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Towards bioinformatics assisted infectious disease control

Vitali Sintchenko, Blanca Gallego, Grace Chung, Enrico Coiera
2009 BMC Bioinformatics  
Results: This framework combines the genetic and geographic data of a pathogen to reconstruct its history and to identify the migration routes through which the strains spread regionally and internationally  ...  This paper proposes a novel framework for bioinformatics assisted biosurveillance and early warning to address the inefficiencies in traditional surveillance as well as the need for more timely and comprehensive  ...  Acknowledgements The authors thank Drs Q Wang, JR Iredell, L Hiley and GL Gilbert for their expert advice and providing genotyping data.  ... 
doi:10.1186/1471-2105-10-s2-s10 pmid:19208185 pmcid:PMC2646247 fatcat:x4jds5naerdhdenvsnltgi3chi

A Wide Survey on Data Mining Approach for Crop Diseases Detection and Prevention [chapter]

Vikas N Nirgude, Sandeep Malik
2021 Advances in Parallel Computing  
During this paper complete survey of several data mining approach for crop disease management has been done.  ...  However, because of absence of maintenance, inappropriate development of fruits and manual investigation there has been scale back in generate the standard of fruits.So, Data Mining Approach used in the  ...  For specific prediction of potentially fruit plant disease, and right time for protection the fruit plant using data mining.  ... 
doi:10.3233/apc210239 fatcat:jpc6bq75h5eijhwgu2dwxrfbny

Implementation of Decision Based Fruits Protection System Using Classification and Clustering Techniques

Dong Jo Kim
2016 Asia-pacific Journal of Convergent Research Interchange  
Data mining techniques are the analytical tools that are used to extract the meaningful information from large data bases.  ...  Automatic methods for the detection of plant diseases before hand is very important for absolute fruit protection.  ...  For the detection of disease can be done in four stages [6] . 1.Data collecting 2.Data pre processing 3.Data processing 4.prediction Data Collecting: For the prediction of possible fruit and plant disease  ... 
doi:10.21742/apjcri.2016.12.04 fatcat:sf475vdbubeknhsoqtnnrplkza

Application of Artificial Intelligence in Fruit Production: A Review

S. Manonmani, S. Senthilkumar, U.S. Akshara Govind, S. Manivannan
2022 Agricultural Science Digest - A Research Journal  
Adaptation of new and latest technological solutions for the improvement of farming might be the only possible way to meet out the food requirement in future.  ...  A data by UN FAO proclaims that the availability of land area for the crop cultivation will be 4% in 2050 with additional population of 2 billion to the existing global population.  ...  In case of cherry fruit, prediction of two most important disease-causing pathogens namely Monilinia laxa and Coccomyces hiemalis were done using data mining (Ilic et al. 2018) .  ... 
doi:10.18805/ag.d-5482 fatcat:euviios25rftnev4dqsidytxtq

Utilization from Computational Methods and Omics Data for Antiviral Drug Discovery to Control of SARS-CoV-2 [chapter]

Ömür Baysal, Ragıp Soner Silme
2021 Origin and Impact of COVID-19 Pandemic Originating From SARS-CoV-2 Infection Across the Globe [Working Title]  
Various novel drugs by using in silico resources and in vivo imaging techniques associated with high-resolution technologies can cause the confidential development of methods for the detection of antiviral  ...  This chapter highlights these approaches and addresses updated knowledge currently used for research and development.  ...  Conflict of interest The authors declare no conflict of interest. Origin and Impact of COVID-19 Pandemic Originating from SARS-CoV-2 Infection...  ... 
doi:10.5772/intechopen.98319 fatcat:6if4r252dbepfjvjwjwponoqme

Gaining Insight into Exclusive and Common Transcriptomic Features Linked with Biotic Stress Responses in Malus

Bipin Balan, Tiziano Caruso, Federico Martinelli
2017 Frontiers in Plant Science  
A total of 13,230 genes of the 12 studies were analyzed with functional data mining tools: 5,215 were upregulated, 8,015 were downregulated.  ...  Identifying key information in transcriptomic data is very important, especially when the "omic" study deals with plant responses to stresses in field conditions where a high number of variables and disturbing  ...  These published data demonstrated their possible application in improving early detection of infections of virus, bacteria, and fungi (Barón et al., 2016) .  ... 
doi:10.3389/fpls.2017.01569 pmid:28955361 pmcid:PMC5601412 fatcat:zs324qbtvneyljtzdv2au65hgu

Advanced methods of plant disease detection. A review

Federico Martinelli, Riccardo Scalenghe, Salvatore Davino, Stefano Panno, Giuseppe Scuderi, Paolo Ruisi, Paolo Villa, Daniela Stroppiana, Mirco Boschetti, Luiz R. Goulart, Cristina E. Davis, Abhaya M. Dandekar
2014 Agronomy for Sustainable Development  
DNA-based and serological methods now provide essential tools for accurate plant disease diagnosis, in addition to the traditional visual scouting for symptoms.  ...  effectively detect early infections directly in the field; (2) biosensors based on phage display and biophotonics can also detect instantaneously infections although they can be integrated with other systems  ...  We thank Minghua Zhang and colleagues for permission to use their data in our Fig. 4 and Jorge Torres-Sánchez and colleagues for permission to use their picture in our  ... 
doi:10.1007/s13593-014-0246-1 fatcat:sdvsemwsire5lftrc242mzxyai

Informatics for Infectious Disease Research and Control [chapter]

Vitali Sintchenko
2009 Infectious Disease Informatics  
For example, functional gene recognition tools GeneMark and GLIMMER employ Hidden Markov models, in which the preceding nucleotide bases are used to predict the next base in a coding region, and the algorithm  ...  Tables 1.1 and 1.2 provide examples of informatics tools for pathogen annotation and analysis.  ... 
doi:10.1007/978-1-4419-1327-2_1 fatcat:usfwlegnrfcjtedpvrzu2vmaue

Malaysian Carica papaya L. var. Eksotika: Current Research Strategies Fronting Challenges

Rogayah Sekeli, Muhammad Hanam Hamid, Roslinda A. Razak, Chien-Yeong Wee, Janna Ong-Abdullah
2018 Frontiers in Plant Science  
Even though Eksotika is a favored commercial variety with good eating and aesthetic quality fruit, its potential for more lucrative distant markets is tarnished with its short-shelf life fruits.  ...  This event changed the outlook of papaya planting from a smallholder crop to a plantation crop.  ...  ACKNOWLEDGMENTS The authors acknowledge Universiti Putra Malaysia for funding the publication of this manuscript.  ... 
doi:10.3389/fpls.2018.01380 pmid:30279695 pmcid:PMC6154280 fatcat:3xws5zcuxnesfcfufypr7wkbii

Forewarned is forearmed: harmonized approaches for early detection of potentially invasive pests and pathogens in sentinel plantings

Carmen Morales-Rodríguez, Sten Anslan, Marie-Anne Auger-Rozenberg, Sylvie Augustin, Yuri Baranchikov, Amani Bellahirech, Daiva Burokienė, Dovilė Čepukoit, Ejup Çota, Kateryna Davydenko, H. Tuğba Doğmuş Lehtijärvi, Rein Drenkhan (+23 others)
2019 NeoBiota  
Discoveries of invasive pests and pathogens previously unknown to science or with unknown host associations yet damaging on novel hosts highlights the necessity of developing novel tools to predict their  ...  Consistency and comparison of results are based on the adoption of common procedures for sampling design and sample processing.  ...  MG was supported by Ministry of Education, Science and Technological Development of the Republic of Serbia, Grant III43002.  ... 
doi:10.3897/neobiota.47.34276 fatcat:itcgvnksbvbv5poounwew2i4ca

A molecular perspective: biology of the emerging pathogen Batrachochytrium dendrobatidis

EB Rosenblum, MC Fisher, TY James, JE Stajich, JE Longcore, LR Gentry, TJ Poorten
2009 Diseases of Aquatic Organisms  
Avenues of future research promise to be particularly fruitful and highlight the need for integrative studies that unite genetic, ecological and spatial data in both Bd and its amphibian hosts.  ...  Here we discuss the promise of genetic and genomic tools for answering these previously intractable questions about the biology and evolutionary history of Bd.  ...  ., National Institutes of Health (P20 RR016448) from the COBRE Program of the National Center for Research Resources to E.B.R., the UK Natural Environmental Research Council to M.C.F. and the Miller Institute  ... 
doi:10.3354/dao02179 pmid:21268975 fatcat:fvdkfm4gmra2ndnlfre4zabuja

Effector-Mining in the Poplar Rust Fungus Melampsora larici-populina Secretome

Cécile Lorrain, Arnaud Hecker, Sébastien Duplessis
2015 Frontiers in Plant Science  
Understanding the molecular mechanisms controlling infection by pathogens appears essential for durable management of tree plantations.  ...  Automatized effector-mining pipelines hold great promise for rapid and systematic identification and prioritization of CSEPs for functional characterization.  ...  SD acknowledges the support of the French ANR for the young scientist grant POPRUST (ANR-2010-JCJC-1709-01) and of the Région Lorraine.  ... 
doi:10.3389/fpls.2015.01051 pmid:26697026 pmcid:PMC4678189 fatcat:33a44fcv65fjjpspoljr273ode

Mining and unearthing hidden biosynthetic potential

Kirstin Scherlach, Christian Hertweck
2021 Nature Communications  
The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products.  ...  These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential.  ...  ChemBioSys, Cluster of Excellence, Balance of the Microverse, and Leibniz Award.  ... 
doi:10.1038/s41467-021-24133-5 pmid:34162873 fatcat:clvhjzvvn5g6pdjd23q733mrm4

Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host–pathogen interaction space

Roland Arnold, Kurt Boonen, Mark G.F. Sun, Philip M. Kim
2012 Methods  
Specifically, this challenge consists of a number of sub-problems: First, prediction of possible pathogen interactors (e.g. effector proteins) is necessary for bacteria and protozoa.  ...  As an application example of the methods covered, we predict host-pathogen interactions of Salmonella and discuss the value of these predictions as a prospective for further research.  ...  Domain-domain based interaction methods are applicable to detect interactions based on HGT from host to pathogen and might be fruitful for viruses considering the described streamlining effect.  ... 
doi:10.1016/j.ymeth.2012.06.011 pmid:22750305 pmcid:PMC7128575 fatcat:l23wwm4wgbhvdfz4ndxfhccasq

Identifying Host Molecular Features Strongly Linked With Responses to Huanglongbing Disease in Citrus Leaves

Bipin Balan, Ana M. Ibáñez, Abhaya M. Dandekar, Tiziano Caruso, Federico Martinelli
2018 Frontiers in Plant Science  
Protein-protein interaction (PPI) network analysis confirmed a possible role for heat shock proteins in curbing disease progression.  ...  Bioinformatic analysis of expression data of four datasets present in NCBI provided 46-68 million reads with an alignment percentage of 72.95-86.76%.  ...  Functional data mining tools were provided.  ... 
doi:10.3389/fpls.2018.00277 pmid:29541089 pmcid:PMC5836289 fatcat:ee2tqimxdbcuzhr4vhpgep2t2m
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