Relevant bibliographies by topics / Bioinformatics tools

Contents

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

Academic literature on the topic 'Bioinformatics tools'

Author: Grafiati
Published: 4 June 2021
Last updated: 26 July 2025

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Journal articles on the topic "Bioinformatics tools"

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Lomberk, Gwen. "Bioinformatics tools." Pancreatology 5, no. 4-5 (2005): 314–15. http://dx.doi.org/10.1159/000086531.

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Moreews, François, Olivier Sallou, Hervé Ménager, et al. "BioShaDock: a community driven bioinformatics shared Docker-based tools registry." F1000Research 4 (December 14, 2015): 1443. http://dx.doi.org/10.12688/f1000research.7536.1.

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Linux container technologies, as represented by Docker, provide an alternative to complex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docke
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Grisham, William, Natalie A. Schottler, Joanne Valli-Marill, Lisa Beck, and Jackson Beatty. "Teaching Bioinformatics and Neuroinformatics by Using Free Web-based Tools." CBE—Life Sciences Education 9, no. 2 (2010): 98–107. http://dx.doi.org/10.1187/cbe.09-11-0079.

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This completely computer-based module's purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together several important bioinformatic tools so students can grasp how these tools are used in answering research questions. Students integrate information gathered from websites dealing with anatomy (Mouse Brain Library), quantitative trait locus analysis (WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, National Center for Biotechnology Information's Entrez Gene, and th
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Zhang, Xiaorong. "Teaching Botany Using Bioinformatics Tools." Creative Education 10, no. 10 (2019): 2137–46. http://dx.doi.org/10.4236/ce.2019.1010155.

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Cantó‐Pastor, Alex, G. Alex Mason, Siobhan M. Brady, and Nicholas J. Provart. "Arabidopsis bioinformatics: tools and strategies." Plant Journal 108, no. 6 (2021): 1585–96. http://dx.doi.org/10.1111/tpj.15547.

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Skuse, Gary R., and Chunguang Du. "Bioinformatics Tools for Plant Genomics." International Journal of Plant Genomics 2008 (June 11, 2008): 1–2. http://dx.doi.org/10.1155/2008/910474.

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Arndt, Timothy. "Visual software tools for bioinformatics." Journal of Visual Languages & Computing 19, no. 2 (2008): 291–301. http://dx.doi.org/10.1016/j.jvlc.2007.06.001.

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Margolis, David J., Nandita Mitra, Bradley Wubbenhorst, and Katherine L. Nathanson. "Filaggrin sequencing and bioinformatics tools." Archives of Dermatological Research 312, no. 2 (2019): 155–58. http://dx.doi.org/10.1007/s00403-019-01956-3.

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Arora, Pankaj Kumar, and Wenxin Shi. "Tools of bioinformatics in biodegradation." Reviews in Environmental Science and Bio/Technology 9, no. 3 (2010): 211–13. http://dx.doi.org/10.1007/s11157-010-9211-x.

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Lomberk, Gwen. "Educational Websites — Bioinformatics Tools II." Pancreatology 9, no. 1-2 (2009): 4–5. http://dx.doi.org/10.1159/000178767.

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Dissertations / Theses on the topic "Bioinformatics tools"

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Sentausa, Erwin. "Time course simulation replicability of SBML-supporting biochemical network simulation tools." Thesis, University of Skövde, School of Humanities and Informatics, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-33.

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<p>Background: Modelling and simulation are important tools for understanding biological systems. Numerous modelling and simulation software tools have been developed for integrating knowledge regarding the behaviour of a dynamic biological system described in mathematical form. The Systems Biology Markup Language (SBML) was created as a standard format for exchanging biochemical network models among tools. However, it is not certain yet whether actual usage and exchange of SBML models among the tools of different purpose and interfaces is assessable. Particularly, it is not clear whether dyna
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Berry, Eric Zachary 1980. "Bioinformatics and database tools for glycans." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/27085.

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Thesis (M. Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2004.<br>Includes bibliographical references (leaves 75-76).<br>Recent advances in biology have afforded scientists with the knowledge that polysaccharides play an active role in modulating cellular activities. Glycosaminoglycans (GAGs) are one such family of polysaccharides that play a very important role in regulating the functions of numerous important signaling molecules and enzymes in the cell. Developing bioinformatics tools has been integral to advancing genomics and p
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Meng, Da. "Bioinformatics tools for evaluating microbial relationships." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Spring2009/d_meng_042209.pdf.

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Thesis (Ph. D.)--Washington State University, May 2009.<br>Title from PDF title page (viewed on June 8, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references.
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Martini, Paolo. "Dissecting the transcriptome complexity with bioinformatics tools." Doctoral thesis, Università degli studi di Padova, 2012. http://hdl.handle.net/11577/3422923.

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Bioinformatics has acquired a lot of importance especially with the advent of genomic approaches. The large amount of data produced by ``omics'' experiments requires appropriate frameworks to handle, store and mine the information and to derive appropriate work hypotheses. Transcriptome is defined as the whole amount of RNA molecules produced by a cell that provides the bridge between the genome and proteins. RNA molecules can be divided in two major classes: protein coding RNAs or messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). While the first class has been the most studied in the last
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Strafford, J. "Docking and bioinformatics tools to guide enzyme engineering." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1339145/.

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The carbon-carbon bond forming ability of transketolase (TK), along with its broad substrate specificity, makes it very attractive as a biocatalyst in industrial organic synthesis. Through the production of saturation mutagenesis libraries focused on individual active site residues, several variants of TK have been discovered with enhanced activities on non-natural substrates. We have used computational and bioinformatics tools to increase our understanding of TK and to guide engineering of the enzyme for further improvements in activity. Computational automated docking is a powerful technique
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Petri, Eric D. C. "Bioinformatics Tools for Finding the Vocabularies of Genomes." Ohio University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1213730223.

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Mahram, Atabak. "FPGA acceleration of sequence analysis tools in bioinformatics." Thesis, Boston University, 2013. https://hdl.handle.net/2144/11126.

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Thesis (Ph.D.)--Boston University<br>With advances in biotechnology and computing power, biological data are being produced at an exceptional rate. The purpose of this study is to analyze the application of FPGAs to accelerate high impact production biosequence analysis tools. Compared with other alternatives, FPGAs offer huge compute power, lower power consumption, and reasonable flexibility. BLAST has become the de facto standard in bioinformatic approximate string matching and so its acceleration is of fundamental importance. It is a complex highly-optimized system, consisting of tens of t
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Stenberg, Johan. "Software Tools for Design of Reagents for Multiplex Genetic Analyses." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6832.

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Parida, Mrutyunjaya. "Exploring and analyzing omics using bioinformatics tools and techniques." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6244.

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During the Human Genome Project the first hundred billion bases were sequenced in four years, however, the second hundred billion bases were sequenced in four months (NHGRI, 2013). As efforts were made to improve every aspect of sequencing in this project, cost became inversely proportional to the speed (NHGRI, 2013). Human Genome Project ended in April 2003 but research in faster and cheaper ways to sequence the DNA is active to date (NHGRI, 2013). On the one hand, these advancements have allowed the convenient and unbiased generation and interrogation of a variety of omics datasets; on the o
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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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Books on the topic "Bioinformatics tools"

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Bosu, Orpita. Bioinformatics: Database, tools, algorithms. Oxford University Press, 2007.

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1978-, Stajich Jason Eric, Hansen David, and SpringerLink (Online service), eds. Bioinformatics: Tools and Applications. Springer-Verlag New York, 2009.

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Association, Information Resources Management. Bioinformatics: Concepts, methodologies, tools, and applications. Medical Information Science Reference, 2013.

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Koča, Jaroslav, Radka Svobodová Vařeková, Lukáš Pravda, et al. Structural Bioinformatics Tools for Drug Design. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-47388-8.

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Malviya, Rishabha, Pramod Kumar Sharma, Sonali Sundram, Rajesh Kumar Dhanaraj, and Balamurugan Balusamy. Bioinformatics Tools and Big Data Analytics for Patient Care. Chapman and Hall/CRC, 2022. http://dx.doi.org/10.1201/9781003226949.

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Schmitz, Ulf. MicroRNA Cancer Regulation: Advanced Concepts, Bioinformatics and Systems Biology Tools. Springer Netherlands, 2013.

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Srinivasa, K. G., G. M. Siddesh, and S. R. Manisekhar, eds. Statistical Modelling and Machine Learning Principles for Bioinformatics Techniques, Tools, and Applications. Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-2445-5.

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Paton, Ray. Computation in Cells and Tissues: Perspectives and Tools of Thought. Springer Berlin Heidelberg, 2004.

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Smagula, Cynthia S. Bioinformation on the World Wide Web: An annotated directory of molecular biology tools. BIOTA Publications, 1996.

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Høiriis, Nielsen Jens, and Jewett Michael C, eds. Metabolomics: A powerful tool in systems biology. Springer, 2007.

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Book chapters on the topic "Bioinformatics tools"

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Imelfort, Michael. "Sequence Comparison Tools." In Bioinformatics. Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-92738-1_2.

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Zweigenbaum, Pierre, and Dina Demner-Fushman. "Advanced Literature-Mining Tools." In Bioinformatics. Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-92738-1_17.

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Luo, Jingchu. "Applied Bioinformatics Tools." In Basics of Bioinformatics. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-38951-1_9.

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Gupta, Aeshna, Disha Gangotia, and Indra Mani. "Bioinformatics Tools and Software." In Advances in Bioinformatics. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-33-6191-1_2.

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Liebler, Daniel C. "Bioinformatics Tools for Proteomics." In Proteomics for Biological Discovery. John Wiley & Sons, Inc., 2006. http://dx.doi.org/10.1002/0470007745.ch15.

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Raman, Maya. "Bioinformatics and Computational Tools." In Fish Structural Proteins and its Derivatives: Functionality and Applications. Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-97-2562-5_5.

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Betsy, C. Judith, and C. Siva. "Bioinformatics Tools and Techniques." In Fisheries Biotechnology and Bioinformatics. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-99-6991-3_22.

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Bandi, Venkat, Carl Gutwin, Jorge Núñez Siri, Eric Neufeld, Andrew Sharpe, and Isobel Parkin. "Visualization Tools for Genomic Conservation." In Plant Bioinformatics. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2067-0_16.

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Bourque, Guillaume, and Glenn Tesler. "Computational Tools for the Analysis of Rearrangements in Mammalian Genomes." In Bioinformatics. Humana Press, 2008. http://dx.doi.org/10.1007/978-1-60327-159-2_20.

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Singh, Gautam B. "Alignment Tools." In Fundamentals of Bioinformatics and Computational Biology. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-11403-3_8.

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Conference papers on the topic "Bioinformatics tools"

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Elmakki, Shimaa M., Marwa M. A. Hadhoud, and Vidan F. Ghoneim. "Investigation of Amyotrophic Lateral Sclerosis Using Bioinformatics Tools." In 2025 42nd National Radio Science Conference (NRSC). IEEE, 2025. https://doi.org/10.1109/nrsc65659.2025.11018550.

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Falvo, Fedra Rosita, and Mario Cannataro. "Explainability in Artificial Intelligence: Techniques, Tools and Applications in Medicine and Bioinformatics." In 2024 Fourth International Conference on Digital Data Processing (DDP). IEEE, 2024. https://doi.org/10.1109/ddp64453.2024.00026.

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Vasireddy, Indrani, K. Ashwini, B. Sriveni, and G. Sri Ramya. "Compositional and Structural Analysis for Non-Insulin Dependent Diabetes through Artificial Intelligence and Bioinformatics Tools." In 2025 7th International Conference on Signal Processing, Computing and Control (ISPCC). IEEE, 2025. https://doi.org/10.1109/ispcc66872.2025.11039575.

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Li, Xin, Yadong Liu, Zhongbo Yang, Yadong Wang, and Tao Jiang. "Comprehensive Benchmarking of Genotype Imputation Tools Using a Large-Scale Chinese Reference Panel." In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2024. https://doi.org/10.1109/bibm62325.2024.10822265.

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Yang, Zhongbo, Zhenhao Lu, Xin Li, Tao Jiang, Yadong Wang, and Yadong Liu. "Comprehensive evaluation of haplotype phasing tools with different strategies across diverse sequence technologies." In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2024. https://doi.org/10.1109/bibm62325.2024.10822156.

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Martins, Inês Branco, Jorge Miguel Silva, and João Rafael Almeida. "A comprehensive study of databases to assess the reliability of metagenomic tools." In 2024 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2024. http://dx.doi.org/10.1109/cibcb58642.2024.10702118.

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Baykal, Pelin Icer, Niko Beerenwinkel, and Serghei Mangul. "Reproducibility of Bioinformatics Tools." In 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). IEEE, 2022. http://dx.doi.org/10.1109/ipdpsw55747.2022.00046.

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Bartlett, Joan C., Yusuke Ishimura, and Lorie A. Kloda. "Scientists' preferences for bioinformatics tools." In the 4th Information Interaction in Context Symposium. ACM Press, 2012. http://dx.doi.org/10.1145/2362724.2362761.

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Cannataro, Mario, and Pietro H. Guzzi. "A taxonomy for bioinformatics tools." In BCB '14: ACM-BCB '14. ACM, 2014. http://dx.doi.org/10.1145/2649387.2660852.

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Skapavets, K., and R. Smolyakova. "BIOINFORMATICS TOOLS FOR METAGENOME SEQUENCING." In SAKHAROV READINGS 2020: ENVIRONMENTAL PROBLEMS OF THE XXI CENTURY. Minsk, ICC of Minfin, 2020. http://dx.doi.org/10.46646/sakh-2020-2-259-262.

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Reports on the topic "Bioinformatics tools"

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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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Beckstrom-Sternberg, Stephen. Bioinformatic Tools for Metagenomic Analysis of Pathogen Backgrounds and Human Microbial Communities. Defense Technical Information Center, 2010. http://dx.doi.org/10.21236/ada581677.

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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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Altindis, E., R. Cozzi, B. Di Palo, et al. Protectome analysis: a new selective bioinformatics tool for bacterial vaccine candidate discovery. Cold Spring Harbor Laboratory, 2014. http://dx.doi.org/10.1101/002089.

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Fromm, Hillel, Paul Michael Hasegawa, and Aaron Fait. Calcium-regulated Transcription Factors Mediating Carbon Metabolism in Response to Drought. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7699847.bard.

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Original objectives: The long-term goal of the proposed research is to elucidate the transcription factors, genes and metabolic networks involved in carbon metabolism and partitioning in response to water deficit. The proposed research focuses on the GTLcalcium/calmodulinbindingTFs and the gene and metabolic networks modulated by these TFs in Arabidopsis thaliana. The specific objectives are as follows. Objective-1 (USA): Physiological analyses of GTL1 loss- and gain-of-function plants under water sufficient and drought stress conditions Objective 2 (USA / Israel-TAU): Characterizion of GTL ta
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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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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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Gershoni, Jonathan M., David E. Swayne, Tal Pupko, et al. Discovery and reconstitution of cross-reactive vaccine targets for H5 and H9 avian influenza. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7699854.bard.

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Research objectives: Identification of highly conserved B-cell epitopes common to either H5 or H9 subtypes of AI Reconstruction of conserved epitopes from (1) as recombinantimmunogens, and testing their suitability to be used as universal vaccine components by measuring their binding to Influenza vaccinated sera of birds Vaccination of chickens with reconstituted epitopes and evaluation of successful vaccination, clinical protection and viral replication Development of a platform to investigate the dynamics of immune response towards infection or an epitope based vaccine Estimate our ability t
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Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, 2002. http://dx.doi.org/10.32747/2002.7587232.bard.

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The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel se
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