Missing Value Estimation

KNNimpute is a fast, robust, and accurate method of estimating missing values for microarray data. Both KNNimpute and SVDimpute methods far surpass the currently accepted solutions (filling missing values with zeros or row average) by taking advantage of the structure of microarray data to estimate missing expression values.

[1]  F. Yates The analysis of replicated experiments when the field results are incomplete , 1933 .

[2]  G. N. Wilkinson Estimation of Missing Values for the Analysis of Incomplete Data , 1958 .

[3]  T. W. Anderson An Introduction to Multivariate Statistical Analysis , 1959 .

[4]  R. Bulger,et al.  Antimicrobial Agents and Chemotherapy , 1969, Nature.

[5]  Gene H. Golub,et al.  Matrix computations , 1983 .

[6]  D. Rubin,et al.  Statistical Analysis with Missing Data. , 1989 .

[7]  W. Loh,et al.  Tree-Structured Classification via Generalized Discriminant Analysis. , 1988 .

[8]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

[9]  D. Botstein,et al.  The transcriptional program of sporulation in budding yeast. , 1998, Science.

[10]  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.

[11]  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.

[12]  J. Mesirov,et al.  Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. , 1999, Science.

[13]  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.

[14]  Laurie J. Heyer,et al.  Exploring expression data: identification and analysis of coexpressed genes. , 1999, Genome research.

[15]  D. Botstein,et al.  Singular value decomposition for genome-wide expression data processing and modeling. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Joshua M. Stuart,et al.  MICROARRAY EXPERIMENTS : APPLICATION TO SPORULATION TIME SERIES , 1999 .

[17]  Christian A. Rees,et al.  Molecular portraits of human breast tumours , 2000, Nature.

[18]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[19]  D Haussler,et al.  Knowledge-based analysis of microarray gene expression data by using support vector machines. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[21]  Ash A. Alizadeh,et al.  'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns , 2000, Genome Biology.

[22]  Russ B. Altman,et al.  Missing value estimation methods for DNA microarrays , 2001, Bioinform..

[23]  Atul J. Butte,et al.  Determining Significant Fold Differences in Gene Expression Analysis , 2000, Pacific Symposium on Biocomputing.

[24]  Tommi S. Jaakkola,et al.  A new approach to analyzing gene expression time series data , 2002, RECOMB '02.

[25]  Thomas Lengauer,et al.  Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Thomas Lengauer,et al.  Methods for optimizing antiviral combination therapies , 2003, ISMB.

[27]  Thomas Lengauer,et al.  Tenofovir Resistance and Resensitization , 2003, Antimicrobial Agents and Chemotherapy.

[28]  Thomas Lengauer,et al.  Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes , 2003, Nucleic Acids Res..

[29]  Thomas Lengauer,et al.  Learning multiple evolutionary pathways from cross-sectional data , 2004, J. Comput. Biol..

[30]  Thomas Lengauer,et al.  Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. , 2005, The Journal of infectious diseases.

[31]  Thomas Lengauer,et al.  Mtreemix: a software package for learning and using mixture models of mutagenetic trees , 2005, Bioinform..