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- ArticleApril 2003
Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 332–340https://doi.org/10.1145/640075.640119Recent 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 ...
- ArticleApril 2003
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 322–331https://doi.org/10.1145/640075.640118We propose a framework for modeling sequence motifs based on the Maximum Entropy principle (MEP).We recommend approximating short sequence motif distributions with the Maximum Entropy Distribution (MED) consistent with low-order marginal constraints ...
- ArticleApril 2003
Physical network models and multi-source data integration
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 312–321https://doi.org/10.1145/640075.640117We develop a new framework for inferring models of transcriptional regulation. The models in this approach, which we call physical models, are constructed on the basis of verifiable molecular attributes of the underlying biological system. The ...
- ArticleApril 2003
Invited: poetry and prose of the sequences
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Page 311https://doi.org/10.1145/640075.640116Nucleotide and amino acid sequences carry many different codes, patterns recognized by numerous different reading devices. To name a few: THE triplet code, gene splicing code, translation framing code, chromatin code. One very basic property of the ...
- ArticleApril 2003
Modeling transcription programs: inferring binding site activity and dose-response model optimization
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 301–310https://doi.org/10.1145/640075.640115The modeling of transcription regulation programs is a major focus of today's biology. The challenge is to utilize diverse high-throughput data (gene expression, promoter binding site localization assays, protein expression) in order to infer the ...
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- ArticleApril 2003
Combining phylogenetic and hidden Markov models in biosequence analysis
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 277–286https://doi.org/10.1145/640075.640111A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models ...
- ArticleApril 2003
Approximation of protein structure for fast similarity measures
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 267–276https://doi.org/10.1145/640075.640110It is shown that structural similarity between proteins can be decided well with much less information than what is used in common similarity measures. The full Cα representation contains redundant information because of the inherent chain topology of ...
- ArticleApril 2003
Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 257–266https://doi.org/10.1145/640075.640109We construct several score functions for use in locating unusually conserved regions in a genome-wide search of aligned DNA from two species. We test these functions on regions of the human genome aligned to the mouse genome. These score functions are ...
- ArticleApril 2003
Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 247–256https://doi.org/10.1145/640075.640108Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human ...
- ArticleApril 2003
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 biologyApril 2003, Pages 237–246https://doi.org/10.1145/640075.640107Recent efforts to characterize genetic variation indicate that humans share large chromosomal blocks, along which little to no recombination is observable. Thus, on a segment-by-segment basis, only a handful of haplotypes account for most human ...
- ArticleApril 2003
Invited: Biology and bioinformatics of halophilism
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Page 236https://doi.org/10.1145/640075.640106Halophilism is a biological response to habitats with extreme salt concentrations. We sequenced the genomes of two extremely halophilic archaea for detailed analysis of life style and adaptation to extreme environments. A central focus are studies on ...
- ArticleApril 2003
A multi-expert system for the automatic detection of protein domains from sequence information
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 224–234https://doi.org/10.1145/640075.640104We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from a database search. Multiple measures are defined to quantify ...
- ArticleApril 2003
Gene selection criterion for discriminant microarray data analysis based on extreme value distributions
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 217–223https://doi.org/10.1145/640075.640103An important issue commonly encountered in the analysis of microarray data is to decide which and how many genes should be selected for further studies. For discriminant microarray data analyses based on statistical models, such as the logistic ...
- ArticleApril 2003
Efficient rule-based haplotyping algorithms for pedigree data
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 197–206https://doi.org/10.1145/640075.640101We study haplotype reconstruction under the Mendelian law of inheritance and the minimum recombination principleon pedigree data. We prove that the problem of finding a mini-mum-recombinant haplotype configuration (MRHC) is in general NP-hard. This is ...
- ArticleApril 2003
Invited: Prediction of protein function
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Page 196https://doi.org/10.1145/640075.640100A genome sequence embodies the potential life of an organism, but implementation of genetic information depends on the functions of the proteins that it encodes. Many proteins of known sequence and even of known structure present challenges to ...
- ArticleApril 2003
Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 176–187https://doi.org/10.1145/640075.640098High-throughput NMR structural biology can play an important role in structural genomics. We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of an homologous structure. These assignments ...
- ArticleApril 2003
Joint classifier and feature optimization for cancer diagnosis using gene expression data
RECOMB '03: Proceedings of the seventh annual international conference on Research in computational molecular biologyApril 2003, Pages 167–175https://doi.org/10.1145/640075.640097Recent research has demonstrated quite convincingly that accurate cancer diagnosis can be achieved by constructing classifiers that are designed to compare the gene expression profile of a tissue of unknown cancer status to a database of stored ...
