Relevant bibliographies by topics / Systems Bioinformatics

Contents

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

Academic literature on the topic 'Systems Bioinformatics'

Author: Grafiati
Published: 3 June 2025
Last updated: 1 August 2025

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Journal articles on the topic "Systems Bioinformatics"

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Lee, Eunjung, and Doheon Lee. "Systems Bioinformatics Research Trends." Journal of Korean Society of Medical Informatics 14, no. 4 (2008): 313. http://dx.doi.org/10.4258/jksmi.2008.14.4.313.

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Lederman, Lynne. "Bioinformatics and Systems Biology." BioTechniques 46, no. 7 (2009): 501–3. http://dx.doi.org/10.2144/000113177.

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Ram, Prahlad T., John Mendelsohn, and Gordon B. Mills. "Bioinformatics and systems biology." Molecular Oncology 6, no. 2 (2012): 147–54. http://dx.doi.org/10.1016/j.molonc.2012.01.008.

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Suter-Crazzolara, C. "Bioinformatics, Databases and Systems." Briefings in Bioinformatics 1, no. 4 (2000): 417–18. http://dx.doi.org/10.1093/bib/1.4.417.

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Fellenberg, Matthias. "Developing integrative bioinformatics systems." BIOSILICO 1, no. 5 (2003): 177–83. http://dx.doi.org/10.1016/s1478-5382(03)02372-2.

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Benoît, Gerald. "Bioinformatics." Annual Review of Information Science and Technology 39, no. 1 (2006): 179–218. http://dx.doi.org/10.1002/aris.1440390112.

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Samudrala, R. "Structural Bioinformatics." Briefings in Bioinformatics 4, no. 3 (2003): 299–301. http://dx.doi.org/10.1093/bib/4.3.299.

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Podkolodnyy, N. L., and O. A. Podkolodnaya. "Ontologies in bioinformatics and systems biology." Vavilov Journal of Genetics and Breeding 19, no. 6 (2016): 652–60. http://dx.doi.org/10.18699/vj15.090.

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Shen, Bairong, Hong-Bin Shen, Tianhai Tian, Qiang Lü, and Guang Hu. "Translational Bioinformatics and Computational Systems Medicine." Computational and Mathematical Methods in Medicine 2013 (2013): 1–2. http://dx.doi.org/10.1155/2013/375641.

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Podkolodnyy, N. L., and O. A. Podkolodnaya. "Ontologies in bioinformatics and systems biology." Russian Journal of Genetics: Applied Research 6, no. 7 (2016): 749–58. http://dx.doi.org/10.1134/s2079059716070091.

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Dissertations / Theses on the topic "Systems Bioinformatics"

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Jauhiainen, Alexandra. "Evaluation and Development of Methods for Identification of Biochemical Networks." Thesis, Linköping University, The Department of Physics, Chemistry and Biology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-2811.

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<p>Systems biology is an area concerned with understanding biology on a systems level, where structure and dynamics of the system is in focus. Knowledge about structure and dynamics of biological systems is fundamental information about cells and interactions within cells and also play an increasingly important role in medical applications. </p><p>System identification deals with the problem of constructing a model of a system from data and an extensive theory of particularly identification of linear systems exists. </p><p>This is a master thesis in systems biology treating identification of b
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Ohler, Nathaniel Tobias. "Metaprogramming bioinformatics in the postgenomic era." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/ohler/OhlerN0506.pdf.

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mattei, gianluca. "Tumor Microenvironment: Bioinformatics and Systems Biology Approaches." Doctoral thesis, Università di Siena, 2019. http://hdl.handle.net/11365/1070301.

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Cancers develop in complex microenvironments whose importance was emerging during last years. In fact, cancer microenvironment influences tumor progression and leads to the raising of chemotherapics resistance. Thus, a shift of the focus from cancer cells to cancer cells in their environment is crucial for studying the molecular and metabolic features of tumors in physiological contexts. Within the microenvironment, cancer associated fibroblasts (CAF) are attracting the attention of scientific community since, up to date, it is clear that they are the main component involved in the organizatio
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Hayes, John A. "A Framework for Implementing Bioinformatics Knowledge-Exploration Systems." W&M ScholarWorks, 2004. https://scholarworks.wm.edu/etd/1539626830.

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Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066627/document.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn
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Malatras, Apostolos. "Bioinformatics tools for the systems biology of dysferlin deficiency." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066627.pdf.

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Le but de mon projet est de créer et d’appliquer des outils pour l’analyse de la biologie des systèmes musculaires en utilisant différentes données OMICS. Ce projet s’intéresse plus particulièrement à la dysferlinopathie due la déficience d’une protéine appelée dysferline qui est exprimée principalement dans les muscles squelettiques et cardiaque. La perte du dysferline due à la mutation (autosomique-récessive) du gène DYSF entraîne une dystrophie musculaire progressive (LGMD2B, MM, DMAT). Nous avons déjà développé des outils bio-informatiques qui peuvent être utilisés pour l’analyse fonctionn
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Markstedt, Olof. "Kubernetes as an approach for solving bioinformatic problems." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-330217.

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The cluster orchestration tool Kubernetes enables easy deployment and reproducibility of life science research by utilizing the advantages of the container technology. The container technology allows for easy tool creation, sharing and runs on any Linux system once it has been built. The applicability of Kubernetes as an approach to run bioinformatic workflows was evaluated and resulted in some examples of how Kubernetes and containers could be used within the field of life science and how they should not be used. The resulting examples serves as proof of concepts and the general idea of how i
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Niklasson, Markus. "Coding to cure : NMR and thermodynamic software applied to congenital heart disease research." Doctoral thesis, Linköpings universitet, Kemi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-142785.

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Regardless of scientific field computers have become pivotal tools for data analysis and the field of structural biology is not an exception. Here, computers are the main tools used for tasks including structural calculations of proteins, spectral analysis of nuclear magnetic resonance (NMR) spectroscopy data and fitting mathematical models to data. As results reported in papers heavily rely on software and scripts it is of key importance that the employed computational methods are robust and yield reliable results. However, as many scientific fields are niched and possess a small potential us
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Ishak, Helena. "Developing a ChIP-seq pipeline that analyzes the human genome and its repetitive sequences." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-335914.

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Tangruksa, Benyapa. "Extracellular vesicles (EVs):roles in cell proliferation and transcriptomic analysis of HUVEC receiving cancerderived EVs." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-20593.

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Extracellular vesicles (EVs) are released by almost  all types of cells. EVs play an    important role in cell-to-cell communication by sending biomolecules such as mRNAs to    other cells via endocytosis. This project aims to understand the roles of EVs and their    potential application as mRNA delivery vehicles by completing two objectives. One       objective was to investigate the EVs’ roles in cell proliferation by routinely removing EVs    from cell-conditioned media, transferring stress-induced EVs to recipient epithelial cells, and examining their cell number. Another objective was to
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Books on the topic "Systems Bioinformatics"

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Krawetz, Stephen, ed. Bioinformatics for Systems Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-440-7.

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Marcus, Frederick B. Bioinformatics and Systems Biology. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78353-4.

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Letovsky, Stanley, ed. Bioinformatics: Databases and Systems. Kluwer Academic Publishers, 2002. http://dx.doi.org/10.1007/b112979.

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Stanley, Letovsky, ed. Bioinformatics: Databases and systems. Kluwer Academic Publishers, 1999.

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Chan, Jonathan H., Yew-Soon Ong, and Sung-Bae Cho, eds. Computational Systems-Biology and Bioinformatics. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-16750-8.

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Opresko, Lee K. Advances in Systems Biology. Springer US, 2004.

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Cesario, Alfredo, and Frederick Marcus, eds. Cancer Systems Biology, Bioinformatics and Medicine. Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-1567-7.

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Institute of Electrical and Electronics Engineers, Inc. Staff. 2004 IEEE Computational Systems Bioinformatics Conference. IEEE Computer Society Press, 2004.

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Zhou, Xiaobo. Computational systems bioinformatics: Methods and biomedical applications. World Scientific, 2008.

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Jin, Yaochu, and Lipo Wang, eds. Fuzzy Systems in Bioinformatics and Computational Biology. Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-89968-6.

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Book chapters on the topic "Systems Bioinformatics"

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Marcus, Frederick B. "Bioinformatics." In Bioinformatics and Systems Biology. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78353-4_2.

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Pazos, Florencio, and Mónica Chagoyen. "Systems." In Practical Protein Bioinformatics. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-12727-9_3.

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Dandekar, Thomas, and Meik Kunz. "Systems Biology Helps to Discover Causes of Disease." In Bioinformatics. Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-65036-3_5.

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Dandekar, Thomas, and Meik Kunz. "Complex Systems Behave Fundamentally in a Similar Way." In Bioinformatics. Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-65036-3_9.

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He, Mingyan, Li Feng, and Jinglin Xia. "Cancer Bioinformatics." In Single Cell Sequencing and Systems Immunology. Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-017-9753-5_13.

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Wishart, David S. "Bioinformatics for Metabolomics." In Bioinformatics for Systems Biology. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-440-7_30.

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Wu, Duojiao, David E. Sanin, and Xiangdong Wang. "Clinical Applications and Systems Biomedicine." In Translational Bioinformatics. Springer Netherlands, 2016. http://dx.doi.org/10.1007/978-94-017-7543-4_13.

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Prusinkiewicz, Przemyslaw. "A look at the visual modeling of plants using L-systems." In Bioinformatics. Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/bfb0033200.

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Marcus, Frederick B. "Systems Biology." In Bioinformatics and Systems Biology. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78353-4_3.

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Tiwary, Basant K. "Systems Biology." In Bioinformatics and Computational Biology. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-4241-8_8.

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Conference papers on the topic "Systems Bioinformatics"

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"Bioinformatics track - bioinformatics track co-chairs." In 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems. IEEE, 2007. http://dx.doi.org/10.1109/bimnics.2007.4610107.

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"Bioinformatics track - chair: Bioinformatics track co-chairs." In 2007 2nd Bio-Inspired Models of Network, Information and Computing Systems. IEEE, 2007. http://dx.doi.org/10.1109/bimnics.2007.4610110.

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Wasnik, S., P. Donachy, T. Harmer, et al. "GeneGrid: From "Virtual" Bioinformatics Laboratory to "Smart" Bioinformatics Laboratory." In Proceedings. 19th IEEE International Symposium on Computer-Based Medical Systems. IEEE, 2006. http://dx.doi.org/10.1109/cbms.2006.90.

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Kolchanov, N. A. "Systems Computer Biology and Bioinformatics." In IX Congress of society physiologists of plants of Russia "Plant physiology is the basis for creating plants of the future". Kazan University Press, 2019. http://dx.doi.org/10.26907/978-5-00130-204-9-2019-17.

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Dong Xu, R. Bondugula, M. Popescu, and J. Keller. "Bioinformatics and Fuzzy Logic." In 2006 IEEE International Conference on Fuzzy Systems. IEEE, 2006. http://dx.doi.org/10.1109/fuzzy.2006.1681805.

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"Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003." In Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003. IEEE, 2003. http://dx.doi.org/10.1109/csb.2003.1227286.

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Giakos, George C., Stefanie Marotta, Suman Shrestha, et al. "Bioinformatics of Lung Cancer." In 2015 IEEE International Conference on Imaging Systems and Techniques (IST). IEEE, 2015. http://dx.doi.org/10.1109/ist.2015.7294524.

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Gough, E. S., and M. D. Kane. "Evaluating Parallel Computing Systems in Bioinformatics." In Third International Conference on Information Technology: New Generations (ITNG'06). IEEE, 2006. http://dx.doi.org/10.1109/itng.2006.62.

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"2004 IEEE Computational Systems Bioinformatics Conference." In Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004. IEEE, 2004. http://dx.doi.org/10.1109/csb.2004.1332397.

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"2004 IEEE Computational Systems Bioinformatics Conference." In Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004. IEEE, 2004. http://dx.doi.org/10.1109/csb.2004.1332399.

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Reports on the topic "Systems Bioinformatics"

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Chakraborty, Srijani. Promises and Challenges of Systems Biology. Nature Library, 2020. http://dx.doi.org/10.47496/nl.blog.09.

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Modern systems biology is essentially interdisciplinary, tying molecular biology, the omics, bioinformatics and non-biological disciplines like computer science, engineering, physics, and mathematics together.
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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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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.

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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specific
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Geib, Christopher, John M. Frazier, and Robert S. Cook. Air Force Genomics, Proteomics, Bioinformatics System, DataCap-Data Collection Module. Phase 1: Development. Defense Technical Information Center, 2004. http://dx.doi.org/10.21236/ada435020.

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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7598153.bard.

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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences betwee
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Barkan, Alice, and Zach Adam. The Role of Proteases in Regulating Gene Expression and Assembly Processes in the Chloroplast. United States Department of Agriculture, 2003. http://dx.doi.org/10.32747/2003.7695852.bard.

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Chloroplasts house many biochemical processes that are essential for plant viability. Foremost, among these is photosynthesis, which requires the protein-rich thylakoid membrane system. The activation of chloroplast genes encoding thylakoid membrane proteins and the targeting and assembly of these proteins together with their nuclear-encoded partners are essential for the elaboration of the thylakoid membrane. Several nuclear-encoded proteins that regulate chloroplast gene expression and that mediate the targeting of proteins to the thylakoid membrane have been identified in recent years, and
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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped
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Burdman, S., E. Welbaum, R. Walcott, and B. Zhao. erial fruit blotch, elucidating the mechanisms of fruit infection by Acidovorax citrulli. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134162.bard.

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Bacterial fruit blotch (BFB) of cucurbits is caused by the Gram-negative bacterium Acidovorax citrulli. BFB affects cucurbit production worldwide, and mainly watermelon and melon. Most A. citrulli strains are divided into two genetically differentiated groups: while group I strains have been mainly associated with melon and other non-watermelon cucurbits, group II strains are more aggressive on watermelon. Like many Gram-negative plant-pathogenic bacteria, A. citrulli relies on a functional type III secretion system (T3SS) for pathogenicity. The T3SS is responsible for direct secretion of bact
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Savaldi-Goldstein, Sigal, and Todd C. Mockler. Precise Mapping of Growth Hormone Effects by Cell-Specific Gene Activation Response. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7699849.bard.

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Plant yield largely depends on a complex interplay and feedback mechanisms of distinct hormonal pathways. Over the past decade great progress has been made in elucidating the global molecular mechanisms by which each hormone is produced and perceived. However, our knowledge of how interactions between hormonal pathways are spatially and temporally regulated remains rudimentary. For example, we have demonstrated that although the BR receptor BRI1 is widely expressed, the perception of BRs in epidermal cells is sufficient to control whole-organ growth. Supported by additional recent works, it is
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Burns, Malcom, and Gavin Nixon. Literature review on analytical methods for the detection of precision bred products. Food Standards Agency, 2023. http://dx.doi.org/10.46756/sci.fsa.ney927.

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The Genetic Technology (Precision Breeding) Act (England) aims to develop a science-based process for the regulation and authorisation of precision bred organisms (PBOs). PBOs are created by genetic technologies but exhibit changes which could have occurred through traditional processes. This current review, commissioned by the Food Standards Agency (FSA), aims to clarify existing terminologies, explore viable methods for the detection, identification, and quantification of products of precision breeding techniques, address and identify potential solutions to the analytical challenges presente
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