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TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Abstract: With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
12,124 citations
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TL;DR: It is shown that feature relevance alone is insufficient for efficient feature selection of high-dimensional data, and a new framework is introduced that decouples relevance analysis and redundancy analysis.
Abstract: Feature selection is applied to reduce the number of features in many applications where data has hundreds or thousands of features. Existing feature selection methods mainly focus on finding relevant features. In this paper, we show that feature relevance alone is insufficient for efficient feature selection of high-dimensional data. We define feature redundancy and propose to perform explicit redundancy analysis in feature selection. A new framework is introduced that decouples relevance analysis and redundancy analysis. We develop a correlation-based method for relevance and redundancy analysis, and conduct an empirical study of its efficiency and effectiveness comparing with representative methods.
1,971 citations
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TL;DR: The data suggest that in the absence of normal stimulation there is a sensitive period of about 3.5 yr during which the human central auditory system remains maximally plastic.
Abstract: ObjectiveThe aim of the present experiment was to assess the consequences of cochlear implantation at different ages on the development of the human central auditory system.DesignOur measure of the maturity of central auditory pathways was the latency of the P1 cortical auditory evoked potential. Be
765 citations
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TL;DR: Short telomeres are a signature in IIPs and likely play a role in their age-related onset, and the clustering of cryptogenic liver cirrhosis with IPF suggests that the telomere shortening can contribute to what appears clinically as idiopathic progressive organ failure in the lung and the liver.
Abstract: Idiopathic interstitial pneumonias (IIPs) have a progressive and often fatal course, and their enigmatic etiology has complicated approaches to effective therapies. Idiopathic pulmonary fibrosis (IPF) is the most common of IIPs and shares with IIPs an increased incidence with age and unexplained scarring in the lung. Short telomeres limit tissue renewal capacity in the lung and germ-line mutations in telomerase components, hTERT and hTR, underlie inheritance in a subset of families with IPF. To examine the hypothesis that short telomeres contribute to disease risk in sporadic IIPs, we recruited patients who have no family history and examined telomere length in leukocytes and in alveolar cells. To screen for mutations, we sequenced hTERT and hTR. We also reviewed the cases for features of a telomere syndrome. IIP patients had shorter leukocyte telomeres than age-matched controls (P < 0.0001). In a subset (10%), IIP patients had telomere lengths below the first percentile for their age. Similar to familial cases with mutations, IPF patients had short telomeres in alveolar epithelial cells (P < 0.0001). Although telomerase mutations were rare, detected in 1 of 100 patients, we identified a cluster of individuals (3%) with IPF and cryptogenic liver cirrhosis, another feature of a telomere syndrome. Short telomeres are thus a signature in IIPs and likely play a role in their age-related onset. The clustering of cryptogenic liver cirrhosis with IPF suggests that the telomere shortening we identify has consequences and can contribute to what appears clinically as idiopathic progressive organ failure in the lung and the liver.
689 citations
Authors
Showing all 202 results
Name | H-index | Papers | Citations |
---|---|---|---|
Chao Zhang | 127 | 3119 | 84711 |
Huan Liu | 110 | 727 | 57903 |
Bruce E. Rittmann | 92 | 693 | 38520 |
Hao Yan | 90 | 324 | 34010 |
George R. Pettit | 89 | 848 | 31759 |
Nongjian Tao | 86 | 458 | 27541 |
Sudhir Kumar | 82 | 524 | 216349 |
Yan Liu | 79 | 203 | 20263 |
Stuart Lindsay | 74 | 347 | 22224 |
Roy Curtiss | 71 | 340 | 16048 |
Randolph M. Nesse | 71 | 209 | 20518 |
Tao Luo | 66 | 723 | 17774 |
George Poste | 64 | 252 | 15890 |
Douglas G. Walker | 63 | 163 | 14631 |
Stephen Albert Johnston | 62 | 239 | 14224 |