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SM algorithms-based encryption scheme for large genomic data files

Digital Communications and Networks 2021年第4期7卷 543-550页

作者： Yatong Jiang Tao Shang Jianwei Liu School of Cyber Science and Technology Beihang UniversityBeijing100083China

With the rapid development of the genomic sequencing technology,the cost of obtaining personal genomic data and effectively analyzing it has been gradually *** analysis and utilization of genomic dam gradually entered the public view,and the leakage of genomic dam privacy has attracted the attention of *** security of genomic data is not only related to the protection of personal privacy,but also related to the biological information security of the ***,there is still *** genomic dam privacy protection scheme using Shangyong Mima(SM)*** this paper,we analyze the widely used genomic dam file formats and design a large genomic dam files encryption scheme based on the SM ***,we design a key agreement protocol based on the SM2 asymmetric cryptography and use the SM3 hash function to guarantee the correctness of the ***,we used the SM4 symmetric cryptography to encrypt the genomic data by optimizing the packet processing of files,and improve the usability by assisting the computing platform with key *** implementation demonstrates that the scheme can be applied to securely transmit the genomic data in the network environment and provide an encryption method based on SM algorithms for protecting the privacy of genomic data.

关键词： genomic data Privacy protection SM algorithm Key agreement protocol Hybrid encryption

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Identifcation of Immunity-related Genes in Arabidopsis and Cassava Using genomic data

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genomics, Proteomics & Bioinformatics 2013年第6期11卷 345-353页

作者： Luis Guillermo Leal A'lvaro Perez Andre's Quintero A'ngela Bayona Juan Felipe Ortiz Anju Gangadharan David Mackey Camilo Lo'pez Liliana Lo'pez-Kleine Department of Statistics Universidad Nacional de Colombia Department of Biology Universidad Nacional de Colombia Department of Molecular Genetics The Ohio State University

Recent advances in genomic and post-genomic technologies have provided the opportu- nity to generate a previously unimaginable amount of information. However, biological knowledge is still needed to improve the understanding of complex mechanisms such as plant immune responses. Better knowledge of this process could improve crop production and management. Here, we used holistic analysis to combine our own microarray and RNA-seq data with public genomic data from Arabidopsis and cassava in order to acquire biological knowledge about the relationships between proteins encoded by immunity-related genes （IRGs） and other genes. This approach was based on a kernel method adapted for the construction of gene networks. The obtained results allowed us to propose a list of new IRGs. A putative function in the immunity pathway was predicted for the new IRGs. The analysis of networks revealed that our predicted IRGs are either well documented or recognized in previous co-expression studies. In addition to robust relationships between IRGs, there is evidence suggesting that other cellular processes may be also strongly related to immunity.

关键词： Arabidopsis Cassava Functional gene prediction genomic data Kernel canonical correlation ajalysi Plant immunity

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Rice bioinformatics in the genomic era: Status and perspectives

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The Crop Journal 2021年第3期9卷 609-621页

作者： Lei Jia Lingjuan Xie Sangting Lao Qian-Hao Zhu Longjiang Fan Hainan Institute of Zhejiang University Yonyou Industrial ParkSanya 572025HainanChina Instituteof Crop Science&Institute of Bioinformatics Zhejiang UniversityHangzhou 310058ZhejiangChina CSIRO Agriculture and Food Black Mountain LaboratoriesGPO Box 1700CanberraACT 2601Australia

Rice is one of cereal crops and a model species for *** the release of the first draft rice genome sequences in 2002,considerable progress has been achieved in rice genomic researches,thanks to rapid development and efficient utilization of bioinformatics methods and *** this review,we summarize the progress of studies of rice genome sequencing and other omics and introduce the wellmaintained bioinformatics databases and tools developed for rice genome resources and *** reviewing the history of rice bioinformatics,we use single-cell sequencing and machine learning as examples showing how bioinformatics integrates emerging technologies and how it continues to develop for future rice research.

关键词： Rice Bioinformatics genomic data database Tool

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Candidate genes for male and female reproductive traits in Canchim beef cattle

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Journal of Animal Science and Biotechnology 2018年第1期9卷 59-68页

作者： Marcos Eli Buzanskas Daniela do Amaral Grossi Ricardo Vieira Ventura Flavio Schramm Schenkel Tatiane Cristina Seleguim Chud Nedenia Bonvino Stafuzza Luciana Diniz Rola Sarah Laguna Conceio Meirelles Fabiana Barichello Mokry Maurício de Alvarenga Mudadu Roberto Hiroshi Higa Marcos Vinícius Gualberto Barbosa da Silva Maurício Mello de Alencar Luciana Correia de Almeida Regitano Danísio Prado Munari Departamento de Zootecnia Universidade Federal da Paraíba(UFPB)AreiaParailba 58397-000Brazil Fast Genetics SaskatoonSK S7K 2K6Canada Beef Improvement Opportunities(BIO) GuelphON N1K 1ESCanada Department of Animal and Poultry Science University of GuelphCentre for Genetic Improvement of Livestock(CGIL)GuelphON N1G 2W1Canada Departamento de Ciencias Exatas Faculdade de Ci6ncias Agrarias e VeterinariasUniversidade Estadual Paulista(Unesp)JaboticabalSao Paulo 14884 900Brazil Departamento de Zootecnia Nucleo de Pesquisa e Conservacao de CervMeosFaculdade de Ciencias Agrarias e VeterinariasUniversidade Estadual Paulista(Unesp)JaboticabalSao Paulo 14884 900Brazil Department of Animal Science Federal University/of Lavras(UFLA)LavrasMinas Gerais 37200 000Brazil Department of Genetics and Evolution Federa University of Sao Carlos(UFSCar)Sao CarlosSao Paulo 13565-905Brazil Embrapa Agricultural Informatics Campinas55o Paulo 13083 886Brazil Embrapa Dairy Cattle Juiz de ForaMinas Gerais 36038 330Brazil Embrapa Southeast Livestock Sao CarlosSao Paulo 13560 970Brazil

Background： Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. data quality control was conducted resulting in 672,778 SNPs and 392 ***： Associated SNPs were observed for scrotal circumference at 420 d of age（435 SNPs）, followed by scrotal circumference at 210 d of age（12 SNPs）, age at first calving（six SNPs）, and age at second calving（four SNPs）. We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and ***： Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless,the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, al relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.

关键词： Animal breeding Composite breed Genome-wide association genomic data Single nucleotide polymorphism

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Challenges and prospects in bridging precision medicine and artificial intelligence in genomic psychiatric treatment

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World Journal of Psychiatry 2024年第8期14卷 1148-1164页

作者： Uchenna Esther Okpete Haewon Byeon Department of Digital Anti-aging Healthcare(BK21) Inje UniversityGimhae 50834South Korea

Precision medicine is transforming psychiatric treatment by tailoring personalized healthcare interventions based on clinical,genetic,environmental,and lifestyle factors to optimize medication *** study investigates how artificial intelligence(AI)and machine learning(ML)can address key challenges in integrating pharmacogenomics(PGx)into psychiatric *** this integration,AI analyzes vast genomic datasets to identify genetic markers linked to psychiatric ***-driven models integrating genomic,clinical,and demographic data demonstrated high accuracy in predicting treatment outcomes for major depressive disorder and bipolar *** study also examines the pressing challenges and provides strategic directions for integrating AI and ML in genomic psychiatry,highlighting the importance of ethical considerations and the need for personalized *** implementation of AI-driven clinical decision support systems within electronic health records is crucial for translating PGx into routine psychiatric *** research should focus on developing enhanced AI-driven predictive models,privacy-preserving data exchange,and robust informatics systems to optimize patient outcomes and advance precision medicine in psychiatry.

关键词： Precision medicine Psychiatric treatment genomic data Machine learning Deep learning Clinical decision making data privacy Review

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