Relevant bibliographies by topics / Genome structure

Academic literature on the topic 'Genome structure'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2023

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Journal articles on the topic "Genome structure"

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Khaitovich, A. B. "CORONAVIRUS (GENOME STRUCTURE, REPLICATION)." Crimea Journal of Experimental and Clinical Medicine 10, no. 4 (2021): 78–95. http://dx.doi.org/10.37279/2224-6444-2020-10-4-78-95.

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The overview presented in the article is a continuation of the publication on coronaviruses. The paper examines modern data on the structure of the genome and the replication process in various types of coronaviruses that cause diseases in humans and are of medical importance. The structure of the genomes of coronaviruses and the functions of genes that encode the structure of viral particles are presented; describes the function of structural genes and auxiliary genes; the role of genes encoding non-structural proteins in the structure of the viral particle and replication of coronaviruses is shown. The analysis of published studies made it possible to comparatively characterize the genomes of highly dangerous coronaviruses: SARS-CoV, MERS-CoV, SARS-CoV-2, describe their differences in structure and in the process of replication. The review analyzes the structure of the genome and the replication process of coronaviruses at the molecular level, taking into account the characteristics of different types of coronaviruses. To analyze the genetic structures and replication of coronaviruses, modern literary sources, articles in the world’s leading medical and biological journals were used.
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Mauger, David M., Michael Golden, Daisuke Yamane, Sara Williford, Stanley M. Lemon, Darren P. Martin, and Kevin M. Weeks. "Functionally conserved architecture of hepatitis C virus RNA genomes." Proceedings of the National Academy of Sciences 112, no. 12 (March 9, 2015): 3692–97. http://dx.doi.org/10.1073/pnas.1416266112.

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Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of liver disease and cancer. The virus has a 9,650-nt, single-stranded, messenger-sense RNA genome that is infectious as an independent entity. The RNA genome has evolved in response to complex selection pressures, including the need to maintain structures that facilitate replication and to avoid clearance by cell-intrinsic immune processes. Here we used high-throughput, single-nucleotide resolution information to generate and functionally test data-driven structural models for three diverse HCV RNA genomes. We identified, de novo, multiple regions of conserved RNA structure, including all previously characterized cis-acting regulatory elements and also multiple novel structures required for optimal viral fitness. Well-defined RNA structures in the central regions of HCV genomes appear to facilitate persistent infection by masking the genome from RNase L and double-stranded RNA-induced innate immune sensors. This work shows how structure-first comparative analysis of entire genomes of a pathogenic RNA virus enables comprehensive and concise identification of regulatory elements and emphasizes the extensive interrelationships among RNA genome structure, viral biology, and innate immune responses.
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Fujishiro, Shin, Naoko Tokuda, and Masaki Sasai. "2P267 Computational chromosome conformation sampling of human diploid genome(21B. Genome biology:Genome structure,Poster)." Seibutsu Butsuri 54, supplement1-2 (2014): S239. http://dx.doi.org/10.2142/biophys.54.s239_3.

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Bernaola-Galván, Pedro, Pedro Carpena, Cristina Gómez-Martín, and Jose L. Oliver. "Compositional Structure of the Genome: A Review." Biology 12, no. 6 (June 13, 2023): 849. http://dx.doi.org/10.3390/biology12060849.

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As the genome carries the historical information of a species’ biotic and environmental interactions, analyzing changes in genome structure over time by using powerful statistical physics methods (such as entropic segmentation algorithms, fluctuation analysis in DNA walks, or measures of compositional complexity) provides valuable insights into genome evolution. Nucleotide frequencies tend to vary along the DNA chain, resulting in a hierarchically patchy chromosome structure with heterogeneities at different length scales that range from a few nucleotides to tens of millions of them. Fluctuation analysis reveals that these compositional structures can be classified into three main categories: (1) short-range heterogeneities (below a few kilobase pairs (Kbp)) primarily attributed to the alternation of coding and noncoding regions, interspersed or tandem repeats densities, etc.; (2) isochores, spanning tens to hundreds of tens of Kbp; and (3) superstructures, reaching sizes of tens of megabase pairs (Mbp) or even larger. The obtained isochore and superstructure coordinates in the first complete T2T human sequence are now shared in a public database. In this way, interested researchers can use T2T isochore data, as well as the annotations for different genome elements, to check a specific hypothesis about genome structure. Similarly to other levels of biological organization, a hierarchical compositional structure is prevalent in the genome. Once the compositional structure of a genome is identified, various measures can be derived to quantify the heterogeneity of such structure. The distribution of segment G+C content has recently been proposed as a new genome signature that proves to be useful for comparing complete genomes. Another meaningful measure is the sequence compositional complexity (SCC), which has been used for genome structure comparisons. Lastly, we review the recent genome comparisons in species of the ancient phylum Cyanobacteria, conducted by phylogenetic regression of SCC against time, which have revealed positive trends towards higher genome complexity. These findings provide the first evidence for a driven progressive evolution of genome compositional structure.
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Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (February 20, 2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.

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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.
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Makałowski, W. "The human genome structure and organization." Acta Biochimica Polonica 48, no. 3 (September 30, 2001): 587–98. http://dx.doi.org/10.18388/abp.2001_3893.

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Genetic information of human is encoded in two genomes: nuclear and mitochondrial. Both of them reflect molecular evolution of human starting from the beginning of life (about 4.5 billion years ago) until the origin of Homo sapiens species about 100,000 years ago. From this reason human genome contains some features that are common for different groups of organisms and some features that are unique for Homo sapiens. 3.2 x 10(9) base pairs of human nuclear genome are packed into 23 chromosomes of different size. The smallest chromosome - 21st contains 5 x 10(7) base pairs while the biggest one -1st contains 2.63 x 10(8) base pairs. Despite the fact that the nucleotide sequence of all chromosomes is established, the organisation of nuclear genome put still questions: for example: the exact number of genes encoded by the human genome is still unknown giving estimations from 30 to 150 thousand genes. Coding sequences represent a few percent of human nuclear genome. The majority of the genome is represented by repetitiVe sequences (about 50%) and noncoding unique sequences. This part of the genome is frequently wrongly called "junk DNA". The distribution of genes on chromosomes is irregular, DNA fragments containing low percentage of GC pairs code lower number of genes than the fragments of high percentage of GC pairs.
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Mukherjee, Partha, Youakim Badr, Srushti Karvekar, and Shanmugapriya Viswanathan. "Coronavirus Genome Sequence Similarity and Protein Sequence Classification." Journal of Digital Science 3, no. 2 (December 28, 2021): 3–18. http://dx.doi.org/10.33847/2686-8296.3.2_1.

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The world currently is going through a serious pandemic due to the coronavirus disease (COVID-19). In this study, we investigate the gene structure similarity of coronavirus genomes isolated from COVID-19 patients, Severe Acute Respiratory Syndrome (SARS) patients and bats genes. We also explore the extent of similarity between their genome structures to find if the new coronavirus is similar to either of the other genome structures. Our experimental results show that there is 82.42% similarity between the CoV-2 genome structure and the bat genome structure. Moreover, we have used a bidirectional Gated Recurrent Unit (GRU) model as the deep learning technique and an improved variant of Recurrent Neural networks (i.e., Bidirectional Long Short Term Memory model) to classify the protein families of these genomes to isolate the prominent protein family accession. The accuracy of Gated Recurrent Unit (GRU) is 98% for labeled protein sequences against the protein families. By comparing the performance of the Gated Recurrent Unit (GRU) model with the Bidirectional Long Short Term Memory (Bi-LSTM) model results, we found that the GRU model is 1.6% more accurate than the Bi-LSTM model for our multiclass protein classification problem. Our experimental results would be further support medical research purposes in targeting the protein family similarity to better understand the coronavirus genomic structure.
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Lloyd, Vett K., and Kathleen Fitzpatrick. "Genome and chromosome structure: Twelve dynamic and evolving genomes." Fly 2, no. 3 (May 19, 2008): 141–44. http://dx.doi.org/10.4161/fly.6379.

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Cassidy, Liam D., and Ashok R. Venkitaraman. "Genome instability mechanisms and the structure of cancer genomes." Current Opinion in Genetics & Development 22, no. 1 (February 2012): 10–13. http://dx.doi.org/10.1016/j.gde.2012.02.003.

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Zhou, Tianming, Ruochi Zhang, and Jian Ma. "The 3D Genome Structure of Single Cells." Annual Review of Biomedical Data Science 4, no. 1 (July 20, 2021): 21–41. http://dx.doi.org/10.1146/annurev-biodatasci-020121-084709.

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The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for enhancing data quality, and the revealing of 3D genome features at single-cell resolution. While much progress has been made in computational method development to analyze single-cell 3D genomes, substantial future work is needed to improve data interpretation and multimodal data integration, which are critical to reveal fundamental connections between genome structure and function among heterogeneous cell populations in various biological contexts.
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Dissertations / Theses on the topic "Genome structure"

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Weintraub, Abraham S. (Abraham Selby). "Transcriptional regulation and genome structure." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/117886.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.
Cataloged from PDF version of thesis. Page 162 blink.
Includes bibliographical references.
The regulation of gene expression is fundamental to the control of cell identity, development and disease. The control of gene transcription is a major point in the regulation of gene expression. Transcription is regulated by the binding of transcription factors to DNA regulatory elements known as enhancers and promoters. This leads to the formation of a DNA loop connecting the enhancer and the promoter resulting in the subsequent transcription of the gene. Thus the structuring of the genome into DNA loops is important in the control of gene expression. This thesis will focus on the role of genome structure in transcriptional regulation. Two key questions in this area that I have attempted to address during my PhD are "how are enhancer-promoter interactions constrained so that enhancers do not operate nonspecifically?" and "are there proteins that facilitate enhancer-promoter looping?" I will describe the identification of DNA loop structures formed by CTCF and cohesin that constrain enhancer-promoter interactions. These structures-termed insulated neighborhoods-are perturbed in cancer and this perturbation results in the inappropriate activation of oncogenes. Additionally, I will describe the identification and characterization of the transcription factor YY1 as a factor that can structure enhancer-promoter loops. Through a combination of genetics, genomics, and biochemistry, my studies have helped to identify insulated neighborhood structures, shown the importance of these structures in the control of gene expression, revealed that these structures are mutated in cancer, and identified YY1 as a structural regulator of enhancer-promoter loops. I believe these studies have produced a deeper understanding of the regulatory mechanisms that connect the control of genome structure to the control of gene transcription.
by Abraham S. Weintraub.
Ph. D.
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Trussart, Marie 1985. "Structure determination of mycoplasma pneumoniae genome." Doctoral thesis, Universitat Pompeu Fabra, 2015. http://hdl.handle.net/10803/552940.

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Des de l’aparició de les tecnologies de seqüenciació d’alt rendiment, els conjunts de dades biològiques han esdevingut cada cop més grans i complexes, la qual cosa els fa pràcticament impossibles d’interpretar manualment. El paradigma de l’aprenentatge automàtic permet fer una anàlisi sistemàtica de les relacions i patrons existents en els conjuts de dades, tot aprofitant l’enorme volum de dades disponibles. No obstant això, una aplicació poc curosa dels principis bàsics de l’aprenentatge automàtic pot conduir a estimacions massa optimistes, un problema prevalent conegut com a sobreajust. En el camp del plegament de proteïnes, en vam trobar exemples en models publicats que afirmaven tenir un alt poder predictiu, però que es comportaven de forma mediocre devant de dades noves. En el camp de l’epigenètica, problemes com la falta de reproducibilitat, qualitat heterogènia i conflictes entre replicats esdevenen evidents quan es comparen diferents conjunts de dades de ChIP-seq. Per superar aquestes limitacions vam desenvolupar Zerone, un discretitzador de ChIP-seq basat en aprenentatge automàtic que és capaç de combinar informació de diferents replicats experimentals i d’identificar automàticament dades de baixa qualitat o irreproduïbles.
Since the appearance of high throughput sequencing technologies, biological data sets have become increasingly large and complex, which renders them practically impossible to interpret directly by a human. The machine learning paradigm allows a systematic analysis of relationships and patterns within data sets, making possible to extract information by leveraging the sheer amount of data available. However, violations of basic machine learning principles may lead to overly optimistic estimates, a prevalent problem known as overfitting. In the field of protein folding, we found examples of this in published models that claimed high predictive power, but that performed poorly on new data. A different problem arises in epigenetics. Issues such as lack of reproducibility, heterogeneous quality and conflicts between replicates become evident when comparing ChIP-seq data sets. To overcome this limitations we developed Zerone, a machine learning-based ChIP-seq discretizer capable of merging information from several experimental replicates and automatically identifying low quality or irreproducible data.
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Axelsson, Tomas. "Evolution of polyploid Brassica genomes : genome structure and the evolution of duplicated genes /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 2000. http://epsilon.slu.se/avh/2000/91-576-5768-8.pdf.

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Windsor, Aaron J. "Transposons in Arabidopsis : structure, activity, genome restructuring." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38542.

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In the following study, I have investigated aberrant integration events of the maize Activator/Dissociation ( Ac/Ds) family of transposable elements (TEs) in Arabidopsis. The purpose of the study was twofold: (i) to identify sequence modifications associated with aberrant transposition that are informative regarding the mechanism of Ac/Ds transposition; and (ii) to extend our understanding of the mechanisms by which class II TEs can influence genome structure. This work focuses on a large inversion identified on chromosome II. A lone Ds element comprises one breakpoint of the inversion and the second breakpoint is composed solely of Arabidopsis sequences. The analysis of the sequence modifications present at both breakpoints indicates that the event was precipitated by the abortive transposition of Ds. This is the first event of its kind identified for an Ac/Ds and the event defines a novel mechanism by which these TEs can induce change within a genome. Further, the presence of deletions at both termini of the implicated Ds suggests that the transposition of Ac/Ds involves fully excised intermediates. To obtain further support for this model, a population of Arabidopsis individuals harboring Ds excision events was screened for reintegrated elements. Several integrations were analyzed at the sequence level and compared to wild-type integration sites. While no genome rearrangements were detected, a number of integrations display small deletions within both the Ds termini and the DNA flanking the elements. These results are consistent with the presence of fully excised Ac/Ds intermediates. Further, the results suggest that dissolution of the transposase active complex at different points in the transposition process will result in the formation of distinct aberrant transposition products. During the characterization of the inversion, a novel Arabidopsis TE family, FARE, was identified. The FARE elements are foldback transposons, a heterogeneous and poorly characteri
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Wu, Huan-Lin. "Studies of protein structure and genome evolution." Thesis, University of Bath, 2006. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432372.

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Majumdar, Rajrupa Sonali. "The conservation of genome structure in Salmonella typhi." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ48365.pdf.

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Weber, Claudia. "Genome structure and determinants of rates of evolution." Thesis, University of Bath, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.557810.

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How might the process of meiotic crossing-over affect the evolution of sequences and genome structure? Much attention has been focussed on the notion that crossing-over modulates the efficacy of selection. Here, we consider how good the evidence for this is. Correlations between recombination and protein rates of evolution, commonly interpreted in the above framework, might be misleading for failing to remove the effects of covariates or misinterpreted by disregarding direct effects of recombination, such as biased gene conversion. Similarly, higher diversity commonly seen in highly recombining domains may not necessarily imply a connection between recombination and diversity. It could, for instance, reflect a covariance with mutation rate variability owing to replication timing effects. This thesis examines not only these links between recombination and gene evolution but in addition asks other recombination-centred questions. Is gene order evolution in part driven by recombination predisposing certain sites to rearrangement? How can we account for the genomic location of recombination? Does, for example, germline expression, recently suggested to predict low recombination rates in mammals, predict recombination rates in flies? With the exception of the second chapter where we investigate the relationship between double strand break formation, recombination and sequence divergence in Saccharomyces cerevisiae, my work considers Drosophila, making use of the 12 genomes resource. While an effect of crossover on divergence owing to more efficient selection cannot be ruled out, we demonstrate that premeiotic double strand breaks also predict slow evolution. Late replication, we show, is associated with increases in both divergence and variation but this does not undermine the recombination-diversity correlation. While recombination is associated with increased rearrangement rates, we find no evidence that germline expressed genes avoid recombination.
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Yamato, Katsuyuki. "Structure and Gene Expression of Rice Mitochondrial Genome." Kyoto University, 1993. http://hdl.handle.net/2433/78042.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第5431号
農博第762号
新制||農||649(附属図書館)
学位論文||H5||N2565(農学部図書室)
UT51-93-F188
京都大学大学院農学研究科農芸化学専攻
(主査)教授 大山 莞爾, 教授 山田 康之, 教授 常脇 恒一郎
学位規則第4条第1項該当
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MERONI, ALICE. "RNA IN DNA: FROM STRUCTURE TO GENOME INSTABILITY." Doctoral thesis, Università degli Studi di Milano, 2018. http://hdl.handle.net/2434/570097.

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The presence of RNA in the genome of living cells is one of the emerging topics of the last two decades and has been implicated in many biological processes. I focused my attention on ribonucleotides (rNMPs) embedded into DNA during genome duplication, as a threat to its integrity. In fact, rNMPs have been classified as the most frequent non-canonical nucleotides introduced during genome duplication by DNA polymerases. Such high incorporation frequency has been related to a physiological role in mismatch repair, but it can be easily turned into a source of genomic instability if rNMPs are not removed from DNA. This task is performed by RNase H activities that enable error-free repair of embedded single and multiple ribonucleotides. I first approached the issue of ribonucleotides incorporation into DNA from a physical point of view. Utilizing Atomic Force Microscopy I studied how ribonucleotides intrusions impact on DNA structure. The results obtained provided new insights on the structural changes imposed by ribonucleotides persistence into DNA. The other part of my Ph.D. project concerned the study of rNMPs incorporation in vivo, using the budding yeast S. cerevisiae as a model organism. The second aim was to unravel the function of the Translesion Synthesis polymerase η (Pol η) when the genome contains residual ribonucleotides and when deoxyribonucleotides (dNTPs) pools are depleted. We found that DNA polymerase η is responsible for the cell lethality observed when dNTPs are scarce and RNase H activities are defective. Therefore, I explored and characterized this unexpected toxic activity. We propose a model where Pol η supports cell survival in low dNTPs conditions by promoting DNA replication using ribonucleotides. While this activity is normally beneficial to wild type cells, it is highly toxic to cells defective for RNase H activities.
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Neuditschko, Markus. "A whole-genome population structure analysis within cattle breeds." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-133991.

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Books on the topic "Genome structure"

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Nicolini, Claudio, ed. Genome Structure and Function. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5550-2.

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Giorgio, Bernardi, ed. Genome structure and evolution. New York: Springer, 1991.

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de, Bruijn F. J., Lupski James R. 1957-, and Weinstock George M. 1949-, eds. Bacterial genomes: Physical structure and analysis. New York: Kluwer Academic, 1999.

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de, Bruijn F. J., Lupski James R. 1957-, and Weinstock George M. 1949-, eds. Bacterial genomes: Physical structure and analysis. New York: Chapman & Hall, 1998.

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Kolchanov, Nikolay, and Ralf Hofestaedt, eds. Bioinformatics of Genome Regulation and Structure. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-7152-4.

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A, Kolchanov N., and Hofestädt Ralf, eds. Bioinformatics of genome regulation and structure. Boston: Kluwer Academic, 2004.

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O'Sullivan, Donal Martin. Genome structure & plasticity in Colletotrichum lindemuthianum. Dublin: University College Dublin, 1997.

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Haddad, Luciana Amaral, ed. Human Genome Structure, Function and Clinical Considerations. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-73151-9.

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Kolchanov, Nikolay, Ralf Hofestaedt, and Luciano Milanesi, eds. Bioinformatics of Genome Regulation and Structure II. Boston, MA: Springer US, 2006. http://dx.doi.org/10.1007/0-387-29455-4.

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Plant cytogenetics: Genome structure and chromosome function. New York: Springer, 2012.

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Book chapters on the topic "Genome structure"

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Black, Lindsay W., and Julie A. Thomas. "Condensed Genome Structure." In Viral Molecular Machines, 469–87. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-1-4614-0980-9_21.

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Symons, Robert H. "Viral Genome Structure." In The Plant Viruses, 57–81. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4684-4937-2_3.

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Watson, J. D., J. M. Thornton, M. L. Tress, G. Lopez, A. Valencia, O. Redfern, C. A. Orengo, I. Sommer, and F. S. Domingues. "Structure to function." In Modern Genome Annotation, 239–62. Vienna: Springer Vienna, 2008. http://dx.doi.org/10.1007/978-3-211-75123-7_12.

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Palacios, Rafael, and Manuel Megías. "Genome Structure of Diazotrophs." In Nitrogen Fixation: From Molecules to Crop Productivity, 269–70. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/0-306-47615-0_144.

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Kellogg, Elizabeth A. "Karyology and Genome Structure." In Flowering Plants. Monocots, 55–61. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-15332-2_5.

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Dolan, James, and Jonathan Leis. "Integrase: Structure, Function, and Mechanism." In Viral Genome Replication, 467–78. Boston, MA: Springer US, 2009. http://dx.doi.org/10.1007/b135974_21.

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Tramontano, A., D. Jones, L. Rychlewski, R. Casadio, P. Martelli, D. Raimondo, and A. Giorgetti. "Structure prediction of globular proteins." In Modern Genome Annotation, 283–307. Vienna: Springer Vienna, 2008. http://dx.doi.org/10.1007/978-3-211-75123-7_14.

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Kim, Nam-Hoon, Murukarthick Jayakodi, and Tae-Jin Yang. "Ginseng Genome Structure and Evolution." In The Ginseng Genome, 85–93. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-30347-1_7.

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Belmont, A. S. "Large-Scale Chromatin Structure." In Genome Structure and Function, 261–78. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5550-2_13.

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Nicolini, C. "Genome Structure — Function from Nuclei to Chromosomes and Nucleosomes." In Genome Structure and Function, 1–37. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5550-2_1.

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Conference papers on the topic "Genome structure"

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Yu, Wenbin. "Structure Genome: Fill the Gap between Materials Genome and Structural Analysis." In 56th AIAA/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference. Reston, Virginia: American Institute of Aeronautics and Astronautics, 2015. http://dx.doi.org/10.2514/6.2015-0201.

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ZHANG, QI, WEI WANG, LEONARD MCMILLAN, FERNANDO PARDO-MANUEL DE VILLENA, and DAVID THREADGILL. "INFERRING GENOME-WIDE MOSAIC STRUCTURE." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2008. http://dx.doi.org/10.1142/9789812836939_0015.

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ZHAO, BANGHUA, and WENBIN YU. "Multiscale Structural Analysis of Honeycomb Sandwich Structure Using Mechanics of Structure Genome." In American Society for Composites 2017. Lancaster, PA: DEStech Publications, Inc., 2017. http://dx.doi.org/10.12783/asc2017/15171.

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"Whole genome sequencing and assembly of Saccharomyces cerevisiae genomes using Oxford Nanopore data." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-037.

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Panfilio, Kristen A. "Trends in bug genome size, gene structure, and gene repertoires." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.93920.

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Peignier, Sergio, Christophe Rigotti, and Guillaume Beslon. "Subspace Clustering Using Evolvable Genome Structure." In GECCO '15: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2739480.2754709.

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"Genome mining for novel bioactive peptides." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-330.

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"Genome and karyotype evolution after whole genome duplication in free-living flatworms of the genus Macrostomum." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-167.

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"Plastid genome evolution in the genus Allium." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-154.

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Misra, Sanchit, Md Vasimuddin, Kiran Pamnany, Sriram P. Chockalingam, Yong Dong, Min Xie, Maneesha R. Aluru, and Srinivas Aluru. "Parallel Bayesian Network Structure Learning for Genome-Scale Gene Networks." In SC14: International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE, 2014. http://dx.doi.org/10.1109/sc.2014.43.

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Reports on the topic "Genome structure"

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Padmanabhan, Radha K. Structure and Functional Studies on Dengue-2 Virus Genome. Fort Belvoir, VA: Defense Technical Information Center, March 1986. http://dx.doi.org/10.21236/ada199075.

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Peng, Jamy C. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity. Office of Scientific and Technical Information (OSTI), January 2007. http://dx.doi.org/10.2172/913167.

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Hegyi, Hedi, and Mark Gerstein. The Relationship between Protein Structure and Function: a Comprehensive Survey with Application to the Yeast Genome. Fort Belvoir, VA: Defense Technical Information Center, January 1999. http://dx.doi.org/10.21236/ada472211.

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Gur, Amit, Edward Buckler, Joseph Burger, Yaakov Tadmor, and Iftach Klapp. Characterization of genetic variation and yield heterosis in Cucumis melo. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7600047.bard.

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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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Dawson, William O., Moshe Bar-Joseph, Charles L. Niblett, Ron Gafny, Richard F. Lee, and Munir Mawassi. Citrus Tristeza Virus: Molecular Approaches to Cross Protection. United States Department of Agriculture, January 1994. http://dx.doi.org/10.32747/1994.7570551.bard.

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Citrus tristeza virus (CTV) has the largest genomes among RNA viruses of plants. The 19,296-nt CTV genome codes for eleven open reading frames (ORFs) and can produce at least 19 protein products ranging in size from 6 to 401 kDa. The complex biology of CTV results in an unusual composition of CTV-specific RNAs in infected plants which includes multiple defective RNAs and mixed infections. The complex structure of CTV populations poses special problems for diagnosis, strain differentiation, and studies of pathogenesis. A manipulatable genetic system with the full-length cDNA copy of the CTV genome has been created which allows direct studies of various aspects of the CTV biology and pathology. This genetic system is being used to identify determinants of the decline and stem-pitting disease syndromes, as well as determinants responsible for aphid transmission.
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Azem, Abdussalam, George Lorimer, and Adina Breiman. Molecular and in vivo Functions of the Chloroplast Chaperonins. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697111.bard.

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We present here the final report for our research project entitled "The molecular and in vivo functions of the chloroplast chaperonins”. Over the past few decades, intensive investigation of the bacterial GroELS system has led to a basic understanding of how chaperonins refold denatured proteins. However, the parallel is limited in its relevance to plant chaperonins, since the plant system differs from GroEL in genetic complexity, physiological roles of the chaperonins and precise molecular structure. Due to the importance of plant chaperonins for chloroplast biogenesis and Rubisco assembly, research on this topic will have implications for many vital applicative fields such as crop hardiness and efficiency of plant growth as well as the production of alternative energy sources. In this study, we set out to investigate the structure and function of chloroplast chaperonins from A. thaliana. Most plants harbor multiple genes for chaperonin proteins, making analysis of plant chaperonin systems more complicated than the GroEL-GroES system. We decided to focus on the chaperonins from A. thaliana since the genome of this plant has been well defined and many materials are available which can help facilitate studies using this system. Our proposal put forward a number of goals including cloning, purification, and characterization of the chloroplast cpn60 subunits, antibody preparation, gene expression patterns, in vivo analysis of oligomer composition, preparation and characterization of plant deletion mutants, identification of substrate proteins and biophysical studies. In this report, we describe the progress we have made in understanding the structure and function of chloroplast chaperonins in each of these categories.
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Breiman, Adina, Jan Dvorak, Abraham Korol, and Eduard Akhunov. Population Genomics and Association Mapping of Disease Resistance Genes in Israeli Populations of Wild Relatives of Wheat, Triticum dicoccoides and Aegilops speltoides. United States Department of Agriculture, December 2011. http://dx.doi.org/10.32747/2011.7697121.bard.

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Wheat is the most widely grown crop on earth, together with rice it is second to maize in total global tonnage. One of the emerging threats to wheat is stripe (yellow) rust, especially in North Africa, West and Central Asia and North America. The most efficient way to control plant diseases is to introduce disease resistant genes. However, the pathogens can overcome rapidly the effectiveness of these genes when they are wildly used. Therefore, there is a constant need to find new resistance genes to replace the non-effective genes. The resistance gene pool in the cultivated wheat is depleted and there is a need to find new genes in the wild relative of wheat. Wild emmer (Triticum dicoccoides) the progenitor of the cultivated wheat can serve as valuable gene pool for breeding for disease resistance. Transferring of novel genes into elite cultivars is highly facilitated by the availability of information of their chromosomal location. Therefore, our goals in this study was to find stripe rust resistant and susceptible genotypes in Israeli T. dicoccoides population, genotype them using state of the art genotyping methods and to find association between genetic markers and stripe rust resistance. We have screened 129 accessions from our collection of wild emmer wheat for resistance to three isolates of stripe rust. About 30% of the accessions were resistant to one or more isolates, 50% susceptible, and the rest displayed intermediate response. The accessions were genotyped with Illumina'sInfinium assay which consists of 9K single nucleotide polymorphism (SNP) markers. About 13% (1179) of the SNPs were polymorphic in the wild emmer population. Cluster analysis based on SNP diversity has shown that there are two main groups in the wild population. A big cluster probably belongs to the Horanum ssp. and a small cluster of the Judaicum ssp. In order to avoid population structure bias, the Judaicum spp. was removed from the association analysis. In the remaining group of genotypes, linkage disequilibrium (LD) measured along the chromosomes decayed rapidly within one centimorgan. This is the first time when such analysis is conducted on a genome wide level in wild emmer. Such a rapid decay in LD level, quite unexpected for a selfer, was not observed in cultivated wheat collection. It indicates that wild emmer populations are highly suitable for association studies yielding a better resolution than association studies in cultivated wheat or genetic mapping in bi-parental populations. Significant association was found between an SNP marker located in the distal region of chromosome arm 1BL and resistance to one of the isolates. This region is not known in the literature to bear a stripe rust resistance gene. Therefore, there may be a new stripe rust resistance gene in this locus. With the current fast increase of wheat genome sequence data, genome wide association analysis becomes a feasible task and efficient strategy for searching novel genes in wild emmer wheat. In this study, we have shown that the wild emmer gene pool is a valuable source for new stripe rust resistance genes that can protect the cultivated wheat.
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Adams, Paul, Hassina Bilheux, Andrzej Joachimiak, Scott Lea, Sean McSweeney, Karolina Michalska, Irina Novikova, et al. Genomes to Structure and Function Workshop Report 2022. Office of Scientific and Technical Information (OSTI), April 2023. http://dx.doi.org/10.2172/1959294.

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Hartmaier, Ryan. Progression of Structural Change in the Breast Cancer Genome. Fort Belvoir, VA: Defense Technical Information Center, August 2012. http://dx.doi.org/10.21236/ada566777.

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Hartmaier, Ryan J. Progression of Structural Change in the Breast Cancer Genome. Fort Belvoir, VA: Defense Technical Information Center, August 2013. http://dx.doi.org/10.21236/ada591079.

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