Gene Function Analysis

In Chap. 5, a granular self-organizing network for clustering and a methodology for gene ranking using the concept of granularity are described.

[1]  Dmitrij Frishman,et al.  MIPS: a database for genomes and protein sequences , 1999, Nucleic Acids Res..

[2]  Ron Shamir,et al.  CLICK and EXPANDER: a system for clustering and visualizing gene expression data , 2003, Bioinform..

[3]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[4]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[5]  T. H. Bø,et al.  LSimpute: accurate estimation of missing values in microarray data with least squares methods. , 2004, Nucleic acids research.

[6]  Tommi S. Jaakkola,et al.  Fast optimal leaf ordering for hierarchical clustering , 2001, ISMB.

[7]  A. Owen,et al.  A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[8]  In suk Lee,et al.  24 Bioinformatic Prediction of Yeast Gene Function , 2007 .

[9]  C. DeLisi,et al.  The society of genes: networks of functional links between genes from comparative genomics , 2002, Genome Biology.

[10]  Kara Dolinski,et al.  Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) , 2002, Nucleic Acids Res..

[11]  Cheng-Yan Kao,et al.  An evolutionary approach for gene expression patterns , 2004, IEEE Transactions on Information Technology in Biomedicine.

[12]  W. Cleveland,et al.  Locally Weighted Regression: An Approach to Regression Analysis by Local Fitting , 1988 .

[13]  E. Southern.  Detection of specific sequences among DNA fragments separated by gel electrophoresis. , 1975, Journal of molecular biology.

[14]  T. Pawson,et al.  Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.

[15]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[16]  Avi Shoshan,et al.  Large-scale protein annotation through gene ontology. , 2002, Genome research.

[17]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[18]  B. Snel,et al.  Comparative assessment of large-scale data sets of protein–protein interactions , 2002, Nature.

[19]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[20]  T. Ideker,et al.  Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae , 2006, Journal of biology.

[21]  Pablo Moscato,et al.  Applying Memetic Algorithms to the Analysis of Microarray Data , 2003, EvoWorkshops.

[22]  E. Krause,et al.  Taxicab Geometry: An Adventure in Non-Euclidean Geometry , 1987 .

[23]  L. Mirny,et al.  Protein complexes and functional modules in molecular networks , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Paul Kellam,et al.  Kaposi's Sarcoma-Associated Herpesvirus Latent and Lytic Gene Expression as Revealed by DNA Arrays , 2001, Journal of Virology.

[25]  Qicheng Ma,et al.  Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks , 2005, BMC Bioinformatics.

[26]  D. Haussler,et al.  Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. , 1998, Journal of molecular biology.

[27]  Shailesh V. Date,et al.  A Probabilistic Functional Network of Yeast Genes , 2004, Science.

[28]  David Venet,et al.  MatArray: a Matlab toolbox for microarray data , 2003, Bioinform..

[29]  Wei Wu,et al.  Evaluation of normalization methods for cDNA microarray data by k-NN classification , 2005, BMC Bioinformatics.

[30]  Peter B. McGarvey,et al.  The Protein Information Resource (PIR) , 2000, Nucleic Acids Res..

[31]  S. Bandyopadhyay,et al.  Evolutionary computation in bioinformatics: a review , 2006, IEEE Transactions on Systems, Man, and Cybernetics, Part C (Applications and Reviews).

[32]  C. Müller,et al.  Large-scale clustering of cDNA-fingerprinting data. , 1999, Genome research.

[33]  Sanghamitra Bandyopadhyay,et al.  Genetic operators for combinatorial optimization in TSP and microarray gene ordering , 2007, Applied Intelligence.

[34]  J. Mesirov,et al.  Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Gavin Sherlock,et al.  Global analysis of gene function in yeast by quantitative phenotypic profiling , 2006, Molecular systems biology.

[36]  P. Bork,et al.  Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Alexander Schliep,et al.  ProClust: improved clustering of protein sequences with an extended graph-based approach , 2002, ECCB.

[38]  J. Weitzman,et al.  Getting the right dose of sex (chromosomes) , 2006, Journal of biology.

[39]  S. Dudoit,et al.  Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. , 2002, Nucleic acids research.

[40]  Hong Wang,et al.  Gene Expression Profiles during the Initial Phase of Salt Stress in Rice , 2001, Plant Cell.

[41]  Tao Han,et al.  Microarray scanner calibration curves: characteristics and implications , 2005, BMC Bioinformatics.

[42]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[43]  S. Spiegelman,et al.  A quantitative assay for DNA-RNA hybrids with DNA immobilized on a membrane. , 1965, Journal of molecular biology.

[44]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[45]  Sanghamitra Bandyopadhyay,et al.  Combining Multisource Information Through Functional-Annotation-Based Weighting: Gene Function Prediction in Yeast , 2009, IEEE Transactions on Biomedical Engineering.

[46]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[47]  Sanghamitra Bandyopadhyay,et al.  Gene ordering in partitive clustering using microarray expressions , 2007, Journal of Biosciences.

[48]  Adam J. Smith,et al.  The Database of Interacting Proteins: 2004 update , 2004, Nucleic Acids Res..

[49]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[50]  David Botstein,et al.  The Stanford Microarray Database , 2001, Nucleic Acids Res..

[51]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[52]  Ron Shamir,et al.  Clustering Gene Expression Patterns , 1999, J. Comput. Biol..