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951,167
Basecalling 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 largescale 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 ..."
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Cited by 1602 (4 self)
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The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current largescale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required
New empirical relationships among magnitude, rupture length, rupture width, rupture area, and surface
, 1994
"... Abstract Source parameters for historical earthquakes worldwide are compiled to develop a series of empirical relationships among moment magnitude (M), surface rupture length, subsurface rupture length, downdip rupture width, rupture area, and maximum and average displacement per event. The resultin ..."
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Cited by 524 (0 self)
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Abstract Source parameters for historical earthquakes worldwide are compiled to develop a series of empirical relationships among moment magnitude (M), surface rupture length, subsurface rupture length, downdip rupture width, rupture area, and maximum and average displacement per event
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
Determining the Number of Factors in Approximate Factor Models
, 2000
"... In this paper we develop some statistical theory for factor models of large dimensions. The focus is the determination of the number of factors, which is an unresolved issue in the rapidly growing literature on multifactor models. We propose a panel Cp criterion and show that the number of factors c ..."
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Cited by 538 (29 self)
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In this paper we develop some statistical theory for factor models of large dimensions. The focus is the determination of the number of factors, which is an unresolved issue in the rapidly growing literature on multifactor models. We propose a panel Cp criterion and show that the number of factors
Factor Graphs and the SumProduct Algorithm
 IEEE TRANSACTIONS ON INFORMATION THEORY
, 1998
"... A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple c ..."
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Cited by 1787 (72 self)
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A factor graph is a bipartite graph that expresses how a "global" function of many variables factors into a product of "local" functions. Factor graphs subsume many other graphical models including Bayesian networks, Markov random fields, and Tanner graphs. Following one simple
FAST VOLUME RENDERING USING A SHEARWARP FACTORIZATION OF THE VIEWING TRANSFORMATION
, 1995
"... Volume rendering is a technique for visualizing 3D arrays of sampled data. It has applications in areas such as medical imaging and scientific visualization, but its use has been limited by its high computational expense. Early implementations of volume rendering used bruteforce techniques that req ..."
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Cited by 541 (2 self)
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Volume rendering is a technique for visualizing 3D arrays of sampled data. It has applications in areas such as medical imaging and scientific visualization, but its use has been limited by its high computational expense. Early implementations of volume rendering used bruteforce techniques that require on the order of 100 seconds to render typical data sets on a workstation. Algorithms with optimizations that exploit coherence in the data have reduced rendering times to the range of ten seconds but are still not fast enough for interactive visualization applications. In this thesis we present a family of volume rendering algorithms that reduces rendering times to one second. First we present a scanlineorder volume rendering algorithm that exploits coherence in both the volume data and the image. We show that scanlineorder algorithms are fundamentally more efficient than commonlyused ray casting algorithms because the latter must perform analytic geometry calculations (e.g. intersecting rays with axisaligned boxes). The new scanlineorder algorithm simply streams through the volume and the image in storage order. We describe variants of the algorithm for both parallel and perspective projections and
2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res
"... The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
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Cited by 788 (5 self)
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The accuracy of multiple sequence alignment program MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, HINSi, FINSi and GINSi, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed
Exploiting Generative Models in Discriminative Classifiers
 In Advances in Neural Information Processing Systems 11
, 1998
"... Generative probability models such as hidden Markov models provide a principled way of treating missing information and dealing with variable length sequences. On the other hand, discriminative methods such as support vector machines enable us to construct flexible decision boundaries and often resu ..."
Abstract

Cited by 538 (11 self)
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Generative probability models such as hidden Markov models provide a principled way of treating missing information and dealing with variable length sequences. On the other hand, discriminative methods such as support vector machines enable us to construct flexible decision boundaries and often
Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods
 J. Mol. Evol
, 1994
"... Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called ..."
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Cited by 540 (28 self)
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Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or nearoptimum fit by the model to the data, and also an acceptable approximation to the continuous dis tribution. The second method, called "fixedrates mod el," classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated.
Construction of Escherichia coli K12 inframe, singlegene knockout mutants: the Keio collection. Mol. Syst. Biol 2:2006.0008
, 2006
"... We have systematically made a set of precisely defined, singlegene deletions of all nonessential genes in Escherichia coli K12. Openreading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a onestep method for inactivation of chromosom ..."
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Cited by 701 (7 self)
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We have systematically made a set of precisely defined, singlegene deletions of all nonessential genes in Escherichia coli K12. Openreading frame coding regions were replaced with a kanamycin cassette flanked by FLP recognition target sites by using a onestep method for inactivation of chromosomal genes and primers designed to create inframe deletions upon excision of the resistance cassette. Of 4288 genes targeted, mutants were obtained for 3985. To alleviate problems encountered in highthroughput studies, two independent mutants were saved for every deleted gene. These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genomewide testing of mutational effects in a common strain background, E. coli K12 BW25113. We were unable to disrupt 303 genes, including 37 of unknown function, which are candidates for essential genes. Distribution is being handled via GenoBase
Results 11  20
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951,167