Relevant bibliographies by topics / Genomics

Academic literature on the topic 'Genomics'

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Published: 4 June 2021
Last updated: 31 August 2024

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Journal articles on the topic "Genomics"

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Tang, Lin. "Genomics beyond complete genomes." Nature Methods 19, no. 1 (January 2022): 29. http://dx.doi.org/10.1038/s41592-021-01374-2.

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Hedges, S. B. "GENOMICS: Vertebrate Genomes Compared." Science 297, no. 5585 (August 23, 2002): 1283b—1285. http://dx.doi.org/10.1126/science.1076231.

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Keller, Evelyn Fox. "Genes, Genomes, and Genomics." Biological Theory 6, no. 2 (June 2011): 132–40. http://dx.doi.org/10.1007/s13752-012-0014-x.

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Karam, Jose A., Shahrokh F. Shariat, Jer-Tsong Hsieh, and Margaret A. Knowles. "Genomics: a preview of genomic medicine." BJU International 102, no. 9b (November 2008): 1221–27. http://dx.doi.org/10.1111/j.1464-410x.2008.07963.x.

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Lazaridis, Konstantinos N., and Gloria M. Petersen. "Genomics, genetic epidemiology, and genomic medicine." Clinical Gastroenterology and Hepatology 3, no. 4 (April 2005): 320–28. http://dx.doi.org/10.1016/s1542-3565(05)00085-6.

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Hollander, Rachelle D. "Social genomics: Genomic inventions in society." Science and Engineering Ethics 8, no. 4 (December 2002): 485–96. http://dx.doi.org/10.1007/s11948-002-0002-9.

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Whitley, Kiara V., Josie A. Tueller, and K. Scott Weber. "Genomics Education in the Era of Personal Genomics: Academic, Professional, and Public Considerations." International Journal of Molecular Sciences 21, no. 3 (January 24, 2020): 768. http://dx.doi.org/10.3390/ijms21030768.

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Since the completion of the Human Genome Project in 2003, genomic sequencing has become a prominent tool used by diverse disciplines in modern science. In the past 20 years, the cost of genomic sequencing has decreased exponentially, making it affordable and accessible. Bioinformatic and biological studies have produced significant scientific breakthroughs using the wealth of genomic information now available. Alongside the scientific benefit of genomics, companies offer direct-to-consumer genetic testing which provide health, trait, and ancestry information to the public. A key area that must be addressed is education about what conclusions can be made from this genomic information and integrating genomic education with foundational genetic principles already taught in academic settings. The promise of personal genomics providing disease treatment is exciting, but many challenges remain to validate genomic predictions and diagnostic correlations. Ethical and societal concerns must also be addressed regarding how personal genomic information is used. This genomics revolution provides a powerful opportunity to educate students, clinicians, and the public on scientific and ethical issues in a personal way to increase learning. In this review, we discuss the influence of personal genomics in society and focus on the importance and benefits of genomics education in the classroom, clinics, and the public and explore the potential consequences of personal genomic education.
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Gurwitz, David, and Yael Bregman-Eschet. "Personal genomics services: whose genomes?" European Journal of Human Genetics 17, no. 7 (March 4, 2009): 883–89. http://dx.doi.org/10.1038/ejhg.2008.254.

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Endy, D. "GENOMICS: Reconstruction of the Genomes." Science 319, no. 5867 (February 29, 2008): 1196–97. http://dx.doi.org/10.1126/science.1155749.

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DiRita, V. J. "GENOMICS: Genomics Happens." Science 289, no. 5484 (September 1, 2000): 1488–89. http://dx.doi.org/10.1126/science.289.5484.1488.

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Dissertations / Theses on the topic "Genomics"

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Batzoglou, Serafim. "Computational genomics : mapping, comparison, and annotation of genomes." Thesis, Massachusetts Institute of Technology, 2000. http://hdl.handle.net/1721.1/8629.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2000.
Includes bibliographical references (leaves 180-191).
The field of genomics provides many challenges to computer scientists and mathematicians. The area of computational genomics has been expanding recently, and the timely application of computer science in this field is proving to be an essential component of the large international effort in genomics. In this thesis we address key issues in the different stages of genome research: planning of a genome sequencing project, obtaining and assembling sequence information, and ultimately study, cross-species comparison, and annotation of finished genomic sequence. We present applications of computational techniques to the above areas: (1) In relation to the early stages of a genome project, we address physical mapping, and we present results on the theoretical problem of finding minimum superstrings of hypergraphs, a combinatorial problem motivated by physical mapping. We also present a statistical and simulation study of "walking with clone-end sequences", an important method for sequencing a large genome.
(cont.) (2) Turning to the problem of obtaining the finished genomic sequence, we present ARACHNE, a prototype software system for assembling sequence data that are derived from sequencing a genome with the "shotgun" method. (3) Finally, we turn to the computational analysis of finished genomic sequence. We present GLASS, a software system for obtaining global pairwise alignments of orthologous finished sequences. We finally use GLASS to perform a comparative structure and sequence analysis of orthologous human and mouse genomic regions, and develop ROSETTA, the first cross-species comparison-based system for the prediction of protein coding regions in genomic sequences.
by Serafin Batzoglou.
Ph.D.
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Roidl, Andreas. "“Functional Genomics”." Diss., lmu, 2007. http://nbn-resolving.de/urn:nbn:de:bvb:19-67491.

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Tiwari, Jitesh. "Assembly and Automated Annotation of the Clostridium scatologenes Genome." TopSCHOLAR®, 2012. http://digitalcommons.wku.edu/theses/1175.

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Clostridium scatologenes is an anaerobic bacterium that demonstrates some unusual metabolic traits such as the production of 3-methyl indole. The availability of genome level sequencing has lent itself to the exploration and elucidation of unique metabolic pathways in other organisms such as Clostridium botulinum. The Clostridium scatologenes genome, with an estimated length 4.2 million bp, was sequenced by the Applied Biosystems Solid method and the Roche 454 pyrosequencing method. The resulting DNA sequences were combined and assembled into 8267 contigs with an average length of 1250 bp with the Newbler Assembler program. Comparision of published subunits of csd gene and assembled contigs identified that one contig contained all three subunits. In addition a gene with similarity to clostridium carboxidivorans butyrate kinase was found lined next to csd gene. An alignment of the contig and csdgene sequences identified three deletions in the contig within the 4066 bases of the alignment. This implies that there is about 0.07% error rate in the sequencing itself requiring more finishing. Even without finishing the genome assembly into single contig, contigs were annotated in RAST pipeline predicting 2521 protein encoding genes (PEGs). The PEGs were classified by their metabolic function and compared to classified PEGs found in the closely related clostridium species, Clostridium carboxidivorans and Clostridium. ljungdahlii, which have similarly sized genomes. According to the RAST analysis, Clostridium scatologenes had 35% subsystem coverage of all known metabolic processes with its 2521 PEGs. This compares to 41% for Clostridium carboxidivorans with 4174 PEGs (29) and 42% for Clostridium ljungdahlii with 4184 PEGs (30), indicating that Clostridium scatologenesmay still have more genes to be identified. Comparison of the percent genes found in the metabolic subsystems was similar except in motility and chemotaxis. The contigs, on which the csd gene and tryptophan metabolizing genes lay, were examined to see if additional genes might support these metabolic pathways. Butyrate kinase was associated with the csd genes but no other associations were found for the two tryptophan metabolizing genes. The tryptophan biosynthesis operon genes were all found on one contig (contig 6771) and were syntenic with other bacterial species.
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St, Jean Andrew Louis. "Haloarchaeal comparative genomics and the local context model of genomic evolution." Thesis, University of Ottawa (Canada), 1996. http://hdl.handle.net/10393/10308.

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Genomics is a rapidly expanding field of research that seeks to study the structure, function and evolution of an organism's genome. Genomic investigations were conducted on three species of haloarchaea, a monophyletic group of prokaryotes belonging to the kingdom Euryarchaeota of the domain Archaea that are adapted to high-salt environments. A physical and genetic map of the genome of Halobacterium salinarum GRB is described. This map and the previously published map of the genome of Haloferax volcanii DS2 were compared with the object of detecting any conservation in the order or spacing of homologous loci between the two genomes. A computer program--COMPAGEN--was developed to aid in the analysis of the data generated by this comparison. No map order conservation could be detected at the 15 kbp average resolution of this comparison between genomes estimated to have diverged 600 million years ago. A second comparison was performed between the chromosomes of Haloferax volcanii DS2 and Haloferax mediterranei ATCC 33500 (R-4). Extensive conservation was found between these two genomes which diverged approximately 80 million years ago showing only three rearrangements: two inversions and a transposition. Conclusions drawn from an analysis of the comparisons include: (1) that higher resolution is required to deal with distantly related genomes, likely making use of sequence data, and (2) that it is important to compare genomes that have diverged at different times if one wishes to investigate the dynamics of genomic evolution within a phylogenetic group. The local context model was developed in an effort to explain the pattern of conservation and divergence seen in these and other prokaryotic genome comparisons. This model states that since the expression of genes is affected by flanking genetic elements, genes will resist changing their position relative to one another so long as this change is likely to alter gene expression in a way deleterious to the cell. The local context model thus provides a force promoting the conservation of genomic map order. The implications of this model for the evolution of the haloarchaea is discussed and future directions of prokaryotic genomics in general is explored.
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Al-Nuaimi, Bashar. "Ancestral Reconstruction and Investigations of Genomics Recombination on Chloroplasts Genomes." Thesis, Bourgogne Franche-Comté, 2017. http://www.theses.fr/2017UBFCD042/document.

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La théorie de l’évolution repose sur la biologie moderne. Toutes les nouvelles espèces émergent d’une espèce existante. Il en résulte que différentes espèces partagent une ascendance commune, telle que représentée dans la classification phylogénétique. L’ascendance commune peut expliquer les similitudes entre tous les organismes vivants, tels que la chimie générale, la structure cellulaire, l’ADN comme matériau génétique et le code génétique. Les individus d’une espèce partagent les mêmes gènes mais (d’ordinaire) différentes séquences d’allèles de ces gènes. Un individu hérite des allèles de leur ascendance ou de leurs parents. Le but des études phylogénétiques est d’analyser les changements qui se produisent dans différents organismes pendant l’évolution en identifiant les relations entre les séquences génomiques et en déterminant les séquences ancestrales et leurs descendants. Une étude de phylogénie peut également estimer le temps de divergence entre les groupes d’organismes qui partagent un ancêtre commun. Les arbres phylogénétiques sont utiles dans les domaines de la biologie, comme la bio informatique, pour une phylogénétique systématique et comparative. L’arbre évolutif ou l’arbre phylogénétique est une exposition ramifiée les relations évolutives entre divers organismes biologiques ou autre existence en fonction des différences et des similitudes dans leurs caractéristiques génétiques. Les arbres phylogénétiques sont construits à partir de données moléculaires comme les séquences d’ADN et les séquences de protéines. Dans un arbre phylogénétique, les nœuds représentent des séquences génomiques et s’appellent des unités taxonomiques. Chaque branche relie deux nœuds adjacents. Chaque séquence similaire sera un voisin sur les branches extérieures, et une branche interne commune les reliera à un ancêtre commun. Les branches internes sont appelées unités taxonomiques hypothétiques. Ainsi, les unités taxonomiques réunies dans l’arbre impliquent d’être descendues d’un ancêtre commun. Notre recherche réalisée dans cette dissertation met l’accent sur l’amélioration des prototypes évolutifs appropriés et des algorithmes robustes pour résoudre les problèmes d’inférence phylogénétiques et ancestrales sur l’ordre des gènes et les données ADN dans l’évolution du génome complet, ainsi que leurs applications.[...]
The theory of evolution is based on modern biology. All new species emerge of an existing species. As a result, different species share common ancestry,as represented in the phylogenetic classification. Common ancestry may explainthe similarities between all living organisms, such as general chemistry, cell structure,DNA as genetic material and genetic code. Individuals of one species share the same genes but (usually) different allele sequences of these genes. An individual inheritsalleles of their ancestry or their parents. The goal of phylogenetic studies is to analyzethe changes that occur in different organisms during evolution by identifying therelationships between genomic sequences and determining the ancestral sequences and theirdescendants. A phylogeny study can also estimate the time of divergence betweengroups of organisms that share a common ancestor. Phylogenetic trees are usefulin the fields of biology, such as bioinformatics, for systematic phylogeneticsand comparative. The evolutionary tree or the phylogenetic tree is a branched exposure the relationsevolutionary between various biological organisms or other existence depending on the differences andsimilarities in their genetic characteristics. Phylogenetic trees are built infrom molecular data such as DNA sequences and protein sequences. Ina phylogenetic tree, the nodes represent genomic sequences and are calledtaxonomic units. Each branch connects two adjacent nodes. Each similar sequencewill be a neighbor on the outer branches, and a common internal branch will link them to acommon ancestor. Internal branches are called hypothetical taxonomic units. Thus,Taxonomic units gathered in the tree involve being descended from a common ancestor. Ourresearch conducted in this dissertation focuses on improving evolutionary prototypesappropriate and robust algorithms to solve phylogenetic inference problems andancestral information about the order of genes and DNA data in the evolution of the complete genome, as well astheir applications
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Gaiarsa, S. "EVOLUTION, COMPARATIVE GENOMICS AND GENOMIC EPIDEMIOLOGY OF BACTERIA OF PUBLIC HEALTH IMPORTANCE." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/525881.

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La presente tesi è incentrata sull'epidemiologia genomica delle infezioni batteriche ospedaliere. L'ambiente ospedaliero è peculiare, in quanto al suo interno si concentrano un elevato numero di agenti batterici, pazienti con un sistema immunitario debole e un uso massiccio di sostanze antimicrobiche. Questa combinazione favorisce lo sviluppo e la selezione di ceppi resistenti agli antibiotici e la diffusione di infezioni opportunistiche: in generale il prosperare dei patogeni nosocomiali. Alcune tecniche all'avanguardia per lo studio di questo tipo di infezioni sono basate sull’uso della genomica e di approcci evoluzionistici: esse permettono di conoscere le caratteristiche genomiche dei ceppi batterici e di ricostruire la loro storia evolutiva. Grazie alla possibilità di sequenziare il DNA ad un prezzo sempre più economico, i progetti di ricerca sono supportati da un numero sempre crescente di genomi e i dati genomici depositati nelle banche dati sono in crescita esponenziale: questo rende possibile eseguire una varietà sempre maggiore di analisi. Il primo lavoro qui riportato descrive l'evoluzione del Clonal Complex 258 (CC258) di Klebsiella pneumoniae. Le mutazioni puntiformi (single nucleotide polymorphism, SNP) hanno permesso di ricostruire la filogenesi globale di tutta la specie e di collocare il CC258 nel suo contesto evolutivo. Successivamente, è stato possibile rilevare la presenza di una ricombinazione di 1,3 Mb nei genomi del clade in analisi. Un’analisi del molecular clock ha poi consentito di datare sia questo che gli altri eventi di ricombinazione scoperti in lavori precedenti. Questi risultati sono stati usati per completare il quadro della storia evolutiva del CC258, caratterizzata da frequenti eventi di macro-ricombinazione. Un’evoluzione rapida e caratterizzata da scambi di elevate quantità di informazioni genomiche è una caratteristica comune ad altri patogeni nosocomiali che sviluppano fenotipi da "superbatteri". Sebbene frequente, il modello di evoluzione per macro-ricombinazioni non è comune a tutti i batteri responsabili di infezioni nosocomiali. Un’eccezione è il ceppo SMAL di Acinetobacter baumannii, presentato in un altro sottoprogetto di questa tesi. In questo lavoro sono stati analizzati i genomi del sequence type (ST) 78 di A. baumannii. La filogenesi e la genomica comparativa hanno rivelato la presenza di due differenti cladi all'interno del ST che presentano differenti "stili" evolutivi. Un gruppo (contenente i genomi SMAL) è caratterizzato da una minore variabilità del contenuto genico e dalla presenza di un numero più elevato di copie di insertion sequence (IS). Una IS interrompe il gene comEC/rec2 in tutti i genomi SMAL. Questo gene codifica per una proteina coinvolta nell’acquisizione del DNA esogeno, quindi la sua inattivazione limita lo scambio di geni. Questo suggerisce una spiegazione per la bassa plasticità genomica. In un altro lavoro presentato in questa tesi, l'epidemiologia genomica è stata applicata per ricostruire la diffusione di un focolaio epidemico di K. pneumoniae in un’unità di terapia intensiva ospedaliera. In un primo momento, è stato utilizzato un approccio filogenetico per separare gli isolati appartenenti all'epidemia da quelli sporadici. Poi le date di isolamento e gli SNP genomici hanno permesso di costruire una rete genomica che modellasse la propagazione delle infezioni nel reparto. La ricostruzione ha indicato una diffusione radiale del patogeno dal paziente zero a tutti gli altri infetti, rivelando così un errore sistematico nelle procedure di biosicurezza dell'ospedale. Questa applicazione quasi forense dell'epidemiologia genomica è stata utilizzata anche in altri due lavori qui presentati, entrambi riguardanti la ricostruzione di infezioni alimentari. In uno degli articoli, incentrato su Salmonella enterica, l’analisi filogenetica è stata eseguita solamente con gli SNP sinonimi al fine di filtrare le mutazioni patoadattative. Nell'altro lavoro sono stati utilizzati dati epidemiologici, tipizzazione molecolare e filogenesi basata sugli SNP per studiare l'infezione di nove isolati di Listeria monocytogenes, che si ritenevano essere parte dello stesso focolaio e alla fine sono risultati genomicamente non correlati. Infine, viene qui presentato anche un articolo di review riguardante l'epidemiologia genomica. L'articolo è focalizzato sulle ultime pubblicazioni ad alto impatto che analizzano l'evoluzione genomica degli agenti patogeni batterici e le dinamiche di propagazione delle epidemie in brevi periodi di tempo. L'articolo descrive, infine, le ultime ricostruzioni epidemiologiche a livello storico, che sono possibili grazie alle moderne tecnologie di isolamento e sequenza del DNA.
The present thesis is focused on genomic epidemiology of bacterial hospital infections. The hospital environment is unique, as it concentrates a high number of bacterial agents, frequent antibiotic use, and patients with weak immune systems. This combination favours the development and selection of antibiotic resistant strains and the spread of opportunistic infections: in general the thriving of nosocomial pathogens. Genomics and evolutionary approaches have emerged as the cutting edge tools for studying this kind of infections, allowing to study the genomic features of bacterial strains and their evolution. Thanks to the possibility to sequence DNA at a constantly cheaper price, research projects are supported by a growing number of genomes and a considerable amount of genomic data is available in the databases, expanding the amount of possible investigations that can be performed. The first work presented here describes the evolution of the Clonal Complex 258 (CC258) of Klebsiella pneumoniae. Single nucleotide polymorphisms (SNPs) allowed to reconstruct the global phylogeny of the entire species and to collocate the CC258 in its evolutionary context. Furthermore, it was possible to detect the presence of a 1.3 Mb recombination in the genomes of the clade in analysis. A molecular clock approach allowed to date this and other previously discovered recombination events. These findings were used to complete the picture of the evolutionary history of CC258, which is characterized by frequent macro-recombination events. A quick evolutive strategy characterized by exchange of high amount of information is a common feature to other nosocomial pathogens, which develop “superbug” phenotypes. Although common, the macro-recombination evolution model is not shared by all nosocomial infection bacteria. One exception is the SMAL strain of Acinetobacter baumannii, presented in another subproject of this thesis. In this work, the genomes of Sequence Type (ST) 78 of A. baumannii were analyzed. Phylogeny and comparative genomics revealed the presence of two different clades within the ST, presenting different evolutive “lifestyles”. One group (containing the SMAL genomes) was characterized by a lower gene content variability and by the presence of a higher copy number of insertion sequences (ISs). One IS interrupts the comEC/rec2 gene in all the SMAL genomes. This gene codes for a protein involved in the exogenous DNA importation, thus its inactivation limits the gene exchange, suggesting an explanation for the low genomic plasticity. In another work presented in this document, genomic epidemiology was applied to reconstruct the spreading routes of a K. pneumoniae epidemic event in an hospital intensive care unit. At first, a phylogenetic approach was used to separate the isolates that belonged to the outbreak from the sporadic ones. Then the isolation dates and genomic SNPs allowed to build a genomic network, which modelled the chain of infection events in the ward. The reconstruction suggested a star-like diffusion of the pathogen from patient zero to the other infected ones, thus revealing a systematic error in the biosafety procedures of the hospital. This almost-forensic application of genomic epidemiology was also used in two other works presented, both of them concerning the reconstruction of food-borne infections. In one of the works, focused on Salmonella enterica, only synonymous SNPs were used as input to a phylogenetic based investigation, in order to filter out pathoadaptative mutations. In the other article, epidemiological data, molecular typing and SNP-based phylogeny were used to investigate the infection of nine Listeria monocytogenes isolates, which were believed to be part of the same outbreak and in the end proved to be genomically unrelated. Lastly, a review paper on genomic epidemiology is also presented. The article is focused on the latest high impact publications analyzing the genome evolution of bacterial pathogens as well as the propagation dynamics of epidemic outbreaks in very short periods of time. The article also describes the latest historical epidemiological studies, which are possible thanks to modern DNA isolation and sequencing technologies.
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Kern, Andrew David. "Drosophila population genomics /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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Loman, Nicholas James. "Comparative bacterial genomics." Thesis, University of Birmingham, 2012. http://etheses.bham.ac.uk//id/eprint/2839/.

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For the most part, diagnostic clinical microbiology still relies on 19th century ideas and techniques, particularly microscopy and laboratory culture. In this thesis I investigate the utility of a new approach, whole-genome sequencing (WGS), to tackle current issues in infectious disease. I present four studies. The first demonstrates the utility of WGS in a hospital outbreak of Acinetobacter baumannii. The second study uses WGS to examine the evolution of drug resistance following antibiotic treatment. I then explore the use of WGS prospectively during an international outbreak of food-borne Escherichia coli infection, which caused over 50 deaths. The final study compares the performance of benchtop sequencers applied to the genome of this outbreak strain and touches on the issue of whether WGS is ready for routine use by clinical and public health laboratories. In conclusion, through this programme of work, I provide ample evidence that whole-genome sequencing of bacterial pathogens has great potential in clinical and public health microbiology. However, a number of technical and logistical challenges have yet to be addressed before such approaches can become routine.
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Lin, Ying. "Development and assessment of machine learning attributes for ortholog detection." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file 0.31 Mb., 65 p, 2006. http://wwwlib.umi.com/dissertations/fullcit/3220791.

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Meng, Da. "Bioinformatics tools for evaluating microbial relationships." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Spring2009/d_meng_042209.pdf.

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Thesis (Ph. D.)--Washington State University, May 2009.
Title from PDF title page (viewed on June 8, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references.
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Books on the topic "Genomics"

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D, Thangadurai, Tang W. 1964-, and Pullaiah T, eds. Genes, genomes, and genomics. New Delhi: Regency Publications, 2006.

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Primrose, Sandy B., and Richard M. Twyman, eds. Genomics. Malden, MA, USA: Blackwell Science Ltd, 2003. http://dx.doi.org/10.1002/9780470751282.

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Starkey, Mike, and Ramnath Elaswarapu, eds. Genomics. Chichester, UK: John Wiley & Sons, Ltd, 2010. http://dx.doi.org/10.1002/9780470711675.

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D, Protopapas Alex, ed. Genomics. Upper Saddle River, NJ: Prentice-Hall, 2005.

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Folta, Kevin M. Genetics and genomics of Rosaceae. New York, NY: Springer, 2009.

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

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Palacios, Rafael, and William E. Newton, eds. Genomes and Genomics of Nitrogen-fixing Organisms. Dordrecht: Springer Netherlands, 2005. http://dx.doi.org/10.1007/1-4020-3054-1.

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Gojōbori, Takashi. Genomu kara mita seibutsu no tayōsei to shinka. Tōkyō: Shupuringā Fearāku Tōkyō, 2003.

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

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Starkey, Michael P., and Ramnath Elaswarapu. Genomics Protocols. New Jersey: Humana Press, 2001. http://dx.doi.org/10.1385/159259235x.

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Book chapters on the topic "Genomics"

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García-Sancho, Miguel, and James Lowe. "Improving and Going Beyond Reference Genomes." In A History of Genomics across Species, Communities and Projects, 255–326. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-06130-1_7.

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AbstractIn this chapter, we show that many of the features of ‘post-genomics’ were present in pre-reference genome research, and the reference genomics of yeast and pig. Due to the problems we identify with the notion of ‘post-genomics’, we instead propose the term ‘post-reference genomics’, which encompasses all the forms of genomic-related research opened up by the existence of a reference sequence. To identify what is distinct about post-reference genomics, we detail the relationship between two modes of research: functional and systematic. We observe how the evolving relationship between these two modes of research differs across species, and attribute this to distinct relationships between scientific communities and the pre-reference genomics or reference genomics work they were involved in. We close by considering the role of reference genomes and other genomic resources in seeding ‘webs of reference’ that enable researchers and other practitioners to explore the possible variation exhibited by a given species.
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García-Sancho, Miguel, and James Lowe. "Conclusion." In A History of Genomics across Species, Communities and Projects, 327–53. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-06130-1_8.

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AbstractIn this concluding chapter, we explore the implications of our historical investigation for research and policies pertaining to genomic data. We outline the particular form of ‘epistemic iteration’ that operates in genomics and further develop the idea of ‘webs of reference’. Through this, we address one of the main consequences of our overarching argument: that problems in bridging ‘translational gaps’ are to a significant extent rooted in the specific model of the International Human Genome Sequencing Consortium. Conversely, the alternative models of genomics that we have explored in the book provide indications as to how to configure work in the life sciences to avoid such gaps between the results of genomics research and outcomes in medicine, agriculture or other spheres of activity. Our consideration of different communities of genomicists and their heterogeneous ways of interacting with their target genomes helps in uncovering the diversity of genomics and comprehending a variety of modes of translation.
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Oliveira, Antônio Costa, Luciano Carlos Maia, Daniel Rosa Farias, and Naciele Marini. "Genomics." In Omics in Plant Breeding, 13–31. Chichester, UK: John Wiley & Sons, Inc, 2014. http://dx.doi.org/10.1002/9781118820971.ch2.

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Paus, Tomáš. "Genomics." In Population Neuroscience, 43–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-36450-1_4.

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Scaglione, Davide, Alberto Acquadro, Ezio Portis, and Sergio Lanteri. "Genomics." In Compendium of Plant Genomes, 163–84. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-20012-1_9.

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Ramsden, Jeremy. "Genomics." In Computational Biology, 203–21. London: Springer London, 2015. http://dx.doi.org/10.1007/978-1-4471-6702-0_13.

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Priyadarshan, P. M. "Genomics." In PLANT BREEDING: Classical to Modern, 541–60. Singapore: Springer Singapore, 2019. http://dx.doi.org/10.1007/978-981-13-7095-3_24.

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Hardy, Billie-Jo, Sarah E. Ali Khan, and Abdallah S. Daar. "Genomics." In Encyclopedia of Global Bioethics, 1–14. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-05544-2_214-1.

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Hardy, Billie-Jo, Sarah E. Ali Khan, and Abdallah S. Daar. "Genomics." In Encyclopedia of Global Bioethics, 1–14. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-05544-2_214-2.

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Peck, Stewart B., Carol C. Mapes, Netta Dorchin, John B. Heppner, Eileen A. Buss, Gustavo Moya-Raygoza, Marjorie A. Hoy, et al. "Genomics." In Encyclopedia of Entomology, 1606. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_1069.

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Conference papers on the topic "Genomics"

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STANLEY, SCOTT, and BENJAMIN A. SALISBURY. "PHYLOGENETIC GENOMICS AND GENOMIC PHYLOGENETICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0047.

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Rubert, Diego P., Jens Stoye, and Fábio H. V. Martinez. "Distance and Similarity Measures in Comparative Genomics." In Concurso de Teses e Dissertações da SBC. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/ctd.2020.11361.

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Research in comparative genomics supports the investigation of important questions in molecular biology, genetics and biomedicine. A central question in this field is the elucidation of similarities and differences between genomes by means of different measures. This summary, submitted to CTD 2020, briefly describes the main contributions, originality and impact possibilities of the thesis entitled "Distance and Similarity Measures in Comparative Genomics", by Diego P. Rubert.
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HUANG, HENG, LI SHEN, PAUL M. THOMPSON, KUN HUANG, JUNZHOU HUANG, and LIN YANG. "IMAGING GENOMICS." In Pacific Symposium on Biocomputing 2018. WORLD SCIENTIFIC, 2017. http://dx.doi.org/10.1142/9789813235533_0028.

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SHEN, LI, and LEE A. D. COOPER. "IMAGING GENOMICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2016. http://dx.doi.org/10.1142/9789813207813_0006.

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Toch, Eran, Netta Rager, Tal Florentin, Dan Linenberg, Daya Sellman, and Noam Shomron. "Augmented-Genomics." In IUI'18: 23rd International Conference on Intelligent User Interfaces. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3180308.3180326.

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Stajano, Frank, Lucia Bianchi, Pietro Liò, and Douwe Korff. "Forensic genomics." In the 7th ACM workshop. New York, New York, USA: ACM Press, 2008. http://dx.doi.org/10.1145/1456403.1456407.

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Besserud, Keith, and Joshua Cotten. "Architectural Genomics." In ACADIA 2008: Silicon + Skin. ACADIA, 2008. http://dx.doi.org/10.52842/conf.acadia.2008.238.

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Abdullah, Tariq, and Ahmed Ahmet. "Genomics Analyser." In UCC '17: 10th International Conference on Utility and Cloud Computing. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3148055.3148072.

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Haussler, David. "Cancer genomics." In the 17th ACM SIGKDD international conference. New York, New York, USA: ACM Press, 2011. http://dx.doi.org/10.1145/2020408.2020414.

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Delderfield, Mark, Lee Kitching, Gareth Smith, David Hoyle, and Iain Buchan. "Shared Genomics: Accessible High Performance Computing for Genomic Medical Research." In 2008 IEEE Fourth International Conference on eScience (eScience). IEEE, 2008. http://dx.doi.org/10.1109/escience.2008.132.

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Reports on the topic "Genomics"

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Best, Stephanie, Clara Gaff, Natalie Taylor, and Helen Brown. Frameworks to support the implementation of genomics into clinical care. The Sax Institute, November 2019. http://dx.doi.org/10.57022/daqw3432.

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Establishing genomics within clinical practice poses many challenges. NSW Ministry of Health commissioned this review to identify frameworks that have been used to support the translation of genomic research into clinical practice. Although the literature on the use and evaluation of frameworks that have actively translated genomics from laboratory to clinical settings is limited the authors were able to draw out key themes and recommendations for NSW and possible future directions, including: a crucial need for formal evaluation of the implementation of genomic medicine in real-world settings, the need for collaboration across disciplines, and the importance of supporting non-geneticist specialist medical professionals to integrate genomics into their practice.
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Simison, W. Brian, and Jeffrey L. Boore. Molluscan Evolutionary Genomics. Office of Scientific and Technical Information (OSTI), December 2005. http://dx.doi.org/10.2172/982432.

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Bentley, Jennifer A., Megan Kregel, and Kyra Bellrichard. Midwest Dairy Day Focuses on Genomics 101: Putting Genomics to Work. Ames (Iowa): Iowa State University, January 2016. http://dx.doi.org/10.31274/ans_air-180814-220.

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Terwilliger, Thomas C. Achievements of structural genomics. Office of Scientific and Technical Information (OSTI), October 2013. http://dx.doi.org/10.2172/1095844.

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Carlson, Jake. Human Genomics - Purdue University. Purdue University Libraries, October 2009. http://dx.doi.org/10.5703/1288284315006.

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Carlson, Jake. Plant Genomics - Purdue University. Purdue University Libraries, October 2009. http://dx.doi.org/10.5703/1288284315011.

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Grigoriev, Igor V. JGI Fungal Genomics Program. Office of Scientific and Technical Information (OSTI), March 2011. http://dx.doi.org/10.2172/1012482.

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Wiwanitkit, Viroj, and Viroj Wiwanitkit. PHYSIOLOGICAL GENOMICS IN MANIA. Buenos Aires: siicsalud.com, September 2017. http://dx.doi.org/10.21840/siic/148771.

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Lennie, Peter. Facilities and Equipment for Genomics/Comparative Functional Genomics at New York University. Office of Scientific and Technical Information (OSTI), June 2006. http://dx.doi.org/10.2172/898062.

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Starkenburg, Shawn. Genomics for Biosecurity and Bioenergy. Office of Scientific and Technical Information (OSTI), August 2020. http://dx.doi.org/10.2172/1657114.

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