Relevant bibliographies by topics / Genome architecture mapping

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers
  5. Reports

Academic literature on the topic 'Genome architecture mapping'

Author: Grafiati
Published: 24 June 2021
Last updated: 29 July 2025

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Journal articles on the topic "Genome architecture mapping"

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Tavallaee, Ghazaleh, and Elias Orouji. "Mapping the 3D genome architecture." Computational and Structural Biotechnology Journal 27 (2025): 89–101. https://doi.org/10.1016/j.csbj.2024.12.018.

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McKay, Daniel J., Alexis V. Stutzman, and Jill M. Dowen. "Advancements in mapping 3D genome architecture." Methods 170 (January 2020): 75–81. http://dx.doi.org/10.1016/j.ymeth.2019.06.002.

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Feng, Yi, Leslie Y. Beh, Wei-Jen Chang, and Laura F. Landweber. "SIGAR: Inferring Features of Genome Architecture and DNA Rearrangements by Split-Read Mapping." Genome Biology and Evolution 12, no. 10 (2020): 1711–18. http://dx.doi.org/10.1093/gbe/evaa147.

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Abstract Ciliates are microbial eukaryotes with distinct somatic and germline genomes. Postzygotic development involves extensive remodeling of the germline genome to form somatic chromosomes. Ciliates therefore offer a valuable model for studying the architecture and evolution of programed genome rearrangements. Current studies usually focus on a few model species, where rearrangement features are annotated by aligning reference germline and somatic genomes. Although many high-quality somatic genomes have been assembled, a high-quality germline genome assembly is difficult to obtain due to it
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Chowdhary, Surabhi, Amoldeep S. Kainth, and David S. Gross. "Methods for mapping three-dimensional genome architecture." Methods 170 (January 2020): 1–3. http://dx.doi.org/10.1016/j.ymeth.2019.10.011.

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Danchin, Antoine, Pascale Guerdoux-Jamet, Ivan Moszer, and Patrick Nitschké. "Mapping the bacterial cell architecture into the chromosome." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 355, no. 1394 (2000): 179–90. http://dx.doi.org/10.1098/rstb.2000.0557.

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A genome is not a simple collection of genes. We propose here that it can be viewed as being organized as a ;‘celluloculus’ similar to the homunculus of preformists, but pertaining to the category of programmes (or algorithms) rather than to that of architectures or structures: a significant correlation exists between the distribution of genes along the chromosome and the physical architecture of the cell. W e review here data supporting this observation, stressing physical constraints operating on the cell's architecture and dynamics, and their consequences in terms of gene and genome structu
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Schmitt, Anthony D., Ming Hu, and Bing Ren. "Genome-wide mapping and analysis of chromosome architecture." Nature Reviews Molecular Cell Biology 17, no. 12 (2016): 743–55. http://dx.doi.org/10.1038/nrm.2016.104.

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Beagrie, Robert A., Antonio Scialdone, Markus Schueler, et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature 543, no. 7646 (2017): 519–24. http://dx.doi.org/10.1038/nature21411.

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Maluszynska, J., and J. S. Heslop-Harrison. "Physical mapping of rDNA loci in Brassica species." Genome 36, no. 4 (1993): 774–81. http://dx.doi.org/10.1139/g93-102.

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The number of major rDNA loci (the genes coding for 18S–5.8S–26S rRNA) was investigated in the economically important Brassica species and their wild relatives by in situ hybridization of an rDNA probe to metaphase chromosomes and interphase nuclei. The diploid species B. nigra (B genome) has two major pairs of rDNA loci, B. oleracea (C genome) has two major pairs and one minor pair of loci, while B. campestris (A genome) has five pairs of loci. Among the three tetraploid species arising from these three diploid ancestors, B. carinata (BBCC genomes) has four loci, B. juncea (AABB genomes) has
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Ramani, Vijay, Darren A. Cusanovich, Ronald J. Hause, et al. "Mapping 3D genome architecture through in situ DNase Hi-C." Nature Protocols 11, no. 11 (2016): 2104–21. http://dx.doi.org/10.1038/nprot.2016.126.

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Burridge, James D., Hannah M. Schneider, Bao-Lam Huynh, Philip A. Roberts, Alexander Bucksch, and Jonathan P. Lynch. "Genome-wide association mapping and agronomic impact of cowpea root architecture." Theoretical and Applied Genetics 130, no. 2 (2016): 419–31. http://dx.doi.org/10.1007/s00122-016-2823-y.

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Dissertations / Theses on the topic "Genome architecture mapping"

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Beagrie, Robert Alexander. "Deciphering mechanisms of gene regulation through novel strategies for mapping genome architecture." Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/55112.

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The regulation of gene expression plays a crucial role in development and disease. Regulation at the level of transcription is intimately linked with the positions of genes within the nucleus, both in terms of their association with structural components such as the nuclear lamina and in terms of their proximity to genomic elements such as enhancers or other genes. Methods based on Chromosome Conformation Capture (3C) have begun to disentangle the complicated relationship between chromatin folding and gene expression. However, 3C-based techniques have important limitations that restrict their
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Loof, Gesa. "Elucidating the influence of chromatin topology on cellular identity in murine pre-implantation development." Doctoral thesis, Humboldt-Universität zu Berlin, 2021. http://dx.doi.org/10.18452/22928.

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Präzise regulierte Genexpression, ist der Schlüssel zu erfolgreicher Embryonal-entwicklung. Die Expression von Zelltyp-spezifischen Transkriptionsfaktoren kann durch räumliche Interaktionen von Promotoren und Enhancern im Nukleus kontrolliert werden, aber auch durch 3D Faltung der DNA in größere organisatorische Einheiten wie “Topologically Associating Domains” (TADs) oder “A/B compartments”. Um die 3D Faltung in den Zelltypen des prä-implantations Embryos zu untersuchen, nutze ich ES und XEN Zellen, die stark dem Epiblast und dem primitiven Endoderm in der inneren Zellmasse des E4.5 Embryos
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Kempfer, Rieke. "Chromatin folding in health and disease: exploring allele-specific topologies and the reorganization due to the 16p11.2 deletion in autism-spectrum disorder." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/22071.

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Die 3D Struktur von Chromosomen im Zellkern reguliert verschiedene Funktionen in der Zelle und Fehler in der 3D Faltung des Genoms können pathogen sein. 3D Genomfaltung kann mit verschiedenen Methoden untersucht werden um Chromatinkontakte, sowie die Position von DNA in Relation zu sub-nuklearen Bereichen oder der Kernmembran zu detektieren. Hier verwende ich GAM und Hi-C um zwei Aspekte der 3D Genomtopologie zu untersuchen, die Allelspezifität von Chromatinkontakten und Kontakte zwischen Chromosomen. Ich untersuche allelspezifische Kontakte in murinen embryonalen Stammzellen und Interaktionen
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Herzig, Paul [Verfasser], Klaus [Gutachter] Pillen, and Jens [Gutachter] Léon. "Genome-wide association studies in a wild barley nested association mapping (NAM) population to reveal the genetic architecture of plant development and quality traits / Paul Herzig ; Gutachter: Klaus Pillen, Jens Léon." Halle (Saale) : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2021. http://d-nb.info/1238074561/34.

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CASELLA, LAURA. "SNP ANALYSIS FOR DROUGHT-RELATED CANDIDATE GENES IN A GERMPLASM COLLECTION AND A TILLING POPULATION OF ITALIAN RICE." Doctoral thesis, Università degli Studi di Milano, 2012. http://hdl.handle.net/2434/203361.

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Rice is the most important food crop in the world, representing the main source of caloric intake for more than one third of the world’s population. Although a great part of the global rice production comes from the developing countries such as China, India, Indonesia and Bangladesh, northern Italy plays a relevant role in terms of rice production providing about 50% of the total European paddy rice production. Due to the nature of the area devoted to rice growth, characterized by large availability of water and an efficient water distribution net, rice in Italy developed in the last two centu
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Powell, Joseph E. "Influence of genomic architecture on the performance of association mapping : application to ascites syndrome in broiler chickens." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/15653.

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Zurek, Paul Roman. "Quantitative Trait Locus Mapping Reveals Regions of the Maize Genome Controlling Root System Architecture." Diss., 2014. http://hdl.handle.net/10161/9399.

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<p>Root system architecture (RSA) is the spatial distribution of roots of individual plants. As part of a collaborative effort I adapted a gellan gum based system for imaging and phenotyping of root systems in maize. This system was first used to perform a survey of 26 distinct maize varieties of the Nested Association Mapping (NAM) population. The analysis of these data showed a large amount of variation between different RSA, in particular demonstrating tradeoffs between architectures favoring sparse, but far reaching, root networks versus those favoring small but dense root networks. To stu
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Lin, R. "Dissecting the genetic architecture of multiple sclerosis." Thesis, 2014. https://eprints.utas.edu.au/22603/1/Final%20Thesis.pdf.

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Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS) triggered by environmental and genetic factors. There is considerable evidence for a significant genetic component to MS susceptibility, such that genome-wide association studies (GWASs) have successfully revealed about 100 common genetic variants associated with MS. However, at least 60% of the overall heritability of MS has not been delineated, so-called “missing heritability”. This thesis describes a series of experiments to further elucidate the “missing heritability” of MS.
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Vinayan, M. T. "Genetic Architecture of Spotted Stem Borer Resistance in Sorghum As Inferred From Qtl Mapping and Synteny with the Maize Genome." Thesis, 2010. http://oar.icrisat.org/6046/1/MT_VinayanPhD_Thesis_2010.pdf.

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The present investigation was carried out to characterize the genetic architecture of spotted stem borer resistance and related agronomic and morphological traits in sorghum. The experimental material for this study consisted of 266 RILs derived from a cross between susceptible parent ICSV 745 and resistant parent PB 15520. These RILs were evaluated for phenotypic traits during the 2007 and 2008 rainy seasons under artificial infestation of stem borer, and were genotyped with 90 polymorphic SSR markers for linkage map construction and QTL analysis. The RILs exhibited wide variation for
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Book chapters on the topic "Genome architecture mapping"

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Fiorillo, Luca, Mattia Conte, Andrea Esposito, et al. "Analysis of Genome Architecture Mapping Data with a Machine Learning and Polymer-Physics-Based Tool." In Euro-Par 2020: Parallel Processing Workshops. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-71593-9_25.

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de Siqueira Gesteira, Gabriel, Guilherme da Silva Pereira, Zhao-Bang Zeng, and Marcelo Mollinari. "Genetic Maps in Sweetpotato." In Compendium of Plant Genomes. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-65003-1_5.

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AbstractThis chapter highlights the research and efforts that have been done to understand the composition of the genome and the mechanisms underlying the genetic inheritance in sweetpotato, with focus on the cultivated hexaploid sweetpotato. The first part of the chapter focuses on dissecting strategies and methods that have been used to study and understand key factors that affect the genetic behavior in polyploid species, with emphasis on linkage analysis, highlighting the most common types of experimental populations used for genetic mapping, the obtention of genotype information, and the
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Zhou, Hao, and Brian J. Steffenson. "Genome-Wide Association Mapping Reveals Genetic Architecture of Durable Spot Blotch Resistance in US Barley Breeding Germplasm." In Advance in Barley Sciences. Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4682-4_22.

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Sowa, Anna S., Lisa Dussling, Jörg Hagmann, and Sebastian J. Schultheiss. "The power of next-generation sequencing and machine learning for causal gene finding and prediction of phenotypes." In Mutation breeding, genetic diversity and crop adaptation to climate change. CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0041.

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Abstract The wide application of next-generation sequencing (NGS) has facilitated and accelerated causal gene finding and breeding in the field of plant sciences. A wide variety of techniques and computational strategies is available that needs to be appropriately tailored to the species, genetic architecture of the trait of interest, breeding system and available resources. Utilizing these NGS methods, the typical computational steps of marker discovery, genetic mapping and identification of causal mutations can be achieved in a single step in a cost- and time-efficient manner. Rather than fo
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da Silva Pereira, Guilherme, Carla Cristina da Silva, João Ricardo Bachega Feijó Rosa, et al. "New Analytical Tools for Molecular Mapping of Quantitative Trait Loci in Sweetpotato." In Compendium of Plant Genomes. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-65003-1_6.

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AbstractQuantitative trait loci(QTL) mapping is an important tool in sweetpotato research, contributing to the understanding of genetic architecture of various traits, including dry matter, nematode resistance, and flesh color. Early QTL work was carried out by using marker information alone via single marker analysis (SMA), or based on parent-specific linkage map using interval mapping (IM), composite interval mapping (CIM), and multiple interval mapping (MIM). Initially developed for inbred diploid species populations, these methods did not fully consider the complex autopolyploid, outcrossi
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Bulayeva, Kazima, Oleg Bulayev, and Stephen Glatt. "Current Problems of Complex Disease Genes Mapping." In Genomic Architecture of Schizophrenia Across Diverse Genetic Isolates. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_1.

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Gebretsadik, Kiros, Daoliang Yu, and Kailiang Bo. "Molecular Mapping of QTLs and Genes for Plant Architecture and Fruit Traits in Cucumber." In Compendium of Plant Genomes. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-88647-9_4.

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Bulayeva, Kazima, Oleg Bulayev, and Stephen Glatt. "Mapping Genes of Schizophrenia in Selected Dagestan Isolates." In Genomic Architecture of Schizophrenia Across Diverse Genetic Isolates. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_4.

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Bulayeva, Kazima, Oleg Bulayev, and Stephen Glatt. "Selection of Populations for Mapping Genes of Complex Diseases." In Genomic Architecture of Schizophrenia Across Diverse Genetic Isolates. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_3.

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Selvakumar, Raman. "An Update on Radish Breeding Strategies: An Overview." In Plant Breeding - New Perspectives [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.108725.

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In tropical, subtropical, and temperate climates, radish (Raphanus sativus L.) is a popular root vegetable. Radish diversity is intense from the eastern Mediterranean to the Caspian Sea. Many radish varieties have varied leaf morphology, root color, size, shape, flavor, vernalization requirements, and maturity times. Early radish variants were long and tapered rather than cylindrical, bulbous, elliptic, or spherical. For black Spanish radish, European-cultivated variety, and Asian-cultivated radish, three separate domestication processes occurred. The original radishes were black, followed by
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Conference papers on the topic "Genome architecture mapping"

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Houtgast, Ernst Joachim, Vlad-Mihai Sima, Koen Bertels, and Zaid Al-Ars. "An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm." In 2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS). IEEE, 2015. http://dx.doi.org/10.1109/samos.2015.7363679.

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Kikuchi, Teruyuki, and Sho Fukaya. "Landslide Susceptibility Map using ViT Architectures With Pre-Slide Topographic Dem of Deep-Seated Landslide Events." In 4th European Regional Conference of IAEG. University of Zagreb Faculty of Civil Engineering, 2024. https://doi.org/10.5592/co/euroengeo.2024.158.

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There has been an increasing demand in recent years for detailed and accurate landslide maps and inventories in disaster-prone areas of subtropical and temperate zones. Standard Landslide susceptibility mapping methods require detailed fieldwork to be conducted by knowledgeable, skilled professionals. When predicting landslides, it is important to understand past landslide cases and prepare for situations in which the same phenomena occur. Developing automatic analysis methods using deep learning can contribute to the sophistication and cost of screening. In this study, models using the automa
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Reports on the topic "Genome architecture mapping"

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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7592655.bard.

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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflow
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Zamir, Dani, Steven Tanksley, and Robert Fluhr. Cloning a Fusarium Resistance Gene in Tomato Based on Knowledge of its Map Position. United States Department of Agriculture, 1995. http://dx.doi.org/10.32747/1995.7604934.bard.

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The objectives of this project were to develop the tools and methodologies for positional cloning of genes in tomato and apply them for the cloning a Fusarium resistance gene - I2.. The feasibility of positional cloning of disease resistance genes was demonstrated for Pto which confers resistance to pseudomonas (Martin et al. 1993). The Fusarium resistance gene was mapped genetically and physically and was found to be in close proximity to TG 105 (Segal et al. 1992). To obtain fine mapping of gene I2, and additional target genes in future projects, a high density linkage map was developed (Tan
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