une information simplifiée et robuste à partir d'un grand ensemble de données. Appliquée à une base de données sur l'activité des régulateurs dans l'hématopoieïse, nous proposons des résultats originaux, en accord avec de précédentes études. La deuxième partie de ce travail s'intéresse à l'organisation 3D du génome, intimement lié à l'expression génique. Elle est accessible grâce à des algorithmes de reconstruction 3D à partir de données de contact entre chromosomes. Nous proposons des améliorations à l'algorithme le plus performant du domaine actuellement, ShRec3D, en permettant d'ajuster la reconstruction en fonction des besoins de l'utilisateurThe human body has more than 200 different cell types each containing an identical copy of the genome but expressing a different set of genes. The control of gene expression is ensured by a set of regulatory mechanisms acting at different scales of time and space. Several diseases are caused by a disturbance of this system, notably some cancers, and many therapeutic applications, such as regenerative medicine, rely on understanding the mechanisms of gene regulation. This thesis proposes, in a first part, an annotation algorithm (GABI) to identify recurrent patterns in the high-throughput sequencing data. The particularity of this algorithm is to take into account the variability observed in experimental replicates by optimizing the rate of false positive and false negative, increasing significantly the annotation reliability compared to the state of the art. The annotation provides simplified and robust information from a large dataset. Applied to a database of regulators activity in hematopoiesis, we propose original results, in agreement with previous studies. The second part of this work focuses on the 3D organization of the genome, intimately linked to gene expression. This structure is now accessible thanks to 3D reconstruction algorithm from contact data between chromosomes. We offer improvements to the currently most efficient algorithm of the domain, ShRec3D, allowing to adjust the reconstruction according to the user needs
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SINHA, AMIT U. « Discovery and Analysis of Genomic Patterns : Applications to Transcription Factor Binding and Genome Rearrangement ». University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1204227723.
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Schiavo, Giuseppina <1986>. « Analysis of the pig genome for the identification of genomic regions affecting production traits ». Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6919/1/Schiavo_Giuseppina_Tesi_Dottorato_XVII_ciclo.pdf.
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The aim of this work was to identify markers associated with production traits in the pig genome using different approaches. We focused the attention on Italian Large White pig breed using Genome Wide Association Studies (GWAS) and applying a selective genotyping approach to increase the power of the analyses.
Furthermore, we searched the pig genome using Next Generation Sequencing (NSG) Ion Torrent Technology to combine selective genotyping approach and deep sequencing for SNP discovery. Other two studies were carried on with a different approach. Allele frequency changes for SNPs affecting candidate genes and at Genome Wide level were analysed to identify selection signatures driven by selection program during the last 20 years.
This approach confirmed that a great number of markers may affect production traits and that they are captured by the classical selection programs.
GWAS revealed 123 significant or suggestively significant SNP associated with Back Fat Thickenss and 229 associated with Average Daily Gain. 16 Copy Number Variant Regions resulted more frequent in lean or fat pigs and showed that different copies of those region could have a limited impact on fat. These often appear to be involved in food intake and behavior, beside affecting genes involved in metabolic pathways and their expression.
By combining NGS sequencing with selective genotyping approach, new variants where discovered and at least 54 are worth to be analysed in association studies.
The study of groups of pigs undergone to stringent selection showed that allele frequency of some loci can drastically change if they are close to traits that are interesting for selection schemes. These approaches could be, in future, integrated in genomic selection plans.
Livres sur le sujet "Genomic analysi"
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Genome clustering : From linguistic models to classification of genetic texts. Berlin : Springer, 2010.
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Y, Galperin Michael, et Koonin Eugene V, dir. Frontiers in computational genomics. Norfolk, U.K : Caister, 2003.
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L, Smith Cassandra, et Human Genome Project, dir. Genomics : The science and technology behind the Human Genome Project. New York : Wiley, 1999.
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Bioinformatics : Genomics and post-genomics. Chichester, England : John Wiley & Sons, 2006.
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P, Jauhar Prem, dir. Methods of genome analysis in plants. Boca Raton : CRC Press, 1996.
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Per, Sunnerhagen, et Piškur Jure, dir. Comparative genomics : Using fungi as models. Berlin : Springer, 2006.
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de, Bruijn F. J., Lupski James R. 1957- et Weinstock George M. 1949-, dir. Bacterial genomes : Physical structure and analysis. New York : Kluwer Academic, 1999.
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de, Bruijn F. J., Lupski James R. 1957- et Weinstock George M. 1949-, dir. Bacterial genomes : Physical structure and analysis. New York : Chapman & Hall, 1998.
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Bickel, David R. Genomics Data Analysis. Boca Raton, FL : CRC Press, 2019. : Chapman and Hall/CRC, 2019. http://dx.doi.org/10.1201/9780429299308.
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India) National Seminar on "Genome Analysis Perspective in the Post-Genomic Era and its Relevance to Society" (2007 Hyderabad. Genome analysis perspective in the post-genomic era and its relevance to society. Hyderabad : School of Human Genome Research and Genetic Disorders and School of Biotechnology, Mahatma Gandhi National Institute of Research and Social Action, 2007.
Trouver le texte intégralChapitres de livres sur le sujet "Genomic analysi"
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Gill, Bikram S. « A Century of Cytogenetic and Genome Analysis : Impact on Wheat Crop Improvement ». Dans Wheat Improvement, 277–97. Cham : Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-90673-3_16.
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AbstractBeginning in the first decade of 1900, pioneering research in disease resistance and seed color inheritance established the scientific basis of Mendelian inheritance in wheat breeding. A series of breakthroughs in chromosome and genome analysis beginning in the 1920s and continuing into the twenty-first century have impacted wheat improvement. The application of meiotic chromosome pairing in the 1920s and plasmon analysis in the 1950s elucidated phylogeny of the Triticum-Aegilops complex of species and defined the wheat gene pools. The aneuploid stocks in the 1950s opened floodgates for chromosome and arm mapping of first phenotypic and later protein and DNA probes. The aneuploid stocks, coupled with advances in chromosome banding and in situ hybridization in the 1970s, allowed precise chromosome engineering of traits in wide hybrids. The deletion stocks in the 1990s were pivotal in mapping expressed genes to specific chromosome bins revealing structural and functional differentiation of chromosomes along their length and facilitating map-based cloning of genes. Advances in whole-genome sequencing, chromosome genomics, RH mapping and functional tools led to the assembly of reference sequence of Chinese Spring and multiple wheat genomes. Chromosome and genomic analysis must be integrated into wheat breeding and wide-hybridizaton pipeline for sustainable crop improvement.
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Chaitanya, K. V. « Orgenellar Genome Analysis ». Dans Genome and Genomics, 89–119. Singapore : Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-15-0702-1_4.
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Ahmad Dar, Mayasar, et Deepmala Sharma. « Revisiting the Genomics and Genetic Codes Using Walsh-Hadamard Spectrum Analysis ». Dans Proceedings of the Conference BioSangam 2022 : Emerging Trends in Biotechnology (BIOSANGAM 2022), 106–13. Dordrecht : Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_11.
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AbstractWalsh-Hadamard spectrum is widely used in the field of science and technology like classification of cancer cells, image processing, speech processing, signal and image compression etc. In this paper, a genomic analysis using Walsh-Hadamard spectrum and cross-correlation has been done. Transformation of genetic code using Walsh-Hadamard spectrum has been given. We redefine the Walsh-Hadamard spectrum in genomics and analyse the origin of mRNA features by using this spectra. Finally, using Walsh-Hadamard spectrum the overall energy of the mRNA sequence has been evaluated.
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Hunter, Sally M., Amy E. McCart Reed, Ian G. Campbell et Kylie L. Gorringe. « Genomic Analysis ». Dans Molecular Pathology in Cancer Research, 83–106. New York, NY : Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6643-1_5.
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Contreras-Moreira, Bruno, Guy Naamati, Marc Rosello, James E. Allen, Sarah E. Hunt, Matthieu Muffato, Astrid Gall et Paul Flicek. « Scripting Analyses of Genomes in Ensembl Plants ». Dans Plant Bioinformatics, 27–55. New York, NY : Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2067-0_2.
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AbstractEnsembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.
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Karolchik, Donna, Gill Bejerano, Angie S. Hinrichs, Robert M. Kuhn, Webb Miller, Kate R. Rosenbloom, Ann S. Zweig, David Haussler et W. James Kent. « Comparative Genomic Analysis Using the UCSC Genome Browser ». Dans Comparative Genomics, 17–33. Totowa, NJ : Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-514-5_2.
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Opperman, Charles H., David McK Bird et Jennifer E. Schaff. « Genomic Analysis of the Root-Knot Nematode Genome ». Dans Cell Biology of Plant Nematode Parasitism, 221–37. Berlin, Heidelberg : Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-85215-5_8.
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Nanni, Luca. « Computational Inference of DNA Folding Principles : From Data Management to Machine Learning ». Dans Special Topics in Information Technology, 79–88. Cham : Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-85918-3_7.
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AbstractDNA is the molecular basis of life and would total about three meters if linearly untangled. To fit in the cell nucleus at the micrometer scale, DNA has, therefore, to fold itself into several layers of hierarchical structures, which are thought to be associated with functional compartmentalization of genomic features like genes and their regulatory elements. For this reason, understanding the mechanisms of genome folding is a major biological research problem. Studying chromatin conformation requires high computational resources and complex data analyses pipelines. In this chapter, we first present the PyGMQL software for interactive and scalable data exploration for genomic data. PyGMQL allows the user to inspect genomic datasets and design complex analysis pipelines. The software presents itself as a easy-to-use Python library and interacts seamlessly with other data analysis packages. We then use the software for the study of chromatin conformation data. We focus on the epigenetic determinants of Topologically Associating Domains (TADs), which are region of high self chromatin interaction. The results of this study highlight the existence of a “grammar of genome folding” which dictates the formation of TADs and boundaries, which is based on the CTCF insulator protein. Finally we focus on the relationship between chromatin conformation and gene expression, designing a graph representation learning model for the prediction of gene co-expression from gene topological features obtained from chromatin conformation data. We demonstrate a correlation between chromatin topology and co-expression, shedding a new light on this debated topic and providing a novel computational framework for the study of co-expression networks.
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Jeukens, Julie, Brian Boyle, Nicholas P. Tucker et Roger C. Levesque. « Strategy for Genome Sequencing Analysis and Assembly for Comparative Genomics of Pseudomonas Genomes ». Dans Methods in Molecular Biology, 565–77. New York, NY : Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-0473-0_43.
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Hamlet, Stephen, Eugen Petcu et Saso Ivanovski. « Genomic Microarray Analysis ». Dans Handbook of Vascular Biology Techniques, 391–405. Dordrecht : Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9716-0_30.
Texte intégralActes de conférences sur le sujet "Genomic analysi"
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Afanasyeva, K. P., A. N. Rusakovich, N. E. Kharchenko, I. D. Aleksandrov et M. V. Aleksandrova. « GENOMIC CHANGES IN THE PROGENY OF DROSOPHILA MELANOGASTER MALES IRRADIATED BY y-RAYS ». Dans SAKHAROV READINGS 2022 : ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. International Sakharov Environmental Institute of Belarusian State University, 2022. http://dx.doi.org/10.46646/sakh-2022-1-328-331.
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The results of sequencing and bioinformatics analysis of genomic changes in 9 F1 progeny of males from the isogenic line D. melanogaster irradiated by Co60 Y—rays at a dose of 40 Gy (LD85) and in 3 control samples are presented. In 9 progeny from irradiated males, a total of 46 genomic changes (32 significant and 15 mosaic de novo mutations) were found, which is equal to a frequency of 5.2 mutations/genome. The spectrum of changes included 33 deletions (17-78 000 bp in size), 4 duplications (322-1371 bp), 4 reciprocal translocations and 6 inversions in X, 2 and 3 chromosomes. In 3 studied control samples, 2 deletions (98 and 128 bp in length) were found in 3 chromosome (frequency - 0.66 mutations/genome). This shows that in the progeny of irradiated males, the frequency of de novo mutations at the genome level is 7.9 times higher than in the control, even without taking into account base substitutions and indels, the analysis of which is ongoing. Almost half of the identified structural changes in the genome affect coding genes. Thus, the results show that next-generation genome sequencing can detect a much wider range of mutations of any size. This indicates a much higher genetic hazard of sparsely ionizing radiation than previously thought.
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Galimova, A. A., E. A. Zaikina et B. R. Kuluev. « SNP analysis of common wheat baking qualities ». Dans 2nd International Scientific Conference "Plants and Microbes : the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.082.
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The allelic states of waxy genes in genomes A, B and D were studied by genome-specific primers in cultivars and lines of common wheat of the pre-Ural steppe. The studied cultivars and lines revealed differences in genotypes for genome A.
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DUBCHAK, INNA, LIOR PACHTER et LIPING WEI. « GENOME-WIDE ANALYSIS AND COMPARATIVE GENOMICS ». Dans Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0011.
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Collins, Corolyn J., Richard B. Levene, Christina P. Ravera, Marker J. Dombalagian, David M. Livingston et Dennis C. Lynch. « MOLECULAR CLONING OF THE HUMAN GENE FOR VON WILLEBRAND FACTOR AND IDENTIFICATION OF THE TRANSCRIPTION INITIATION SITE ». Dans XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642830.
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Most patients with von Willebrand's disease appear to have a defect affecting the level of expression of the von Willebrand factor (vWf) gene. Thus, an understanding of the pathogenesis of von Willebrand's disease will require an analysis of the structure and function of the vWf gene in normals and in patients. To begin such analyses, we have screened a human genomic cosmid library with probes obtained from vWf cDNA and isolated a colinear segment spanning ≈175 kb in five overlapping clones. This segment extends ≈25 kb upstream and ≈5 kb downstream of the transcription start and stop sites for vWf mRNA, implying the vWf gene has a length of ≈150 kb. Within one of these clones, the vWf transcription initiation sites have been mapped. A portion of the promoter region has been sequenced, revealing a typical TATA box, a downstream CCAAT box, and a perfect downstream repeat of the 8 base pairs containing the major transcription start site. Primer extension analysis suggests that sequences contained within the downstream repeat of the transcription start site may be used as minor initiation sites in endothelial cells. Transfection studies are underway to evaluate the role of sequences within this promoter region in gene regulatory activity. Comparative restriction analyses of cloned and chromosomal DNA segments strongly suggests that no major alterations ocurred during cloning and that there is only one complete copy of the vWf gene in the human haploid genome. Similar analyses of DNA from vWf-expressing endothelial cells and non-expressing white blood cells suggests that no major rearrangements are associated with vWf gene expression. Finally, cross hybridization patterns among seven mammalian species suggests a strong conservation of genomic sequences encoding the plasma portion of vWf, but a lower degree of conservation of sequences encoding the N terminal region of provWf.
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Hamon, Morgan, Kirn Cramer, Sachin Jambovane, Jing Dai, Ali Khademhosseini et Jong Wook Hong. « Wide Range Logarithmic Gradient Formation for Cell Response ». Dans ASME 2011 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2011. http://dx.doi.org/10.1115/sbc2011-53710.
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Recently, the number of potential drug targets has dramatically increased because of the recent completion of the human genome sequencing and the progress in genomics and proteomics. In parallel, the number of new drugs for those targets has also been increased due to the use of combinatorial synthesis and the increased access to natural molecules [1]. However, this has not increased consequently the number of approved new drugs delivered to patients [2]. Indeed the drug discovery process is still limited by numbers of challenges; among them the need to analyze in more rapid and accurate manner precious sample of drug candidates.
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Heidaritabar, M., A. Huisman, M. C. A. M. Bink, P. Charagu et G. Plastow. « 261. Genome-wide association analyses and genomic prediction for pork meat quality traits using whole-genome sequence ». Dans World Congress on Genetics Applied to Livestock Production. The Netherlands : Wageningen Academic Publishers, 2022. http://dx.doi.org/10.3920/978-90-8686-940-4_261.
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Mansani, Fabio Postiglione, Márcia Magalhães Fernandes et Ruffo de Freitas-Junior. « IMPACT OF THE MAMMAPRINT GENETIC SIGNATURE ON THE DECALONATION OF THE CHEMOTHERAPY TREATMENT IN A MEDIUM INCOME COUNTRY – STUDY OF REAL LIFE ». Dans Abstracts from the Brazilian Breast Cancer Symposium - BBCS 2021. Mastology, 2021. http://dx.doi.org/10.29289/259453942021v31s2023.
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Introduction: Genetic signatures have been used in the attempt of de-escalate the treatment of breast carcinoma, reducing the indication for adjuvant chemotherapy (CTAd) in patients with luminal tumors with high clinical risk. The MINDACT trial, using the 70 gene platform MammaPrintTM, analyzing a cohort of European patients, showed that it was possible to save 46% of the use of CTAd in this population. However, there is a lack of information regarding the impact of this platform in the low- and medium-income countries (LMIC). Objective: The objective of this study was to analyze the Brazilian population with luminal breast cancer with high clinical risk, subjected to genomic analysis by the MammaPrintTM signature, the percentage of de-escalation of the systemic treatment, saving patients with low genomic risk from chemotherapy, using the MINDACT trial criteria. Methodology: Data were collected from 815 patients who underwent the MammaPrintTM genetic platform, provided by the GenCell Pharma database, from several Brazilian states, with luminal profile, by immunohistochemistry (IHC), breast carcinoma, and high clinical risk by the criteria of the MINDACT trial. The percentage of these patients who had a low genomic risk was calculated using MammaPrintTM. Patients were categorized by age group and menopausal status. The correlation of low and high clinical and genomic risks was also analyzed according to the Brazilian macro-regions, considering the municipal human development index (MHDI). MammaPrintTM values ³0.355 were considered to be genomic ultra-low risk. Results: The age of the patients ranged between 29 and 97 years. Of the 815 patients, 14 (1.71%) had a non-luminal profile to BluePrintTM and were excluded, although demonstrating that there was a strong statistical significance between IHC and BluePrintTM. Out of 801 luminal profile patients of high clinical risk to MammaPrintTM, 477 had low genomic risk, representing a percentage of 59.5%. Of the patients with low genomic risk 124 (15.48%) were ultra-low risk, considering the cutoff of 0.355. When assessing the age group, low genomic risk represents 46% of patients aged below 35 years, 51% of those aged between 35 and 49 years old, 61% aged between 50 and 70 years, and 64% of patients aged above 70 years old. Taking into consideration the menopausal status, 51% of low genomic risk were premenopause and 62% were postmenopause women. The correlation between the MHDI of the Brazilian macro regions and the presence of breast cancer of high genomic risk was not statistically significant. Conclusions: The use of the MammaPrintTM genetic signature in a Brazilian cohort, with high clinical risk, demonstrated that 59.5% of the patients could be spared from CTAd, more markedly in the postmenopause women, which represents 62% of the sample. This real-life study showed that for LMICs, MammaPrintTM can generate an even more significant CTAd de-escalation than that observed in the European cohort by the MINDACT study. A broader assessment with analysis of the clinical outcome is needed to confirm these results.
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Nordentoft, Iver K., Karin Birkenkamp-Demtroder, Philippe Lamy, Thomas Reinert, Niels Fristrup, Jakob Skou Pedersen, Søren Vang et al. « Abstract 3153 : Whole genome and transcriptome analysis reveals novel genomic alterations in bladder cancer. » Dans Proceedings : AACR 104th Annual Meeting 2013 ; Apr 6-10, 2013 ; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-3153.
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Liu, Wei Yi, Hui-I. Hsiao et Shih Yao Dai. « Genomic analysis with MapReduce ». Dans 2015 IEEE International Conference on Big Data (Big Data). IEEE, 2015. http://dx.doi.org/10.1109/bigdata.2015.7363891.
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Cristea, Paul Dan, Rodica Tuduce, Jan Cornelis et Adrian Munteanu. « Nucleotide genomic signal analysis ». Dans 2008 International Conference on Signals and Electronic Systems. IEEE, 2008. http://dx.doi.org/10.1109/icses.2008.4673398.
Texte intégralRapports d'organisations sur le sujet "Genomic analysi"
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Zhang, Hongbin B., David J. Bonfil et Shahal Abbo. Genomics Tools for Legume Agronomic Gene Mapping and Cloning, and Genome Analysis : Chickpea as a Model. United States Department of Agriculture, mars 2003. http://dx.doi.org/10.32747/2003.7586464.bard.
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The goals of this project were to develop essential genomic tools for modern chickpea genetics and genomics research, map the genes and quantitative traits of importance to chickpea production and generate DNA markers that are well-suited for enhanced chickpea germplasm analysis and breeding. To achieve these research goals, we proposed the following research objectives in this period of the project: 1) Develop an ordered BAC library with an average insert size of 150 - 200 kb (USA); 2) Develop 300 simple sequence repeat (SSR) markers with an aid of the BAC library (USA); 3) Develop SSR marker tags for Ascochyta response, flowering date and grain weight (USA); 4) Develop a molecular genetic map consisting of at least 200 SSR markers (Israel and USA); 5) Map genes and QTLs most important to chickpea production in the U.S. and Israel: Ascochyta response, flowering and seed set date, grain weight, and grain yield under extreme dryland conditions (Israel); and 6) Determine the genetic correlation between the above four traits (Israel). Chickpea is the third most important pulse crop in the world and ranks the first in the Middle East. Chickpea seeds are a good source of plant protein (12.4-31.5%) and carbohydrates (52.4-70.9%). Although it has been demonstrated in other major crops that the modern genetics and genomics research is essential to enhance our capacity for crop genetic improvement and breeding, little work was pursued in these research areas for chickpea. It was absent in resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. For instance, there were no large-insert BAC and BIBAC libraries, no sufficient and user- friendly DNA markers, and no intraspecific genetic map. Grain sizes, flowering time and Ascochyta response are three main constraints to chickpea production in drylands. Combination of large seeds, early flowering time and Ascochyta blight resistance is desirable and of significance for further genetic improvement of chickpea. However, it was unknown how many genes and/or loci contribute to each of the traits and what correlations occur among them, making breeders difficult to combine these desirable traits. In this period of the project, we developed the resources, tools and infrastructure that are essential for chickpea genomics and modern genetics research. In particular, we constructed the proposed large-insert BAC library and an additional plant-transformation-competent BIBAC library from an Israeli advanced chickpea cultivar, Hadas. The BAC library contains 30,720 clones and has an average insert size of 151 kb, equivalent to 6.3 x chickpea haploid genomes. The BIBAC library contains 18,432 clones and has an average insert size of 135 kb, equivalent to 3.4 x chickpea haploid genomes. The combined libraries contain 49,152 clones, equivalent to 10.7 x chickpea haploid genomes. We identified all SSR loci-containing clones from the chickpea BAC library, generated sequences for 536 SSR loci from a part of the SSR-containing BACs and developed 310 new SSR markers. From the new SSR markers and selected existing SSR markers, we developed a SSR marker-based molecular genetic map of the chickpea genome. The BAC and BIBAC libraries, SSR markers and the molecular genetic map have provided essential resources and tools for modern genetic and genomic analyses of the chickpea genome. Using the SSR markers and genetic map, we mapped the genes and loci for flowering time and Ascochyta responses; one major QTL and a few minor QTLs have been identified for Ascochyta response and one major QTL has been identified for flowering time. The genetic correlations between flowering time, grain weight and Ascochyta response have been established. These results have provided essential tools and knowledge for effective manipulation and enhanced breeding of the traits in chickpea.
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Katzir, Nurit, James Giovannoni, Marla Binzel, Efraim Lewinsohn, Joseph Burger et Arthur Schaffer. Genomic Approach to the Improvement of Fruit Quality in Melon (Cucumis melo) and Related Cucurbit Crops II : Functional Genomics. United States Department of Agriculture, janvier 2010. http://dx.doi.org/10.32747/2010.7592123.bard.
Texte intégralRésumé :
Background: Genomics tools for enhancement of melon research, with an emphasis on fruit, were developed through a previous BARD project of the PIs (IS -333-02). These included the first public melon EST collection, a database to relay this information to the research community and a publicly available microarray. The current project (IS-3877- 06) aimed to apply these tools for identification of important genes for improvement of melon (Cucumis melo) fruit quality. Specifically, the research plans included expression analysis using the microarray and functional analyses of selected genes. The original project objectives, as they appeared in the approved project, were: Objective 1: Utilization of a public melon microarray developed under the existing project to characterize melon transcriptome activity during the ripening of normal melon fruit (cv. Galia) in order to provide a basis for both a general view of melon transcriptome activity during ripening and for comparison with existing transcriptome data of developing tomato and pepper fruit. Objective 2: Utilization of the same public melon microarray to characterize melon transcriptome activity in lines available in the collection of the Israeli group, focusing on sugar, organic acids and aroma metabolism, so as to identify potentially useful candidates for functional analysis and possible manipulation, through comparison with the general fruit development profile resulting from (1) above. Objective 3: Expansion of our existing melon EST database to include publicly available gene expression data and query tools, as the US group has done with tomato. Objective 4: Selection of 6-8 candidate genes for functional analysis and development of DNA constructs for repression or over-expression. Objective 5: Creation of transgenic melon lines, or transgenic heterologous systems (e.g. E. coli or tomato), to assess putative functions and potential as tools for molecular enhancement of melon fruit quality, using the candidate gene constructs from (4).
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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor et Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, janvier 2016. http://dx.doi.org/10.32747/2016.7600047.bard.
Texte intégralRésumé :
Project objectives: 1) Characterization of variation for yield heterosis in melon using Half-Diallele (HDA) design. 2) Development and implementation of image-based yield phenotyping in melon. 3) Characterization of genetic, epigenetic and transcriptional variation across 25 founder lines and selected hybrids. The epigentic part of this objective was modified during the course of the project: instead of characterization of chromatin structure in a single melon line through genome-wide mapping of nucleosomes using MNase-seq approach, we took advantage of rapid advancements in single-molecule sequencing and shifted the focus to Nanoporelong-read sequencing of all 25 founder lines. This analysis provides invaluable information on genome-wide structural variation across our diversity 4) Integrated analyses and development of prediction models Agricultural heterosis relates to hybrids that outperform their inbred parents for yield. First generation (F1) hybrids are produced in many crop species and it is estimated that heterosis increases yield by 15-30% globally. Melon (Cucumismelo) is an economically important species of The Cucurbitaceae family and is among the most important fleshy fruits for fresh consumption Worldwide. The major goal of this project was to explore the patterns and magnitude of yield heterosis in melon and link it to whole genome sequence variation. A core subset of 25 diverse lines was selected from the Newe-Yaar melon diversity panel for whole-genome re-sequencing (WGS) and test-crosses, to produce structured half-diallele design of 300 F1 hybrids (MelHDA25). Yield variation was measured in replicated yield trials at the whole-plant and at the rootstock levels (through a common-scion grafted experiments), across the F1s and parental lines. As part of this project we also developed an algorithmic pipeline for detection and yield estimation of melons from aerial-images, towards future implementation of such high throughput, cost-effective method for remote yield evaluation in open-field melons. We found extensive, highly heritable root-derived yield variation across the diallele population that was characterized by prominent best-parent heterosis (BPH), where hybrids rootstocks outperformed their parents by 38% and 56 % under optimal irrigation and drought- stress, respectively. Through integration of the genotypic data (~4,000,000 SNPs) and yield analyses we show that root-derived hybrids yield is independent of parental genetic distance. However, we mapped novel root-derived yield QTLs through genome-wide association (GWA) analysis and a multi-QTLs model explained more than 45% of the hybrids yield variation, providing a potential route for marker-assisted hybrid rootstock breeding. Four selected hybrid rootstocks are further studied under multiple scion varieties and their validated positive effect on yield performance is now leading to ongoing evaluation of their commercial potential. On the genomic level, this project resulted in 3 layers of data: 1) whole-genome short-read Illumina sequencing (30X) of the 25 founder lines provided us with 25 genome alignments and high-density melon HapMap that is already shown to be an effective resource for QTL annotation and candidate gene analysis in melon. 2) fast advancements in long-read single-molecule sequencing allowed us to shift focus towards this technology and generate ~50X Nanoporesequencing of the 25 founders which in combination with the short-read data now enable de novo assembly of the 25 genomes that will soon lead to construction of the first melon pan-genome. 3) Transcriptomic (3' RNA-Seq) analysis of several selected hybrids and their parents provide preliminary information on differentially expressed genes that can be further used to explain the root-derived yield variation. Taken together, this project expanded our view on yield heterosis in melon with novel specific insights on root-derived yield heterosis. To our knowledge, thus far this is the largest systematic genetic analysis of rootstock effects on yield heterosis in cucurbits or any other crop plant, and our results are now translated into potential breeding applications. The genomic resources that were developed as part of this project are putting melon in the forefront of genomic research and will continue to be useful tool for the cucurbits community in years to come.
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Tamanaha, C. R., S. P. Mulvaney, K. A. Wahowski, M. C. Tondra, L. J. Whitman et R. J. Colton. Cellular Genomic Analysis with GMR Sensor Arrays. Fort Belvoir, VA : Defense Technical Information Center, octobre 2003. http://dx.doi.org/10.21236/ada482671.
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Stern, David. Hidden Chloroplast Functions Revealed Through Deep Genomic Analysis. Office of Scientific and Technical Information (OSTI), novembre 2017. http://dx.doi.org/10.2172/1409823.
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Price, Lance B. Genomic Analysis of Complex Microbial Communities in Wounds. Fort Belvoir, VA : Defense Technical Information Center, juillet 2009. http://dx.doi.org/10.21236/ada585789.
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Price, Lance B. Genomic Analysis of Complex Microbial Communities in Wounds. Fort Belvoir, VA : Defense Technical Information Center, janvier 2012. http://dx.doi.org/10.21236/ada561076.
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Fluhr, Robert, et Volker Brendel. Harnessing the genetic diversity engendered by alternative gene splicing. United States Department of Agriculture, décembre 2005. http://dx.doi.org/10.32747/2005.7696517.bard.
Texte intégralRésumé :
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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Stevens, Rick. Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models. Office of Scientific and Technical Information (OSTI), août 2010. http://dx.doi.org/10.2172/1234257.
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Tang, Shao-Jun. A Functional Genomic Analysis of NF1-Associated Learning Disabilities. Fort Belvoir, VA : Defense Technical Information Center, février 2005. http://dx.doi.org/10.21236/ada435850.
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