Results 1  10
of
617,732
Finding community structure in networks using the eigenvectors of matrices
, 2006
"... We consider the problem of detecting communities or modules in networks, groups of vertices with a higherthanaverage density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as “modularity ” over possible div ..."
Abstract

Cited by 500 (0 self)
 Add to MetaCart
We consider the problem of detecting communities or modules in networks, groups of vertices with a higherthanaverage density of edges connecting them. Previous work indicates that a robust approach to this problem is the maximization of the benefit function known as “modularity ” over possible divisions of a network. Here we show that this maximization process can be written in terms of the eigenspectrum of a matrix we call the modularity matrix, which plays a role in community detection similar to that played by the graph Laplacian in graph partitioning calculations. This result leads us to a number of possible algorithms for detecting community structure, as well as several other results, including a spectral measure of bipartite structure in networks and a new centrality measure that identifies those vertices that occupy central positions within the communities to which they belong. The algorithms and measures proposed are illustrated with applications to a variety of realworld complex networks.
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 ..."
Abstract

Cited by 540 (28 self)
 Add to MetaCart
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
Good ErrorCorrecting Codes based on Very Sparse Matrices
, 1999
"... We study two families of errorcorrecting codes defined in terms of very sparse matrices. "MN" (MacKayNeal) codes are recently invented, and "Gallager codes" were first investigated in 1962, but appear to have been largely forgotten, in spite of their excellent properties. The ..."
Abstract

Cited by 741 (23 self)
 Add to MetaCart
We study two families of errorcorrecting codes defined in terms of very sparse matrices. "MN" (MacKayNeal) codes are recently invented, and "Gallager codes" were first investigated in 1962, but appear to have been largely forgotten, in spite of their excellent properties
Estimating the Support of a HighDimensional Distribution
, 1999
"... Suppose you are given some dataset drawn from an underlying probability distribution P and you want to estimate a "simple" subset S of input space such that the probability that a test point drawn from P lies outside of S is bounded by some a priori specified between 0 and 1. We propo ..."
Abstract

Cited by 766 (29 self)
 Add to MetaCart
Suppose you are given some dataset drawn from an underlying probability distribution P and you want to estimate a "simple" subset S of input space such that the probability that a test point drawn from P lies outside of S is bounded by some a priori specified between 0 and 1. We
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 ..."
Abstract

Cited by 1602 (4 self)
 Add to MetaCart
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
MEGA5: Molecular evolutionary genetics analysis using maximum . . .
, 2011
"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
Abstract

Cited by 6858 (19 self)
 Add to MetaCart
) analyses for inferring evolutionary trees, selecting bestfit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates sitebysite. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared
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 ..."
Abstract

Cited by 946 (9 self)
 Add to MetaCart
repeats by percent identity and frequency of indels between adjacent pattern copies and use statistically based recognition criteria. We demonstrate the algorithm's speed and its ability to detect tandem repeats that have undergone extensive mutational change by analyzing four sequences: the human
A Simple Estimator of Cointegrating Vectors in Higher Order Cointegrated Systems
 ECONOMETRICA
, 1993
"... Efficient estimators of cointegrating vectors are presented for systems involving deterministic components and variables of differing, higher orders of integration. The estimators are computed using GLS or OLS, and Wald Statistics constructed from these estimators have asymptotic x2 distributions. T ..."
Abstract

Cited by 507 (3 self)
 Add to MetaCart
Efficient estimators of cointegrating vectors are presented for systems involving deterministic components and variables of differing, higher orders of integration. The estimators are computed using GLS or OLS, and Wald Statistics constructed from these estimators have asymptotic x2 distributions
Powerlaw distributions in empirical data
 ISSN 00361445. doi: 10.1137/ 070710111. URL http://dx.doi.org/10.1137/070710111
, 2009
"... Powerlaw distributions occur in many situations of scientific interest and have significant consequences for our understanding of natural and manmade phenomena. Unfortunately, the empirical detection and characterization of power laws is made difficult by the large fluctuations that occur in the t ..."
Abstract

Cited by 589 (7 self)
 Add to MetaCart
in the tail of the distribution. In particular, standard methods such as leastsquares fitting are known to produce systematically biased estimates of parameters for powerlaw distributions and should not be used in most circumstances. Here we describe statistical techniques for making accurate parameter
Results 1  10
of
617,732