A novel hierarchical clustering algorithm for gene sequences
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Shengrui Wang | Qingshan Jiang | Yanjie Wei | Dan Wei | Q. Jiang | Shengrui Wang | Yanjie Wei | Dan Wei
[1] Bernhard Haubold,et al. Efficient estimation of pairwise distances between genomes , 2009, Bioinform..
[2] Ernesto Picardi,et al. EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data , 2009, BMC Bioinformatics.
[3] Qi Dai,et al. Numerical characteristics of word frequencies and their application to dissimilarity measure for sequence comparison. , 2011, Journal of theoretical biology.
[4] B. Blaisdell. A measure of the similarity of sets of sequences not requiring sequence alignment. , 1986, Proceedings of the National Academy of Sciences of the United States of America.
[5] Daniel A. Ashlock,et al. Classifying synthetic and biological DNA sequences with side effect machines , 2008, 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
[6] Adam Godzik,et al. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..
[7] Michael S. Waterman,et al. Introduction to computational biology , 1995 .
[8] Chun Li,et al. Relative entropy of DNA and its application , 2005 .
[9] I. Uchiyama. Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes , 2006, Nucleic acids research.
[10] Brian Everitt,et al. Cluster analysis , 1974 .
[11] Jonas S. Almeida,et al. Alignment-free sequence comparison-a review , 2003, Bioinform..
[12] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[13] Susan R. Wilson. INTRODUCTION TO COMPUTATIONAL BIOLOGY: MAPS, SEQUENCES AND GENOMES. , 1996 .
[14] Mihai Pop,et al. Alignment and clustering of phylogenetic markers - implications for microbial diversity studies , 2010, BMC Bioinformatics.
[15] T. Mahalakshmi,et al. Visualization Of Genomic Data Using Inter-Nucleotide Distance Signals , 2005 .
[16] Rodrigo Lopez,et al. Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..
[17] Andrei V. Kelarev,et al. Clustering Algorithms for ITS Sequence Data with Alignment Metrics , 2006, Australian Conference on Artificial Intelligence.
[18] Paul A. Gore,et al. 11 – Cluster Analysis , 2000 .
[19] Susan M. Bridges,et al. Interactive clustering for exploration of genomic data , 2002 .
[20] S. Pääbo,et al. Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders , 1998, Journal of Molecular Evolution.
[21] Christian Gautier,et al. Statistical method for predicting protein coding regions in nucleic acid sequences , 1987, Comput. Appl. Biosci..
[22] Shengrui Wang,et al. CLUSS: Clustering of protein sequences based on a new similarity measure , 2007, BMC Bioinformatics.
[23] Elon Portugaly,et al. Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space , 2008, ISMB.
[24] Qingshan Jiang,et al. A DNA sequence distance measure approach for phylogenetic tree construction , 2010, 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA).
[25] Tiee-Jian Wu,et al. Statistical Measures of DNA Sequence Dissimilarity under Markov Chain Models of Base Composition , 2001, Biometrics.
[26] George C. Tseng,et al. Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data , 2007, Bioinform..
[27] Ting Chen,et al. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering , 2011, Bioinform..
[28] Xiao Sun,et al. A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. , 2008, Biochemical and Biophysical Research Communications - BBRC.
[29] P. Chaudhuri,et al. SWORDS: A statistical tool for analysing large DNA sequences , 2002, Journal of Biosciences.
[30] FayyadUsama,et al. Hierarchical Clustering Algorithms for Document Datasets , 2005 .
[31] Bernhard Haubold,et al. Alignment-free detection of local similarity among viral and bacterial genomes , 2011, Bioinform..
[32] Koichi Nishigaki,et al. A mathematical consideration of the word-composition vector method in comparison of biological sequences , 2011, Biosyst..
[33] Eva M. Neumann-Held. The Gene Is Dead — Long Live the Gene! Conceptualizing Genes the Constructionist Way , 1999 .
[34] Magnus Rattray,et al. A Methodology for Comparative Functional Genomics , 2007, J. Integr. Bioinform..
[35] Gesine Reinert,et al. Alignment-Free Sequence Comparison (I): Statistics and Power , 2009, J. Comput. Biol..
[36] Aibing Zhang,et al. New method for comparing DNA primary sequences based on a discrimination measure , 2010, Journal of Theoretical Biology.
[37] BMC Bioinformatics , 2005 .
[38] Anton J. Enright,et al. GeneRAGE: a robust algorithm for sequence clustering and domain detection , 2000, Bioinform..
[39] Xiang Fang,et al. An improved string composition method for sequence comparison , 2008, BMC Bioinformatics.
[40] A. S.,et al. Estimating the Entropy of DNA Sequences , 1997 .
[41] Kuan Yang,et al. Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana , 2008, Planta.
[42] D. Davison,et al. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. , 1997, Biometrics.
[43] Robert C. Edgar,et al. MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.
[44] Stephen S-T Yau,et al. A new distribution vector and its application in genome clustering. , 2011, Molecular phylogenetics and evolution.
[45] Chinatsu Aone,et al. Fast and effective text mining using linear-time document clustering , 1999, KDD '99.
[46] Sokal Rr,et al. Biometry: the principles and practice of statistics in biological research 2nd edition. , 1981 .
[47] George Karypis,et al. A Comparison of Document Clustering Techniques , 2000 .
[48] Mohamed S. Kamel,et al. Enhanced bisecting k-means clustering using intermediate cooperation , 2009, Pattern Recognit..
[49] Bernhard Haubold,et al. Alignment-free estimation of nucleotide diversity , 2011, Bioinform..
[50] F. James Rohlf,et al. Biometry: The Principles and Practice of Statistics in Biological Research , 1969 .
[51] Jian Pei,et al. Classification, Clustering, Features and Distances of Sequence Data , 2007 .
[52] Bo Zhao,et al. A novel clustering method via nucleotide-based Fourier power spectrum analysis , 2011, Journal of Theoretical Biology.
[53] Steve Baker,et al. Integrated gene and species phylogenies from unaligned whole genome protein sequences , 2002, Bioinform..
[54] Jun Wang,et al. A Poisson model of sequence comparison and its application to coronavirus phylogeny , 2009, Mathematical Biosciences.
[55] Peter Sperisen,et al. JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture , 2005, BMC Bioinformatics.
[56] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[57] Roderic D. M. Page,et al. TreeView: an application to display phylogenetic trees on personal computers , 1996, Comput. Appl. Biosci..
[58] Jun Wang,et al. WSE, a new sequence distance measure based on word frequencies , 2008, Mathematical Biosciences.
[59] Jeffery P. Demuth,et al. The Evolution of Mammalian Gene Families , 2006, PloS one.
[60] D. Lipman,et al. Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[61] George Karypis,et al. Hierarchical Clustering Algorithms for Document Datasets , 2005, Data Mining and Knowledge Discovery.
[62] G. Karypis,et al. Criterion Functions for Document Clustering ∗ Experiments and Analysis , 2001 .