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Polygene-based evolution

Shuaiqiang Wang, Byron J. Gao, Shuangling Wang, Guibao Cao, Yilong Yin
2012 Proceedings of the 21st ACM international conference on Information and knowledge management - CIKM '12  
In polygene-based evolutionary algorithms (PGEAs), the evolution unit is polygene, i.e., a set of co-regulated genes.  ...  In this paper, we introduce polygene-based evolution, a novel framework for evolutionary algorithms (EAs) that features distinctive operations in the evolution process.  ...  frequent pattern mining techniques and select elite ones with a CBA-based approach.  ... 
doi:10.1145/2396761.2398616 dblp:conf/cikm/WangGWCY12 fatcat:4bzeusimtzf3lci5gjisgagkza

Techniques of SNP Genotyping and Remote Sensing Applied for Elucidation of the Contribution of Polygene and Environmental Factors to Inter-individual Variation in Skin Pigmentation Phenotype

Sumiko Anno, Susumu Kudo, Keita Hamasaki, Kazunari Matsumura, Takushi Yamamoto, Koretsugu Ogata
2005 Journal of Physiological Anthropology and Applied Human Science  
We present a conceptual framework for applying techniques of SNP genotyping as a molecular biological approach and remote sensing as an ecological approach to elucidation of the contribution of polygene  ...  Acknowledgements This work is supported by Japan Society for the Promotion of Science (JSPS) grants and NASA's Earth Science and Public Health Program, NASA Goddard Space Flight Center with the RS data  ...  A combination of machine learning, statistical analysis, modeling techniques and database technology, data mining finds patterns and subtle relationships in a large database and infers rules that allow  ... 
doi:10.2114/jpa.24.483 pmid:16079603 fatcat:gjms6c5xengf3n6z5zafokznwi

Advances in Computational Methods for Genetic Diseases

Francesco Camastra, Roberto Amato, Maria Donata Di Taranto, Antonino Staiano
2015 Computational and Mathematical Methods in Medicine  
Xue et al. proposes, in the context of gene expression data, a patternbased subspace clustering or OPSM (order-preserving submatrix model), based on frequent sequential pattern.  ...  "A New Approach for Mining Order-Preserving Submatrices Based on all Common Subsequences" by Y.  ... 
doi:10.1155/2015/645649 pmid:26167201 pmcid:PMC4488520 fatcat:iq5hw3d26bhnhfxp4ubexjd4gq

A review on Machine Learning Techniques for Neurological disorders estimation by Analyzing EEG Waves

Vijaykumar Janga, Prof. E Sreenivasa Reddy
2017 International Journal of Trend in Scientific Research and Development  
Hence, an better feature representation is actually key to an effective suite of data mining and machine learning algorithms in the examination of neurological disorders.  ...  With the fast improvement of neuroimaging data acquisition strategies, there has been a significant growth in learning neurological disorders among data mining and machine learning communities.  ...  This paper presents a literature review of machine learning algorithms that are frequently used psychological health sector handling.  ... 
doi:10.31142/ijtsrd7082 fatcat:yf44mwfip5b55cgq3jyn45liba

Biological network analysis: insights into structure and functions

X. Ma, L. Gao
2012 Briefings in Functional Genomics  
In detail, we first reviewed the interactome topological properties of biological networks, the methods for structure and functional patterns.  ...  STATIC-BASED STRUCTURE AND FUNCTIONAL PATTERNS DISCOVERY It is well known that the topological structure is associated with biological functions.  ...  Motifs are subgraphs that appear more frequently than expected, whereas modules are subgraphs with a high degree of clustering.  ... 
doi:10.1093/bfgp/els045 pmid:23184677 fatcat:uq3hg5ura5a6be2nqua4numfme

Computational intelligence for genetic association study in complex diseases: review of theory and applications

Arpad Kelemen, Athanasios V. Vasilakos, Yulan Liang
2009 International Journal of Computational Intelligence in Bioinformatics and Systems Biology  
Comprehensive evaluation of common genetic variations through association of SNP structure with common complex disease in the genome-wide scale is currently a hot area in human genome research thanks for  ...  They employed an approximate and noisy fitness function based on the ReliefF data mining algorithm and applied to synthetic data sets with individual features having no marginal effects.  ...  Genetic Programming (GP) is closely related to genetic algorithms. It makes use of genetic algorithms and they are a stochastic, population based, evolutionary approaches for search and optimisation.  ... 
doi:10.1504/ijcibsb.2009.024041 fatcat:s5qhnexpezgypdsau54nvi365i

Candidate Gene Identification Approach: Progress and Challenges

Mengjin Zhu, Shuhong Zhao
2007 International Journal of Biological Sciences  
There were many statistical algorithms or computational methods, and of which some included data-mining analysis [59] , hidden Markov analysis [60] , cluster analysis (similarity-based method) [61]  ...  causative allelic variant that may be of biomedical, economic and evolutionary interest were mined in succession.  ... 
doi:10.7150/ijbs.3.420 pmid:17998950 pmcid:PMC2043166 fatcat:du3nopokybbepfrhb4wa67fvkm

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

Sudhir Kumar, Joel T. Dudley, Alan Filipski, Li Liu
2011 Trends in Genetics  
One reason for the lack of evolutionary conservation of positions associated with complex diseases is that their effects appear later in life, which means that these variants are frequently inherited without  ...  An early examination of the evolutionary patterns of the occurrence of a small set of 37 nSNVs associated with complex diseases did not find any tendency for these variations to occur at sites with high  ... 
doi:10.1016/j.tig.2011.06.004 pmid:21764165 pmcid:PMC3272884 fatcat:skstblolnjbspejtnux25bzrkq

Integrating molecular networks with genetic variant interpretation for precision medicine

Emidio Capriotti, Kivilcim Ozturk, Hannah Carter
2018 Wiley Interdisciplinary Reviews: Systems Biology and Medicine  
These studies lay the foundation for using networks to predict variant effects at scale using machine-learning or algorithmic approaches.  ...  Nevertheless the simple one-variant one-phenotype model valid for many monogenic diseases does not capture the complexity of polygenic traits and disorders.  ...  Approaches have included random walk-based algorithms (Rosvall & Bergstrom, 2008) and nonnegative matrix factorization (Zhang, Wang, & Zhang, 2007) .  ... 
doi:10.1002/wsbm.1443 pmid:30548534 pmcid:PMC6450710 fatcat:yzgesn3eybb7dmhnmckqboiewi

Bioinformatics tools for development of fast and cost effective simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs)
English

Gupta Sushmita, Bharalee Raju, Das Ranjita, Thakur Debajit
2013 African Journal of Biotechnology  
This has opened a new era in crop molecular breeding with identification and/or development of a new class of useful DNA markers called genic molecular markers (GMMs).  ...  This mini-review mainly provides an overview of different bioinformatics tools available and its use in marker development with particular reference to SNP and SSR markers.  ...  ., 2002) which draws a keyword tree and matches it with a technique adapted from bibliographic searches, based on the Aho-Corasick algorithm.  ... 
doi:10.5897/ajb12.1410 fatcat:7vxb34dylvehbop2fu2olk2l6a

Pharmacogenomics in the treatment of mood disorders: Strategies and Opportunities for personalized psychiatry

Azmeraw T. Amare, Klaus Oliver Schubert, Bernhard T. Baune
2017 The EPMA Journal  
The third strategy aims to the development of multivariable diagnostic or prognostic algorithms (tools) combining individual's genomic information (polygenic score) with other predictors (e.g., omics pillars  ...  The first strategy can be to implement diagnostic, therapeutic, or prognostic genetic testing based on candidate genes or gene products.  ...  A similar GWAS on the patterns of treatment response using the STAR*D subjects having sustained (n = 869) versus unsustained (n = 247) patterns and a replication attempt at the Genome-Based Therapeutic  ... 
doi:10.1007/s13167-017-0112-8 pmid:29021832 pmcid:PMC5607053 fatcat:7hyxzfdmb5er3l24dbx4fwyxgq

Combining genotype, phenotype, and environmental data to delineate site-adjusted provenance strategies for ecological restoration [article]

Carolina S. Carvalho, Brenna R. Forester, Simone K. Mitre, Ronnie Alves, Vera L. Imperatriz-Fonseca, Silvio J. Ramos, Luciana C. Resende-Moreira, José O. Siqueira, Leonardo C. Trevelin, Cecilio F. Caldeira, Markus Gastauer, Rodolfo Jaffé
2019 bioRxiv   pre-print
Whereas local provenances where found optimal to restore the moderately disturbed site, a mixture of genotypes was the most promising strategy to recover a highly degraded mining site, to which local provenances  ...  In addition to the soil samples gathered along with plant tissue, we collected 50 extra soil samples from a highly degraded mine site (the mine pit from an exhausted mine) and seven soil samples from a  ...  Indeed most fitness-related traits in plants have a polygenic basis (Falke et al., 2013) , including tolerance to soil with phytotoxic levels of heavy metals (Arnold et al., 2016) .  ... 
doi:10.1101/2019.12.11.872747 fatcat:rznuxgez2razpmrevhxszmsu6y

Evolutionary triangulation: informing genetic association studies with evolutionary evidence

Minjun Huang, Britney E. Graham, Ge Zhang, Reed Harder, Nuri Kodaman, Jason H. Moore, Louis Muglia, Scott M. Williams
2016 BioData Mining  
Evolutionary Triangulation (ET) exploits this evolutionary differentiation by comparing population structure among three populations with variable patterns of disease prevalence.  ...  By selecting populations based on patterns where two have similar rates of disease that differ substantially from a third, we performed a proof of principle analysis for this method.  ...  Genetic association mining and identification of additional phenotypes Genetic associations of ET genes with diseases were analyzed based on data retrieved from the HuGE Navigator [6] (http://www.cdc.gov  ... 
doi:10.1186/s13040-016-0091-7 pmid:27042214 pmcid:PMC4818851 fatcat:tsq5unbwybcflhwi37mte2pzlm

Can Modern Evolutionary Theory Explain Macroevolution? [chapter]

Douglas J. Futuyma
2015 Interdisciplinary Evolution Research  
Ever since the Evolutionary Synthesis of the 1930s and 1940s, some biologists have expressed doubt that the Synthetic Theory, based principally on mutation, genetic variation, and natural selection, adequately  ...  This chapter describes the Evolutionary Synthesis and the challenges to it and addresses the extent to which the modern formulation of the Synthetic Theory (ST) adequately addresses the observations that  ...  attention to a passage in The Origin of Species in which Darwin seems to foreshadow punctuated equilibria, to Alan Love for enlightening discussion of the relationship of developmental biology to the Evolutionary  ... 
doi:10.1007/978-3-319-15045-1_2 fatcat:qe5rw6qpwbgwphjdlbdde4fjyi

In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant

Abdel Aouacheria, Vincent Navratil, Wenyu Wen, Ming Jiang, Dominique Mouchiroud, Christian Gautier, Manolo Gouy, Mingjie Zhang
2005 Oncogene  
In this cancer-oriented study, we detail an SNP mining strategy based on the analysis of expressed sequence tags among publicly available databases.  ...  These genotypic markers can be used to assay how alleles of candidate genes correlate with the malignant phenotype, and may provide new clues into the genetic modifications that characterize cancer onset  ...  Future studies may deal with insertion-deletion patterns or chromosomal translocations that could be common events in tumoral cells.  ... 
doi:10.1038/sj.onc.1208745 pmid:15897869 fatcat:cpjvbh6jevf3zdvhbifrgauarm
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