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RESEARCH Open Access On the design of clone-based haplotyping

by Christine Lo, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church, Vineet Bafna, Kun Zhang
"... Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable ..."
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, but with variable yields due to incompletely understood parameter choices. Results: We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together

A comparison of bayesian methods for haplotype reconstruction from population genotype data.

by Matthew Stephens , Peter Donnelly , Dr Matthew Stephens - Am J Hum Genet , 2003
"... In this report, we compare and contrast three previously published Bayesian methods for inferring haplotypes from genotype data in a population sample. We review the methods, emphasizing the differences between them in terms of both the models ("priors") they use and the computational str ..."
Abstract - Cited by 557 (7 self) - Add to MetaCart
individuals to assist in this endeavor, but in general such data may be either unavailable or only partially informative. We focus here on the problem of statistically inferring haplotypes from unphased genotype data for a sample of ("unrelated") individuals from a population. Several approaches

On the design of clone-based haplotyping

by Christine Lo , Rui Liu , Jehyuk Lee , Kimberly Robasky , Susan Byrne , Carolina Lucchesi , John Aach , George Church , Vineet Bafna , Kun Zhang - Genome Biol , 2013
"... Abstract Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but wit ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
Abstract Background: Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising

permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. On the design of clone-based haplotyping

by Christine Lo, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church, Vineet Bafna, Kun Zhang, Christine Lo, Rui Liu, Jehyuk Lee, Kimberly Robasky, Susan Byrne, Carolina Lucchesi, John Aach, George Church , 2013
"... This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. On the design of clone-based haplotyping ..."
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This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. On the design of clone-based haplotyping

Adaptive Fraud Detection

by Tom Fawcett, Foster Provost - DATA MINING AND KNOWLEDGE DISCOVERY , 1997
"... One method for detecting fraud is to check for suspicious changes in user behavior. This paper describes the automatic design of user profiling methods for the purpose of fraud detection, using a series of data mining techniques. Specifically, we use a rule-learning program to uncover indicators of ..."
Abstract - Cited by 221 (19 self) - Add to MetaCart
high-confidence alarms. The system has been applied to the problem of detecting cellular cloning fraud based on a database of call records. Experiments indicate that this automatic approach performs better than hand-crafted methods for detecting fraud. Furthermore, this approach can adapt

Consed: a graphical tool for sequence finishing

by David Gordon , Chris Abajian , Phil Green - Genome Res , 1998
"... Sequencing of large clones or small genomes is generally done by the shotgun approach Although complete automation of data processing in shotgun sequencing is clearly desirable and may be feasible in the near future, at present finishing still requires extensive human intervention. This is customa ..."
Abstract - Cited by 207 (0 self) - Add to MetaCart
Sequencing of large clones or small genomes is generally done by the shotgun approach Although complete automation of data processing in shotgun sequencing is clearly desirable and may be feasible in the near future, at present finishing still requires extensive human intervention

Dynamic Programming Algorithms for Haplotype Block Partitioning: Applications to Human Chromosome 21 Haplotype Data

by Kui Zhang, Fengzhu Sun, Michael S. Waterman, Ting Chen - Proc. Natl. Acad. Sci. USA , 2003
"... Recent studies have shown that the human genome has a haplotype block structure such that it can be divided into discrete blocks of limited haplotype diversity. Patil et al. [6] and Zhang et al. [12] developed algorithms to partition haplotypes into blocks with minimum number of tag SNPs for the ent ..."
Abstract - Cited by 127 (8 self) - Add to MetaCart
for the entire chromosome. However, it is not clear how to partition haplotypes into blocks with restricted number of SNPs when only limited resources are available. In this paper, we first formulated this problem as finding a block partition with a fixed number of tag SNPs that can cover the maximal percentage

On the Complexity of Several Haplotyping Problems

by Rudi Cilibrasi, Leo Van Iersel, Steven Kelk, John Tromp - Proceedings of the 5th International Workshop on Algorithms in Bioinformatics (WABI 2005), LNBI 3692 , 2005
"... Abstract In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More specifically, we show that an interesting, restricted case o ..."
Abstract - Cited by 22 (4 self) - Add to MetaCart
Abstract In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More specifically, we show that an interesting, restricted case

Models and Algorithms for Haplotyping Problem

by Xiang-sun Zhang, Rui-sheng Wang, Ling-yun Wu, Luonan Chen - Current Bioinformatics , 2006
"... Abstract: One of the main topics in genomics is to determine the relevance of DNA variations with some genetic disease. Single nucleotide polymorphism (SNP) is the most frequent and important form of genetic variation which involves a single DNA base. The values of a set of SNPs on a particular chro ..."
Abstract - Cited by 10 (1 self) - Add to MetaCart
chromosome copy define a haplotype. Because of its importance in the studies of complex disease association, haplotyping is one of the central problems in bioinformatics. There are two classes of in silico haplotyping problems, i.e., single individual haplotyping and population haplotyping. In this review

Efficient reconstruction of haplotype structure via perfect phylogeny

by Eleazar Eskin, Eran Halperin, Richard M. Karp - Journal of Bioinformatics and Computational Biology , 2003
"... Each person’s genome contains two copies of each chromosome, one inherited from the father and the other from the mother. A person’s genotype specifies the pair of bases at each site, but does not specify which base occurs on which chromosome. The sequence of each chromosome separately is called a h ..."
Abstract - Cited by 75 (12 self) - Add to MetaCart
Each person’s genome contains two copies of each chromosome, one inherited from the father and the other from the mother. A person’s genotype specifies the pair of bases at each site, but does not specify which base occurs on which chromosome. The sequence of each chromosome separately is called a
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