Haplotype phasing: existing methods and new developments

SR Browning, BL Browning - Nature Reviews Genetics, 2011 - nature.com
Determination of haplotype phase is becoming increasingly important as we enter the era of
large-scale sequencing because many of its applications, such as imputing low-frequency …

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

P Librado, J Rozas - Bioinformatics, 2009 - academic.oup.com
Motivation: DnaSP is a software package for a comprehensive analysis of DNA
polymorphism data. Version 5 implements a number of new features and analytical methods …

Toward intelligent training of supervised image classifications: directing training data acquisition for SVM classification

GM Foody, A Mathur - Remote Sensing of Environment, 2004 - Elsevier
Conventional approaches to training a supervised image classification aim to fully describe
all of the classes spectrally. To achieve a complete description of each class in feature …

A comprehensive literature review of haplotyping software and methods for use with unrelated individuals

RM Salem, J Wessel, NJ Schork - Human Genomics, 2005 - Springer
Interest in the assignment and frequency analysis of haplotypes in samples of unrelated
individuals has increased immeasurably as a result of the emphasis placed on haplotype …

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool'CubeX'

TR Gaunt, S Rodríguez, INM Day - BMC bioinformatics, 2007 - Springer
Background The frequency of a haplotype comprising one allele at each of two loci can be
expressed as a cubic equation (the'Hill equation'), the solution of which gives that frequency …

[图书][B] Handbook of computational molecular biology

S Aluru - 2005 - taylorfrancis.com
The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …

Haplotype reconstruction from SNP fragments by minimum error correction

RS Wang, LY Wu, ZP Li, XS Zhang - Bioinformatics, 2005 - academic.oup.com
Motivation: Haplotype reconstruction based on aligned single nucleotide polymorphism
(SNP) fragments is to infer a pair of haplotypes from localized polymorphism data gathered …

Uncovering signal transduction networks from high-throughput data by integer linear programming

XM Zhao, RS Wang, L Chen, K Aihara - Nucleic acids research, 2008 - academic.oup.com
Signal transduction is an important process that transmits signals from the outside of a cell to
the inside to mediate sophisticated biological responses. Effective computational models to …

[PDF][PDF] Efficient haplotype inference with Boolean satisfiability

I Lynce, J Marques-Silva - National conference on artificial intelligence …, 2006 - cdn.aaai.org
One of the main topics of research in genomics is determining the relevance of mutations,
described in haplotype data, as causes of some genetic diseases. However, due to …

SAT in bioinformatics: Making the case with haplotype inference

I Lynce, J Marques-Silva - … Conference on Theory and Applications of …, 2006 - Springer
Mutation in DNA is the principal cause for differences among human beings, and Single
Nucleotide Polymorphisms (SNPs) are the most common mutations. Hence, a fundamental …