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2,955,980
Efficient similarity search in sequence databases
, 1994
"... We propose an indexing method for time sequences for processing similarity queries. We use the Discrete Fourier Transform (DFT) to map time sequences to the frequency domain, the crucial observation being that, for most sequences of practical interest, only the first few frequencies are strong. Anot ..."
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Cited by 505 (21 self)
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. Another important observation is Parseval's theorem, which specifies that the Fourier transform preserves the Euclidean distance in the time or frequency domain. Having thus mapped sequences to a lowerdimensionality space by using only the first few Fourier coe cients, we use Rtrees to index
Graphical models, exponential families, and variational inference
, 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building largescale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
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Cited by 800 (26 self)
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of probability distributions — are best studied in the general setting. Working with exponential family representations, and exploiting the conjugate duality between the cumulant function and the entropy for exponential families, we develop general variational representations of the problems of computing
Pfam protein families database
 Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
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Cited by 748 (13 self)
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Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI Gen
A greedy algorithm for aligning DNA sequences
 J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
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Cited by 576 (16 self)
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For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy
The Encyclopedia of Integer Sequences
"... This article gives a brief introduction to the OnLine Encyclopedia of Integer Sequences (or OEIS). The OEIS is a database of nearly 90,000 sequences of integers, arranged lexicographically. The entry for a sequence lists the initial terms (50 to 100, if available), a description, formulae, programs ..."
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Cited by 866 (15 self)
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This article gives a brief introduction to the OnLine Encyclopedia of Integer Sequences (or OEIS). The OEIS is a database of nearly 90,000 sequences of integers, arranged lexicographically. The entry for a sequence lists the initial terms (50 to 100, if available), a description, formulae
Multiple sequence alignment with the Clustal series of programs
 Nucleic Acids Res
, 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
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Cited by 725 (5 self)
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The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also
A Note on the Confinement Problem
, 1973
"... This not explores the problem of confining a program during its execution so that it cannot transmit information to any other program except its caller. A set of examples attempts to stake out the boundaries of the problem. Necessary conditions for a solution are stated and informally justified. ..."
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Cited by 532 (0 self)
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This not explores the problem of confining a program during its execution so that it cannot transmit information to any other program except its caller. A set of examples attempts to stake out the boundaries of the problem. Necessary conditions for a solution are stated and informally justified.
Tandem repeats finder: a program to analyze DNA sequences
, 1999
"... A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, co ..."
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Cited by 946 (9 self)
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, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem
The Extended Linear Complementarity Problem
, 1993
"... We consider an extension of the horizontal linear complementarity problem, which we call the extended linear complementarity problem (XLCP). With the aid of a natural bilinear program, we establish various properties of this extended complementarity problem; these include the convexity of the biline ..."
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Cited by 776 (28 self)
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We consider an extension of the horizontal linear complementarity problem, which we call the extended linear complementarity problem (XLCP). With the aid of a natural bilinear program, we establish various properties of this extended complementarity problem; these include the convexity
Results 1  10
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2,955,980