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Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - 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 ..."
Abstract - Cited by 748 (13 self) - Add to MetaCart
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

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 1052 (38 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

Graphical models, exponential families, and variational inference

by Martin J. Wainwright, Michael I. Jordan , 2008
"... The formalism of probabilistic graphical models provides a unifying framework for capturing complex dependencies among random variables, and building large-scale multivariate statistical models. Graphical models have become a focus of research in many statistical, computational and mathematical fiel ..."
Abstract - Cited by 800 (26 self) - Add to MetaCart
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

BoosTexter: A Boosting-based System for Text Categorization

by Robert E. Schapire , Yoram Singer
"... This work focuses on algorithms which learn from examples to perform multiclass text and speech categorization tasks. Our approach is based on a new and improved family of boosting algorithms. We describe in detail an implementation, called BoosTexter, of the new boosting algorithms for text catego ..."
Abstract - Cited by 658 (20 self) - Add to MetaCart
This work focuses on algorithms which learn from examples to perform multiclass text and speech categorization tasks. Our approach is based on a new and improved family of boosting algorithms. We describe in detail an implementation, called BoosTexter, of the new boosting algorithms for text

2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement opti-ons, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
Abstract - Cited by 788 (5 self) - Add to MetaCart
The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement opti-ons, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed

The CONSORT Statement: Revised Recommendations for Improving the Quality of Reports of Parallel-Group Randomised Trials. The Lancet

by David Moher, Msc Kenneth, F. Schulz, Douglas G. Altman, For The Consort Group
"... To comprehend the results of a randomized, controlled trial (RCT), readers must understand its design, conduct, analysis, and inter-pretation. That goal can be achieved only through complete trans-parency from authors. Despite several decades of educational ef-forts, the reporting of RCTs needs impr ..."
Abstract - Cited by 759 (15 self) - Add to MetaCart
improvement. Investigators and editors developed the original CONSORT (Consolidated Standards of Reporting Trials) statement to help authors improve reporting by using a checklist and flow diagram. The revised CONSORT statement presented in this paper incorporates new evidence and addresses some criticisms

Debt, deficits and finite horizons

by Olivier J. Blanchard, Debt Comments, Suggestions Andy Abel, Alan Auerbach, Robert Barro, Guillernio Calvo, Rudi Dornbusch, Greg Mankiw, Franco Modigliani, Robert Solow, Olivier J. Blanchard - Journal of Political Economy , 1985
"... Weitzman have improved this paper. I thank NSF for financial ..."
Abstract - Cited by 579 (1 self) - Add to MetaCart
Weitzman have improved this paper. I thank NSF for financial

The separation of ownership and control in East Asian Corporations

by Stijn Claessens, Simeon Djankov, Larry H. P. Lang - Journal of Financial Economics , 2000
"... We examine the separation of ownership and control for 2,980 corporations in nine East Asian countries. In all countries, voting rights frequently exceed cash-#ow rights via pyramid structures and cross-holdings. The separation of ownership and control is most pronounced among family-controlled &quo ..."
Abstract - Cited by 573 (17 self) - Add to MetaCart
We examine the separation of ownership and control for 2,980 corporations in nine East Asian countries. In all countries, voting rights frequently exceed cash-#ow rights via pyramid structures and cross-holdings. The separation of ownership and control is most pronounced among family

Wrappers for Feature Subset Selection

by Ron Kohavi, George H. John - AIJ SPECIAL ISSUE ON RELEVANCE , 1997
"... In the feature subset selection problem, a learning algorithm is faced with the problem of selecting a relevant subset of features upon which to focus its attention, while ignoring the rest. To achieve the best possible performance with a particular learning algorithm on a particular training set, a ..."
Abstract - Cited by 1522 (3 self) - Add to MetaCart
the strengths and weaknesses of the wrapper approach andshow a series of improved designs. We compare the wrapper approach to induction without feature subset selection and to Relief, a filter approach to feature subset selection. Significant improvement in accuracy is achieved for some datasets for the two

Nonmonotonic Reasoning, Preferential Models and Cumulative Logics

by Sarit Kraus, Daniel Lehmann, Menachem Magidor , 1990
"... Many systems that exhibit nonmonotonic behavior have been described and studied already in the literature. The general notion of nonmonotonic reasoning, though, has almost always been described only negatively, by the property it does not enjoy, i.e. monotonicity. We study here general patterns of ..."
Abstract - Cited by 624 (14 self) - Add to MetaCart
of nonmonotonic reasoning and try to isolate properties that could help us map the field of nonmonotonic reasoning by reference to positive properties. We concentrate on a number of families of nonmonotonic consequence relations, defined in the style of Gentzen [13]. Both proof-theoretic and semantic points
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