The EM algorithm and the rise of computational biology

DOI10.1214/09-STS312MaRDI QIDQ906519zbMATH OpenFDO

Authors Xiaodan Fan, Yuan Yuan, Jun S. Liu

Publication date 22 January 2016

Published in Statistical Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1104.2180, https://projecteuclid.org/euclid.ss/1300108232

zbMATH Keywords

EM algorithmcomputational biology

Mathematics Subject Classification ID

Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Genetics and epigenetics (92D10) History of mathematics in the 20th century (01A60) History of statistics (62-03) Research exposition (monographs, survey articles) pertaining to biology (92-02) History of biology (92-03) Computational methods for problems pertaining to biology (92-08)

Abstract: In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists. Of interest to us is the key role played by the EM algorithm during this transformation. We survey the use of the EM algorithm in a few important computational biology problems surrounding the "central dogma"; of molecular biology: from DNA to RNA and then to proteins. Topics of this article include sequence motif discovery, protein sequence alignment, population genetics, evolutionary models and mRNA expression microarray data analysis.

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Cited in

(1)

• Statistical Inference in Evolutionary Models of DNA Sequences via the EM Algorithm

Describes a project that uses

Uses Software

• HMMGEP
• PhyME
• Pfam
• T-coffee
• MUSCLE
• ClustalW
• ProbCons
• 3DCoffee
• PAML
• MAFFT
• fastDNAml
• HAPLO

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