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43,361
Base-calling of automated sequencer traces using phred. I. Accuracy Assessment
- GENOME RES
, 1998
"... The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obta ..."
Abstract
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Cited by 1653 (4 self)
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improved accuracy of the data processing software and reliable accuracy measures to reduce the need for human involvement in error correction and make human review more efficient. Here, we describe one step toward that goal: a base-calling program for automated sequencer traces, phred, with improved
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
- Biostatistics,
, 2003
"... SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting of f ..."
Abstract
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Cited by 854 (33 self)
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SUMMARY In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix GeneChip R system with the objective of improving upon currently used measures of gene expression. Our analyses make use of three data sets: a small experimental study consisting
Summaries of Affymetrix GeneChip probe level data
- Nucleic Acids Res
, 2003
"... High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11±20 pairs of pr ..."
Abstract
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Cited by 471 (21 self)
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of probes. In order to obtain expression measures it is necessary to summarize the probe level data. Using two extensive spike-in studies and a dilution study, we developed a set of tools for assessing the effectiveness of expression measures. We found that the performance of the current version
Atmospheric Modeling, Data Assimilation and Predictability
, 2003
"... Numerical weather prediction (NWP) now provides major guidance in our daily weather forecast. The accuracy of NWP models has improved steadily since the first successful experiment made by Charney, Fj!rtoft and von Neuman (1950). During the past 50 years, a large number of technical papers and repor ..."
Abstract
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Cited by 626 (33 self)
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Numerical weather prediction (NWP) now provides major guidance in our daily weather forecast. The accuracy of NWP models has improved steadily since the first successful experiment made by Charney, Fj!rtoft and von Neuman (1950). During the past 50 years, a large number of technical papers
Mining Sequential Patterns: Generalizations and Performance Improvements
- RESEARCH REPORT RJ 9994, IBM ALMADEN RESEARCH
, 1995
"... The problem of mining sequential patterns was recently introduced in [3]. We are given a database of sequences, where each sequence is a list of transactions ordered by transaction-time, and each transaction is a set of items. The problem is to discover all sequential patterns with a user-specified ..."
Abstract
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Cited by 759 (5 self)
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-specified minimum support, where the support of a pattern is the number of data-sequences that contain the pattern. An example of a sequential pattern is "5 % of customers bought `Foundation' and `Ringworld' in one transaction, followed by `Second Foundation ' in a later transaction". We
Improved prediction of signal peptides -- SignalP 3.0
- J. MOL. BIOL.
, 2004
"... We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cle ..."
Abstract
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Cited by 654 (7 self)
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that the cleavage site position and the amino acid composition of the signal peptide are correlated, new features have been included as input to the neural network. This addition, combined with a thorough error-correction of a new data set, have improved the performance of the predictor significantly over Signal
Trade Liberalization, Exit, and Productivity Improvements: Evidence from Chilean Plants
- Review of Economic Studies
, 2002
"... This paper empirically investigates the effects of liberalized trade on plant productivity in the case of Chile. Chile presents an interesting setting to study this relationship since it underwent a massive trade liberalization that significantly exposed its plants to competition from abroad during ..."
Abstract
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Cited by 555 (16 self)
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on consistent estimates of the input coefficients. In the second step, I identify the impact of trade on plants’ productivity in a regression framework allowing variation in productivity over time and across tradedand nontraded-goods sectors. Using plant-level panel data on Chilean manufacturers, I find
Dynamic Itemset Counting and Implication Rules for Market Basket Data
, 1997
"... We consider the problem of analyzing market-basket data and present several important contributions. First, we present a new algorithm for finding large itemsets which uses fewer passes over the data than classic algorithms, and yet uses fewer candidate itemsets than methods based on sampling. We in ..."
Abstract
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Cited by 615 (6 self)
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investigate the idea of item reordering, which can improve the low-level efficiency of the algorithm. Second, we present a new way of generating "implication rules," which are normalized based on both the antecedent and the consequent and are truly implications (not simply a measure of co
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999
- Nucleic Acids Res
, 1999
"... SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other ..."
Abstract
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Cited by 624 (5 self)
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SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration
Bagging predictors
, 1996
"... Bagging predictors is a method for generating multiple versions of a predictor and using these to get an aggregated predictor. The aggregation averages over the versions when predicting a numerical outcome and does a plurality vote when predicting a class. The multiple versions are formed by making ..."
Abstract
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Cited by 3650 (1 self)
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by making bootstrap replicates of the learning set and using these as new learning sets. Tests on real and simulated data sets using classification and regression trees and subset selection in linear regression show that bagging can give substantial gains in accuracy. The vital element is the instability
Results 1 - 10
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43,361
