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A fast algorithm for genome-wide haplotype pattern mining

Søren Besenbacher, Christian NS Pedersen, Thomas Mailund
2009 BMC Bioinformatics  
The Haplotype Pattern Mining (HPM) method is a machine learning approach to do exactly this. Results: We present a new, faster algorithm for the HPM method.  ...  We show that the new approach speeds up the HPM method with a factor of 2 on a genome-wide dataset with 5009 individuals typed in 491208 markers using default parameters and more if the pattern length  ...  Conclusion We have developed a new algorithm for the haplotype pattern mining method and shown that it outperforms the original algorithm on genome wide association data.  ... 
doi:10.1186/1471-2105-10-s1-s74 pmid:19208179 pmcid:PMC2648728 fatcat:bd7hbssu5fggpfh22hxkmd4pje

A survey of data mining methods for linkage disequilibrium mapping

Päivi Onkamo, Hannu Toivonen
2006 Human Genomics  
Here, the current data mining-based methods for linkage disequilibrium mapping and phenotype analyses are reviewed.  ...  Data mining methods areg aining more interesta sp otential tools in mapping and identification of complex disease loci.  ...  Haplotype patternm ining (HPM) wast he first such method (http://www.cs.helsinki.fi/group/genetics/). 20 The algorithm finds all haplotype fragments (patterns) of arbitraryl ength -p ossibly up to some  ... 
doi:10.1186/1479-7364-2-5-336 pmid:16595078 pmcid:PMC3500183 fatcat:7qwqfnldtbbojodbeujhyc26ci

LD-Spline: Mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium

William S Bush, Guanhua Chen, Eric S Torstenson, Marylyn D Ritchie
2009 BioData Mining  
We compared the LD-Spline haplotype block partitioning approach to that of the four gamete rule and the Gabriel et al. approach using simulated data; in addition, we processed two commonly used genome-wide  ...  Gene-centric analysis tools for genome-wide association study data are being developed both to annotate single locus statistics and to prioritize or group single nucleotide polymorphisms (SNPs) prior to  ...  Acknowledgements Our thanks to the International HapMap Project for making populationbased collections of LD statistics freely available.  ... 
doi:10.1186/1756-0381-2-7 pmid:19954552 pmcid:PMC2795743 fatcat:g3tac4pfjbextll4i3hh3cakau

HapBoost: A Fast Approach to Boosting Haplotype Association Analyses in Genome-Wide Association Studies

Xiang Wan, Can Yang, Qiang Yang, Hongyu Zhao, Weichuan Yu
2013 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We present a fast method named HapBoost for finding haplotype associations, which can be applied to quickly screen the whole genome.  ...  Genome-wide association study (GWAS) has been successful in identifying genetic variants that are associated with complex human diseases.  ...  HapMiner is a data mining approach that utilizes a density-based clustering algorithm to find haplotype associations.  ... 
doi:10.1109/tcbb.2013.6 pmid:23702557 fatcat:wwyjz75krbcd5m6hirormk3kz4

Intelligent mining of large-scale bio-data: Bioinformatics applications

Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Rafii Yusop, Mahboobe Sadat Golestan Hashemi, Mohammad Hossein Nadimi Shahraki, Hamid Rastegari, Gous Miah, Farzad Aslani
2017 Biotechnology & Biotechnological Equipment  
Consequently, a challenging and valuable area for research in artificial intelligence has been created.  ...  Data mining, as biology intelligence, attempts to find reliable, new, useful and meaningful patterns in huge amounts of data.  ...  Hence, there is a wide scope for production of reference genome sequences and discovery of such SNPs using NGS technologies for further understanding of plant genetics and genomics.  ... 
doi:10.1080/13102818.2017.1364977 fatcat:qmbiss53wfggtc7ayj2ysgt5rq

Statistical advances and challenges for analyzing correlated high dimensional SNP data in genomic study for complex diseases

Yulan Liang, Arpad Kelemen
2008 Statistics Survey  
In this paper, we present a review of recent statistical advances and challenges for analyzing correlated high dimensional SNP data in genomic association studies for complex diseases.  ...  The review includes both general feature reduction approaches for high dimensional correlated data and more specific approaches for SNPs data, which include unsupervised haplotype mapping, tag SNP selection  ...  A nonparametric method called Haplotype Pattern Mining (HPM) was proposed to identify disease associated haplotype patterns from case-control data.  ... 
doi:10.1214/07-ss026 fatcat:ayqcurtk6bavhp2jf6ea4cc2ci

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  ...  There have been fast growing interests in developing and applying computational intelligence in disease mapping using SNP and haplotype data.  ...  However, in parallel with molecular biology, methods of computational intelligence also share their origins in the 1950s, with refinement over time into a wide array of algorithms useful for data mining  ... 
doi:10.1504/ijcibsb.2009.024041 fatcat:s5qhnexpezgypdsau54nvi365i

Whole-genome haplotyping approaches and genomic medicine

Gustavo Glusman, Hannah C Cox, Jared C Roach
2014 Genome Medicine  
Here, we review advances in whole-genome haplotyping approaches and discuss the importance of haplotypes for genomic medicine.  ...  The main approaches for phasing genomic sequence data are molecular haplotyping, genetic haplotyping, and population-based inference.  ...  GG and JCR received support from and the National Institute of General Medical Sciences Center for Systems Biology (P50 GM076547). We thank the anonymous reviewers for their contributions.  ... 
doi:10.1186/s13073-014-0073-7 pmid:25473435 pmcid:PMC4254418 fatcat:3cwkvkr4k5bfba3cobsey4mphq

A Review on New Horizons of Bioinformatics in Next Generation Sequencing, Viral and Cancer Genomics

Rahul Kumar Sharma
2016 International Journal of Biomedical Data Mining  
Genomics and molecular biology has always been a constant source of inspiration and motivational research for worldwide researchers in field of biology and biotechnology.  ...  Mostly genomic data is composed of sequencing results at a higher scale and that is why manual curating and handling of these data is quite difficult.  ...  Several tools can be implemented for this process, which include Short Read Assembly into Haplotypes, Quasispecies Reconstruction algorithm and QuasiRecomb.  ... 
doi:10.4172/2090-4924.1000122 fatcat:fqklmjq4rrhizg3czyg5ggfg2e

A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

Hari D. Upadhyaya, Deepak Bajaj, Shouvik Das, Maneesha S. Saxena, Saurabh Badoni, Vinod Kumar, Shailesh Tripathi, C. L. L. Gowda, Shivali Sharma, Akhilesh K. Tyagi, Swarup K. Parida
2015 Plant Molecular Biology  
delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea. have contributed  ...  The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41 % combined PVE) for flowering time differentiation  ...  Shouvik Das acknowledges the Department of Biotechnology (DBT), Government of India for Junior Research Fellowship award.  ... 
doi:10.1007/s11103-015-0377-z pmid:26394865 fatcat:fkq3buuhlvfvda27snekejhby4

Whole genome association mapping by incompatibilities and local perfect phylogenies

Thomas Mailund, Søren Besenbacher, Mikkel H Schierup
2006 BMC Bioinformatics  
approaches such as HapMiner and Haplotype Pattern Mining (HPM) despite being significantly faster.  ...  Using Blossoc, genome wide chip-based surveys of 3 million SNPs in 1000 cases and 1000 controls can be analysed in less than two CPU hours.  ...  Waldron for providing data for the comparison in Fig. 8 , to S. Zöllner and J. Pritchard for providing data for the comparison in Fig. 9 , to H.  ... 
doi:10.1186/1471-2105-7-454 pmid:17042942 pmcid:PMC1624851 fatcat:knyldrrgozhqxdupge7ujuskkm

FastTagger: An efficient algorithm for genome-wide tag SNP selection using multi-marker linkage disequilibrium

Guimei Liu, Yue Wang, Limsoon Wong
2010 BMC Bioinformatics  
FastTagger is a practical and scalable algorithm to solve this problem.  ...  Many algorithms have been developed to find a small subset of SNPs called tag SNPs that are sufficient to infer all the other SNPs.  ...  Acknowledgements This work was supported in part by an A*STAR grant SERC 072 101 0016 (Liu, Wong) and an NUS NGS scholarship (Wang).  ... 
doi:10.1186/1471-2105-11-66 pmid:20113476 pmcid:PMC3098109 fatcat:pln3xrorqrdnfocrxlpr4ynp74

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  
A revision of current bioinformatics tools for development of genic molecular markers is, therefore, crucial in this phase.  ...  These markers represent the functional component of the genome in contrast to all other random DNA markers (RMMs).  ...  Haplotypes in this context represent the different alleles of a gene in a dataset. The haplotype reconstruction is based on a mathematical algorithm.  ... 
doi:10.5897/ajb12.1410 fatcat:7vxb34dylvehbop2fu2olk2l6a

Probabilistic graphical models for genetic association studies

R. Mourad, C. Sinoquet, P. Leray
2011 Briefings in Bioinformatics  
Probabilistic graphical models have been widely recognized as a powerful formalism in the bioinformatics field, especially in gene expression studies and linkage analysis.  ...  Finally, we give promising directions for future research in this field.  ...  Acknowledgements The authors are grateful to the three anonymous reviewers for helping to improve this article.  ... 
doi:10.1093/bib/bbr015 pmid:21450805 fatcat:yh3v7vyopngczbqtmcqfs73rbm

LINKAGE DISEQUILIBRIUM STUDY WITH A PARALLEL ADAPTIVE GA

L. VERMEULEN-JOURDAN, C. DHAENENS, E-G. TALBI
2005 International Journal of Foundations of Computer Science  
In this article, we model a linkage disequilibrium study (genomic study) as an optimization problem where a given objective function has to be optimized.  ...  Results of this study show that exact algorithms are not adapted to this specific problem and lead us to the development of a parallel dedicated adaptive multipopulation genetic algorithm that is able  ...  In these articles, authors introduce a method for linkage disequilibrium mapping: haplotype pattern mining (HPM).  ... 
doi:10.1142/s0129054105002978 fatcat:56cq3722crbavpahiou5ndqqbe
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