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The Pfam protein families database

by Alex Bateman, Lachlan Coin, Richard Durbin, Robert D. Finn, Volker Hollich, Ajay Khanna, Mhairi Marshall, Simon Moxon, Erik L. L. Sonnhammer, David J. Studholme, Corin Yeats, Sean R. Eddy - Nucleic Acids Res , 2002
"... Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations includ ..."
Abstract - Cited by 1070 (39 self) - Add to MetaCart
Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations

A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res

by Michaelw. Pfaffl
"... Use of the real-time polymerase chain reaction (PCR) to amplify cDNA products reverse transcribed from mRNA is on the way to becoming a routine tool in molecular biology to study low abundance gene expression. Real-time PCR is easy to perform, provides the necessary accuracy and produces reliable as ..."
Abstract - Cited by 1088 (4 self) - Add to MetaCart
as well as rapid quantification results. But accurate quantification of nucleic acids requires a reproducible methodology and an adequate mathematical model for data analysis. This study enters into the particular topics of the relative quantification in real-time RT–PCR of a target gene transcript

Mining the Network Value of Customers

by Pedro Domingos, Matt Richardson - In Proceedings of the Seventh International Conference on Knowledge Discovery and Data Mining , 2002
"... One of the major applications of data mining is in helping companies determine which potential customers to market to. If the expected pro t from a customer is greater than the cost of marketing to her, the marketing action for that customer is executed. So far, work in this area has considered only ..."
Abstract - Cited by 568 (11 self) - Add to MetaCart
|can be extremely eective, but is still a black art. Our work can be viewed as a step towards providing a more solid foundation for it, taking advantage of the availability of large relevant databases. Categories and Subject Descriptors H.2.8 [Database Management]: Database Applications| data mining

Learning Stochastic Logic Programs

by Stephen Muggleton , 2000
"... Stochastic Logic Programs (SLPs) have been shown to be a generalisation of Hidden Markov Models (HMMs), stochastic context-free grammars, and directed Bayes' nets. A stochastic logic program consists of a set of labelled clauses p:C where p is in the interval [0,1] and C is a first-order r ..."
Abstract - Cited by 1194 (81 self) - Add to MetaCart
Stochastic Logic Programs (SLPs) have been shown to be a generalisation of Hidden Markov Models (HMMs), stochastic context-free grammars, and directed Bayes' nets. A stochastic logic program consists of a set of labelled clauses p:C where p is in the interval [0,1] and C is a first

Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

by Jean-paul Ryckaert, Giovanni Ciccotti, Herman J. C. Berendsen - J. Comput. Phys , 1977
"... A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method ..."
Abstract - Cited by 704 (6 self) - Add to MetaCart
(MD), which has been widely used in the past for studying simple liquids and solids, has more recently been applied to molecular systems with internal degrees of freedom such as N, [l], H,O [2] and even C,H,, [3]. In applying the MD method three problems arise: (a) the choice of a suitable mechanical

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
PHASE, version 2.0, available online (http://www.stat.washington.edu/stephens/ software.html). Current high-throughput genotyping technologies, when applied to DNA from a diploid individual, are able to determine which two alleles are present at each locus but not the haplotype information (that is

Loopy belief propagation for approximate inference: An empirical study. In:

by Kevin P Murphy , Yair Weiss , Michael I Jordan - Proceedings of Uncertainty in AI, , 1999
"... Abstract Recently, researchers have demonstrated that "loopy belief propagation" -the use of Pearl's polytree algorithm in a Bayesian network with loops -can perform well in the context of error-correcting codes. The most dramatic instance of this is the near Shannon-limit performanc ..."
Abstract - Cited by 676 (15 self) - Add to MetaCart
;belief revision") version, Weiss For the case of networks with multiple loops, Richard son To summarize, what is currently known about loopy propagation is that ( 1) it works very well in an error correcting code setting and (2) there are conditions for a single-loop network for which it can be guaranteed

Brain magnetic resonance imaging with contrast dependent on blood oxygenation.

by S Ogawa , T M Lee , A R Kay , D W Tank - Proc. Natl. Acad. Sci. USA , 1990
"... ABSTRACT Paramagnetic deoxyhemoglobin in venous blood is a naturally occurring contrast agent for magnetic resonance imaging (MRI). By accentuating the effects of this agent through the use of gradient-echo techniques in high fields, we demonstrate in vivo images of brain microvasculature with imag ..."
Abstract - Cited by 648 (1 self) - Add to MetaCart
be used to provide in vivo real-time maps of blood oxygenation in the brain under normal physiological conditions. BOLD contrast adds an additional feature to magnetic resonance imaging and complements other techniques that are attempting to provide positron emission tomographylike measurements related

Relative absorptive capacity and interorganizational learning

by Peter J. Lane, Michael Lubatkin - STRATEGIC MANAGEMENT JOURNAL , 1998
"... Much of the prior research on interorganizational learning has focused on the role of absorptive capacity, a firm’s ability to value, assimilate, and utilize new external knowledge. However, this definition of the construct suggests that a firm has an equal capacity to learn from all other organizat ..."
Abstract - Cited by 463 (2 self) - Add to MetaCart
organizations. We reconceptualize the firm-level construct absorptive capacity as a learning dyad-level construct, relative absorptive capacity. One firm’s ability to learn from another firm is argued to depend on the similarity of both firms ’ (1) knowledge bases, (2) organizational structures and compensation

The design of Postgres

by Michael Stonebraker, Lawrence A. Rowe - In Proceedings of the SIGMOD Conference , 1986
"... This paper presents the preliminary design of a new database management system, called POSTGRES, that is the successor to the INGRES relational database system. The main design goals of the new system are to: 1) provide better support for complex objects, 2) provide user extendibility for data types ..."
Abstract - Cited by 431 (23 self) - Add to MetaCart
This paper presents the preliminary design of a new database management system, called POSTGRES, that is the successor to the INGRES relational database system. The main design goals of the new system are to: 1) provide better support for complex objects, 2) provide user extendibility for data
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