Family trio phasing and missing data recovery (2009)
Dumitru Brinza, Jingwu He, Weidong Mao, Alexander Zelikovsky
Abstract: Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt...
De novo fragment assembly with short mate-paired reads: Does the read length matter? (2009)
Chaisson, Mark J., Brinza, Dumitru, Pevzner, Pavel A.
Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of...
Greedy Approach to Reliable Disease Susceptibility Prediction (2008)
Dumitru Brinza, Irina Astrovskaya, Er Zelikovsky
Abstract. One of the main problems in genetic epidemiology is to robustly predict genetic susceptibility to complex diseases based on the data from case/control studies. This becomes computationally...
Risk Factor Searching Heuristics for SNP Case-Control Studies (2008)
This paper addresses the computational challenge facing association analysis of case-control studies – searching an enormous amount of possible gene interactions. A complex risk factor (RF) is...
Gulsah Altun, Hae-jin Hu, Dumitru Brinza, Robert W. Harrison, Alex Zelikovsky, Yi Pan
Abstract—The Support Vector Machine is a powerful methodology for solving problems in nonlinear classification, function estimation and density estimation. When data are not linearly separable,...
1 Optimization Methods for Genotype Data Analysis in Epidemiological Studies (2008)
Dumitru Brinza, Jingwu He, Er Zelikovsky
Recent improvement in accessibility of high-throughput DNA sequencing brought a great deal of attention to disease association and susceptibility studies. Successful genome-wide searches for...
18 OPTIMIZATION METHODS FOR GENOTYPE DATA ANALYSIS IN EPIDEMIOLOGICAL STUDIES (2008)
Dumitru Brinza, Jingwu He, Er Zelikovsky
Recent improvement in accessibility of high throughput DNA sequencing brought a great deal of attention to disease association and susceptibility studies. Successful genome-wide searches for...
2SNP: Scalable Phasing Method for Trios and Unrelated Individuals (2008)
Abstract — Emerging microarray technologies allow affordable typing of very long genome sequences. A key challenge in analyzing of such huge amount of data is scalable and accurate computational...
Case(Control)-Free Multi-SNP Combinations in Case-Control Studies (2008)
Several genome-wide searches for disease-associated gene variations have been recently reported (Spinola et al, 2006; Herbert et al, 2006). However, complex diseases can be caused by combinations of...
Phasing and Missing Data Recovery in Family (2008)
Dumitru Brinza, Jingwu He, Weidong Mao, Er Zelikovsky
Abstract. Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt...
Summary: 2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for...
Family Trio Phasing and Missing Data Recovery ∗ (2008)
Dumitru Brinza, Jingwu He, Weidong Mao, Alexander Zelikovsky
Abstract: Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt...
In this paper we analyze the SNP data (GAW Problem Set 2) for rheumatoid arthritis (RA) trying to check if it is caused by combinations of several unlinked gene variations. We apply here improved...
Association testing by haplotype-sharing methods applicable to whole-genome analysis (2007)
Nolte, Ilja M, De Vries, André R, Spijker, Geert T, Jansen, Ritsert C, Brinza, Dumitru, Zelikovsky, Alexander, ...
Abstract We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and...
Association testing by haplotype-sharing methods applicable to whole-genome analysis (2007)
Nolte, Ilja M., Vries, André R. De, Spijker, Geert T., Jansen, Ritsert C., Brinza, Dumitru, Zelikovsky, Alexander, ...
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS...
Discrete algorithms for analysis of genotype data (2007)
Thesis (Ph. D.)--Georgia State University, 2007.
DISCRETE ALGORITHMS FOR ANALYSIS OF GENOTYPE DATA (2007)
Under Direction, Alexander Zelikovsky, Dumitru Brinza
Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to search and...
Discrete Methods for Association Search and Status Prediction (2007)
Abstract—Recent improvements in high-throughput genotyping technology make possible genome-wide association studies and status prediction (classification) for common complex diseases. This paper...
Combinatorial Methods for Disease Association Search and Susceptibility Prediction (2006)
Abstract. Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to...
Combinatorial Search Methods for Multi-SNP Disease Association (2006)
Dumitru Brinza, Jingwu He, Er Zelikovsky
Abstract — Recent improvements in the accessibility of highthroughput genotyping have brought a deal of attention to genome-wide association studies for common complex diseases. Although, such...
Genotype Susceptibility and Integrated Risk Factors for Complex Diseases (2006)
Weidong Mao, Dumitru Brinza, Nisar Hundewale, Stefan Gremalschi, Er Zelikovsky
Abstract — Recent improvements in the accessibility of highthroughput genotyping have brought a great deal of attention to disease association and susceptibility studies. This paper explores...
Zelikovsky A: Phasing of 2-SNP Genotypes based on Non-Random Mating Model (2006)
Abstract. Emerging microarray technologies allow genotyping of long genome sequences resulting in huge amount of data. A key challenge is to provide an accurate phasing of very long single nucleotide...
Combinatorial Methods for Disease Association Search and Susceptibility Prediction (2006)
Abstract. Accessibility of high-throughput genotyping technology makes possible genome-wide association studies for common complex diseases. When dealing with common diseases, it is necessary to...
2SNP: scalable phasing based on 2-SNP haplotypes (2006)
Brinza, Dumitru, Zelikovsky, Alexander
Summary: 2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for...
Family trio phasing and missing data recovery (2005)
Dumitru Brinza, Jingwu He, Weidong Mao, Alexander Zelikovsky
Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt to fill...
Family trio phasing and missing data recovery (2005)
Dumitru Brinza, Jingwu He, Weidong Mao, Alexander Zelikovsky
Although there exist many phasing methods for unrelated adults or pedigrees, phasing and missing data recovery for data representing family trios is lagging behind. This paper is an attempt to fill...
A Combinatorial Method for Predicting Genetic Susceptibility to Complex Diseases (2005)
Weidong Mao, Jingwu He, Dumitru Brinza, Alex Zelikovsky
Abstract — Recent improvements in the accessibility of highthroughput genotyping have brought a great deal of attention to disease association and susceptibility studies. This paper explores...
2SNP: scalable phasing based on 2-SNP haplotypes (2005)
Brinza, Dumitru, Zelikovsky, Alexander
Summary: 2SNP software package implements a new very fast scalable algorithm for haplotype inference based on genotype statistics collected only for pairs of SNPs. This software can be used for...
Association testing by haplotype-sharing methods applicable to whole-genome analysis
Nolte, Ilja M, De Vries, André R, Spijker, Geert T, Jansen, Ritsert C, Brinza, Dumitru, Zelikovsky, Alexander, ...
We propose two new haplotype-sharing methods for identifying disease loci: the haplotype sharing statistic (HSS), which compares length of shared haplotypes between cases and controls, and the CROSS...
De novo fragment assembly with short mate-paired reads: Does the read length matter?
Chaisson, Mark J., Brinza, Dumitru, Pevzner, Pavel A.
Increasing read length is currently viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of...