Relevant bibliographies by topics / Genome architecture mapping

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

Academic literature on the topic 'Genome architecture mapping'

Author: Grafiati
Published: 24 June 2021
Last updated: 8 February 2022

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Journal articles on the topic "Genome architecture mapping"

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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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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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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 (August 13, 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 its smaller DNA content and abundance of repetitive sequences. To overcome these hurdles, we propose a new pipeline, SIGAR (Split-read Inference of Genome Architecture and Rearrangements) to infer germline genome architecture and rearrangement features without a germline genome assembly, requiring only short DNA sequencing reads. As a proof of principle, 93% of rearrangement junctions identified by SIGAR in the ciliate Oxytricha trifallax were validated by the existing germline assembly. We then applied SIGAR to six diverse ciliate species without germline genome assemblies, including Ichthyophthirius multifilii, a fish pathogen. Despite the high level of somatic DNA contamination in each sample, SIGAR successfully inferred rearrangement junctions, short eliminated sequences, and potential scrambled genes in each species. This pipeline enables pilot surveys or exploration of DNA rearrangements in species with limited DNA material access, thereby providing new insights into the evolution of chromosome rearrangements.
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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 (February 29, 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 structure. If such a correlation exists, it derives from some selection pressure: simple and general physical principles acting at the level of the cell structure are discussed. As a first case in point we see the piling up of planar modules as a stable, entropy–driven, architectural principle that could be at the root of the coupling between the architecture of the cell and the location of genes at specific places in the chromosome. W e propose that the specific organization of certain genes whose products have a general tendency to form easily planar modules is a general motor for architectural organization in the bacterial cell. A second mechanism, operating at the transcription level, is described that could account for the efficient building up of complex structures. As an organizing principle we suggest that exploration by biological polymers of the vast space of possible conformation states is constrained by anchoring points. In particular, we suggest that transcription does not always allow the 5 ′ –end of the transcript to go free and explore the many conformations available, but that, in many cases, it remains linked to the transcribing RNA polymerase complex in such a way that loops of RNA, rather than threads with a free end, explore the surrounding medium. In bacteria, extension of the loops throughout the cytoplasm would therefore be mediated by the de novo synthesis of ribosomes in growing cells. Termination of transcription and mRNA turnover would accordingly be expected to be controlled by sequence features at both the 3 ′ – and 5 ′ –ends of the molecule. These concepts are discussed taking into account in vitro analysis of genome sequences and experimental data about cell compartmentalization, mRNA folding and turnover, as well as known structural features of protein and membrane complexes.
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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 (September 1, 2016): 743–55. http://dx.doi.org/10.1038/nrm.2016.104.

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Beagrie, Robert A., Antonio Scialdone, Markus Schueler, Dorothee C. A. Kraemer, Mita Chotalia, Sheila Q. Xie, Mariano Barbieri, et al. "Complex multi-enhancer contacts captured by genome architecture mapping." Nature 543, no. 7646 (March 2017): 519–24. http://dx.doi.org/10.1038/nature21411.

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Ramani, Vijay, Darren A. Cusanovich, Ronald J. Hause, Wenxiu Ma, Ruolan Qiu, Xinxian Deng, C. Anthony Blau, et al. "Mapping 3D genome architecture through in situ DNase Hi-C." Nature Protocols 11, no. 11 (September 29, 2016): 2104–21. http://dx.doi.org/10.1038/nprot.2016.126.

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Maluszynska, J., and J. S. Heslop-Harrison. "Physical mapping of rDNA loci in Brassica species." Genome 36, no. 4 (August 1, 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 five major pairs and one minor pair of loci, and B. napus (AACC genomes) has six pairs of loci, indicating that the number of loci has been reduced during evolution. The complexity of the known rDNA restriction fragment length polymorphism patterns gave little indication of number of rDNA loci. It is probable that chromosome rearrangements have occurred during evolution of the amphidiploid species. The data will be useful for physical mapping of genes relative to rDNA loci, micro- and macro-evolutionary studies and analysis of aneuploids including addition and substitution lines used in Brassica breeding programs.Key words: Brassica, centromeric DNA, genetic maps, nuclear architecture, ribosomal DNA, evolution, Brassicaceae, Cruciferae, gene mapping.
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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 (November 18, 2016): 419–31. http://dx.doi.org/10.1007/s00122-016-2823-y.

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Thoen, Manus P. M., Nelson H. Davila Olivas, Karen J. Kloth, Silvia Coolen, Ping-Ping Huang, Mark G. M. Aarts, Johanna A. Bac-Molenaar, et al. "Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping." New Phytologist 213, no. 3 (October 4, 2016): 1346–62. http://dx.doi.org/10.1111/nph.14220.

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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 ability to address important biological questions. Crucially, they struggle to detect interactions involving three or more genomic features because they rely on ligation of DNA fragment ends. To address these limitations, I implemented and optimized Genome Architecture Mapping (GAM), a ligation-free approach for determining genome topology. GAM infers the spatial proximity between genomic elements by measuring their co-segregation in thin nuclear slices, and places no upper limit on the number of regions that can be detected in a simultaneous interaction. I apply GAM to mouse embryonic stem cells and develop a computational pipeline to analyse the resulting dataset. GAM independently verifies key features of chromosome folding identified by 3C-based methods, including topologically associating domains (TADs). Using a statistical model, we find many non-random interactions spanning tens of megabases, which preferentially involve interactions between active genes and enhancers, between pairs of active genes and between pairs of enhancers at 30 kb resolution. We also explore simultaneous, three-way contacts between TADs and identify super-enhancers and highly-transcribed TADs as the most likely to interact at higher multiplicity. Strikingly, we uncover an antagonistic relationship between lamina association and TAD triplet formation. Finally, we show that GAM can be used to measure chromatin compaction and radial positioning.
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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 ähneln. Um den Zusammenhang zwischen 3D DNA Faltung und zellulärer Identität zu erforschen, habe ich GAM, ATAC-seq und RNA-seq Daten von ES und XEN Zellen produziert. Um die Genom-Architektur im Embryo zu untersuchen, habe ich außerdem die GAM Methode an den Mausembryo angepasst und kann dadurch erstmals genomweit DNA-Faltung in den spezifischen Zelltypen der inneren Zellmasse des prä-implantations Embryos zeigen. ES und XEN Zellen zeigen viele differentiell exprimierte Gene, sowie starke Veränderungen in der Chromatin-Organisation, beispielweise in der Bildung von reprimierten Chromatinnetzwerken in ESCs, die wichtige XEN Gene wie Gata6 und Lama1 enthalten, während diese nicht aktiv sind. XEN-spezifische Genexpression ist oft mit der Präsenz von XEN-spezifischen “TAD boundaries” gekoppelt. Der Sox2 Locus zeigt eine ESC-spezifische Organisation mit aktiven Genen, und Regionen die von den Transkriptionsfaktoren SOX2, NANOG und OCT4 gebunden sind. Die starke Reorganisation der Genom-Architektur in wichtigen Loci wie Gata6 und Sox2 konnte ich mit in vivo GAM Daten bestätigen und finde ähnliche Unterschiede zwischen den beiden Zelltypen der inneren Zellmasse wie im in vitro Model. Diese Ergebnisse zeigen, wie wichtig es ist, Zelltypen getrennt zu untersuchen und, dass eine Verbindung zwischen zellulärer Identität und der Faltung des Genoms in der Embryonalentwicklung besteht.
Tightly controlled gene regulation is key to functional metazoan embryonic development. The expression of cell-fate determining transcription factors orchestrates the establishment of the various lineages of the embryo. Gene expression is often regulated via specific chromatin organisation. To investigate cell type-specific differences in chromatin folding in early embryonic development, I used in vitro models of the two distinct cell populations in the blastocyst ICM. In mouse ES and XEN cells, I mapped 3D genome conformation using Genome Architecture Mapping (GAM), chromatin accessibility using ATAC-seq, and gene expression using total RNA-seq. To enable the mapping of 3D genome folding directly in the blastocyst ICM, I adapted GAM for cell type-specific selection of nuclei, by integrating immunofluorescence detection of markers, and generated the first genome-wide chromatin contact maps that distinguish ICM cell types. I report that the ES and XEN cell lineages undergo abundant large scale rearrangements of genome architecture and exhibit high numbers of differentially expressed genes. For example, extra-embryonic endoderm genes, such as Lama1 and Gata6, form silent hubs in ESCs, potentially connecting maintenance of pluripotency to 3D structure of the genome. Further, I show that the expression of XEN cell-specific genes relates to the formation of XEN cell-specific TAD boundaries. Chromatin contacts at the Sox2 locus exhibit an ESC-specific organisation around binding of pluripotency transcription factors OCT4, NANOG and SOX2, into hubs of high gene activity. The observations detected in in vitro models, were investigated in smaller GAM datasets produced using the in vivo counterparts in the ICM. Overall, in vivo data confirmed the high degree of chromatin rearrangement among the two cell types, specifically in loci of lineage driving genes. The findings from in vivo data further underscore the connection of genome topology and cellular identity.
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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 zwischen Chromosomen im Zusammenhang mit Autismus Spektrum Störung auf ihre Relevanz in der Regulation von Genen. Zur allelspezifischen Detektion von Chromatinkontakten generierte ich einen GAM Datensatz der tausende von nuklearen Cryodünnschnitten enthält. Die Generierung dieser Daten beinhaltete die Entwicklung einer verbesserten Version der GAM Methode zur Produktion von großen Datensätzen in Hochdurchsatz. Hier zeige ich, dass GAM effizient Haplotyp-spezifische Chromatinkontakte bestimmen kann. Erste Untersuchungen von allelspezifischer 3D Genomtopologie zeigten weitreichende Unterschiede zwischen den Allelen, welche „A/B compartments“ und spezifische Chromatinkontakte beinhalten, wie zum Beispiel am Imprinting Locus H19/Igf2. Zur Untersuchung von interchromosomalen Kontakten detektierte ich Chromatinkontakte mit Hi-C im Kontext einer genomischen Deletion am humanen 16p11.2 Locus, assoziiert mit Autismus Spektrum Störung. Ich zeige hier, dass die Deletion am 16p11.2 Locus zu der Reorganisation von spezifischen interchromosomalen Kontakten zwischen 16p11.2 und Chromosom 18 führt, und stelle eine Hypothese auf wie diese interchromosomalen Kontakte zur ektopischen Aktivierung von Pcdh Genen auf Chromosom 18 führen. Protocadherins haben wichtige Funktionen in neuronaler Konnektivität, ein Prozess dessen Störung zur Manifestierung von Autismus Spektrum Störung beitragen könnte.
The 3D folding of interphase chromosomes inside the nucleus regulates important nuclear functions and once disrupted can lead to the manifestation of disease. Different techniques can be used to map 3D genome folding and detect pairwise and multiway interactions of the genome, or map the positions of DNA with respect to subnuclear compartments or the nuclear lamina. Here, I use GAM and Hi-C to explore two aspects of 3D genome topology, the allele specificity of chromatin contacts and long-range contacts between chromosomes, respectively. I detect specific contacts of the parental alleles in mouse embryonic stem cells and interactions between chromosomes in the context of congenital disease and study them with regard to their functionality and importance in mammalian gene regulation. For detecting chromatin contacts with allele specificity, I produced a GAM dataset containing thousands of nuclear slices. The collection of this data was accompanied by the development of a high-throughput version of GAM that allows the generation of large datasets. I show that GAM can determine haplotype-specific chromatin contacts with high efficiencies. First explorations of allele-specific chromatin topologies reveal many differences between the parental alleles, including allele-specific compartments A and B, and specific chromatin contacts, for example at the imprinted H19/Igf2 locus. For the exploration of inter-chromosomal contacts in disease, I mapped chromatin interactions with Hi-C in the context of a CNV at the human 16p11.2 locus, associated with autism spectrum disorders. Here, I show that the deletion at the 16p11.2 locus results in the rearrangement of specific inter-chromosomal contacts between the 16p11.2 locus and chromosome 18 and propose a role for these inter-chromosomal contact changes in the upregulation of the nearby Pcdhb gene cluster, which comprises protocadherin genes with important functions in neuronal connectivity during development.
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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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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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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 study this further I imaged and phenotyped the B73 (compact) x Ki3 (exploratory) mapping population. These data were used to map 102 quantitative trait loci (QTL). A large portion of these QTL had large, ranging from 5.48% to 23.8%. Majority of these QTLs were grouped into 9 clusters across the genome, with each cluster favoring either the compact of exploratory RSA. In summary, our study demonstrates the power of the gellan based system to locate loci controlling root system architecture of maize, by combining rapid and highly detailed imaging techniques with semi-automated computation phenotyping.


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Book chapters on the topic "Genome architecture mapping"

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Fiorillo, Luca, Mattia Conte, Andrea Esposito, Francesco Musella, Francesco Flora, Andrea M. Chiariello, and Simona Bianco. "Analysis of Genome Architecture Mapping Data with a Machine Learning and Polymer-Physics-Based Tool." In Euro-Par 2020: Parallel Processing Workshops, 321–32. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-71593-9_25.

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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, 257–67. Dordrecht: Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-4682-4_22.

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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, 1–19. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_1.

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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, 71–101. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_4.

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Houtgast, Ernst Joachim, Vlad-Mihai Sima, Koen Bertels, and Zaid Al-Ars. "GPU-Accelerated BWA-MEM Genomic Mapping Algorithm Using Adaptive Load Balancing." In Architecture of Computing Systems – ARCS 2016, 130–42. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-30695-7_10.

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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, 37–70. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31964-3_3.

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Hayat, Khezir, Adem Bardak, Mehboob-ur-Rahman, Hafiz Muhammad Imran, Furqan Ahmad, Donay Parlak, Muhammad Azam, et al. "Association Mapping for Improving Fiber Quality in Upland Cottons." In Plant Breeding - Current and Future Views. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.94405.

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Improved fiber yield is considered a constant goal of upland cotton (Gossypium hirsutum) breeding worldwide, but the understanding of the genetic basis controlling yield-related traits remains limited. Dissecting the genetic architecture of complex traits is an ongoing challenge for geneticists. Two complementary approaches for genetic mapping, linkage mapping and association mapping have led to successful dissection of complex traits in many crop species. Both of these methods detect quantitative trait loci (QTL) by identifying marker–trait associations, and the only fundamental difference between them is that between mapping populations, which directly determine mapping resolution and power. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information with the development of high-throughput genotyping, phenotyping will be a major challenge for genetic mapping studies. We believe that high-quality phenotyping and appropriate experimental design coupled with new statistical models will accelerate progress in dissecting the genetic architecture of complex traits.
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Pezzat, Michel, Hector Perez-Meana, Toru Nakashika, and Mariko Nakano. "Many-to-Many Symbolic Multi-Track Music Genre Transfer." In Knowledge Innovation Through Intelligent Software Methodologies, Tools and Techniques. IOS Press, 2020. http://dx.doi.org/10.3233/faia200572.

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This paper shows the feasibility of a variant of the Generative Adversarial Network (GAN), called Star GAN, for music genre transfer. This method is noteworthy in that it simultaneously learns many-to-many mappings across different attribute domains using a single generator network. A similar architecture to research in MuseGAN and CycleGAN is applied. Also, as in MGTGAN, Desert Camel MIDI dataset is use for training and testing.
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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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