Relevant bibliographies by topics / Comparative genomics

Academic literature on the topic 'Comparative genomics'

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Published: 4 June 2021
Last updated: 30 July 2024

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Journal articles on the topic "Comparative genomics"

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Furlong, Rebecca F., and Ziheng Yang. "Comparative genomics: Comparative genomics coming of age." Heredity 91, no. 6 (October 22, 2003): 533–34. http://dx.doi.org/10.1038/sj.hdy.6800372.

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HURST, L. D. "Comparative Genomics." Journal of Medical Genetics 38, no. 11 (November 1, 2001): 807. http://dx.doi.org/10.1136/jmg.38.11.807.

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Hardison, Ross C. "Comparative Genomics." PLoS Biology 1, no. 2 (November 17, 2003): e58. http://dx.doi.org/10.1371/journal.pbio.0000058.

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Hochachka✠, P., T. P. Mommsen, and P. Walsh. "Comparative Genomics." Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 133, no. 4 (December 2002): 461–62. http://dx.doi.org/10.1016/s1096-4959(02)00170-7.

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Elgar, G. "Comparative Genomics." Briefings in Bioinformatics 2, no. 2 (January 1, 2001): 200–202. http://dx.doi.org/10.1093/bib/2.2.200.

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Miller, Webb, Kateryna D. Makova, Anton Nekrutenko, and Ross C. Hardison. "COMPARATIVE GENOMICS." Annual Review of Genomics and Human Genetics 5, no. 1 (September 22, 2004): 15–56. http://dx.doi.org/10.1146/annurev.genom.5.061903.180057.

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Bachhawat, Anand K. "Comparative genomics." Resonance 11, no. 8 (August 2006): 22–40. http://dx.doi.org/10.1007/bf02855776.

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Copeland, N. G. "GENOMICS: Enhanced: Mmu 16--Comparative Genomic Highlights." Science 296, no. 5573 (May 31, 2002): 1617–18. http://dx.doi.org/10.1126/science.1073127.

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Pain, Arnab, Lisa Crossman, and Julian Parkhill. "Comparative Apicomplexan genomics." Nature Reviews Microbiology 3, no. 6 (May 10, 2005): 454–55. http://dx.doi.org/10.1038/nrmicro1174.

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Holding, Cathy. "Caenorhabditis comparative genomics." Genome Biology 4 (2003): spotlight—20031118–08. http://dx.doi.org/10.1186/gb-spotlight-20031118-02.

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Dissertations / Theses on the topic "Comparative genomics"

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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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Axelsson, Erik. "Comparative Genomics in Birds." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7432.

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Eriksen, Niklas. "Combinatorial methods in comparative genomics." Doctoral thesis, KTH, Mathematics, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3508.

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Manee, Manee. "Comparative genomics of noncoding DNA." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/comparative-genomics-of-noncoding-dna(d16aa46c-b8a2-4e6c-b825-d4246d3775fa).html.

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High levels of primary sequence conservation are observed in many noncoding regions of eukaryotic genomes. These conserved noncoding elements (CNEs) have shown to be robust indicators of functionally constrained elements. Nevertheless, the function of only a small fraction of such CNEs is known and their role in genome biology remains largely a mystery. Comparative genomics analysis in model organisms can shed light on CNE function and evolution of noncoding DNA in general. Recently, it has been reported that short CNEs in the Drosophila genome are typically very AT-rich but have unusually high levels of GC content in a much larger (~500 bp) window around them. To understand whether these "side effects" are dependent on their CNE definition or are a more general feature of the Drosophila genome, we analysed base composition of CNEs from two different CNE detection methods. We found side effects are real, but are restricted to a subset of CNEs in the genome. An alternative hypothesis to explain the existence of CNEs is the mutational cold spot hypothesis. Previous work using SNPs was shown evidence that CNEs are not mutational cold spots. Here, non-reference transposable elements (TEs) were used to test cold spot hypothesis. A significant reduction in levels of non-reference TEs was found in intronic and intergenic CNEs compared to the expected number of insertions. TEs in intergenic CNEs were also found at lower allele frequencies than TEs in intergenic spacers. Furthermore, we used simulation to explore the effects of insertion/deletion (indel) evolution on noncoding DNA sequences with and without constrained noncoding elements. We assessed several indel-capable simulators to test expected outcomes with no selectively constrained elements. Simulations with constrained elements show that sequences grow in length even when the deletion rate is exactly the same as the insertion rate. This result can be interpreted as being due to purifying selection on CNEs acting to remove an excess of deletion over insertions. Together, the results presented here provide insights into the evolution of noncoding DNA in one of the most important model organisms.
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Mikkelsen, Tarjei Sigurd 1978. "Mammalian comparative genomics and epigenomics." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/52808.

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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references.
The human genome sequence can be thought of as an instruction manual for our species, written and rewritten over more than a billion of years of evolution. Taking a complete inventory of our genome, dissecting its genes and their functional components, and elucidating how these genes are selectively used to establish and maintain cell types with markedly different behaviors, are key challenges of modern biology. In this thesis we present contributions to our understanding of the structure, function and evolution of the human genome. We rely on two complementary approaches. First, we study signatures of evolutionary processes that have acted on the genome using comparative sequence analysis. We generate high quality draft genome sequences of the chimpanzee, the dog and the opossum. These species share a last common ancestor with humans approximately 6 million, 80 million and 140 million years ago, respectively, and therefore provide distinct perspectives on our evolutionary history. We apply computational methods to explore the functional organization of the genome and to identify genes that contribute to shared and species-specific traits. Second, we study how the genome is bound by proteins and packaged into chromatin in distinct cell types. We develop new methods to map protein-DNA interactions and DNA methylation using single-molecule based sequencing technology. We apply these methods to identify new functional sequence elements based on characteristic chromatin signatures, and to explore the relationship between DNA sequence, chromatin and cellular state.
by Tarjei Sigurd Mikkelsen.
Ph.D.
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Ryder, Carol D. "Comparative genomics of Brassica oleracea." Thesis, University of Warwick, 2012. http://wrap.warwick.ac.uk/51651/.

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The scientific case made by the AUTHOR’S comparative Brassica oleracea genomics work is presented through 5 peer reviewed research papers. In order to achieve a comprehensive understanding of the evolution of B. oleracea the identification of unique genome characteristics, established using comparative genomics, is required. The genome characteristics established within these papers deliver significant contributions to original knowledge. These include a detailed illustration of how macro scale synteny varies markedly between the B. oleracea and A. thaliana genomes; unambiguous integration of the B. oleracea cytogenetic and genetic linkage maps; a cross species characterisation of a large collinear inverted segmental duplication on a single B. oleracea chromosome establishing that the relative physical distances have stayed approximately the same; retrotransposon copy number estimations and characterisation of their genomic organisation and isolation, characterisation and cross species analysis of a C genome specific repeat. For each paper the AUTHOR’S individual scientific contribution to each aspect of the work is described in detail. Both individually and as a body of work these publications substantially advance the fields of comparative, Brassica and genomic research.
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Dong, Xin. "Comparative genomics of rickettsia species." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM5054/document.

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Le genre Rickettsia, sont des petites bactéries Gram-négatives et symbiotes intracellulaires obligatoires des eucaryotes. Les Rickettsia sont surtout connus pour leur pathogénicité et pour provoquer des maladies graves chez l'homme et les autres animaux. À ce jour, 26 espèces valides de Rickettsies ont été identifiées dans le monde entier, dont 20 sont des agents pathogènes éprouvées. Toutes les espèces de Rickettsies validées sont associées à des arthropodes. Les phylogénies basées sur divers marqueurs moléculaires ont présenté des topologies discordantes, avec seulement R. bellii et R. canadensis qui ne sont classées ni parmi la fièvre boutonneuse groupe rickettsies, ni parmi le typhus groupe rickettsies. En utilisant les méthodes avancées de séquençage de génomes entiers, nous avons obtenu et analysé quatre séquences génomiques de Rickettsies : R. helvetica, R. honei, R. australis et R. japonica. Via la phylogénomique qui constitue une nouvelle stratégie permettant de mieux comprendre leur évolution, l'on remarque que ces micro-organismes ont subi une évolution génomique réduite au cours de spécialisation en intracellulaire. Plusieurs caractéristiques évolutives, comme le réarrangement des gènes, la réduction génomique, le transfert horizontal de gènes et l'acquisition d'ADN égoïste, ont formé les génomes Rickettsia d'aujourd'hui. Ces processus peuvent jouer un rôle important pour équilibrer la taille du génome afin de l'adapter au mode de vie intracellulaire. En outre, la pathogénicité des rickettsies peut être associée à la réduction génomique
The Rickettsia genus is composed of small, Gram-negative, bacteria that are obligate intracellular eukaryotic symbionts. Members of the genus Rickettsia are best known for infecting and causing severe diseases in humans and other animals. To date, 26 valid Rickettsia species have been identified worldwide, including 20 that are proven pathogens. All validated Rickettsia species are associated to arthropods that act as vectors and/or reservoirs. The phylogenies based on various molecular markers have resulted in discrepant topologies, with R. bellii and R. canadensis being classified neither among spotted fever nor typhus group rickettsiae. In this thesis, using the advanced whole genomic sequencing methods, we have and analyzed the genomic sequences from four Rickettsia species, including R. helvetica, R. honei, R. australis and R. japonica. Phylogenomics constitute a new strategy to better understand their evolution. These microorganisms underwent a reductive genomic evolution during their specialization to their intracellular lifestyle. Several evolutive characteristics, such as gene rearrangement, reduction, horizontal gene transfer and aquisition of selfish DNA, have shaped Rickettsia genomes. These processes may play an important role in free-living bacteria for balancing the size of genome in order to adapt the intracellular life style. In addition, in contrast with the concept of bacteria becoming pathogens by acquisition of virulence factors, rickettsial pathogenecity may be linked to genomic reduction of metabolism and regulation pathways
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Sentausa, Erwin. "Intraspecies comparative genomics of Rickettsia." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM5082/document.

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Le genre Rickettsia est composé de bactéries Gram-négatives, intracellulaires obligatoires qui causent un éventail de maladies humaines à travers le monde. Des nouvelles techniques ont permis de progresser dans l'identification et la classification des Rickettsia, y compris l'introduction de méthodes moléculaires comme la comparaison de séquences de gènes (ARNr 16S, ompA, ompB, gltA, sca4 …) et la création du statut de sous-espèce. La génomique et les techniques de séquençage de nouvelle génération ont permis d’accéder à une nouvelle façon d’en apprendre davantage sur la pathogenèse et l'évolution de Rickettsia. La première partie de cette thèse est une revue sur les avantages et les limites de la génomique en taxonomie des procaryotes, tandis que la seconde partie est constituée des analyses génomiques de cinq sous-espèces de Rickettsia et une nouvelle espèce de Rickettsia. En utilisant des méthodes de séquençage à haut débit, nous avons obtenu les génomes de R. sibirica sibirica, R. sibirica mongolitimonae, R. conorii indica, R. conorii caspia, R. conorii israelensis et R. gravesii. Ce travail constitue la base d’autres études qui permettront de mieux comprendre les mécanismes physiopathologiques, l’évolution, et la taxonomie des rickettsies
The Rickettsia genus is composed of Gram-negative, obligate intracellular bacteria that cause a range of human diseases around the world. New techniques have led to progress in the identification and classification of Rickettsia, including the introduction of molecular methods like sequence comparison (16S rRNA, ompA, ompB, gltA, sca4 …) and the creation of the subspecies status. Genomics and next-generation sequencing have opened a new way to learn more about the pathogenesis and evolution of Rickettsia. The first part of this thesis is a review on the advantages and limitations of genomics in prokaryotic taxonomy, while the second part consists of the genomic analyses of five Rickettsia subspecies and a new Rickettsia species. Using high-throughput sequencing methods, we obtained the draft genomes of R. sibirica sibirica, R. sibirica mongolitimonae, R. conorii indica, R. conorii caspia, R. conorii israelensis, and R. gravesii. This work can be a basis of further studies to increase the understanding on the disease-causing mechanisms, evolutionary relationships, and taxonomy of rickettsiae
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Benevides, Leandro. "Comparative Genomics of Faecalibacterium spp." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS129.

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Dans le côlon humain, le genre Faecalibacterium est le membre principal du groupe Clostridium leptum et comprend le deuxième genre représentatif le plus commun dans les échantillons fécaux, après Clostridium coccoides. Il a été reconnu comme une bactérie importante favorisant la santé intestinale et est aujourd'hui considéré comme un probiotique de prochaine génération. Jusqu'à récemment, on croyait qu'il n'y avait qu'une seule espèce dans ce genre, mais depuis 2012, certaines études ont commencé à suggérer l'existence de deux phylogroupes dans le genre. Cette nouvelle proposition de reclassification dans ce genre augmente l'importance de nouvelles études, toutes souches confondues, pour mieux comprendre la diversité, les interactions avec l'hôte et les aspects sécuritaires dans son utilisation comme probiotique. Brièvement, dans ce travail, nous introduisons les analyses de génomique comparative au genre Faecalibacterium en effectuant une étude phylogénétique profonde et en évaluant les aspects de sécurité pour son utilisation comme probiotique. Les analyses phylogénétiques comprenaient non seulement l'utilisation classique du gène de l'ARNr 16S, mais aussi l'utilisation de 17 génomes et techniques complets comme le typage de séquence multi-locus (wgMLST), l'identité nucléotidique moyenne (ANI), le synténie génique et le pangénome. C'est aussi le premier travail à combiner une analyse du développement du pangénome avec l'analyse ANI afin de corroborer l'attribution de souches à de nouvelles espèces. Les analyses phylogénétiques ont confirmé l'existence de plus d'une espèce dans le genre Faecalibacterium. De plus, l'évaluation de la sécurité impliquait (1) la prédiction des régions acquises horizontalement (îlots de résistance aux antibiotiques, îlots métaboliques et régions phagiques), (2) la prédiction des voies métaboliques, (3) la recherche de gènes liés à la résistance aux antibiotiques et des bactériocines. Ces analyses ont identifié des îlots génomiques dans tous les génomes, mais aucun d'entre eux n'est exclusif à une souche ou à une génospécie. En outre, ont été identifiés 8 gènes liés aux mécanismes de résistance aux antibiotiques répartis entre les génomes. 126 voies métaboliques ont été prédites et parmi certaines ont été mises en évidence: la dégradation du bisphénol A, le métabolisme du butanoate et la biosynthèse de la streptomycine. En outre, nous avons étudié le contexte génomique d'une protéine (molécule anti-inflammatoire microbienne - MAM) décrite pour la première fois par notre groupe. Cette recherche montre que la MAM apparaît proche des gènes liés au processus de sporulation et, dans certaines souches, proche d'un transporteur ABC
Within the human colon, the genus Faecalibacterium is the main member of the Clostridium leptum cluster and comprises the second-most common representative genus in fecal samples, after Clostridium coccoides. It has been recognized as an important bacterium promoting the intestinal health and today is considered as a potential next generation probiotic. Until recently, it was believed that there was only one species in this genus, but since 2012, some studies have begun to suggest the existence of two phylogroups into the genus. This new proposition of reclassification into this genus increases the importance of new studies, with all strains, to better understand the diversity, the interactions with the host and the safety aspects in its use as probiotic. Briefly, in this work we introduce the comparative genomics analyzes to the genus Faecalibacterium performing a deep phylogenetic study and evaluating the safety aspects for its use as a probiotic. The phylogenetic analyzes included not only the classical use of 16S rRNA gene, but also the utilization of 17 complete genomes and techniques like whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome. Also, this is the first work to combine an analysis of pangenome development with ANI analysis in order to corroborate the assignment of strains to new species. The phylogenetic analyzes confirmed the existence of more than one species into the genus Faecalibacterium. Moreover, the safety assessment involved the (1) prediction of horizontally acquired regions (Antibiotic resistance islands, Metabolic islands and phage regions), (2) prediction of metabolic pathways, (3) search of genes related to antibiotic resistance and (4) search of bacteriocins. These analyzes identified genomic islands in all genomes, but none of than are exclusive to one strain or genospecies. Also, were identified 8 genes related to antibiotic resistance mechanisms distributed among the genomes. 126 metabolic pathways were predicted and among than some were highlighted: Bisphenol A degradation, Butanoate metabolism and Streptomycin biosynthesis. In addition, we studied the genomic context of one protein (Microbial Anti-inflammatory Molecule - MAM) first described by our group. This investigation shows that MAM appears close to genes related to sporulation process and, in some strains, close to an ABC-transporter
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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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Books on the topic "Comparative genomics"

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

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Nicholas, Bergman H. Comparative Genomics. New Jersey: Humana Press, 2007. http://dx.doi.org/10.1385/1597455148.

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Nicholas, Bergman H. Comparative Genomics. New Jersey: Humana Press, 2007. http://dx.doi.org/10.1385/1597455156.

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Jin, Lingling, and Dannie Durand, eds. Comparative Genomics. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-06220-9.

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Blanchette, Mathieu, and Aïda Ouangraoua, eds. Comparative Genomics. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-00834-5.

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Tesler, Glenn, and Dannie Durand, eds. Comparative Genomics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2007. http://dx.doi.org/10.1007/978-3-540-74960-8.

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Tannier, Eric, ed. Comparative Genomics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16181-0.

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Bergman, Nicholas H., ed. Comparative Genomics. Totowa, NJ: Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-514-5.

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Bergman, Nicholas H., ed. Comparative Genomics. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-515-2.

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Nelson, Craig E., and Stéphane Vialette, eds. Comparative Genomics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-87989-3.

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Book chapters on the topic "Comparative genomics"

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Eloe-Fadrosh, Emiley A., Christopher J. Mungall, Mark Andrew Miller, Montana Smith, Sujay Sanjeev Patil, Julia M. Kelliher, Leah Y. D. Johnson, et al. "A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics." In Comparative Genomics, 587–609. New York, NY: Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3838-5_20.

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AbstractComparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimum Information about any (x) Sequence (MIxS) reporting standard for genomic data. To facilitate the use of the GSC’s MIxS reporting standard, we provide a description of the structure and terminology, how to navigate ontologies for required terms in MIxS, and demonstrate practical usage through a soil metagenome example.
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Hardison, Ross C. "Comparative Genomics." In Vogel and Motulsky's Human Genetics, 557–87. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-37654-5_21.

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Ozen, Asli Ismihan, Tammi Vesth, and David W. Ussery. "Comparative Genomics." In The Prokaryotes, 209–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-30194-0_11.

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Sankoff, David, and Joseph H. Nadeau. "Comparative Genomics." In Comparative Genomics, 3–7. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4309-7_1.

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Cheng, Jan-Fang, James R. Priest, and Len A. Pennacchio. "Comparative Genomics." In Methods in Molecular Biology, 229–51. Totowa, NJ: Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-030-0_13.

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Xia, Xuhua. "Comparative Genomics." In Handbook of Statistical Bioinformatics, 567–600. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-16345-6_26.

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Dicks, J., and G. Savva. "Comparative Genomics." In Handbook of Statistical Genetics, 160–99. Chichester, UK: John Wiley & Sons, Ltd, 2008. http://dx.doi.org/10.1002/9780470061619.ch5.

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Neale, David B., and Nicholas C. Wheeler. "Comparative Genomics." In The Conifers: Genomes, Variation and Evolution, 463–76. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-46807-5_17.

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Avison, Matthew B. "Comparative Genomics." In Genomics, Proteomics, and Clinical Bacteriology, 47–69. Totowa, NJ: Humana Press, 2004. http://dx.doi.org/10.1385/1-59259-763-7:047.

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Backofen, Rolf, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler. "Comparative RNA Genomics." In Comparative Genomics, 363–400. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7463-4_14.

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Conference papers on the topic "Comparative genomics"

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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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Narasimhan, Giri. "Invited: Comparative microbial genomics." In 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS). IEEE, 2011. http://dx.doi.org/10.1109/iccabs.2011.5729947.

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Ideker, Trey. "PROTEIN NETWORK COMPARATIVE GENOMICS." In Proceedings of the Conference CSB 2006. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2006. http://dx.doi.org/10.1142/9781860947575_0004.

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DUBCHAK, INNA, LIOR PACHTER, and LIPING WEI. "GENOME-WIDE ANALYSIS AND COMPARATIVE GENOMICS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799623_0011.

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PEREGRÍN-ALVAREZ, JOSÉ M., and CHRISTOS A. OUZOUNIS. "THE COMPARATIVE GENOMICS OF PROTEIN INTERACTIONS." In Proceedings of the 18th International Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2007. http://dx.doi.org/10.1142/9781860949852_0012.

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Smith, Jack A., Melissa Romanus, Pradeep Kumar Mantha, Yaakoub El Khamra, Thomas C. Bishop, and Shantenu Jha. "Scalable online comparative genomics of mononucleosomes." In XSEDE '13: Extreme Science and Engineering Discovery Environment: Gateway to Discovery. New York, NY, USA: ACM, 2013. http://dx.doi.org/10.1145/2484762.2484819.

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"Comparative characteristics of barley hybrids by the anthocyanins content in grain." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-114.

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Goni Urriza, Marisol, Bahia Khalfaoui-Hassani, Mathilde Monperrus, and Remy Guyoneaud. "Comparative Genomics on Mercury Methylators (Pseudo)Desulfovibrio Strains." In Goldschmidt2020. Geochemical Society, 2020. http://dx.doi.org/10.46427/gold2020.857.

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Pai, Tun-Wen, Meng-Chang Hsiao, Chien-Ming Chen, Wen-Shyong Tzou, and Ron-Shan Chen. "An SSR Comparative Genomics Database and Its Applications." In 2008 International Conference on Complex, Intelligent and Software Intensive Systems. IEEE, 2008. http://dx.doi.org/10.1109/cisis.2008.148.

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Galvão, Gustavo Rodrigues, and Zanoni Dias. "Algorithms for Sorting by Reversals or Transpositions, with Application to Genome Rearrangement." In XXIX Concurso de Teses e Dissertações da SBC. Sociedade Brasileira de Computação - SBC, 2020. http://dx.doi.org/10.5753/ctd.2016.9145.

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The problem of finding the minimum sequence of rearrangements that transforms one genome into another is a well-studied problem that finds application in comparative genomics. Representing genomes as permutations, in which genes appear as elements, that problem can be reduced to the combinatorial problem of sorting a permutation using a minimum number of rearrangements. Such combinatorial problem varies according to the types of rearrangements considered. The PhD thesis summarized in this paper presents exact, approximation, and heuristic algorithms for solving variants of the permutation sorting problem involving two types of rearrangements: reversals and transpositions.
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Reports on the topic "Comparative genomics"

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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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Ge, Hong, Yao-Yu E. Chang, Shuping Zhao, Min Tong, Mong-Hsun Tsai, Joseph J. Temenak, Allen L. Richards, and Wei-Mei Ching. Comparative Genomics of Ricketttsia prowazekii Madrid E and Breinl Strains. Fort Belvoir, VA: Defense Technical Information Center, January 2004. http://dx.doi.org/10.21236/ada455008.

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Voss, Stephen R. Application of Comparative Functional Genomics to Identify Regeneration-Specific Genes. Fort Belvoir, VA: Defense Technical Information Center, August 2014. http://dx.doi.org/10.21236/ada613190.

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Lewinsohn, Efraim, Peter Facchini, and Frederic Marsolais. Comparative Functional Genomics as a Platform to Investigate Ephedrine Alkaloid Biosynthesis in Plants. United States Department of Agriculture, January 2009. http://dx.doi.org/10.32747/2009.7613886.bard.

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Borodovsky, M. New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes. Office of Scientific and Technical Information (OSTI), April 2013. http://dx.doi.org/10.2172/1073499.

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Qiu, D., Q. Tu, Zhili He, and Jizhong Zhou. Comparative Genomics Analysis and Phenotypic Characterization of Shewanella putrefaciens W3-18-1: Anaerobic Respiration, Bacterial Microcompartments, and Lateral Flagella. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/986497.

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Dubcovsky, Jorge, Tzion Fahima, Tamar Krugman, and Tyson Howell. Positional cloning of a rye QTL responsible for water stress resistance in wheat based on radiation mapping and comparative genomics. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604265.bard.

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Katzir, Nurit, James Giovannoni, and Joseph Burger. Genomic approach to the improvement of fruit quality in melon (Cucumis melo) and related cucurbit crops. United States Department of Agriculture, June 2006. http://dx.doi.org/10.32747/2006.7587224.bard.

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Fruit quality is determined by numerous genetic traits that affect taste, aroma, texture, pigmentation, nutritional value and duration of shelf-life. The molecular basis of many of these important traits is poorly understood and it’s understanding offers an excellent opportunity for adding value to agricultural products. Improvement of melon fruit quality was the primary goal of the project. The original objectives of the project were: The isolation of a minimum of 1000 fruit specific ESTs. The development of a microarray of melon fruit ESTs. The analysis of gene expression in melon using melon and tomato fruit enriched microarrays. A comprehensive study of fruit gene expression of the major cucurbit crops. In our current project we have focused on the development of genomics tools for the enhancement of melon research with an emphasis on fruit, specifically the first public melon EST collection. We have also developed a database to relay this information to the research community and developed a publicly available microarray. The release of this information was one of the catalysts for the establishment of the International Cucurbit Genomic Initiative (ICuGI, Barcelona, Spain, July 2005) aimed at collecting and generating up to 100,000 melon EST sequences in 2006, leveraging a significant expansion of melon genomic resources. A total of 1000 ESTs were promised under the original proposal (Objective 1). Non-subtracted mature fruit and young fruit flesh of a climacteric variety in addition to a non-climacteric variety resulted in the majority of additional EST sequences for a total of 4800 attempted reads. 3731 high quality sequences from independent ESTs were assembled, representing 2,467 melon unigenes (1,873 singletons, 594 contigs). In comparison, as of June 2004, a total of 170 melon mRNA sequences had been deposited in GENBANK. The current project has thus resulted in nearly five- fold the number of ESTs promised and ca. 15-fold increase in the depth of publicly available melon gene sequences. All of these sequences have been deposited in GENBANK and are also available and searchable via multiple approaches in the public database (http://melon.bti.cornell.edu). Our database was selected as the central location for presentation of public melon EST data of the International Cucurbit Genomic Initiative. With the available unigenes we recently constructed a microarray, which was successfully applied in hybridizations (planned public release by August 2006). Current gene expression analyses focus on fruit development and on comparative studies between climacteric and non-climacteric melons. Earlier, expression profiling was conducted using macroarrays developed at the preliminary stage of the project. This analysis replaced the study of tomato microarray following the recommendations of the reviewers and the panel of the original project. Comparative study between melon and other cucurbit crops have begun, mainly with watermelon, in collaboration with Dr. Amnon Levi (USDA-ARS). In conclusion, all four objectives have been addressed and achieved. In the continuation project that have been approved we plan to apply the genomic tools developed here to achieve detailed functional analyses of genes associated with major metabolic pathway.
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Clark, Steven M. Comparative Genomic Hybridization Onto Dense Arrays of DNA Clones: Development and Application to Breast Cancer Genomes. Fort Belvoir, VA: Defense Technical Information Center, September 1998. http://dx.doi.org/10.21236/ada357608.

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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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