An almost linear-time algorithm for graph realization
Mathematics of Operations Research
Inferring Evolutionary History from DNA Sequences
SIAM Journal on Computing
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Large scale reconstruction of haplotypes from genotype data
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Efficient rule-based haplotyping algorithms for pedigree data
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Resolution of haplotypes and haplotype frequencies from SNP genotypes of pooled samples
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Finding Founder Sequences from a Set of Recombinants
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
The Haplotyping problem: an overview of computational models and solutions
Journal of Computer Science and Technology
Maximum likelihood resolution of multi-block genotypes
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Bayesian haplo-type inference via the dirichlet process
ICML '04 Proceedings of the twenty-first international conference on Machine learning
An approximation algorithm for haplotype inference by maximum parsimony
Proceedings of the 2005 ACM symposium on Applied computing
An Efficient Algorithm for Perfect Phylogeny Haplotyping
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Polynomial and APX-hard cases of the individual haplotyping problem
Theoretical Computer Science - Pattern discovery in the post genome
Islands of Tractability for Parsimony Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotyping with missing data via perfect path phylogenies
Discrete Applied Mathematics
SODA '07 Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms
The phasing of heterozygous traits: Algorithms and complexity
Computers & Mathematics with Applications
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Experimental analysis of a new algorithm for partial haplotype completion
International Journal of Bioinformatics Research and Applications
A fast haplotype inference method for large population genotype data
Computational Statistics & Data Analysis
Haplotype Inferring Via Galled-Tree Networks Is NP-Complete
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
Genotype Sequence Segmentation: Handling Constraints and Noise
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
The Undirected Incomplete Perfect Phylogeny Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Discrete Applied Mathematics
Pure Parsimony Xor Haplotyping
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
A Decomposition of the Pure Parsimony Haplotyping Problem
ISBRA '09 Proceedings of the 5th International Symposium on Bioinformatics Research and Applications
Influence of Tree Topology Restrictions on the Complexity of Haplotyping with Missing Data
TAMC '09 Proceedings of the 6th Annual Conference on Theory and Applications of Models of Computation
Haplotype Inference in Complex Pedigrees
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
On the Approximability of Some Haplotyping Problems
AAIM '09 Proceedings of the 5th International Conference on Algorithmic Aspects in Information and Management
Haplotype Inference Constrained by Plausible Haplotype Data
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Haplotype inference using a genetic algorithm
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Algorithm for haplotype resolution and block partitioning for partial XOR-genotype data
Journal of Biomedical Informatics
Empirical exploration of perfect phylogeny haplotyping and haplotypers
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Algorithm for haplotype inferring via galled-tree networks with simple galls
ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Combinatorial problems arising in SNP and haplotype analysis
DMTCS'03 Proceedings of the 4th international conference on Discrete mathematics and theoretical computer science
Genome-wide compatible SNP intervals and their properties
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
SplittingHeirs: inferring haplotypes by optimizing resultant dense graphs
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Phylogeny - and parsimony-based haplotype inference with constraints
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Xor perfect phylogeny haplotyping in pedigrees
ICIC'10 Proceedings of the Advanced intelligent computing theories and applications, and 6th international conference on Intelligent computing
Insights on haplotype inference on large genotype datasets
BSB'10 Proceedings of the Advances in bioinformatics and computational biology, and 5th Brazilian conference on Bioinformatics
Pure Parsimony Xor Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotype Inference Constrained by Plausible Haplotype Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogenetic network inferences through efficient haplotyping
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
On the complexity of SNP block partitioning under the perfect phylogeny model
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
Constructing camin-sokal phylogenies via answer set programming
LPAR'06 Proceedings of the 13th international conference on Logic for Programming, Artificial Intelligence, and Reasoning
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
On the genealogy of asexual diploids
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
HAPLOFREQ: estimating haplotype frequencies efficiently
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
A linear-time algorithm for the perfect phylogeny haplotyping (PPH) problem
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Experimental analysis of a new algorithm for partial haplotype completion
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
Influence of tree topology restrictions on the complexity of haplotyping with missing data
Theoretical Computer Science
The binary perfect phylogeny with persistent characters
Theoretical Computer Science
Using genetic algorithm in reconstructing single individual haplotype with minimum error correction
Journal of Biomedical Informatics
Semi-supervised clustering algorithm for haplotype assembly problem based on MEC model
International Journal of Data Mining and Bioinformatics
COCOON'07 Proceedings of the 13th annual international conference on Computing and Combinatorics
A heuristic algorithm for haplotype reconstruction from aligned weighted SNP fragments
International Journal of Bioinformatics Research and Applications
Minimum mosaic inference of a set of recombinants
CATS '11 Proceedings of the Seventeenth Computing: The Australasian Theory Symposium - Volume 119
Minimum mosaic inference of a set of recombinants
CATS 2011 Proceedings of the Seventeenth Computing on The Australasian Theory Symposium - Volume 119
FNphasing: A Novel Fast Heuristic Algorithm for Haplotype Phasing Based on Flow Network Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Hi-index | 0.00 |
The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A prototype Haplotype Mapping strategy is presently being finalized by an NIH working-group. The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7].In this paper we explore the algorithmic implications of the key (and now realistic) "no-recombination in long blocks" observation, for the problem of inferring haplotypes in populations. We observe that the no-recombination assumption is very powerful. This assumption, along with the standard population-genetic assumption of infinite sites [23, 14] imposes severe combinatorial constraints on the permitted solutions to the haplotype inference problem, leading to an efficient deterministic algorithm to deduce all features of the permitted haplotype solution(s) that can be known with certainty. The technical key is to view haplotype data as disguised information about paths in an unknown tree, and the haplotype deduction problem as a problem of reconstructing the tree from that path information. This formulation allows us to exploit deep theorems and algorithms from graph and matroid theory to efficiently find one permitted solution to the haplotype problem; it gives a simple test to determine if it is the unique solution; if not, we can implicitly represent the set of all permitted solutions so that each can be efficiently created.