microarray 2000

Microarray

&
Data

Analysis

2000

More papers from the Critical Assessment of Techniques for Microarray Data Mining Workshop (Dec 18-19, 2000)

Orly Alter, Patrick O Brown, David Botstein (2000),
"Singular value decomposition for genome-wide expression data processing and modeling",
Proceedings of the National Academy of Sciences, 97(18):10101-10106.
[ webpage from the author] [ PDF ]
RB Altman, S Raychaudhur, JM Stuart, X Liu, PM Smal (2000),
"Pattern recognition of genomic features with microarrays: site typing of Mycobacterium Tuberculosis strains",
ISMB'00.
A Ben-Dor, L Bruhn, N Friedman, I Nachman, M Schummer, Z Yakhini (2000)
"Tissue classification with gene expression profiles",
Journal of Computational Biology, 7(3/4):559-583.
T Beißbarth, K Fellenberg, B Brors, R Arribas-Prat, JM Boer, NC Hauser, M Scheideler, JD Hoheisel, G Schütz, A Poustka, M Vingron (2000),
"Processing and quality control of DNA array hybridization data",
Bioinformatics, 16:1014-1022.
[ PDF]
B Brors (2000),
"Qualitätsstandards für DNA chip-analysen" (in german)
Medizinische Genetik, 12:301-303.
Nobert Brandle, Horng-Yang Chen, Horst Bischof (2000),
"Robust parametric and semi-parametric spot fitting for spot array images",
ISMB'00.
A Brazma, J Vilo (2000),
"Gene expression data analysis",
FEBS Letters, 480:17-24.
MPS Brown, WN Grundy, D Lin, C Sugnet, M Ares, Jr. D Haussler (2000),
"Knowledge-based analysis of microarray gene expression data by using support vector machines",
Proceedings of the National Academy of Sciences, 97:262-267.
[ abstract] [ PDF ]
AJ Butte, IS Kohane (2000),
"Mutual information relevance networks: functional genomics clustering using pairwise entropy measurements",
PSB00, 5:415-426.
Andrea Califano, Gustavo Stolovitzky, Yuhai Tu (2000),
"Analysis of gene expression microarrays for phenotype classification",
ISMB'00.
A J Carlisle, V V Prabhu, A Elkahloun, J Hudson, J M Trent, W M Linehan, E D Williams, M R Emmert-Buck, L A Liotta, P J Munson, D B Krizman (2000),
"Development of a Prostate cDNA Microarray and statistical gene expression analysis package",
Molecular Carcinogenesis, 28:12-22.
Yidong Chen, Vishnu G Kamat, Edward R Dougherty, Michael L Bittner, Paul S Meltzer, Jeffrey M Trent (2000),
"Expression ratio statistics and its applications to microarray data analysis",
Proceedings of SPIE, 3926:142-149,
Y Cheng, GM Church (2000),
"Biclustering of expression data",
ISMB'00.
BA Cohen, RD Mitra, JD Hughes, GM Church (2000),
"A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression",
Nature Genetics, 26(2):183-186.
P D'haeseleer, S Liang, R Somogyi (2000),
"Genetic network inference: from co-expression clustering to reverse engineering",
Bioinformatics, 16(8):707-726.
RM Ewing, JM Claverie (2000),
"EST database as multi-conditional gene expression datasets",
PSB00, 5:427-439.
N Friedman, M Linial, I Nachman, D Pe'er (2000),
"Using Bayesian networks to analyze expression data",
Journal of Computational Biology, 7(3/4):601-620.
S Fuhrman, MJ Cunningham, X Wen, G Zweiger, JJ Seihamer, R Somogyi (2000),
"The application of Shannon entropy in the identification of putative drug targets",
Biosystem, 55:5-14.
[ abstract] [ PDF ]
TS Furey, N Cristiannini, N Duffy, DW Bednarski, M Schummer, D Haussler (2000),
"Support vector machine classification and validation of cancer tissue samples using microarray expression data",
Bioinformatics, 16(10):906-914.
Terry Gaasterland, Stefan Bekiranov (2000),
"Making the most of microarray data" (news & views),
Nature Genetics, 24(3):204-206.
G Getz, E Levine, E Domany (2000),
"Coupled two-way clustering analysis of gene microarray data",
Proceedings of the National Academy of Sciences, 97(22):12079-12084.
G Getz, E Levine, E Domany, MQ Zhang (2000),
"Super-paramagnetic clustering of yeast gene expression profile",
Physica A, 279:457-464.
SR Gullans (2000),
"Of microarrays and meandering data points",
Nature Genetics, 26:4-5.
T Hastie, O Alter, G Sherlock, M Eigen, R Tibshirani, D Bostein, P Brown (2000),
"Imputation of missing values in DNA microarrays", Technical Report, Stanford University.
Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C Chan, David Botstein, Patrick Brown (2000),
" 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns ",
Genome Biology , 1(2): research0003.1-0003.21.
[ PDF ]
P Hegde, R Qi, K Abernathy, C Gay, S Dharap, R Gaspard, JE Hughes, E Snesrud, N Lee N, J Quackenbush (2000),
"A concise guide to cDNA microarray analysis", Biotechniques, 29(3):548-550.
Neal S Holter, Madhusmita Mitra, Amos Maritan, Marek Cieplak, Jayanth R Banavar, and Nina V Fedoroff (2000),
"Fundamental patterns underlying gene expression profiles: simplicity from complexity",
Proceedings of the National Academy of Sciences, 97(15):8409-8414.
[ PDF]
TR Hughes, MJ Marton, AR Jones, CJ Roberts, R Stoughton, CD Armour, HA Bennett, H Dai, YD He, MJ Kidd, AM King, MR Meyer, D Slade, PY Lum, SB Stepaniants, DD Shoemaker, D Gachotte, K Chakraburtty, J Simon, M Bard, SH Friend (2000),
"Functional discovery via a compendium of expression profiles",
Cell, 102:109-126.
T Ideker, V Thorsson, AF Siegel, LE Hood (2000),
"Testing for differentially-expressed genes by maximum-likelihood analysis of microarray data",
Journal of Computational Biology, 7(6):805-818. Mamoru Kato, Tatsuhiko Tsunoda, Toshihisa Takagi (2000),
"Inferring genetic networks from DNA microarray data by multiple regression analysis",
Genome Informatics, 11:118-128.
M Kathleen Kerr, Mitchell Martin, Gary A Churchill (2000),
"Analysis of variance for gene expression microarray data",
Journal of Computational Biology, 7:819-837.
Hirohisa Kishino, Peter J. Waddell (2000),
"Correspondence analysis of genes and tissue types and finding genetic links from microarray data",
Genome Informatics, 11:83-95.
Seungchan Kim, Edward R Dougherty, Michael L Bittner, Yidong Chen, Krishnamoorthy Sivakumar, Paul S Meltzer, Jeffery M Trent (2000),
"General nonlinear framework for the analysis of gene interaction via multivariate expression arrays",
Journal of Biomedical Optics, 5(4):411-424.
Mei-Ling Ting Lee, Frank C Kuo, G A Whitmore, Jeffrey Sklar (2000),
"Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations ",
97(18):9834-9838. Proceedings of the National Academy of Sciences,
[ PDF]
B Liao, W Hale, CB Epstein, RA Butow, HR Garner (2000),
"MAD: a suite of tools for microarray data management and processing",
Bioinformatics, 16(10):946-947.
DJ Lockhart, EA Winzeler (2000),
"Genomics, gene expression and DNA arrays",
Nature, 405(6788):827-836.
E Manduchi, G R Grant, S E McKenzie, G C Overton, S Surrey, C J Stoeckert (2000),
"Generation of patterns from gene expression data by assigning confidence to differentially expressed genes",
Bioinformatics, 16(8):685-698.
[ PDF]
Kalim U Mir, Edwin M Southern (2000),
"Sequence variation in genes and genomic DNA: methods for large-scale analysis",
Annual Review of Genome and Human Genetics, 1:329-360.
[ PDF]
EJ Moler, ML Chow, IS Mian (2000),
"Analysis of molecular profile data using generative and discriminative methods",
Physiological Genomics, 4(2):109-126.
Juan Carlos Oliveros, Christian Blaschke, Javier Herrero, Joaquín Dopazo, Alfonso Valencia (2000),
"Expression profiles and biological function",
Genome Informatics, 11: 106-117.
Charles M Perou, Patrick O Brown, David Botstein (2000),
"Tumor classification using gene expression patterns from DNA microarrays",
New Technologies for Life Sciences: A Trends Guide, 67-76.
MR Pocock, TJP Hubbard (2000),
"A browser for expression data",
Bioinformatics, 16(4):402-403.
S Raychaudhuri, JM Stuart, RB Altman, (2000),
"Principal components analysis to summarize microarray experiments: application to sporulation time series",
PSB00, 5:452-463.
[ PDF]
Soumya Raychaudhuri, Joshua M Stuart, Xuemin Liu, Peter M Small, Russ B Altman (2000),
"Pattern recognition of genomic features with microarrays: site typing of Mycobacterium Tuberculosis Strains",
ISMB'00.
SA Rifkin, K Atteson, J Kim (2000),
"Constraint structure analysis of gene expression",
Functional Integrative Genomics, 1(3):174-185.
D T Ross, U Scherf, M B Eisen, C M Perou, C Rees, P Spellman, V Iyer, S S Jeffrey, M Van de Rijn, M Waltham, A Pergamenschikov, J C F Lee, D Lashkari, D Shalon, T G Myers, J N Weinstein, D Botstein, P O Brown (2000),
"Systematic variation in gene expression patterns in human cancer cell lines",
Nature Genetics, 24(3):227-235.
[ abstract] [ companion webpage from the authors ]
DB Searls (2000),
"Bioinformatics tools for whole genomes",
Annual Review of Genomics and Human Genetics, 1:251-279.
[ PDF ]
EE Schadt, C Li, C Su, WH Wong (2000),
"Analyzing high-density oligonucleotide gene expression array data",
Journal of Cellular Biochemistry, 80(2):192-202.
U Scherf, D T Ross, M Waltham, L H Smith, J K Lee, L Tanabe, K W Kohn, W C Reinhold, T G Myers, D T Andrews, D A Scudiero, M B Eisen, E A Sausville, Y Pommier, D Botstein, P O Brown & J N Weinstein (2000),
"A gene expression database for the molecular pharmacology of cancer",
Nature Genetics, 24(3):236-244.
Johannes Schuchhardt, Dieter Beule, Arif Malik, Eryc Wolski, Holger Eickhoff, Hans Lehrach and Hanspeter Herzel (2000),
"Normalization strategies for cDNA microarrays" (NAR methods online),
Nucleic Acids Research,28(10):E47.
R Sharan, R Shamir (2000),
"CLICK: A clustering algorithm with applications to gene expression analysis",
ISMB'00.
Hagit Shatkay, Stephen Edwards, W John Wilbur, Mark Boguski (2000),
"Genes, themes, and microarray: using information retrieval for large-scale gene analysis",
ISMB'00.
G Sherlock (2000),
"Analysis of large-scale gene expression data",
Current Opinions on Immunology, 12:201-205.
D Slonim, P Tamayo, J Mesirov, TR Golub, E Lander (2000)
"Class prediction and discovery using gene expression data"
RECOMB'00.
DJ Stewart (2000),
"Making and using DNA microarrays: a short course at Cold Spring Harbor Laboratory" (insight/outlook),
Genome Research, 10(1):1-3.
G Stolovitzky, A Califono, Y Tu (2000),
"Analysis of gene expression microarrays for phenotype classification",
ISMB'00.
A Wagner (2000),
"Robustness against mutations in genetic networks of yeast",
Nature Genetics, 24:355-361.
AHC van Kampen, BDC van Schaik, E Pauws, EMC Michiels, JM Ruijter, HN Caron, R Versteeg, SH Heisterkamp, JAM Leunissen, F Baas, M van der Mee (2000),
"USAGE: a web-based approach towards the analysis of SAGE data",
Bioinformatics, 16(10):899-905.
E van Someren, LFA Wessels, MJT Reinders (2000),
"Linear modeling of genetic networks from experimental data",
ISMB'00.
J Vilo, B Alvia, I Jonassen, A Robinson, E Ukkonen (2000),
"Mining for putative regulatory elements in the yeast genome using gene expression data",
ISMB'00.
Peter J Waddell, Hirohisa Kishino (2000),
"Cluster inference methods and graphical models evaluated on NCI60 microarray gene expression data",
Genome Informatics, 11:129-140.
E Wang, LD Miller, GA Ohnmacht, ET Liu, FM Marincola (2000), "High-fidelity mRNA amplification for gene profiling", Nature Biotechnology, 18:457-459.
D Wolf, CO Gray, A de Saizieu (2000),
"Visualising gene expression in its metabolic context",
Briefings in Bioinformatics, 1(3):297-304.
P J Woolf, Y Wang (2000),
"A fuzzy logic approach to analyzing gene expression data",
Physiological Genomics, 3(1):9-15.
M Xiong, L Jin, W Li, E Boerwinkle (2000),
"Computational methods for gene expression-based tumor classification",
Biotechniques, 29(6):1264-1268.
[abstract]
K Zhang, H Zhao (2000),
"Assessing reliability of gene clusters from gene expression data",
Functional Integrative Genomics, 1(3):156-173.
J Zhu, MQ Zhang (2000),
"Cluster, function and promoter: analysis of yeast expression array",
PSB00, 5:476-487.
[ PDF ]
A Zien, R Kuffner, R Zimmer, T Lengauer (2000),
"Analysis of gene expression data with pathway scores",
ISMB'00.
[ PDF ]