Relevant bibliographies by topics / Biomolecular Visualization

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Biomolecular Visualization'

Author: Grafiati
Published: 6 September 2023
Last updated: 31 July 2025

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Journal articles on the topic "Biomolecular Visualization"

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DOI, Junta. "Biomolecular Visualization." Journal of the Visualization Society of Japan 10, no. 39 (1990): 222–27. http://dx.doi.org/10.3154/jvs.10.222.

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Duncan, Bruce S., Tom J. Macke, and Arthur J. Olson. "Biomolecular visualization using AVS." Journal of Molecular Graphics 13, no. 5 (1995): 271–82. http://dx.doi.org/10.1016/0263-7855(95)00067-4.

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Song, Cheng Long, Chen Zou, Wen Ke Wang, and Si Kun Li. "An Integrated Framework for Biological Data Visualization." Advanced Materials Research 846-847 (November 2013): 1145–48. http://dx.doi.org/10.4028/www.scientific.net/amr.846-847.1145.

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In the field of bioinformatics visualization, integrating software and data in different levels is the development trend. This paper presents an integration framework for biomolecular structure and genome sequences visualization. The framework can effectively support the data and software interoperability of biomolecular structure / genome sequences visualization. Based on the framework, we developed an integrated visualization system, which provides some new comprehensive visualization functions. Preliminary trial showed that the framework has a good prospect in the research of bioinformatics
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Perlasca, Paolo, Marco Frasca, Cheick Tidiane Ba, et al. "Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools." PLOS ONE 15, no. 12 (2020): e0244241. http://dx.doi.org/10.1371/journal.pone.0244241.

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The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that e
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Xie, Jiang, Zhonghua Zhou, Kai Lu, Luonan Chen, and Wu Zhang. "Visualization of biomolecular networks' comparison on cytoscape." Tsinghua Science and Technology 18, no. 5 (2013): 515——521. http://dx.doi.org/10.1109/tst.2013.6616524.

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He, Weiwei, Yen-Lin Chen, Serdal Kirmizialtin, and Lois Pollack. "Visualization of biomolecular structures by WAXS and MD." Acta Crystallographica Section A Foundations and Advances 77, a1 (2021): a124. http://dx.doi.org/10.1107/s0108767321098755.

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Yi Ronggui, Xie Jiang, Zhang Huiran, Zhang Wu, and Shigeo Kawata. "BNVC: A Web-Oriented Biomolecular Network Visualization Platform." Journal of Next Generation Information Technology 4, no. 3 (2013): 151–59. http://dx.doi.org/10.4156/jnit.vol4.issue3.18.

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Kozlíková, B., M. Krone, M. Falk, et al. "Visualization of Biomolecular Structures: State of the Art Revisited." Computer Graphics Forum 36, no. 8 (2016): 178–204. http://dx.doi.org/10.1111/cgf.13072.

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Ando, Toshio, Takayuki Uchihashi, Noriyuki Kodera, et al. "High-speed AFM and nano-visualization of biomolecular processes." Pflügers Archiv - European Journal of Physiology 456, no. 1 (2007): 211–25. http://dx.doi.org/10.1007/s00424-007-0406-0.

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You, Qian, Shiaofen Fang, and Jake Yue Chen. "Gene Terrain: Visual Exploration of Differential Gene Expression Profiles Organized in Native Biomolecular Interaction Networks." Information Visualization 9, no. 1 (2008): 1–12. http://dx.doi.org/10.1057/ivs.2008.3.

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We propose a new network visualization technique using scattered data interpolation and surface rendering, based upon a foundation layout of a scalar field. Contours of the interpolated surfaces are generated to support multi-scale visual interaction for data exploration. Our framework visualizes quantitative attributes of nodes in a network as a continuous surface by interpolating the scalar field, therefore avoiding scalability issues typical in conventional network visualizations while also maintaining the topological properties of the original network. We applied this technique to the stud
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Dissertations / Theses on the topic "Biomolecular Visualization"

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Heberle, Henry. "Uma abordagem visual para análise comparativa de redes biomoleculares com apoio de diagramas de Venn." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/55/55134/tde-19032015-115427/.

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Sistemas biológicos podem ser representados por redes que armazenam não apenas informações de conectividade, mas também informações de características de seus nós. No contexto biomolecular, esses nós podem representar proteínas, metabólitos, entre outros tipos de moléculas. Cada molécula possui características anotadas e armazenadas em bases de dados como o Gene Ontology. A comparação visual dessas redes depende de ferramentas que permitam o usuário identificar diferenças e semelhanças entre as anotações feitas sobre as moléculas (atributos) e também sobre as interações conhecidas (conexões).
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Andrei, Raluca Mihaela. "Intuitive visualization of surface properties of biomolecules." Doctoral thesis, Scuola Normale Superiore, 2012. http://hdl.handle.net/11384/85945.

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In living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as Electrostatic Potential (EP) and hydropathy expressed as Molecular Lipophilic Potential (MLP). The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by phisicochemical programs and visualized as range of colours that vary according to the tool used and imposes the necessity o
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Bivall, Petter. "Touching the Essence of Life : Haptic Virtual Proteins for Learning." Doctoral thesis, Linköpings universitet, Medie- och Informationsteknik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-58994.

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This dissertation presents research in the development and use of a multi-modal visual and haptic virtual model in higher education. The model, named Chemical Force Feedback (CFF), represents molecular recognition through the example of protein-ligand docking, and enables students to simultaneously see and feel representations of the protein and ligand molecules and their force interactions. The research efforts have been divided between educational research aspects and development of haptic feedback techniques. The CFF model was evaluated in situ through multiple data-collections in a univers
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Ljunglöf, Anders. "Direct observation of biomolecule adsorption and spatial distribution of functional groups in chromatographic adsorbent particles." Doctoral thesis, Uppsala University, Surface Biotechnology, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1602.

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<p>Confocal microscopy has been used as a tool for studying adsorption of biomolecules to individual chromatographic adsorbent particles. By coupling a fluorescent dye to protein molecules, their penetration into single adsorbent particles could be observed visually at different times during batch uptake. By relating the relative fluorescence intensity obtained at different times to the value at equilibrium, the degree of saturation versus time could be constructed. The use of two different fluorescent dyes for protein labeling and two independent detectors, allowed direct observation of a two
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Sun, Xinyu. "The Control and Visualization of Intermolecular Interactions in Self-Assembly: From Star-Like and Dendron-Like Ionic Hybrid Macromolecules to Biomolecules." University of Akron / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=akron161980047445729.

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Masood, Talha Bin. "Geometric and Topological Methods for Biomolecular Visualization." Thesis, 2017. http://etd.iisc.ac.in/handle/2005/4324.

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Biomolecules like proteins are the basic building blocks of living systems. It has been observed that the structure of a biomolecule plays an important role in defining its function. In this thesis, we describe novel geometric and topological techniques to understand the structure of molecules. In particular, we focus on the problems related to identification and visualization of cavities and channels in proteins. Cavities refer to empty regions within the molecule, while channels are pathways through the cavities. We pursue an integrated geometric and topological approach towards solving the
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Masood, Talha Bin. "Geometric and Topological Methods for Biomolecular Visualization." Thesis, 2018. http://etd.iisc.ac.in/handle/2005/4300.

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Biomolecules like proteins are the basic building blocks of living systems. It has been observed that the structure of a biomolecule plays an important role in defining its function. In this thesis, we describe novel geometric and topological techniques to understand the structure of molecules. In particular, we focus on the problems related to identification and visualization of cavities and channels in proteins. Cavities refer to empty regions within the molecule, while channels are pathways through the cavities. We pursue an integrated geometric and topological approach towards solving the
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King, Ji-Jao, and 金繼昭. "Virtual Visualization of Biomolecules with Chromatic Anaglyph in Personal Computer." Thesis, 1996. http://ndltd.ncl.edu.tw/handle/66307541488158333566.

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碩士<br>國立中興大學<br>分子生物研究所<br>85<br>The relationship of macro biomolecular structure and function is veryimportant in the biological and biochemical system. Because of macrobiomolecular complexity, it is difficult to observe and analyze their threedimension conformations and quaternary structures. In order to solve theseproblems, we can use picture presentation to study and compare the structuresof macro biomolecules such as proteins and nucleic acids.
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(11198013), Kevin Wee. "Creation, deconstruction, and evaluation of a biochemistry animation about the role of the actin cytoskeleton in cell motility." Thesis, 2021.

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<p>External representations (ERs) used in science education are multimodal ensembles consisting of design elements to convey educational meanings to the audience. As an example of a dynamic ER, an animation presenting its content features (i.e., scientific concepts) via varying the feature’s depiction over time. A production team invited the dissertation author to inspect their creation of a biochemistry animation about the role of the actin cytoskeleton in cell motility and the animation’s implication on learning. To address this, the author developed a four-step methodology entitled the Mult
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Books on the topic "Biomolecular Visualization"

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Wang, Jason T. L., Bruce A. Shapiro, and Dennis Shasha, eds. Pattern Discovery in Biomolecular Data. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780195119404.001.0001.

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Finding patterns in biomolecular data, particularly in DNA and RNA, is at the center of modern biological research. These data are complex and growing rapidly, so the search for patterns requires increasingly sophisticated computer methods. Pattern Discovery in Biomolecular Data provides a clear, up-to-date summary of the principal techniques. Each chapter is self-contained, and the techniques are drawn from many fields, including graph theory, information theory, statistics, genetic algorithms, computer visualization, and vision. Since pattern searches often benefit from multiple approaches,
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Book chapters on the topic "Biomolecular Visualization"

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Natarajan, Vijay, Patrice Koehl, Yusu Wang, and Bernd Hamann. "Visual Analysis of Biomolecular Surfaces." In Mathematics and Visualization. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-72630-2_14.

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Halm, Andreas, Eva Eggeling, and Dieter W. Fellner. "Embedding Biomolecular Information in a Scene Graph System." In Mathematics and Visualization. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-21608-4_14.

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Simmerling, Carlos, Ron Elber, and Jing Zhang. "MOIL-View — A Program for Visualization of Structure and Dynamics of Biomolecules and STO — A Program for Computing Stochastic Paths." In Modelling of Biomolecular Structures and Mechanisms. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0497-5_20.

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Endo, Masayuki. "Single-Molecule Visualization of Biomolecules in the Designed DNA Origami Nanostructures Using High-Speed Atomic Force Microscopy." In Modified Nucleic Acids in Biology and Medicine. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-34175-0_17.

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Agamennone, Mariangela, Alessandro Nicoli, Sebastian Bayer, et al. "Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions." In Biomolecular Interactions Part A. Elsevier, 2021. http://dx.doi.org/10.1016/bs.mcb.2021.06.012.

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Howell, Gareth, and Kyle Dent. "Bioimaging: light and electron microscopy." In Tools and Techniques in Biomolecular Science. Oxford University Press, 2013. http://dx.doi.org/10.1093/hesc/9780199695560.003.0017.

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This chapter discusses the use of light and electron microscopy techniques to image biological structures. Bioimaging enables the visualization of different biological processes such as protein transport, the development or effect of disease, and mutations on a cellular and subcellular scale, and provides structural information on cells, organelles, and individual macromolecular complexes. The chapter looks at the technologies commonly used in studying cells and protein structures such as confocal microscopy, deconvolution microscopy, transmission electron microscopy, and scanning electron mic
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Shrestha, Bindesh. "Visualization in imaging mass spectrometry." In Introduction to Spatial Mapping of Biomolecules by Imaging Mass Spectrometry. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-12-818998-6.00003-6.

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Joshi, Hem Ch, Prabha Pant, Harsh Kumar Chauhan, and Anil Verma. "Revolutionizing Drug Discovery." In Advances in Chemical and Materials Engineering. IGI Global, 2025. https://doi.org/10.4018/979-8-3693-7473-3.ch008.

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Mass spectrometry (MS) has revolutionized drug discovery, offering unparalleled accuracy in identifying and quantifying biomolecules. Recent advancements, such as high-resolution MS, have enhanced sensitivity and resolution, enabling precise molecular characterization. Techniques like liquid chromatography-MS (LC-MS) and quantitative MS, including multiple reaction monitoring (MRM), have improved drug metabolism and pharmacokinetics studies. Imaging mass spectrometry (IMS) allows for the spatial visualization of drug distribution in tissues, providing insights into drug efficacy and safety. Th
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Costa, Everton Ricardo Carneiro, Adriana Ferreira Souza, Galba Maria de Campos Takaki, and Rosileide Fontenele da Silva Andrade. "Bioemulsifier production by Penicillium Citrinum UCP 1183 and microstructural characterization of emulsion droplets." In CONNECTING EXPERTISE MULTIDISCIPLINARY DEVELOPMENT FOR THE FUTURE. Seven Editora, 2023. http://dx.doi.org/10.56238/connexpemultidisdevolpfut-168.

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Bioemulsifying compounds (BE) are biomolecules of high molecular weight produced by microorganisms and have as their main action the ability to emulsify and stabilize emulsions. In this context, the objective of this work was to investigate the potential of the fungus Penicillium citrinum in the production of bioemulsifier from substrates of renewable origin (milhocine and whey) and to characterize by optical microscopy the droplets of the emulsion formed. For this purpose, Penicillium citrinum was grown in sabouraud medium at 28ºC until the mycelial carpet was obtained. After growth, 20 8mm d
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Madkour, Loutfy H. "Carbon Nanocomposites." In Emerging Engineering Technologies and Industrial Applications. IGI Global, 2024. http://dx.doi.org/10.4018/979-8-3693-1335-0.ch005.

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Successful deployment of carbon nanocomposites in many applications, such as sensing, energy storage, and catalysis, relies on the selection, synthesis, and tailoring of the surface properties. Carbon nanotubes, due to their large surface areas, unique surface properties, and needle-like shape, can deliver a lot of therapeutic agents, including DNA, siRNAs and proteins to the target disease sites. Carbon nanotubes can be readily excreted through the renal route by means of degradation through myeloperoxidase enzyme. Nanotubes are categorized as single-walled carbon nanotubes and multiple walle
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Conference papers on the topic "Biomolecular Visualization"

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Liu, Zhanping, and Robert J. Moorhead II. "Visualization of confocal microscopic biomolecular data." In Medical Imaging, edited by Robert L. Galloway, Jr. and Kevin R. Cleary. SPIE, 2005. http://dx.doi.org/10.1117/12.593652.

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Lindow, Norbert, Daniel Baum, Ana-Nicoleta Bondar, and Hans-Christian Hege. "Dynamic channels in biomolecular systems: Path analysis and visualization." In 2012 IEEE Symposium on Biological Data Visualization (BioVis). IEEE, 2012. http://dx.doi.org/10.1109/biovis.2012.6378599.

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Zhang, Huiran, Xiaolong Shen, Dongbo Dai, Weimin Xu, Jiang Xie, and Shigeo Kawata. "An efficient and interactive problem solving environment (PSE) for biomolecular networks visualization." In 2014 International Conference on Information Science, Electronics and Electrical Engineering (ISEEE). IEEE, 2014. http://dx.doi.org/10.1109/infoseee.2014.6947785.

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SANNER, M. F., B. S. DUNCAN, C. J.CARRILLO, and A. J. OLSON. "INTEGRATING COMPUTATION AND VISUALIZATION FOR BIOMOLECULAR ANALYSIS: AN EXAMPLE USING PYTHON AND AVS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1998. http://dx.doi.org/10.1142/9789814447300_0039.

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Bin Masood, Talha, and Vijay Natarajan. "An integrated geometric and topological approach to connecting cavities in biomolecules." In 2016 IEEE Pacific Visualization Symposium (PacificVis). IEEE, 2016. http://dx.doi.org/10.1109/pacificvis.2016.7465257.

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Howze, Patrick H., Naga S. Annamdevula, Anh-Vu Phan, D. J. Pleshinger, Thomas Rich, and Silas Leavesley. "Improving visualization of cAMP gradients using algorithmic modelling." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XX, edited by James F. Leary, Attila Tarnok, and Jessica P. Houston. SPIE, 2022. http://dx.doi.org/10.1117/12.2607772.

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Yamada, Hirofumi. "Functional Visualization of Biomolecules by FM-AFM and 3D Force Mapping Method." In 2021 International Conference on Solid State Devices and Materials. The Japan Society of Applied Physics, 2021. http://dx.doi.org/10.7567/ssdm.2021.g-5-01.

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Liu, Yang, Jianquan Xu, and Hongqiang Ma. "Visualization of disrupted chromatin folding at nanoscale in early carcinogenesis via super-resolution microscopy." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XIX, edited by James F. Leary, Attila Tarnok, and Irene Georgakoudi. SPIE, 2021. http://dx.doi.org/10.1117/12.2579259.

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Mai, Hanning, Simon P. Poland, Francesco Mattioli Della Rocca, et al. "Flow cytometry visualization and real-time processing with a CMOS SPAD array and high-speed hardware implementation algorithm." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVIII, edited by Daniel L. Farkas, James F. Leary, and Attila Tarnok. SPIE, 2020. http://dx.doi.org/10.1117/12.2544759.

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Abraham, Thomas, Gary Clawson, Christopher McGovern, et al. "Multiphoton and harmonic generation imaging methods enable direct visualization of drug nanoparticle carriers in conjunction with vasculature in fibrotic prostate tumor mouse model." In Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII, edited by Daniel L. Farkas, James F. Leary, and Attila Tarnok. SPIE, 2019. http://dx.doi.org/10.1117/12.2508833.

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Reports on the topic "Biomolecular Visualization"

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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other c
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Bajaj, Chandrajit L. Modeling and Visualization for Polymers, Surfaces and Biomolecules. Defense Technical Information Center, 1997. http://dx.doi.org/10.21236/ada336368.

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