Thematische Bibliographien / 3D genome structure

Inhaltsverzeichnis

  1. Zeitschriftenartikel
  2. Dissertationen
  3. Bücher
  4. Buchteile
  5. Konferenzberichte
  6. Berichte der Organisationen

Auswahl der wissenschaftlichen Literatur zum Thema „3D genome structure“

Autor: Grafiati
Veröffentlicht am 18. Mai 2024

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Zeitschriftenartikel zum Thema "3D genome structure"

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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 (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 e
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Mohanta, Tapan Kumar, Awdhesh Kumar Mishra, and Ahmed Al-Harrasi. "The 3D Genome: From Structure to Function." International Journal of Molecular Sciences 22, no. 21 (2021): 11585. http://dx.doi.org/10.3390/ijms222111585.

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The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding fact
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Huang, Kai, Yue Li, Anne R. Shim, et al. "Physical and data structure of 3D genome." Science Advances 6, no. 2 (2020): eaay4055. http://dx.doi.org/10.1126/sciadv.aay4055.

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With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topolog
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Heinz, Sven, Lorane Texari, Michael G. B. Hayes, et al. "Transcription Elongation Can Affect Genome 3D Structure." Cell 174, no. 6 (2018): 1522–36. http://dx.doi.org/10.1016/j.cell.2018.07.047.

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Wlasnowolski, Michal, Michal Sadowski, Tymon Czarnota, et al. "3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome." Nucleic Acids Research 48, W1 (2020): W170—W176. http://dx.doi.org/10.1093/nar/gkaa388.

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Abstract Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue o
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Shepherd, Jeremiah J., Lingxi Zhou, William Arndt, Yan Zhang, W. Jim Zheng, and Jijun Tang. "Exploring genomes with a game engine." Faraday Discuss. 169 (2014): 443–53. http://dx.doi.org/10.1039/c3fd00152k.

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More and more evidence indicates that the 3D conformation of eukaryotic genomes is a critical part of genome function. However, due to the lack of accurate and reliable 3D genome structural data, this information is largely ignored and most of these studies have to use information systems that view the DNA in a linear structure. Visualizing genomes in real time 3D can give researchers more insight, but this is fraught with hardware limitations since each element contains vast amounts of information that cannot be processed on the fly. Using a game engine and sophisticated video game visualizat
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Poblete, Simón, and Horacio V. Guzman. "Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models." Viruses 13, no. 8 (2021): 1555. http://dx.doi.org/10.3390/v13081555.

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Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based
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Trieu, Tuan, and Jianlin Cheng. "3D genome structure modeling by Lorentzian objective function." Nucleic Acids Research 45, no. 3 (2016): 1049–58. http://dx.doi.org/10.1093/nar/gkw1155.

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Li, Chao, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, and Yixue Li. "The 3DGD: a database of genome 3D structure." Bioinformatics 30, no. 11 (2014): 1640–42. http://dx.doi.org/10.1093/bioinformatics/btu081.

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Tjong, Harianto, Wenyuan Li, Reza Kalhor, et al. "Population-based 3D genome structure analysis reveals driving forces in spatial genome organization." Proceedings of the National Academy of Sciences 113, no. 12 (2016): E1663—E1672. http://dx.doi.org/10.1073/pnas.1512577113.

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Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Our approach incorporates the stochastic natu
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Dissertationen zum Thema "3D genome structure"

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Mendieta, Esteban Julen 1992. "Chromatin 3D modelling from sparse 3C-based datasets." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/670311.

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Genome spatial organisation and transcriptional activity are tightly coordinated to ensure the correct function of the cell. Thus, proper understanding of the chromatin organisation is needed to deepen into the processes regulating the activity of specific loci of interest. In this matter, Chromatin Conformation Capture (3C)-based technologies have helped to increase the understanding of the genomic interaction landscape. Particularly, sparse 3C technologies, like promoter capture Hi-C (pcHi-C), have focused on specific interactions of interest to unveil the interaction landscape associated wi
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Han, Chenggong. "Statistical models and computational methods for studying DNA differential methylation and 3D genome structure." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1595417277891892.

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Segueni, Julie. "DNA methylation changes CTCF binding and reorganizes 3D genome structure in breast cancer cells." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL020.

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Les génomes des mammifères adoptent une organisation 3D fonctionnelle où les interactions entre les enhancers et les promoteurs des gènes sont contenues à l'intérieur de domaines d'association topologique (TADs). La protéine insulatrice CTCF a deux rôles dans ce processus : sa liaison aux promoteurs permettant la formation de boucles enhancers-promoteurs (structure intra-TAD) et sa liaison aux frontières des TADs empêchant la formation de boucles ectopiques entre domaines voisins. Surtout, les perturbations de la liaison de la protéine CTCF à des sites particuliers dans des cellules cancéreuse
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Varoquaux, Nelle. "Inférence de la structure tri-dimensionnelle du génome." Thesis, Paris, ENMP, 2015. http://www.theses.fr/2015ENMP0059/document.

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La structure de l'ADN, des chromosomes et l'organisation du génome sont des sujets fascinants du monde de la biologie. La plupart de la recherche s'est concentrée sur la structure unidimensionnelle du génome, étudiant comment les gènes et les chromosomes sont organisés, et le lien entre l'organisation unidimensionnelle et la régulation des gènes, l'épissage, la méthylation… Cependant, le génome est avant tout organisé dans un espace euclidien tridimensionnel, et cette structure 3D, bien que moins étudiée, joue elle aussi un rôle important dans la fonction génomique de la cellule. La capture de
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Svensson, Niclas. "Structure from Motion with Unstructured RGBD Data." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-302553.

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This thesis covers the topic of depth- assisted Structure from Motion (SfM). When performing classic SfM, the goal is to reconstruct a 3D scene using only a set of unstructured RGB images. What is attempted to be achieved in this thesis is adding the depth dimension to the problem formulation, and consequently create a system that can receive a set of RGBD images. The problem has been addressed by modifying an already existing SfM pipeline and in particular, its Bundle Adjustment (BA) process. Comparisons between the modified framework and the baseline framework resulted in conclusions regardi
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Votroubek, Lukáš. "Webový server pro predikci 3D struktury proteinu." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2013. http://www.nusl.cz/ntk/nusl-236225.

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This work deals with proteins, especially with their structure and kinds of tertiary, or 3D, structure prediction. Tertiary structure prediction is very important for function prediction of this vitally important substance. Bioinformatics do this prediction much more effective and faster, because classical methods of structure prediction directly from molecule are very expensive and slow. On the other hand they are much more exact. Objective of this thesis is to describe tertiary structure prediction methods, describe used tools and possibility of automatic communication with them.  Next objec
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Berselli, Michele. "Development and Application of Informatics Tools for the Detection and Analysis of Non-Canonical DNA Structures." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3425749.

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The DNA is a flexible and heterogeneous molecule that can adopt different local conformations alternative to the classical double-helix. These noncanonical structures are known as non-B DNAs. These conformers appear to play an important role in different physiological and pathological cellular conditions and influence many biochemical properties of the genome. The formation of these structures is dependent upon specific features of the DNA sequence and different patterns may lead to the formation of different non-B DNAs. Due to lack of updated and flexible computational methods, during these
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Manoharan, Malini. "Genomic, structural and functional characterization of odorant binding proteins in olfaction of mosquitoes involved in infectious disease transmission." Phd thesis, Université de la Réunion, 2011. http://tel.archives-ouvertes.fr/tel-00979587.

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The role of odorant binding proteins in the olfaction of mosquitoes, the primary mechanism of human host recognition, has been an important focus of biological research in the field of infectious disease transmission by these insects. This thesis provides an in depth knowledge of these proteins in three mosquito species Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus. A large scale analysis on these genomes has been carried out towards the identification of the odorant binding proteins in the mosquito genomes. Identification of many new OBP members, in particular in the Aedes aegyp
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Matala, Ilunga Benjamin. "Une correction à l’échelle et progressive des données Hi-C révèlent des principes fondamentaux de l’organisation tridimensionnelle et fonctionnelle du génome." Thèse, 2016. http://hdl.handle.net/1866/18662.

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Au cours des dernières années, de nouvelles évidences semblent indiquer que, tout autant que sa séquence, l’organisation d’un génome dans l’espace et le temps est importante pour comprendre la fonction de celui-ci. Une des avancées fonda- mentales sur le sujet a été de présenter à l’échelle du génome la carte des inter- actions ADN-ADN. Ces interactions sont essentiellement de 2 types, soit entre chromosomes ou entre régions du même chromosome. Par la suite, la modélisa- tion a permis de visualiser et appréhender la structure tridimensionnelle (3D) du génome à partir des donn
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Bücher zum Thema "3D genome structure"

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Tiana, Guido, and Luca Giorgetti. Modeling the 3D Conformation of Genomes. Taylor & Francis Group, 2019.

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Tiana, Guido, and Luca Giorgetti. Modeling the 3D Conformation of Genomes. Taylor & Francis Group, 2019.

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The connection of brains theory: Brain,brain waves,mind,physiology of brain,cosmic memory,humanaly memory,unlimited memory,limited memory,limbic system,thalamus,hypothalamus,midbrain,cortex, cerebral cortex, cerebral cortex ,cerebellum,cerebellar cortex,neuron,neurons,gray neurons,white neuronal,CNS,think,thoughts,Nervous system,Monkey brain,Brain Animals,Animal memory,central nervous system,smart energy,intelligent energy, intelligence creation,smartness animals,physiology of thinking,the cosmic memory,thinking system,limbic system, the cerebral cortex, brain waves, Humanaly understanding, universal memory, five senses, experiences, Human Magical Talent, book "Human Magical Talent", empirical understanding, the Spherical shape of the head,Walking on two legs, structural differences of the skull, genotype of cortical neurons, cortical neurons, past experiences, see, hear, touch, Clever behaviors, up the cortical lobes of the brain, cortical lobes, cortical lobes of the brain, Fornal lobe, planning and decisions, , planning, decisions, temporal lobe, occipital lobe, deeper parts of the brain, deep processing, brain through, genetics, phenotype,genotype, the cortical lobes, cortical lobes, HMT theory, HMT, communication of brains theory, 2% difference of the genome of brain neurons, The spherical shape of the human head, grooves of the brain, grooves, Neocortex neurons, Neocortex, brain grooves, brain proteins, catecholamines, mental habits, human cognitive abilities ,mental experience , dream, Sensory receptors, Dendrit , dendritic spines, motor neurons, hippocampus, sensory dendrites, meaningful electrical pulses, brain reactions, experiences received, shape of the brain(3D oval mode), dendritic branches , brain satellite dish full of grooves, pyramidal neurons of the neocortex , Purkinje neurons, fantastic brain, fantastic mind, grooves on the surface of the brain, grooves in the cortex, mammalian brain, cognitive abilities, human brain neurons, creativity determine, animal creativity, HMT talent, Creativity in humans, science of psychology, psychology, The idea of HMT, negative thoughts, Mental Experience, the connection of the brain to cosmic memory,koorosh behzad,. archive.org publisher, 2022.

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Buchteile zum Thema "3D genome structure"

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Polles, Guido, Nan Hua, Asli Yildirim, and Frank Alber. "Genome Structure Calculation through Comprehensive Data Integration." In Modeling the 3D Conformation of Genomes. CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-11.

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Casadio, R., P. Fariselli, P. L. Martelli, A. Pierleoni, I. Rossi, and G. von Heijne. "The state of the art of membrane protein structure prediction: from sequence to 3D structure." In Modern Genome Annotation. Springer Vienna, 2008. http://dx.doi.org/10.1007/978-3-211-75123-7_15.

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Ivanisenko, V. A., S. S. Pintus, D. A. Grigorovich, L. N. Ivanisenko, V. A. Debelov, and A. M. Matsokin. "PDBSiteScan: A Program Searching for Functional Sites in Protein 3D Structures." In Bioinformatics of Genome Regulation and Structure. Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-7152-4_20.

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Papale, Andrea, and Angelo Rvosay. "Structure and Microrheology of Genome Organization: From Experiments to Physical Modeling." In Modeling the 3D Conformation of Genomes. CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-7.

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Paro, Renato, Ueli Grossniklaus, Raffaella Santoro, and Anton Wutz. "Biology of Chromatin." In Introduction to Epigenetics. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-68670-3_1.

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AbstractThis chapter provides an introduction to chromatin. We will examine the organization of the genome into a nucleosomal structure. DNA is wrapped around a globular complex of 8 core histone proteins, two of each histone H2A, H2B, H3, and H4. This nucleosomal arrangement is the context in which information can be established along the sequence of the DNA for regulating different aspects of the chromosome, including transcription, DNA replication and repair processes, recombination, kinetochore function, and telomere function. Posttranslational modifications of histone proteins and modifications of DNA bases underlie chromatin-based epigenetic regulation. Enzymes that catalyze histone modifications are considered writers. Conceptually, erasers remove these modifications, and readers are proteins binding these modifications and can target specific functions. On a larger scale, the 3-dimensional (3D) organization of chromatin in the nucleus also contributes to gene regulation. Whereas chromosomes are condensed during mitosis and segregated during cell division, they occupy discrete volumes called chromosome territories during interphase. Looping or folding of DNA can bring regulatory elements including enhancers close to gene promoters. Recent techniques facilitate understanding of 3D contacts at high resolution. Lastly, chromatin is dynamic and changes in histone occupancy, histone modifications, and accessibility of DNA contribute to epigenetic regulation.
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Wang, Yubo, Yanlin Feng, Deyan Wang, and Tao Ma. "Structural Variations and 3D Structure of the Populus Genus." In Compendium of Plant Genomes. Springer International Publishing, 2024. http://dx.doi.org/10.1007/978-3-031-50787-8_2.

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Benedetti, Fabrizio, Dusan Racko, Julien Dorier, and Andrzej Stasiak. "Introducing Supercoiling into Models of Chromosome Structure." In Modeling the 3D Conformation of Genomes. CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-6.

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Gherardi, Marco, Vittore Scolari, Remus Thei Dame, and Marco Cosentino Lagomarsino. "Chromosome Structure and Dynamics in Bacteria: Theory and Experiments." In Modeling the 3D Conformation of Genomes. CRC Press, 2019. http://dx.doi.org/10.1201/9781315144009-9.

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Bhowmick, Biplab Kumar. "Possibility of Uncoding Structural Organization of Genome in Rice Research: Prospects and Approaches by 3D Genome Sequencing." In Applications of Bioinformatics in Rice Research. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-3997-5_1.

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Sætre, Glenn-Peter, and Mark Ravinet. "Sequencing the genome and beyond." In Evolutionary Genetics. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198830917.003.0010.

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Science is defined by continual progress and new technologies. This final chapter starts with introducing what it means to sequence and assemble a reference genome. It is easy to forget that the true genome is not linear but has structure and function. In this chapter the genome is explored as a 3D entity—from how it is transcribed, to how proteins interact with it, and finally to how it is actually structured. This also gives an opportunity to focus on epigenetics and how to interpret processes such as DNA methylation in an evolutionary context. The second part of the chapter focuses on ways we can interact with the genome—exploring how we might test the function and role that candidate genes play. The chapter introduces transgenics, in particular the transformative technology of CRISPR/CAS9, and explores how this might change the face of evolutionary biology in the near future.
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Konferenzberichte zum Thema "3D genome structure"

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"3D-,odels creation based on solid tumor." 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-2020-311.

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Trieu, Tuan, and Jianlin Cheng. "3D Genome Structure Modeling by Lorentzian Objective Function." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM, 2017. http://dx.doi.org/10.1145/3107411.3107455.

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"Simulating of 3D genome data with predefined chromosomal rearrangements." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-062.

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"Insights into the 3D-genome organization in malaria mosquitoes." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-059.

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"3D-2 heterogeneous breast cancer models." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-489.

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"Laser 3D-modeling in research of molecular features of skin lymphatic vessels in the patients with urticaria pigmentosa." 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-2020-296.

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"Multi-class abdominal aortic aneurysm segmentation via 3D neural networks." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-674.

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"Processing of serial microscopic images for 3D reconstruction of plant tissues." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-375.

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"Autophagy activation in 3D-spheroid leads to the mesenchymal stem cells rejuvenation." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-623.

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"804 BGRS/SB-2022 Artificial intelligence (AI) of 3D MRI images for neurooncology." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-466.

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Berichte der Organisationen zum Thema "3D genome structure"

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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are
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