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References
- 1
-
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gassenbeek, M., Mesirov,
J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield,
D.D., and Lander, E. S.
Molecular Classification of Cancer: Class Discovery and Class
Prediction by Gene Expression Monitoring.
Science, Vol. 286(15):531-537, October 1999.
- 2
-
Holter, N. S., Mitra, M., Maritan, A., Cieplak, M., Banavar, J. R., and
Fedoroff, N. V.
Fundamental Patterns Underlying Gene Expression Profiles: Simplicity
from Complexity.
Proc. Natl. Acad. Sci. USA, Vol. 97(15):8409-8414, July 2000.
- 3
-
Tamayo, P. , Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E.,
Lander, E. S., and Golub, T. R.
Interpreting Patterns of Gene Expression with Self-Organizing Maps:
Methods and Application to Hematopoietic Differentiation.
Proc. Natl. Acad. Sci. USA, Vol. 96(6):2907-2912, March 1999.
- 4
-
Hastie, T., Tibshirani, T., Botstein, D., and Brown., P.
Supervised Harvesting of Expression Trees.
Genome Biology, Vol. 2(1):0003.1-0003.12, January 2001.
- 5
-
Brazma, A., and Vilo, J.
Minireview: Gene Expression Data Analysis.
Federation of European Biochemical Societies, 480:17-24, June
2000.
- 6
-
Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickhoff, H., Lehrach, H.,
and Herzel, H.
Normalization Strategies for cDNA Microarrays.
Nucleic Acids Research, Vol. 28(10), 2000.
- 7
-
Manduchi, E., Grant, G. R., McKenzie, S. E., Overton, G. C., Surrey, S., and
Stoeckert, C. J. Jr.
Generation of Patterns from Gene Expression Data by Assigning
Confidence to Differentially Expressed Genes.
Bioinformatics, Vol. 16(8):685-698, 2000.
- 8
-
Dudoit, S., Yang, Y. H., Callow, M. J., and Speed, T. P.
Statistical Methods for Identifying Differentially Expressed Genes
in Replicated cDNA Microarray Experiments.
Technical report 578, Stanford University, Department of Biochemistry
Stanford University School of Medicine, August 2000.
- 9
-
Brown, M. P. S., Grundy, W. N., Lin, D., Cristianini, N., Sugnetn, C. W.,
Furey, Ares, M. Jr., and Haussler, D.
Knowledge-Based Analysis of Microarray Gene Expression Data by Using
Support Vector Machines.
Proc. Natl. Acad. Sci. USA, Vol. 97(1):262-267, January 2000.
- 10
-
Alter, O., Brown, P. O., and Bostein, D.
Singular Value Decomposition for Genome-wide Expression Data
Processing and Modeling.
Proc. Natl. Acad. Sci. USA, Vol. 97(18):10101-10106, Auguest
2000.
- 11
-
Getz, G., Levine, E., and Domany, E.
Coupled Two-way Clustering Analysis of Gene Microarray Data.
Proc. Natl. Acad. Sci. USA, Vol. 97(22):12079-12084, October
2000.
- 12
-
Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D.
Cluster Analysis and Display of Genome-wide Expression Patterns.
Proc. Natl. Acad. Sci. USA, Vol. 95:14863-14868, December
1998.
- 13
-
Brazma, A., Ukkonen, E., Jonassen, I., and Vilo, J.
Predicting Gene Regulatory Elements in Silico on a Genomic Scale.
Genome Research, Vol. 8(11):1202-1215, 1998.
- 14
-
Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D, and
Levine, A. J.g.
Broad Patterns of Gene Expression Revealed by Clustering Analysis of
Tumor and Normal Colon Tissues Probed by Oligonucleotide Array.
Proc. Natl. Acad. Sci. USA, Vol. 96(12):6745-6750, June 1999.
- 15
-
Izidore S. Lossos, Ash A. Alizadeh, Michael B. Eisen, Wing C. Chan, Patirck O.
Brown, David Bostein, Louis M. Staudt, and Ronald Levy.
Ongoing Immunoglobulin Somatic Mutation in Germinal Center B
Cell-Like But Not in Activated B Cell-Like Diffuse Large Cell Lumphomas.
Proc. Natl. Acad. Sci. USA, Vol. 97(18):10209-10213, Auguest
2000.
- 16
-
Jean-Michel Claverie.
Computational Methods for the Identification of Genes in Vertebrate
Genomic Sequences.
Human Molecular Genetics, Vol. 6(10):1735-1744, 1997.
- 17
-
Ron Shamir, and Roded Sharan.
CLICK: A Clustering Algorithm for Gene Expression Analysis.
Department of Computer Science, Tel-Aviv University.
- 18
-
Mark J. van der Laan, and Jennifer F. Bryan.
Gene Expression Analysis with the Parametric Bootstrap.
University of California, Berkeley June 27, 2000.
- 19
-
Holter, N. S., Maritan, A., Cieplak, M., Fedoroff, N. V., and Banavar, J. R.
Dynamic Modeling of Gene Expression Data.
Proc. Natl. Acad. Sci. USA, Vol. 98(4):1693-1698, February
2001.
- 20
-
Wen, X. L., Fuhrman, S., Michaels, G. S., Carr, D. B., Smith, S., Barker, J.
L., and Somogyi, R.
Large-Scale Temporal Gene Expression Mapping of Central Nervous
System Development.
Proc. Natl. Acad. Sci. USA, Vol. 95(1):334-339, January 1998.
- 21
-
Trevor Hastie, Robert Tibshirani, Michael B Eisen, Ash Alizadeh, Ronald Levy,
Louis Staudt, Wing C. Chan, Botstein, D., and Patrick Brown.
Gene Shaving as a Method for Identifying Distinct Sets of Genes with
Similar Expression Patterns.
Genome Biology, Vol. 2(1):0003.1-0003.21, August 2000.
- 22
-
Marina Sapir, and Gary A. Churchill.
Estimating the Posterior Probability of Differential Gene Expression
from Microarray Data.
The Jackson Laboratory, Bar Harbor, ME.
- 23
-
Jean-Michael Claverie.
Computational Methods for the Identification of Differential and
Coordinated Gene Expression.
Human Molecular Genetics, Vol.8(10):1821-1832, 1999.
- 24
-
Stephane Audic, and Jean-Michael Claverie.
The Sigificance of Digital Gene Expression Profiles.
Genome Research, Vol.7(10):986-995, 1997.
- 25
-
Ash A. Alizadeh, Michael B. Eisen, R. Eric Davis, Chi Ma, Izidore S. Lossos,
Adreas Rosenwald, Jennifer C. Boldrick, Hajeer Sabet, Truc Tran, Xin Yu, John
I. Powell, Liming Yang, Gerald E. Marti, Tory Moore, James Hudson Jr, Lisheng
Lu, David B. Lewis, Robert Tibshirani, Gavin Sherlock, Wing C. Chan, Timothy
C. Greiner, Dennis D. Weisenburger, James O. Armitage, Roger Warnke, Ronald
Levy, Wyndham Wilson, Michael R. Grever, John C. Byrd, Botstein, D., Brown,
P. O., and Louis M. Staudt.
Distinct Types of Diffuse Large B-Cell Lymphoma Identified by Gene
Expression Profiling.
Nature, Vol.403:503-511, February 2000.
- 26
-
S. Chu, J. Derisi, M. Eisen, J. Mulholland, D. Botstein, P. B. Brown, and I.
Herskowitz.
The Transcriptional Program of Sporulation in Budding Yeast.
Science, Vol.282(23):699-705, October 1998.
- 27
-
John N. Winstein, Timothy G. Myers, Patrick M. O'Connor, Stephen H. Friend,
Albert J. Fornace, Jr., Kurt W. Kohn, Tito Fojo, Susan E. Bates, Lawrence V.
Rubinstein, N. Leigh Anderson, John K. Buolamwini, William W. van Osdol, Anne
P. Monks, Dominic A. Scudiero, Edward A. Sausville, Daniel W. Zaharevitz,
Barry Bunow, Vellarkad N. Viswanadhan, George S. Johnson, Robert E. Wittes,
and Kenneth D. Paul.
An Information-Intensive Approach to the Molecular Pharmacology of
Cancer.
Science, 275(17):343-349, January 1998.
- 28
-
Yee Hwa Yang, Dudoit, S., Percy Lu, and Terence P. Speed.
Normalization for cDNA Microarry Data.
Technical Report 584, Statistics Dept, UC Berkeley, January 2001.
- 29
-
Charles M. Perou, Stefanie S. Jeffrey, Matt Van De Rijn, Christian A. Rees,
Michael B. Eisen, Douglas T. Ross, Alexander Pergamenschiko, Cheryl F.
Williams, Shirley X. Zhu, Jeffrey C.F. Lee, Deval Lashkari, Dari Shalon,
Brown, P. O., and Davaid Botstein.
Distinctive Gene Expression Patterns in Human Mammary Epithelial
Cells and Breast Cancers.
Proc. Natl. Acad. Sci. USA, Vol. 96(16):9212-9217, August
1999.
- 30
-
Rob M. Ewing, Alia Ben Kahla, Olivier Poirot, Fabrice Lopez, Stephane Audic,
and Jean-Michel Claverie.
Large-Scale Statistical Analyses of Rice ESTs Reveal Correlated
Patterns of Gene Expression.
Genome Research, Vol.9(10):950-959, 1999.
- 31
-
Michael G. Walker, Wayne Volkmuth, Einat Sprinzak, David Hodgson, and Tod
Klingler.
Prediction of Gene Function by Genome-Scale Expression Analysis:
Prostate Cance-Associated Genes.
Genome Research, Vol.9(12):1198-1203, 1999.
- 32
-
Michael Q. Zhang.
Discriminant Analysis and Its Application in DNA Sequence Motif
Recognition.
Briefings in Bioinformatics, Vol.1(4):1-12, November 2000.
- 33
-
Eric P. Xing, and Richard M. Karp.
CLIFF: Clustering of High-Dimensional Microarray Data via Iterative
Feature Filtering Using Normalized Cuts.
Bioinformatics, Vol.17 Suppl.(1):S306-S315, 2001.
- 34
-
Patrik D'haeseleer, Shoudan Liang, and Roland Somogyi.
Tutorial: Gene Expression Data Analysis and Modeling.
Pacific Symposium on Biocomputing, January 1999.
- 35
-
Sven Bilke.
Shuffling Yeast Gene Expression Data.
University of Lund, Sweden, May 2001.
- 36
-
Biedl, T., Brejova, B., Demaine, E. Hamel, A., and Vinar, T.
Optimal Arrangement of Leaves in the Tree Representing Hierarchical
Clustering of Gene Expression Data.
Technical report 2001-14, University of Waterloo, Canada, 2001.
- 37
-
Viann Chan, Nick Hontzeas, and Vincent Park.
Gene Expression.
University of Warterloo, December 2000.
- 38
-
Dudoit, S., Jane Fridlyand, and Terry Speed.
Comparison of Discrimination Methods for the Classification of
Tumors Using Gene Expression Data.
Technical Report 576, Statistics Dept, UC Berkeley, 2000.
- 39
-
G. R. Grant, E. Manduchi, and C. J. Stoeckert Jr.
Using Non-Parametric Methods in the Context of Multiple Testing to
Identify Differentially Expressed Genes.
CBIL, PCBI, 2001.
- 40
-
Andrew D.Keller, Michel Schummer, Walter L.Ruzzo, and Lee Hood.
Bayesian Classification of DNA Array Expression Data.
Technical Report UW-CSE-2000-08-01, University of Washington, 2000.
- 41
-
M. Kathleen Kerr, Cindy Afshari, Lee Bennett, Pierre Bushel, Jeanelle
Martinez, Nigel Walker, and Gary A. Churchill.
Statistical Analysis of a Gene Expression Microarray Experiment with
Replication.
Statistical Genetics Group, the Jackson Laboratory, May 2001.
- 42
-
M. Kathleen Kerr.
Bootstrapping Cluster Analysis: Assessing the Reliability of
Conclusions from Microarray Experiments.
Statistical Genetics Group, the Jackson Laboratory, 2001.
- 43
-
Laura Lazzeroni, and Art Owen.
Plaid Models for Gene Expression Data.
Dept Statistics, Stanford University, March 2000.
- 44
-
Leping Li, Pierre Bushel, Lee Pedersen, Thomas Darden, Hisham Hamadeh, Lee
Bennett, Cindy Afshari, Rick Paules, David Umbach, and Clarice Weinberg.
Computational Analysis of Leukemia Microarray Expression Data Using
the GA/KNN Method and Other Existing Tools.
NIEHS, 2001.
- 45
-
Li, W. T.
Zipf's Law in Importance of Genes for Cancer Classification Using
Microarray Data.
Lab of Statistical Genetics, Rockefeller University, April 2001.
- 46
-
Li, W. T., and Yang, Y. N.
How Many Genes Are Needed for a Discriminant Microarray Data
Analysis.
Lab of Statistical Genetics, Rockefeller University, March 2001.
- 47
-
Felix Naef, Daniel A. Lim, Nila Patil, and Marcelo O. Magnasco.
From Features to Expression: High-Density Oligonucleotide Array
Analysis Revisited.
Lab of Mathematical Physics and Neurogenesis, Rockefeller University,
February 2001.
- 48
-
Wei Pan, Jizhen Lin, and Chap T. Le.
How Many Replicates of Arrays Are Required to Detect Gene Expression
Changes in Microarray Experiments? a Mixture Model Approach.
University of Minnesota, July 2001.
- 49
-
Wei Pan, Jizhen Lin, and Chap T. Le.
A Mixture Model Approach to Detecting Differentially Expressed Genes
with Microarray Data.
University of Minnesota, June 2001.
- 50
-
David Rocke, and Blythe Durbin.
A Model for Measurement Error for Gene Expression Arrays.
University of California, Davis, 2001.
- 51
-
West, M., Nevins, J. R., Marks, J. R., Spang, R., Blanchette, C., and Zuzan,
H.
DNA Microarray Data Analysis and Regression Modeling for Genetic
Expression Profiling.
Duke University, 2001.
- 52
-
Yeung, K. Y., Haynor, D. R., and Ruzzo, W. L.
Validating Clustering for Gene Expression Data.
Bioinformatics, Vol.17(4):309-318, 2001.
- 53
-
John Aach, and George M. Church.
Aligning Gene Expression Time Series with Time Warping Algorithms.
Bioinformatics, Vol.17(6):495-508, 2001.
- 54
-
Pierre Baldi, and Anthony D. Long.
A Bayesian Framework for the Analysis of Microarray Expression Data:
Regularized t-test and Statistical Inferences of Gene Changes.
Bioinformatics, Vol.17(6):509-519, 2001.
- 55
-
Yoseph Barash, and Nir Friedman.
Context-Specific Bayesian Clustering for Gene Expression Data.
In RECOMB 2001: Proceedings of the Fifth Annual International
Conference on Computational Biology, pages 12-20. ACM Press, 2001.
- 56
-
Ben-Dor, A., Friedman, N., and Yakhini, Z.
Class Discovery in Gene Expression Data.
In RECOMB 2001: Proceedings of the Fifth Annual International
Conference on Computational Biology, pages 31-38. ACM Press, 2001.
- 57
-
A. J. Butte, J. Ye, G. Niederfellner, K. Rett, H. U. Häring, M. F.White, and
I. S. Kohane.
Determining Significant Fold Differences in Gene Expression
Analysis.
In Pacific Symposium on Biocomputing, pages 6-17, 2001.
- 58
-
Javier Herrero, Alfonso Valencia, and Joaquín Dopazo.
A Hierarchical Unsupervised Growing Neural Network for Clustering
Gene Expression Patterns.
Bioinformatics, Vol.17(2):126-136, 2001.
- 59
-
Hanspeter Herzel, Dieter Beule, Szymon Kielbasa, Jan Korbel, Christine Sers,
Arif Malik, Holger Eickhoff, Hans Lehrach, and Johannes Schuchhardt.
Extracting Information from cDNA Arrays.
Chaos, Vol.11(1):98-107, 2001.
- 60
-
Maha Abdellatif.
Leading the Way Using Microarray, A More Comprehensive Approach for
Discovery of Gene Expression Patterns.
Circulation Research, 86:919-920, May 2000.
- 61
-
M. Kathleen Kerr, and Gary A. Churchill.
Statistical Design and the Analysis of Gene Expression Microarrays.
Statistical Genetics Group, the Jackson Laboratory, 2001.
- 62
-
M. Kathleen Kerr, and Gary A. Churchill.
Experimental Design for Gene Expression Microarrays.
Bioinformatics, Vol.17(2):183-201, 2001.
- 63
-
Khan, J., Wei, J. S., Ringnér, M., Saal, L. H., Ladanyi, M., Westermann, F.,
Berthold, F., Schwab, M., Antonescu, C. R., Peterson, C., and Meltzer, P. S.
Classification and Diagnostic Prediction of Cancers Using Gene
Expression Profiling and Artificial Neural Networks.
Nature Medicine, Vol.7(6):673-679, 2001.
- 64
-
Ju Han Kim, Lucila Ohno-Machado, and Isaac S. Kohane.
Unsupervised Learning from Complex Data: the Matrix Incision Tree
Algorithm.
In Pacific Symposium on Biocomputing, pages 30-41, 2001.
- 65
-
Gregory T. Klus, Andrew Song, Ari Schick, Mattias Wahde, and Zoltan Szallasi.
Mutual Information Analysis as a Tool to Assess the Role of
Aneuploidy in the Generation of Cancer-Associated Differential Gene
Expression Patterns.
In Pacific Symposium on Biocomputing, pages 42-51, 2001.
- 66
-
Cheng Li, and Wing Hung Wong.
Model-Based Analysis of Oligonucleotide Arrays: Expression Index
Computation and Outlier Detection.
Proc. Natl. Acad. Sci. USA, Vol. 98(1):31-36, January 2001.
- 67
-
Stuart M. Arfin, Anthony D. Long, Elaine T. Ito, Lorenzo Tolleri, Michelle M.
Riehle, Eriks S.Paegle, and G. Wesley Hatfield.
Global Gene Expression Profiling in Escherichia Coli K12.
The Journal of Biological Chemistry, Vol.275(38):29672-29684,
2000.
- 68
-
AlexanderV. Lukashin, and Rainer Fuchs.
Analysis of Temporal Gene Expression Profiles: Clustering by
Simulated Annealing and Determining the Optimal Number of Clusters.
Bioinformatics, Vol.17(5):405-414, 2001.
- 69
-
Daniel R. Masys, John B. Welsh, J. Lynn Fink, Michael Gribskov, Igor
Klacansky, and Jacques Corbeil.
Use of Keyword Hierarchies to Interpret Gene Expression Patterns.
Bioinformatics, Vol.17(4):319-326, 2001.
- 70
-
M. A. Newton, C. M. Kendziorski, C. S. Richmond, F. R. Blattner, and K. W.
Tsui.
On Differential Variability of Expression Ratios: Improving
Statistical Inference about Gene Expression Changes from Microarray Data.
Journal of Computational Biology, Vol.17(4):319-326, 2001.
- 71
-
Park, P. J., Pagano, M., and Bonetti, M.
A Nonparametric Scoring Algorithm for Identifying Informative Genes
from Microarray Data.
In Pacific Symposium on Biocomputing, pages 52-63, 2001.
- 72
-
Pavlidis, P., Weston, J., Cai, J. S., and Grundy, W. N.
Gene Functional Classification from Heterogeneous Data.
In RECOMB 2001: Proceedings of the Fifth Annual International
Conference on Computational Biology, pages 249-255. ACM Press, 2001.
- 73
-
Dana Pe'er,Aviv Regev, Gal Elidan, and Nir Friedman.
Inferring Subnetworks from Perturbed Expression Profiles.
Bioinformatics, Vol.1(1):1-9, 2001.
- 74
-
Paul J. Planet, Rob DeSalle, Mark Siddall, Timothy Bael, Indra Neil Sarkar,
and Scott E. Stanley.
Systematic Analysis of DNA Microarray Data: Ordering and
Interpreting Patterns of Gene Expression.
Genome Research, Vol.11(7):1149-1155, 2001.
- 75
-
Eran Segal, Ben Taskar, Audrey Gasch, Nir Friedman, and Daphne Koller.
Rich Probabilistic Methods for Gene Expression.
In 9th International Conference on Intelligent Systems For
Molecular Biology (ISMB 2001), 2001.
- 76
-
D. D. Shoemaker, E. E. Schadt, C. D. Armour, Y. D. He, P. Garrett-Engele, P.
D. McDonagh, P. M. Loerch, A. Leonardson, P. Y. Lum, G. Cavet, L. F. Wu, S.
J. Altschuler, S. Edwards, J. King, J. S. Tsang, G. Schimmack, J. M.
Schelter, J. Koch, M. Ziman, M. J. Marton, B. Li, P. Cundiff, T. Ward, J.
Castle, M. Krolewski, M. R. Meyer, M. Mao, J. Burchard, M. J. Kidd, H. Dai,
J. W. Phillips, P. S. Linsley, R. Stoughton, S. Scherer, and M. S. Boguski.
Experimental Annotation of the Human Genome Using Microarray
Technology.
Nature, Vol.409:922-927, 2001.
- 77
-
Siedow, J. N.
Meeting Report: Making Sense of Microarrays.
Genome Biology, Vol.2(2):reports4003.1-4003.2, 2001.
- 78
-
R. Sásik, T Hwa, N. Iranfar, and W.F. Loomis.
Percolation Clustering: A Novel Algorithm Applied to the Clustering
of Gene Expression Patterns in Dictyostelium Development.
In Pacific Symposium on Biocomputing, pages 335-347, 2001.
- 79
-
C. Stoeckert, A. Pizarro, E. Manduchi, M. Gibson, B. Brunk, J. Crabtree, J.
Schug, S. Shen-Orr, and G. C. Overton.
A Relational Schema for Both Array-Based and Sage Gene Expression
Expriments.
Bioinformatics, Vol.17(4):300-308, 2001.
- 80
-
Thomas, J. G., Olson, J. M., Tapscott, S. J., and Zhao, L. P.
An Efficient and Robust Statistical Modeling Approach to Discover
Differentially Expressed Genes Using Genomic Expression Profiles.
Genome Research, Vol. 11(7):1227-1236, 2001.
- 81
-
Olga Troyanskaya, Michael Cantor, Gavin Sherlock, Pat Brown, Trevor Hastie,
Robert Tibshirani, David Botstein, and Russ B. Altman.
Missing Value Estimation Methods for DNA Microarrays.
Bioinformatics, Vol.17(6):520-525, 2001.
- 82
-
Tusher, V. G., Tibshirani, R., and Chu, G.
Significance Analysis of Microarrays Applied to the Ionizing
Radiation Response.
Proc. Natl. Acad. Sci. USA, Vol. 98(9):5116-5121, April 2001.
- 83
-
Eric P. Xing, Michael I. Jordan, and Richard M. Karp.
Feature Selection for High-Dimensional Genomic Microarray Data.
In The Eighteenth International Conference on Machine Learning
(ICML2001), 2001.
- 84
-
Yeung, K. Y., and Ruzzo, W. L.
An Empirical Study On Principal Component Analysis for Clustering
Gene Expression Data.
Technical Report UW-CSE-01-04-02, University of Washington, 2001.
- 85
-
Zhang, H. P., Yu, C. Y., Singer, B., and Xiong, M. M.
Recursive Partitioning for Tumor Classification with Gene Expression
Microarray Data.
Proc. Natl. Acad. Sci. USA, Vol. 98(12):6730-6735, June 2001.
- 86
-
Altman, R. B., Raychaudhur, S., Stuart, J. M., Liu, X. M., and Small, P. M.
Pattern Recognition of Genomic Features with Microarrays: Site
Typing of Mycobacterium Tuberculosis Strains.
ISMB'00, 2000.
- 87
-
A. Ben-Dor, L. Bruhn, N. Friedman, I. Nachman, M. Schummer, and Z. Yakhini.
Tissue Classification with Gene Expression Profiles.
Journal of Computational Biology, Vol.7(3/4):559-584, 2000.
- 88
-
T. Beißbarth, K. Fellenberg, B. Brors, R. Arribas-Prat, J. M. Boer, N. C.
Hauser, M. Scheideler, J. D. Hoheisel, G. Schütz, A. Poustka, and M.Vingron.
Processing and Quality Control of DNA Array Hybridization Data.
Bioinformatics, Vol.16(11):1014-1022, 2000.
- 89
-
A. J. Butte, and I. S. Kohane.
Mutual Information Relevance Networks: Functional Genomic Clustering
Using Pairwise Entropy Measurements.
In Pacific Symposium on Biocomputing, pages 415-426, 2000.
- 90
-
Andrea Califano, Gustavo Stolovitzky, and Yuhai Tu.
Analysis of Gene Expression Microarrays for Phenotype
Classification.
ISMB'00, 2000.
- 91
-
Yizong Cheng, andGeorge M. Church.
Biclustering of Expression Data.
ISMB'00, 2000.
- 92
-
Patrik D'haeseleer, Shoudan Liang, and Roland Somogyi.
Genetic Network Inference: from Co-Expression Clustering to Reverse
Engineering.
Bioinformatics, Vol.16(8):707-726, 2000.
- 93
-
Nir Friedman, Michal Linial, Iftach Nachman, and Dana Pe'er.
Using Bayesian Networks to Analyze Expression Data.
Journal of Computational Biology, Vol.7(3/4):601-620, 2000.
- 94
-
Stefanie Fuhrman, Mary Jane Cunningham, Xiling Wen, Gary Zweiger, Jeffrey J.
Seilhamer, and Roland Somogyi.
The Application of Shannon Entropy in the Identification of Putative
Drug Targets.
Biosystem, Vol.55(1-3):5-14, 2000.
- 95
-
Furey, T. S., Cristianini, N., Duffy, N., Bednarski, D. W., Schummer, M., and
Haussler, D.
Support Vector Machine Classification and Validation of Cancer
Tissue Samples Using Microarray Expression Data.
Bioinformatics, Vol.16(10):909-914, 2000.
- 96
-
Getz, G., Levine, E., Domany, E., and Zhang, M. Q.
Super-Paramagnetic Clustering of Yeast Gene Expression Profiles.
Physica A, Vol.279:457-464, 2000.
- 97
-
Kerr, Martin, and Churchill.
Analysis of Variance for Gene Expression Microarray Data.
Journal of Computational Biology, Vol.7:819-837, 2000.
- 98
-
Mei-Ling Ting Lee, Frank C. Kuo, G.A. Whitmore, and Jeffrey Sklar.
Importance of Replication in Microarray Gene Expression Studies:
Statistical Methods and Evidence from Repetitive cDNA Hybridizations.
Proc. Natl. Acad. Sci. USA, Vol. 97(18):9834-9838, August
2000.
- 99
-
Kalim U. Mir, and Edwin M. Southern.
Sequence Variation in Genes and Genomic DNA: Methods for Large-Scale
Analysis.
Annual Review of Genome and Human Genetics, Vol. 1:329-360,
2000.
- 100
-
Moler, E. J., Chow, M. L., and Mian, I. S.
Analysis of Molecular Profile Data Using Generative and
Discriminative Methods.
Physiological Genomics, Vol. 4(2):109-126, 2000.
- 101
-
Raychaudhuri, S., Stuart, J. M., and Altman, R. B.
Principal Components Analysis to Summarize Microarray Experiments:
Application to Sporulation Time Series.
In Pacific Symposium on Biocomputing, pages 415-426, 2000.
- 102
-
David B. Searls.
Bioinformatics Tools for Whole Genomes.
Annual Review of Genome and Human Genetics, Vol. 1:251-279,
2000.
- 103
-
Eric E. Schadt, Cheng Li, Cheng Su, and Wing H. Wong.
Analyzing High-Density Oligonucleotide Gene Expression Array Data.
Journal of Cellular Biochemistry, Vol. 80(2):192-202, October
2000.
- 104
-
Uwe Scherf , Douglas T. Ross , Mark Waltham , Lawrence H. Smith, Jae K. Lee,
Lorraine Tanabe, Kurt W. Kohn, William C. Reinhold , Timothy G. Myers, Darren
T.Andrews, Dominic A. Scudiero, Michael B. Eisen, Edward A. Sausville , Yves
Pommier , David Botstein, Patrick O. Brown , and John N. Weinstein.
A Gene Expression Database for the Molecular Pharmacology of
Cancer.
Nature Genetics, Vol. 24(3):236-244, March 2000.
- 105
-
Hagit Shatkay, Stephen Edwards, W. John Wilbur, and Mark Boguski.
Genes, Themes and Microarrays - Using Information Retrieval for
Large-Scale Gene Analysis.
In 8th International Conference on Intelligent Systems For
Molecular Biology (ISMB 2000), 2000.
- 106
-
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, and Eric S.
Lander.
Class Prediction and Discovery Using Gene Expression Data.
In RECOMB 2000: Proceedings of the Fifth Annual International
Conference on Computational Biology. ACM Press, 2000.
- 107
-
David J. Stewart.
Making and Using DNA Microarrays: A Short Course at Cold Spring
Harbor Laboratory.
Genome Research, Vol.10(1):1-3, 2000.
- 108
-
A. H. C. van Kampen, B. D. C. van Schaik, E. Pauws, E. M. C. Michiels, J. M.
Ruijter, H. N. Caron, R. Versteeg, S. H. Heisterkamp, J. A. M.Leunissen, F.
Baas, and M. van der Mee.
Usage: A Web-Based Approach Towards the Analysis of SAGE Data.
Bioinformatics, Vol.16(10):899-905, 2000.
- 109
-
E. P. van Someren, L. F. A. Wessels, and M. J. T. Reinders.
Linear Modeling of Genetic Networks from Experimental Data.
In 8th International Conference on Intelligent Systems For
Molecular Biology (ISMB 2000), 2000.
- 110
-
Jaak Vilo, Alvis Brazma, Inge Jonassen, Alan Robinson, and Esko Ukkonen.
Mining for Putative Regulatory Elements in the Yeast Genome Using
Gene Expression Data.
In 8th International Conference on Intelligent Systems For
Molecular Biology (ISMB 2000), 2000.
- 111
-
Peter J. Woolf, and Y. Wang.
A Fuzzy Logic Approach to Analyzing Gene Expression Data.
Physiological Genomics, Vol. 3(1):9-15, 2000.
- 112
-
J. Zhu, and M. Q. Zhang.
Cluster, Function and Promoter: Analysis of Yeast Expression Array.
In Pacific Symposium on Biocomputing, pages 476-487, 2000.
- 113
-
A. Zien, R. Kuffner, R. Zimmer, and T. Lengauer.
Analysis of Gene Expression Data with Pathway Scores.
In 8th International Conference on Intelligent Systems For
Molecular Biology (ISMB 2000), 2000.
- 114
-
T. Akutsu, S. Miyano, and S. Kuhara.
Identification of Genetic Networks from a Small Number of Gene
Expression Patterns Under the Boolean Network Model.
In Pacific Symposium on Biocomputing, pages 17-28, 1999.
- 115
-
Ting Chen, Vladimir Filkov, and Steven S. Skiena.
Identifying Gene Regulatory Networks from Experimental Data.
In RECOMB 1999: Proceedings of the Fifth Annual International
Conference on Computational Biology, 1999.
- 116
-
P. D'haeseleer, X. Wen, S. Fuhrman, and R. Somogyi;.
Linear Modeling of mRNA Expression Levels During CNS Developement
and Injury.
In Pacific Symposium on Biocomputing, pages 41-52, 1999.
- 117
-
Ralf Herwig, Albert J. Poustka, Christine Müller, Christof Bull, Hans Lehrach,
and John O'Brien.
Large-Scale Clustering of cDNA-Fingerprinting Data.
Genome Research, Vol.9(11):1093-1105, 1999.
- 118
-
Laurie J. Heyer, Semyon Kruglyak, and Shibu Yooseph.
Exploring Expression Data: Identification and Analysis of
Coexpressed Genes.
Genome Research, Vol.9(11):1106-1115, 1999.
- 119
-
Sui Huang.
Gene Expression Profiling, Genetic Networks, and Cellular States: An
Integrating Concept for Tumorigenesis and Drug Discovery.
Journal of Molecular Medicine, Vol.77(6):469-480, 1999.
- 120
-
Richard M. Karp, Roland Stoughton, and Ka Yee Yeung.
Algorithms for Choosing Differential Gene Expression Experiments.
In RECOMB 1999: Proceedings of the Fifth Annual International
Conference on Computational Biology, 1999.
- 121
-
Z. Szallasi.
Genetic Network Analysis in Light of Massively Parallel Biological
Data Acquisition.
In Pacific Symposium on Biocomputing, pages 5-16, 1999.
- 122
-
Robert Tibshirani, Trevor Hastie, Mike Eisen, Doug Ross, Botstein, D., and Pat
Brown.
Clustering Methods for the Analysis of DNA Microarray Data.
Technical report, Stanford University, October 1999.
- 123
-
D. C. Weaver, C. T. Workman, and G. D. Stormo.
Modeling Regulatory Networks with Weight Matrices.
In Pacific Symposium on Biocomputing, pages 112-123, 1999.
- 124
-
Michael Q. Zhang.
Large-Scale Gene Expression Data Analysis: A New Challenge to
Computational Biologists.
Genome Research, Vol.9(8):681-688, 1999.
- 125
-
M. G. Samsonova and V. N. Serov.
NetWork: An Interactive Interface to the Tools for Analysis of
Genetic Network Structure and Dynamics.
In Pacific Symposium on Biocomputing, pages 102-111, 1999.
- 126
-
S. Liang, S. Fuhrman, and R. Somogyi.
REVEAL, a General Reverse Engineering Algorithm for Inference of
Genetic Network Architectures.
In Pacific Symposium on Biocomputing, pages 18-29, 1998.
- 127
-
G. S. Michaels, D. B. Carr, M. Askenazi, S. Fuhrman, X. Wen, and R. Somogyi.
Cluster Analysis and Data Visualization of Large-Scale Gene
Expression Data.
In Pacific Symposium on Biocomputing, pages 42-53, 1998.
- 128
-
Paul T. Spellman, Gavin Sherlock, Michael Q. Zhang, Vishwanath R. Iyer, Kirk
Anders, Michael B. Eisen, Brown, P. O., Botstein, D., and Bruce Futcher.
Comprehensive Identification of Cell Cycle-regulated Genes of the
Yeast Saccharomyces cerevisiae by Microarray Hybridization.
Molecular Biology of the Cell, Vol. 9(12):3273-3297, December
1998.
- 129
-
A. Watson, A. Mazumder, M. Stewart, and S. Balasubramanian.
Technology for Microarray Analysis of Gene Expression.
Current Opinion in Biotechnology, Vol. 9(6):609-614, 1998.
- 130
-
Vingron, M., and Hoheisel, J.
Computational Aspects of Expression Data.
J Mol Med, Vol. 77:3-7, 1999.
- 131
-
Deval A. Lashkari, Joseph L. DeRisi, John H. McCusker, Allen F. Namath, Cristl
Gentile, Seung Y. Hwang, Brown, P. O., and Ronald W. Davis.
Yeast Microarrays for Genome Wide Parallel Genetic and Gene
Expression Analysis.
Proc. Natl. Acad. Sci. USA, Vol. 94(24):13057-13062, November
1997.
- 132
-
Mark Schena, Dari Shalon, Renu Heller, Andrew Chai, Brown, P. O., and Ronald
W. Davis.
Parallel Human Genome Analysis: Microarray-Based Expression
Monitoring of 1000 Genes.
Proc. Natl. Acad. Sci. USA, Vol. 93(20):10614-10619, October
1996.
- 133
-
KaYee Yeung, Chris Fraley, Alejandro Murua, Adrian E. Raftery, and Walter L.
Ruzzo.
Model-Based Clustering and Data Transformations for Gene Expression
Data.
University of Washington, April 2001.
- 134
-
Rainer Spang, Harry Zuzan, Mike West, Joseph Nevins, Carrie Blanchette,
Jeffrey R. Marks.
Prediction and Uncertainty in the Analysis of Gene Expression
Profiles.
Duke University, 2000.
- 135
-
Danh V. Nguyen, and David M. Rocke.
Tumor Classification by Partial Least Squares Using Microarray Gene
Expression Data.
University of California, Davis, February 2001.
- 136
-
Russ B Altman, and Soumya Raychaudhuri.
Whole-Genome Expression Analysis: Challenges Beyond Clustering.
Curr. Opin. Struct. Biol., Vol. 11(3):377-381, June 2001.
- 137
-
Dan Coleman, Xioapeng Dong, Johanna Hardin, David M. Rocke, and David L.
Woodru.
Some Computational Issues in Cluster Analysis with No a piori
Metric.
University of California, Davis, March 1999.
- 138
-
R. M. Hu, Z. G. Han, H. D. Song, Y. D. Peng, Q. H. Huang, S. X. Ren, Y. J. Gu,
C. H. Huang, Y. B. Li, C. L. Jiang, G. Fu, Q. H. Zhang, B. W. Gu, M. Dai, Y.
F. Mao, G. F. Gao, R. Rong, M. Ye, J. Zhou, S. H. Xu, J. Gu, J. X. Shi, W. R.
Jin, C. K. Zhang, T. M. Wu, G. Y. Huang, Z. Chen, M. D. Chen, and J. L.
Chen.
Gene Expression Profiling in the Human
Hypothalamus-Pituitary-Adrenal Axis and Full-Length cDNA Cloning.
Proc. Natl. Acad. Sci. USA, Vol. 97(17):9543-9548, August
2000.
- 139
-
Samuel T. Nadler, Jonathan P. Stoehr, Kathryn L. Schueler, Gene Tanimoto,
Brian S. Yandell, and Alan D. Attie.
The Expression of Adipogenic Genes Is Decreased in Obesity and
Diabetes Mellitus.
Proc. Natl. Acad. Sci. USA, Vol. 97(21):11371-11376, October
2000.
- 140
-
Arkady B. Khodursky, Brian J. Peter, Nicholas R. Cozzarelli, Botstein, D.,
Brown, P. O., and Charles Yanofsky.
DNA Microarray Analysis of Gene Expression in Response to
Physiological and Genetic Changes That Affect Tryptophan Metabolism in
Escherichia coli.
Proc. Natl. Acad. Sci. USA, Vol. 97(22):12170-12175, October
2000.
- 141
-
Zou, S., Meadows, S., Sharp, L., Jan, L., and Jan, Y.
Genome-Wide Study of Aging and Oxidative Stress Response in
Drosophila Melanogaster.
Proc. Natl. Acad. Sci. USA, Vol. 97(25):13726-13731, December
2000.
- 142
-
Jiang, M., Ryu, J., Kiraly, M., Duke, K., Reinke, V., and Kim, S.
Genome-Wide Analysis of Developmental and Sex-Regulated Gene
Expression Profiles in Caenorhabditis Elegans.
Proc. Natl. Acad. Sci. USA, Vol. 98(1):218-223, January 2001.
- 143
-
Virtaneva, K., Wright, F., Tanner, S., Yuan, B., Lemon, W., Caligiuri, M.,
Bloomfield, C., Chapelle, A., and Krahe, R.
Expression Profiling Reveals Fundamental Biological Differences in
Acute Myeloid Leukemia with Isolated Trisomy 8 and Normal Cytogenetic.
Proc. Natl. Acad. Sci. USA, Vol. 98(3):1124-1129, January
2001.
- 144
-
Welsh, J. B., Zarrinkar, P. P., Sapinoso, L. M., Kern, S. G., Behling, C. A.,
Monk, B. J., Lockhart, D., J., Burger, R. A., and Hampton, G. M.
Analysis of Gene Expression Profiles in Normal and Neoplastic
Ovarian Tissue Samples Identifies Candidate Molecular Markers of Epithelial
Ovarian Cancer.
Proc. Natl. Acad. Sci. USA, Vol. 98(3):1176-1181, January
2001.
- 145
-
Martin, K., J., Graner, E., Li, Y., Price, L. M., Kritzman, B. M., Fournier,
M. V., Rhei, E., and Pardee, A. B.
High-Sensitivity Array Analysis of Gene Expression for the Early
Detection of Disseminated Breast Tumor Cells in Peripheral Blood.
Proc. Natl. Acad. Sci. USA, Vol. 98(5):2646-2651, February
2001.
- 146
-
Hakak, Y., Walker, J. R., Li, C., Wong, W. H., Davis, K. L., Buxbaum, J. D.,
Haroutunian, V., and Fienberg, A. A.
Genome-Wide Expression Analysis Reveals Dysregulation of
Myelination-Related Genes in Chronic Schizophrenia.
Proc. Natl. Acad. Sci. USA, Vol. 98(8):4746-4751, April 2001.
- 147
-
Mody, M., Cao, Y. X., Cui, Z. Z., Tay, K. Y., Shyong, A., Shimizu, E., Pham,
K., Schultz, P., Welsh, D., and Tsien, J. Z.
Genome-Wide Gene Expression Profiles of the Developing Mouse
Hippocampus.
Proc. Natl. Acad. Sci. USA, Vol. 98(15):8862-8867, July 2001.
- 148
-
Vishwanath R. Iyer, Christine E. Horak, Charles S. Scafek, David Botsteink,
Michael Snyder, and Patrick O. Brown.
Genomic Binding Sites of the Yeast Cell-Cycle Transcription Factors
SBF and MBF.
Nature, Vol. 409(25):533-538, January 2001.
- 149
-
Zoltan Szallasi.
Genetic Network Analysis - from the Bench to Computers and Back the
Millennium End Version.
Uniformed Services University of the Health Sciences, 2001.
Bethesda, MD, 20814.
- 150
-
Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Albert Neutzner, Jorg D.
Hoheisel, and Martin Vingron.
Correspondence Analysis Applied to Microarray Data.
Proc. Natl. Acad. Sci. USA, Vol. 98(19):10781-10786, September
2001.
- 151
-
Chandra P. Leo, Ursula A. Vitt, and Aaron J.W. Hsueh.
The Ovarian Kaleidoscope Database: An Online Resource for the
Ovarian Research Community.
Endocrinology, Vol. 141(9):3052-3054, 2000.
- 152
-
David R. Bickel.
Robust Cluster Analysis of DNA Microarray Data: An Application of
Nonparametric Correlation Dissimilarity.
Medical College of Georgia, July 2001.
- 153
-
Anthony D. Long, Harry J. Mangalam, Bob Y. P. Chan, Lorenzo Tolleri, G. Wesley
Hatfield, and Pierre Baldi.
Improved Statistical Inference from DNA Microarray Data Using
Analysis of Variance and a Bayesian Statistical Framework.
The Journal of Biological Chemistry, 276(23):19937-19944,
June 2001.
- 154
-
Yi Lin, Samuel T. Nadler, Alan D. Attie, and Brian S. Yandell.
Mining for Low-Abundance Transcripts in Microarray Data.
Technical Report 1031, Department of Statistics, University of
Wisconsin-Madison, Madison, WI 53706, January 2001.
- 155
-
M. Kathleen Kerr and Gary A. Churchill.
Bootstrapping Cluster Analysis: Assessing the Reliability of
Conclusions from Microarray Experiments.
Proc. Natl. Acad. Sci. USA, Vol. 98(16):8961-8965, July 2001.
- 156
-
C. Romualdi, S. Bortoluzzi, and G. A. Danieli.
Detecting Differentially Expressed Genes in Multiple Tag Sampling
Experiments: Comparative Evaluation of Statistical Tests.
Human Molecular Genetics, Vol. 10(19):2133-2141, 2001.
- 157
-
Bradley Efron, John D. Storey, Robert Tibshirani.
Microarrays, Empirical Bayes Methods, and False Discovery Rates.
Stanford University, July 2001.
- 158
-
Robert Tibshirani, Trevor Hastie, Balasubramanian Narasimhan, Michael Eisen,
Gavin Sherlock, Pat Brown and David Bostein.
Exploratory Screening of Genes and Clusters from Microarray
Experiments.
Stanford University, 2001.
- 159
-
Robert Tibshirani, Guenther Walther, andTrevor Hastie.
Estimating the Number of Clusters in a Dataset Via Gap Statistic.
Stanford University, March 2000.
- 160
-
Carl S. Brown, Paul C. Goodwin, and Peter K. Sorger.
Image Metrics in the Statistical Analysis of DNA Microarray Data.
Proc. Natl. Acad. Sci. USA, Vol. 98(16):8944-8949, July 2001.
- 161
-
Lue Ping Zhao, Ross Prentice, and Linda Breeden.
Statistical modeling of large microarray data sets to identify
stimulus-response profiles.
Proc. Natl. Acad. Sci. USA, Vol. 98(10):5631-5636, May 2001.
- 162
-
Mike West, Carrie Blanchette, Holly Dressman, Erich Huang, Seiichi Ishida,
Rainer Spang, Harry Zuzan, John A. Olson, Jr. , Jeffrey R. Marks, and Joseph
R. Nevins.
Predicting the Clinical Status of Human Breast Cancer by Using Gene
Expression Profiles.
Proc. Natl. Acad. Sci. USA, Vol. 98(20):11462-11467, September
2001.
- 163
-
Masayuki Takahashi, Daniel R. Rhodes, Kyle A. Furge, Hiro-omi Kanayama, Susumu
Kagawa, Brian B. Haab, and Bin Tean Teh.
Gene Expression Profiling of Clear Cell Renal Cell Carcinoma: Gene
Identification and Prognostic Classification.
Proc. Natl. Acad. Sci. USA, Vol. 98(17):9754-9759, Auguse
2001.
- 164
-
Tetsuya S. Tanaka, Saied A. Jaradat, Meng K. Lim, George J. Kargul, Xiaohong
Wang, Marija J. Grahovac, Serafino Pantano, Yuri Sano, Yulan Piao, Ramaiah
Nagaraja, Hirofumi Doi, William H. Wood III, Kevin G. Becker, and Minoru S.
H. Ko.
Genome-Wide Expression Profiling of Mid-Gestation Placenta and
Embryo Using a 15,000 Mouse Developmental cDNA Microarray.
Proc. Natl. Acad. Sci. USA, Vol. 98(16):9127-9132, August
2001.
- 165
-
Therese Sorlie, Charles M. Perou, Robert Tibshirani, Turid Aas, Stephanie
Geisler, Hilde Johnsen, Trevor Hastie, Michael B. Eisen, Matt van de Rijn,
Stefanie S. Jeffrey, Thor Thorsen, Hanne Quist, John C. Matese, Brown, P. O.,
David Botstein, Per Eystein Lonning, and Anne-Lise Borresen-Dale.
Gene Expression Patterns of Breast Carcinomas Distinguish Tumor
Subclasses with Clinical Implications.
Proc. Natl. Acad. Sci. USA, Vol. 98(19):10869-10874, September
2001.
- 166
-
A. E. Murray, D. Lies,G.Li, K. Nealson, J. Zhou, and J. M. Tiedje.
DNA/DNA Hybridization to Microarrays Reveals Gene-Specific
Differences Between Closely Related Microbial Genomes.
Proc. Natl. Acad. Sci. USA, Vol. 98(17):9853-9858, August
2001.
- 167
-
Yee Sook Cho, Meyoung-Kon Kim, Chris Cheadle, Catherine Neary, Kevin G.
Becker, and Yoon S. Cho-Chung.
Antisense DNAs As Multisite Genomic Modulators Identified by DNA
Microarray.
Proc. Natl. Acad. Sci. USA, Vol. 98(17):9819-9823, August
2001.
- 168
-
Corrella S. Detweiler, Dolores B. Cunanan, and Stanley Falkow.
Host Microarray Analysis Reveals a Role for the Salmonella Response
Regulator phoP in Human Macrophage Cell Death.
Proc. Natl. Acad. Sci. USA, Vol. 98(10):5850-5855, May 2001.
- 169
-
Nina Salama, Karen Guillemin, Timothy K. McDaniel, Gavin Sherlock, Lucy
Tompkins, and Stanley Falkow.
A Whole-Genome Microarray Reveals Genetic Diversity Among
Helicobacter Pylori Strains.
Proc. Natl. Acad. Sci. USA, Vol. 97(26):14668-14673, December
2000.
- 170
-
Peer M. Schenk, Kemal Kazan, Iain Wilson, Jonathan P. Anderson, Todd Richmond,
Shauna C. Somerville, and John M. Manners.
Coordinated Plant Defense Responses in Arabidopsis Revealed by
Microarray Analysis.
Proc. Natl. Acad. Sci. USA, Vol. 97(21):11655-11660, October
2000.
- 171
-
Arkady B. Khodursky, Brian J. Peter, Molly B. Schmid, Joseph DeRisi, Botstein,
D., Patrick O. Brown, and Nicholas R. Cozzarelli.
Analysis of Topoisomerase Function in Bacterial Replication Fork
Movement: Use of DNA Microarrays.
Proc. Natl. Acad. Sci. USA, Vol. 97(17):9419-9424, August
2000.
- 172
-
Priya Sudarsanam, Vishwanath R. Iyer, Patrick O. Brown, and Fred Winston.
Whole-Genome Expression Analysis of snfy/swi Mutants of
Saccharomyces Cerevisiae.
Proc. Natl. Acad. Sci. USA, Vol. 97(7):3364-3369, March 2000.
- 173
-
D. W. Voehringer, D. L. Hirschberg, J. Xiao, Q. Lu, M. Roederer, C. B. Lock,
L. A. Herzenberg, L. Steinman, and L. A. Herzenberg.
Gene Microarray Identification of Redox and Mitochondrial Elements
That Control Resistance Or Sensitivity to Apoptosis.
Proc. Natl. Acad. Sci. USA, Vol. 97(6):2680-2685, March 2000.
- 174
-
J. D. Porter, S. Khanna, H. J. Kaminski, J.S.Rao, A. P. Merriam, C. R.
Richmonds, P. Leahy, J.Li, and F. H. Andrade.
Extraocular Muscle Is Defined by a Fundamentally Distinct Gene
Expression Profile.
Proc. Natl. Acad. Sci. USA, Vol. 98(21):12062-12067, October
2001.
- 175
-
Paul E. Neiman, Alanna Ruddell, Christine Jasoni, Gil Loring, Sandra Jo
Thomas, Kimberly A. Brandvold, Ruey-min Lee, Joan Burnside, and Jeffrey
Delrow.
Analysis of Gene Expression During Myc Oncogene-Induced
Lymphomagenesis in the Bursa of Fabricius.
Proc. Natl. Acad. Sci. USA, Vol. 98(11):6378-6383, May 2001.
- 176
-
Andrew Y. Gracey, Joshua V. Troll, and George N. Somero.
Hypoxia-Induced Gene Expression Profiling in the Euryoxic Fish
Gillichthys Mirabilis.
Proc. Natl. Acad. Sci. USA, Vol. 98(14):1993-199, February
2001.
- 177
-
Atul J. Butte, Pablo Tamayo, Donna Slonim, Todd R. Golub, and Isaac S.
Kohane.
Discovering Functional Relationships Between RNA Expression and
Chemotherapeutic Susceptibility Using Relevance Networks.
Proc. Natl. Acad. Sci. USA, Vol. 97(22):12182-12186, October
2000.
- 178
-
S. Brian Wilson, Sally C. Kent, Heidi F. Horton, Andrew A. Hill, Paul L.
Bollyky, David A. Hafler, Jack L. Strominger, and Michael C. Byrne.
Multiple Differences in Gene Expression in Regulatory
V
24J
Q T Cells from Identical Twins Discordant for Type I
Diabetes.
Proc. Natl. Acad. Sci. USA, Vol. 97(13):7411-7416, June 2000.
- 179
-
Gregg Johannes, Mark S. Carter, Michael B. Eisen, Brown, P. O., and Peter
Sarnow.
Identification of Eukaryotic mRNAs That Are Translated At Reduced
Cap Binding Complex eIF4F Concentrations Using a cDNA Microarray.
Proc. Natl. Acad. Sci. USA, Vol. 96(23):13118-13123, November
1999.
- 180
-
S. K. Loftus, Y. Chen, G. Gooden, J. F.Ryan, G. Birznieks, M.Hilliard, A. D.
Baxevanis, M. Bittner, P.Meltzer, J.Trent, and W. Pavan.
Informatic Selection of a Neural Crest-Melanocyte cDNA Set for
Microarray Analysis.
Proc. Natl. Acad. Sci. USA, Vol. 96(15):9277-9280, August
1999.
- 181
-
Tracy L. Ferea, Botstein, D., Brown, P. O., and R. Frank Rosenzweig.
Systematic Changes in Gene Expression Patterns Following Adaptive
Evolution in Yeast.
Proc. Natl. Acad. Sci. USA, Vol. 96(15):9721-9726, August
1999.
- 182
-
Ziv Bar-Joseph, David K. Gifford, and Tommi S. Jaakkola.
Fast Optimal Leaf Ordering for Hierarchical Clustering.
Bioinformatics, Vol. 17 Supplement 1:S22-S29, 2001.
- 183
-
Derek Y. Chiang, Brown, P. O., and Michael B. Eisen.
Visualizing Associations Between Genome Sequences and Gene
Expression Data Using Genome-Mean Expression Profiles.
Bioinformatics, Vol. 17 Supplement 1:S49-S55, 2001.
- 184
-
Lawrence Hunter, Ronald C. Taylor, Sonia M. Leach, and Richard Simon.
GEST: A Gene Expression Search Tool Based On A Novel Bayesian
Similarity Metric.
Bioinformatics, Vol. 17 Supplement 1:S115-S122, 2001.
- 185
-
Fabian Model, Peter Adorj¨¢n, Alexander Olek, and Christian Piepenbrock.
Feature Selection for DNA Methylation Based Cancer Classification.
Bioinformatics, Vol. 17 Supplement 1:S157-S164, 2001.
- 186
-
D. Venet, F. Pecasse, C. Maenhaut, and H. Bersini.
Separation of Samples into Their Constituents Using Gene Expression
Data.
Bioinformatics, Vol. 17 Supplement 1:S279-S287, 2001.
- 187
-
Alexander Zien, Thomas Aigner, Ralf Zimmer, and Thomas Lengauer.
Centralization: A New Method for the Normalization of Gene
Expression Data.
Bioinformatics, Vol. 17 Supplement 1:S323-S331, 2001.
- 188
-
Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, Sayan Mukherjee, Ryan M.
Rifkin, Michael Angelo, Michael Reich, Eric Lander, Jill Mesirov, and Todd
Golub.
Molecular Classification of Multiple Tumor Types.
Bioinformatics, Vol. 17 Supplement 1:S316-S322, 2001.
- 189
-
Robert Stevens, Carole Goble, Patricia Baker, and Andy Brass.
A Classification of Tasks in Bioinformatics.
Bioinformatics, Vol. 17(2):180-188, 2001.
- 190
-
Pierre Baldi, Soren Brunak, Yves Chauvin, Claus A. F. Andersen, and Henrik
Nielsen.
Assessing the Accuracy of Prediction Algorithms for Classification:
An Overview.
Bioinformatics, Vol. 16(5):412-424, 2000.
- 191
-
Anja von Heydebreack, Wolfgang Hubert, Annemarie Poustka and Martin Vingron.
Identifying Splits with Clear Separation: A New Class Discovery
Method for Gene Expression Data.
Bioinformatics, Vol. 1(1):1-8, 2001.
- 192
-
Ira J. Blader, Ian D. Manger, and John C. Boothroyd.
Microarray Analysis Reveals Previously Unknown Changes in Toxoplasma
gondii-infected Human Cells.
The Journal of Biological Chemistry, Vol. 276(26):24223-24231,
June 2001.
- 193
-
Charles B. Epstein, James A. Waddle, Walker Hale IV, Varshal Dave, Janet
Thornton, Timothy L. Macatee, Harold R. Garner, and Ronald A. Butow.
Genome-Wide Responses to Mitochondrial Dysfunction.
Molecular Biology of the Cell, Vol. 12:297-308, February 2001.
- 194
-
Nobuo Ogawa, Joseph DeRisi, and Patrick O. Brown.
New Components of A System for Phosphate Accumulation and
Polyphosphate Metabolism in Saccharomyces Cerevisiae Revealed by Genomic
Expression Analysis.
Molecular Biology of the Cell, Vol. 11:4309-4321, December
2000.
- 195
-
Audrey P. Gasch, Mingxia Huang, Sandra Metzner, Botstein, D., Stephen J.
Elledge, and Patrick O. Brown.
Genomic Expression Responses to DNA-damaging Agents and the
Regulatory Role of the Yeast ATR Homolog Mec1p.
Molecular Biology of the Cell, Vol.:2987-3003, October 2001.
- 196
-
Francois Bertucci, Karine Bernard, Beatrice Loriod, Yi-Chung Chang, Samuel
Granjeaud, Daniel Birnbaum, Catherine Nguyen, Konan Peck, and Bertrand R.
Jordan.
Sensitivity Issues in DNA Array-Based Expression Measurements and
Performance of Nylon Microarrays for Small Samples.
Human Molecular Genetics, Vol. 8(9):1715-1723, June 1999.
- 197
-
George C. Tseng, Min-Kyu Oh, Lars Rohlin, James C. Liao, and Wing Hung Wong.
Issues in cDNA Microarray Analysis: Quality Filtering, Channel
Normalization, Models of Variations and Assessment of Gene Effects.
Nucleic Acids Research, Vol. 29(12):2549-2557, 2001.
- 198
-
Huibin Yue, P. Scott Eastman, Bruce B. Wang, James Minor, Michael H.
Doctolero, Rachel L. Nuttall, Robert Stack, John W. Becker, Julie
R.Montgomery, Marina Vainer, and Rick Johnston.
An Evaluation of the Performance of cDNA Microarrays for Detecting
Changes in Global mRNA Expression.
Nucleic Acids Research, Vol. 29(8):e41, 2001.
- 199
-
Justen Andrews, Gerard G. Bouffard, Chris Cheadle, Jining L, Kevin G. Becker,
and Brian Oliver.
Gene Discovery Using Computational and Microarray Analysis of
Transcription in the Drosophila Melanogaster Testis.
Genome Research, Vol. 10(12):2030-2043, December 2000.
- 200
-
Matthew J. Callow, Dudoit, S., Elaine L. Gong, Terence P. Speed, and Edward M.
Rubin.
Microarray Expression Profiling Identifies Genes with Altered
Expression in HDL-Deficient Mice.
Genome Research, Vol. 10(12):2022-2029, December 2000.
- 201
-
Robert Lucito, Joseph West, Andrew Reiner, Joan Alexander, Diane Esposito,
Bhubaneswar Mishra, Scott Powers, Larry Norton, and Michael Wigler.
Detecting Gene Copy Number Fluctuations in Tumor Cells by Microarray
Analysis of Genomic Representations.
Genome Research, Vol. 10(11):1726-1736, November 2000.
- 202
-
John Aach, Wayne Rindone, and George M. Church.
Systematic Management and Analysis of Yeast Gene Expression Data.
Genome Research, Vol. 10(4):431-445, April 2000.
- 203
-
Paul J. Planet, Rob DeSalle, Mark Siddall, Timothy Bael, Indra Neil Sarkar,
and Scott E. Stanley.
Systematic Analysis of DNA Microarray Data: Ordering and
Interpreting Patterns of Gene Expression.
Genome Research, Vol. 11(7):1149-1155, July 2001.
- 204
-
Daniel A. Notterman, Uri Alon, Alexander J. Sierk, and Arnold J. Levine.
Transcriptional Gene Expression Profiles of Colorectal Adenoma,
Adenocarcinoma, and Normal Tissue Examined by Oligonucleotide Arrays.
Cancer Research, 61:3124-3130, April 2001.
- 205
-
Paul Bertone and Mark Gerstein.
The New Direction in Bioinformatics: Integrative Data Mining for
Genomics and Proteomics.
Yale University, New Haven, CT 06520, 2001.
- 206
-
Reinhard Guthke, Wolfgang Schmidt-Heck, Daniel Hahn and Michael Pfaff.
Gene Expression Data Mining for Functional Genomics.
Hans Knöll Institute for Natural Product Research,Jena, Germany,
2001.
- 207
-
Uwe Scherf, Douglas T. Ross, Mark Waltham, Lawrence H. Smith, Jae K. Lee,
Lorraine Tanabe, Kurt W. Kohn, William C. Reinhold, Timothy G. Myers, Darren
T. Andrews, Dominic A. Scudiero, Michael B. Eisen, Edward A. Sausville, Yves
Pommier, Botstein, D., Brown, P. O., and John N. Weinstein.
A Gene Expression Database for the Molecular Pharmacology of
Cancer.
Nature Genetics, Vol. 24:236-244, March 200.
- 208
-
Eric Mjolsness, and Dennis DeCoste.
Machine Learning for Science: State of the Art and Future
Prospects.
Science, Vol. 293(14):2051-2055, September 2001.
- 209
-
Trey Ideker, Timothy Galitski, and Leroy Hood.
A New Approach to Decoding Life: Systems Biology.
Annu. Rev. Genomics Hum. Genet., 2:343-372, July 2001.
- 210
-
Vishwanath R. Iyer, Michael B. Eisen, Douglas T. Ross, Greg Schuler, Troy
Moore, Jeffrey C. F. Lee, Jeffrey M. Trent, Louis M. Staudt, James Hudson
Jr., Mark S. Boguski, Deval Lashkari, Dari Shalon, Botstein, D., Patrick O.
Brown.
The Transcriptional Program in the Response of Human Fibroblasts to
Serum.
Science, Vol. 283(1):83-87, January 1999.
- 211
-
Katherine J. Martin and Arthur B. Pardee.
Identifying Expressed Genes.
Proc. Natl. Acad. Sci. USA, Vol. 97(8):3789-3791, April 2000.
- 212
-
G. Emilien, M. Ponchon, C. Caldas, O. Isacson and J. M. Maloteaux.
Impact of Genomics on Drug Discovery and Clinical Medicine.
Q J Med, 93:391-423, 2000.
- 213
-
Steven M. Albelda and Dean Sheppard.
Functional Genomics and Expression Profiling Be There or Be Square.
Am. J. Respir. Cell Mol. Biol., Vol. 23:265-269, 2000.
- 214
-
Naftali Kaminski.
Bioinformatics A User's Perspective.
Am. J. Respir. Cell Mol. Biol., Vol. 23:705-711, 2000.
- 215
-
Bertucci, F., Houlgatte, R., Benziane, A., Granjeaud, S., Adélaïde, J.,
Tagett, R., Loriod, B., Jacquemier, J., Viens, P., Jordan, B., Birnbaum, D.,
Nguyen, C.
Gene Expression Profiling of Primary Breast Carcinomas Using Arrays
of Candidate Genes.
Human Molecular Genetics, Vol. 9(20):2981-2991, 2000.
- 216
-
Chow, M. L., Moler, E. J., Mian, I. S.
Identifying Marker Genes in Transcription Profiling Data Using a
Mixture of Feature Relevance Experts.
Physiol Genomics, Vol. 5:99-111, July 2001.
- 217
-
Robert O. Stuart, Kevin T. Bush, and Sanjay K. Nigam.
Changes in Global Gene Expression Patterns During Development and
Maturation of the Rat Kidney.
Proc. Natl. Acad. Sci. USA, Vol. 98(10):5649-5654, May 2001.
- 218
-
Shiyong Li, Douglas T. Ross, Marshall E. Kadin, Brown, P. O., and Mariusz A.
Wasik.
Comparative Genome-Scale Analysis of Gene Expression Profiles in T
Cell Lymphoma Cells during Malignant Progression Using a Complementary DNA
Microarray.
American Journal of Pathology, Vol. 158(4):1231-1237, April
2001.
- 219
-
Lawrance, I. C., Fiocchi, C., Chakravarti, S.
Ulcerative Colitis and Crohn's Disease: Distinctive Gene Expression
Profiles and Novel Susceptibility Candidate Genes.
Human Molecular Genetics, Vol. 10(5):445-456, July 2001.
- 220
-
Andrew N. Young, Mahul B. Amin, Carlos S. Moreno, So Dug Lim, Cynthia Cohen,
John A. Petros, Fray F. Marshall, and Andrew S. Neish.
Expression Profiling of Renal Epithelial Neoplasms, A Method for
Tumor Classification and Discovery of Diagnostic Molecular Markers.
American Journal of Pathology, Vol. 158(5):1639-1651, May
2001.
- 221
-
B. K. Dieckgraefe, W. F. Stenson, J. R. Korzenik, P. E. Swanson, and C. A.
Harrington.
Analysis of Mucosal Gene Expression in Inflammatory Bowel Disease by
Parallel Oligonucleotide Arrays.
Physiol Genomics, Vol. 4:1-11, 2000.
- 222
-
James M. Markert, Catherine M. Fuller, G. Yancey Gillespie, James K. Bubien,
Lee Anne Mclean, Robert L. Hong, Kailin Lee, Steven R. Gullans, Timothy B.
Mapstone, and Dale J. Benos.
Differential Gene Expression Profiling in Human Brain Tumors.
Physiol Genomics, Vol. 5:21-33, 2001.
- 223
-
Jason Comander, Griffin M. Weber, Michael A. Gimbrone, Jr., and Guillermo
Garcia-Cardena.
Argus A New Database System for Web-Based Analysis of Multiple
Microarray Data Sets.
Genome Research, Vol. 11:1603-1610, 2001.
- 224
-
Aitman, T. J.
Science, Medicine, and the Future DNA Microarrays in Medical
Practice.
BMJ, Vol. 323(15):611-615, September 2001.
- 225
-
Thomas J. Giordano, Kerby A. Shedden, Donald R. Schwartz, Rork Kuick, Jeremy
M. G. Taylor, Nana Lee, David E. Misek, Joel K. Greenson, Sharon L. R.
Kardia, David G. Beer, Gad Rennert, Kathleen R. Cho, Stephen B. Gruber, Eric
R. Fearon, and Samir Hanash.
Organ-Specific Molecular Classification of Primary Lung, Colon, and
Ovarian Adenocarcinomas Using Gene Expression Profiles.
American Journal of Pathology, Vol. 159(4):1231-1238, October
2001.
- 226
-
Arul M. Chinnaiyan, Markus Huber-Lang, Chandan Kumar-Sinha, Terrence R.
Barrette, Sunita Shankar-Sinha, Vidya J. Sarma, Vaishalee A. Padgaonkar, and
Peter A. Ward.
Molecular Signatures of Sepsis, Multiorgan Gene Expression Profiles
of Systemic Inflammation.
American Journal of Pathology, Vol. 159(4):1199-1209, October
2001.
- 227
-
M. C. K. Yang, Q. G. Ruan, J. J. Yang, S. Eckenrode, S. Wu, R. A. Mcindoe, and
J.X.She.
A Statistical Method for Flagging Weak Spots Improves Normalization
and Ratio Estimates in Microarrays.
Physiol Genomics, 7:45-53, 2001.
- 228
-
Boer, J. M., Huber, W. K., Sultmann, H., Wilmer, F., von Heydebreck, A., Haas,
S., Korn, B., Gunawan, B., Vente, A., Fuzesi, L., Vingron, M., Poustka, A. .
Identification and Classification of Differentially Expressed Genes
in Renal Cell Carcinoma by Expression Profiling on a Global Human
31,500-Element cDNA Array.
Genome Research, 11:1861-1870, 2001.
- 229
-
Mitchell E. Garber, Olga G. Troyanskaya, Karsten Schluens, Simone Petersen,
Zsuzsanna Thaesler, Manuela Pacyna-Gengelbach, Matt van de Rijn, Glenn D.
Rosen, Charles M. Perou, Richard I. Whyte, Russ B. Altman, Brown, P. O.,
Botstein, D., and Iver Petersen.
Diversity of Gene Expression in Adenocarcinoma of The Lung.
Proc. Natl. Acad. Sci. USA, Vol. 98(24):13784-13789, November
2001.
- 230
-
Arindam Bhattacharjee, William G. Richards, Jane Staunton, Cheng Li , Stefano
Monti, Priya Vasa, Christine Ladd, Javad Beheshti, Raphael Bueno, Michael
Gillette, Massimo Loda, Griffin Weber, Eugene J. Mark, Eric S. Lander, Wing
Wong, Bruce E. Johnson, Todd R. Golub, David J. Sugarbaker, and Matthew
Meyerson.
Classification of Human Lung Carcinomas by Mrna Expression Profiling
Reveals Distinct Adenocarcinoma Subclasses.
Proc. Natl. Acad. Sci. USA, Vol. 98(24):13790-13795, November
2001.
- 231
-
Russell S. Thomas, David R. Rank, Sharron G. Penn, Gina M. Zastrow, Kevin R.
Hayes, Kalyan Pande, Edward Glover, Tomi Silander, Mark W. Craven, Janardan
K. Reddy, Stevan B. Jovanovich, and Christopher A. Bradfield.
Identification of Toxicologically Predictive Gene Sets Using Cdna
Microarrays.
Molecular Pharmacology, Vol. 60(6):1189-1194, 2001.
- 232
-
Jae K. Lee.
Analysis Issues for Gene Expression Array Data.
Clinical Chemistry, 47(8):1350-1352, 2001.
- 233
-
A M Snijders, G A Meijer, R H Brakenhoff,A J C vandenBrule, P J van Diest.
Microarray Techniques in Pathology: Tool Or Toy?
J Clin Pathol: Mol Pathol, Vol. 53:289-294, July 2000.
- 234
-
Joseph L. DeRisi, Vishwanath R. Iyer, Patrick O. Brown.
Exploring the Metabolic and Genetic Control of Gene Expression on a
Genomic Scale.
Science, Vol. 278(24):680-686, October 1997.
- 235
-
Kevin P. White, Scott A. Rifkin, Patrick Hurban, David S. Hogness.
Microarray Analysis of Drosophila Development During Metamorphosis.
Science, Vol. 286(10):2179-2184, December 1999.
- 236
-
Scott A. Jelinsky, Preston Estep, George M. Church, and Leona D. Samson.
Regulatory Networks Revealed by Transcriptional Profiling of Damaged
Saccharomyces cerevisiae Cells: Rpn4 Links Base Excision Repair with
Proteasomes.
Molecular And Cellular Biology, Vol. 20(21):8157-8167, 2000.
- 237
-
E. J. Moler, D. C. Radisky, and I. S. Mian.
Integrating Naive Bayes Models and External Knowledge to Examine
Copper and Iron Homeostasis in S. Cerevisiae.
Physiol Genomics, 4:127-135, 2000.
- 238
-
Lars M. Jakt, Liang Cao, Kathryn S.E. Cheah, and David K. Smith.
Assessing Clusters and Motifs from Gene Expression Data.
Genome Research, 11:112-123, 2001.
- 239
-
Trey Ideker, Vesteinn Thorsson, Jeffrey A. Ranish, Rowan Christmas, Jeremy
Buhler, Jimmy K. Eng, Roger Bumgarner, David R. Goodlett, Ruedi Aebersold,
and Leroy Hood.
Integrated Genomic and Proteomic Analyses of a Systematically
Perturbed Metabolic Network.
Science, Vol. 292(4):929-934, May 2001.
- 240
-
Jason C. Mills, and Jeffrey I. Gordon.
A New Approach for Filtering Noise from High-Density Oligonucleotide
Microarray Datasets.
Nucleic Acids Research, Vol. 29(15):1-13, July 2001.
- 241
-
Douglas B. Kell, Robert M. Darby, and John Draper.
Genomic Computing. Explanatory Analysis of Plant Expression
Profiling Data Using Machine Learning.
Plant Physiology, Vol. 126:943-951, July 2001.
- 242
-
Peter F. Lemkin, Gregory C. Thornwall, Katherine D. Walton, and Lothar
Hennighausen.
The Microarray Explorer Tool for Data Mining of cDNA Microarrays:
Application for the Mammary Gland.
Nucleic Acids Research, Vol. 28(22):4452-4459, 2000.
- 243
-
Ralf Herwig, Pia Aanstad, Mattew Clark, and Hans Lehrach.
Statistical Evaluation of Differential Experssion on cDNA Nylon
Arrays with Replicated Experiments.
Nucleic Acids Research, Vol. 29(23):117-126, 2001.
- 244
-
Naftali Kaminski, John D. Allard, Jean F. Pittet, Fengrong Zuo, Mark J. D.
Griffiths, David Morris, Xiaozhu Huang, Dean Sheppard, and Renu A. Heller.
Global Analysis of Gene Expression in Pulmonary Fibrosis Reveals
Distinct Programs Regulating Lung Inflammation and Fibrosis.
Proc. Natl. Acad. Sci. USA, Vol. 97(4):1778-1783, February
2000.
- 245
-
Andreas Wagner.
Decoupled Evolution of Coding Region and Mrna Expression Patterns
after Gene Duplication: Implications for The Neutralist-Selectionist Debate.
Proc. Natl. Acad. Sci. USA, Vol. 97(12):6579-6584, June 2000.
- 246
-
Carl J. Friddle, Teiichiro Koga, Edward M. Rubin, and James Bristow.
Expression Profiling Reveals Distinct Sets of Genes Altered during
Induction and Regression of Cardiac Hypertrophy.
Proc. Natl. Acad. Sci. USA, Vol. 97(12):6745-6750, June 2000.
- 247
-
van Tilborg, A. A.G., de Vries, A., de Bont, M., Groenfeld, L. E., van der
Kwast, T. H., Zwarthoff, E. C. .
Molecular evolution of multiple recurrent cancers of the bladder.
Human Molecular Genetics, Vol. 9(20):2973-2980, July 2001.
- 248
-
S E Wildsmith, and F J Elcock.
Microarrays under the Microscope.
J Clin Pathol: Mol Pathol, 54:8-16, 2001.
- 249
-
Ding, Y., Lawrence, C. E.
Statistical Prediction of Single-Stranded Regions in RNA Secondary
Structure and Application to Predicting Effective Antisense Target Sites and
Beyond.
Nucleic Acids Research, Vol. 29(5):1034-1046, 2001.
- 250
-
Bruce J. Aronow, Brian D. Richardson, and Stuart Handwerger.
Microarray Analysis of Trophoblast Differentiation: Gene Expression
Reprogramming in Key Gene Function Categories.
Physiol Genomics, 6:105-116, 2001.
- 251
-
Audrey P. Gasch, Paul T. Spellman, Camilla M. Kao, Orna Carmel-Harel, Michael
B. Eisen, Gisela Storz, Botstein, D., and Patrick O. Brown.
Genomic Expression Programs in the Response of Yeast Cells to
Environmental Changes.
Molecular Biology of the Cell, Vol. 11:4241-4257, December
2000.
- 252
-
Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg
TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW.
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle.
Molecular Cell, Vol. 2(1):65-73, July 1998.
- 253
-
Douglas T. Ross, Uwe Scherf, Michael B. Eisen, Charles M. Perou, Christian
Rees, Paul Spellman, Vishwanath Iyer, Stefanie S. Jeffrey, Matt Van de Rijn,
Mark Waltham, Alexander Pergamenschikov, Jeffrey C.F. Lee, Deval Lashkari,
Dari Shalon, Timothy G. Myers, John N. Weinstein, Botstein, D., and Patrick
O. Brown.
Systematic Variation in Gene Expression Patterns in Human Cancer
Cell Lines.
Nature Genetics, Vol. 24:227-235, March 2000.
- 254
-
Hedenfalk, I., Duggan, D., Chen, Y. D., Radmacher, M., Bittner, M., Simon, R.,
Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O. P., Wilfond, B.,
Borg, A., and Trent, J.
Gene-Expression Profiles in Hereditary Breast Cancer.
The New England Journal of Medicine, Vol. 344(8):539-548,
February 2001.
- 255
-
Michel Schummer, WaiLap V. Ng, Roger E. Bumgarner, Peter S. Nelson, Bernhard
Schummer, David W. Bednarski, Laurie Hassell, Rae Lynn Baldwin, Beth Y.
Karlan, Leroy Hood.
Comparative Hybridization of an Array of 21500 Ovarian cDNAs for the
Discovery of Genes Overexpressed in Ovarian Carcinomas.
Gene, Vol. 238:375-385, 1999.
- 256
-
Stephen A. Chervitz, L. Aravind, Gavin Sherlock, Catherine A. Ball, Eugene V.
Koonin, Selina S. Dwight, Midori A. Harris, Kara Dolinski, Scott Mohr, Temple
Smith, Shuai Weng, J. Michael Cherry, David Botstein.
Comparison of the Complete Protein Sets of Worm and Yeast: Orthology
and Divergence.
Science, Vol. 282(11):2022-2028, December 1998.
- 257
-
Brian B. Haab, Maitreya J. Dunham, and Patrick O. Brown.
Protein Microarrays for Highly Parallel Detection and Quantitation
of Specific Proteins and Antibodies in Complex Solutions.
Genome Biology, Vol.2(2):0004.1-0004.13, January 2001.
- 258
-
Lieb J. D., Liu X., Botstein D. , Brown P. O.
Promoter-Specific Binding of Rap1 Revealed by Genome-wide Maps of
Protein-DNA Association.
Nature Genetics, Vol. 28(4):327-334, 2001.
- 259
-
Thomas J. Lyons, Audrey P. Gasch, L. Alex Gaither, Botstein, D., Brown, P. O.,
and David J. Eide.
Genome-wide Characterization of the Zap1p Zinc-Responsive Regulon in
Yeast.
Proc. Natl. Acad. Sci. USA, Vol. 97(14):7957-7962, July 2000.
- 260
-
Charles M. Perou, Therese Surlie, Michael B. Eisen, Matt van de Rijn, Stefanie
S. Jeffreyk, Christian A. Rees, Jonathan R. Pollack, Douglas T. Ross, Hilde
Johnsen, Lars A. Akslen, Oystein Fluge, Alexander Pergamenschikov, Cheryl
Williams, Shirley X. Zhu, Per E. Lunning, Anne-Lise Burresen-Dale, Patrick O.
Brown, and David Botstein.
Molecular Portraits of Human Breast Tumours.
Nature, Vol. 406:747-752, 2000.
- 261
-
Valerie Reinke, Harold E. Smith, Jeremy Nance, John Wang, Carrie Van Doren,
Rebecca Begley, Steven J. M. Jones, Elizabeth B. Davis, Stewart Scherer,
Samuel Ward, and Stuart K. Kim.
A Global Profile of Germline Gene Expression in C. elegans.
Molecular Cell, Vol. 6:605-616, September 2000.
- 262
-
Elizabeth A. Winzeler, Daniel D. Shoemaker, Anna Astromoff, Hong Liang, Keith
Anderson, Bruno Andre, Rhonda Bangham, Rocio Benito, Jef D. Boeke, Howard
Bussey, Angela M. Chu, Carla Connelly, Karen Davis, Fred Dietrich, Sally
Whelen Dow, Mohamed El Bakkoury, Francüoise Foury, Stephen H. Friend, Erik
Gentalen, Guri Giaever, Johannes H. Hegemann, Ted Jones, Michael Laub, Hong
Liao, Nicole Liebundguth, David J. Lockhart, Anca Lucau-Danila, Marc Lussier,
Nasiha MÕRabet, Patrice Menard, Michael Mittmann, Chai Pai, Corinne
Rebischung, Jose L. Revuelta, Linda Riles, Christopher J. Roberts, Petra
Ross-MacDonald, Bart Scherens, Michael Snyder, Sharon Sookhai-Mahadeo,
Reginald K. Storms, Steeve Veronneau, Marleen Voet, Guido Volckaert, Teresa
R. Ward, Robert Wysocki, Grace S. Yen, Kexin Yu, Katja Zimmermann, Peter
Philippsen, Mark Johnston, Ronald W. Davis.
Functional Characterization of the S. cerevisiae Genome by Gene
Deletion and Parallel Analysis.
Science, Vol. 285(6):901-906, August 1999.
- 263
-
Jennifer C. Boldrick, Ash A. Alizadeh, Maximilian Diehn, Dudoit, S., Chih Long
Liu, Christopher E. Belcher, Botstein, D., Louis M. Staudt, Patrick O. Brown,
and David A. Relman.
Stereotyped and Specific Gene Expression Programs in Human Innate
Immune Responses to Bacteria.
Proc. Natl. Acad. Sci. USA, Vol. 99(2):972-977, January 2002.
- 264
-
Justin Courcelle, Arkady Khodursky, Brian Peter, Brown, P. O., and Philip C.
Hanawalt.
Comparative Gene Expression Profiles Following UV Exposure in
Wild-Type and SOS-Deficient Escherichia coli.
Genetics Society of America, Vol. 158:41-64, May 2001.
- 265
-
Claudia Gross, Mark Kelleher, Vishwanath R. Iyer, Brown, P. O., and Dennis R.
Winge.
Identification of the Copper Regulon in Saccharomyces cerevisiae by
DNA Microarrays.
The Journal of Biological Chemistry, Vol. 275(41):32310-32316,
October 2000.
- 266
-
Huang J., Lih C. J., Pan K. H., Cohen S.N.
Global Analysis of Growth Phase Responsive Gene Expression and
Regulation of Antibiotic Biosynthetic Pathways in Streptomyces Coelicolor
Using Dna Microarrays.
Genes Dev., Vol. 15(23):3183-3192, 2001.
- 267
-
Kenneth M. Kuhn, Joseph L. Derisi, Patrick O. Brown, and Peter Sarnow.
Global and Specific Translational Regulation in the Genomic Response
of Saccharomyces cerevisiae to a Rapid Transfer from a Fermentable to a
Nonfermentable Carbon Source.
Molecular and Cellular Biology, Vol. 21(3):916-927, February
2001.
- 268
-
Robert Schaffer, Jeff Landgraf, Monica Accerbi, Vernadette Simon, Matt Larson,
and Ellen Wisman.
Microarray Analysis of Diurnal and Circadian-Regulated Genes in
Arabidopsis.
The Plant Cell, Vol. 13:113-123, January 2001.
- 269
-
Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B.
Two Yeast Forkhead Genes Regulate the Cell Cycle and Pseudohyphal
Growth.
Nature, 406(6791):90-94, 2000.
- 270
-
Diehn M., Eisen M. B., Botstein D., Brown P. O.
Large-Scale Identification of Secreted and Membrane-Associated Gene
Products Using DNA Microarrays.
Nature Genetics, 25(1):58-62, May 2000.
- 271
-
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF,
Jeffrey SS, Botstein D, Brown PO.
Genome-Wide Analysis of DNA Copy-Number Changes Using cDNA
Microarrays.
Nature Genetics, Vol.23(1):41-46, September 1999.
- 272
-
Stefania Bortoluzzi, Fabio Alessi, Chiara Romualdi, and Gian Antonio Danieli.
The Human Adult Skeletal Muscle Transcriptional Profile
Reconstructed by a Novel Computational Approach.
Genome Research, Vol. 10:344-349, 2000.
- 273
-
Whitfield, M. L., Sherlock, G., Alok Saldanha, John I. Murray, Catherine A.
Ball, Karen E. Alexander, John C. Matese, Charles M. Perou, Myra M. Hurt,
Brown, P. O., and David Botstein1.
Identification of Genes Periodically Expressed in the Human Cell
Cycle and Their Expression in Tumors.
MBC, Vol.:-, 2002.
- 274
-
Rosenwald, A., Alizadeh, A. A., Widhopf, G., Simon, R., Davis, R. E., Yu, X.,
Yang, L., Pickeral, O. K, Rassenti, L. Z, Powell, J., Botstein, D., Byrd, J.
C., Grever, M. R., Cheson, B. D., Chiorazzi, N., Wilson, W. H., Kipps, T. J.,
Brown, P. O., Staudt, L. M.
Relation of Gene Expression Phenotype to Immunoglobulin Mutation
Genotype in B Cell Chronic Lymphocytic Leukemia.
J Exp Med, Vol. 11(194):1639-1647, December 2001.
- 275
-
Joachim Theilhaber, Timothy Connolly, Sergio Roman-Roman, Steven Bushnell,
Amanda Jackson, Kathy Call, Teresa Garcia, and Roland Baron .
Finding Genes in the C2C12 Osteogenic Pathway by k-Nearest-Neighbor
Classification of Expression Data.
Genome Research, Vol. 12:165-176, 2002.
- 276
-
Kuang-Hung Pan, Chih-Jian Lih, and Stanley N. Cohen.
Analysis of DNA Microarrays Using Algorithms That Employ Rule-Based
Expert Knowledge.
Proc. Natl. Acad. Sci. USA, Vol. 99(4):2118-2123, February
2002.
- 277
-
A. Tsodikov, A. Szabo, and D. Jones.
Adjustments and Measures of Differential Expression for Microarray
Data.
Bioinformatics, Vol.18(2):251-260, 2002.
- 278
-
Ghosh, D., and Chinnaiyan, A. M.
Mixture Modelling of Gene Expression Data from Microarray
Expreiments.
Bioinformatics, Vol.18(2):275-286, July 2002.
- 279
-
Mattias Wahde, Gregory T. Klus, Michael L. Bittner, Yidong Chen, and Zoltan
Szallasi .
Assessing the Significance of Consistently Mis-Regulated Genes in
Cancer Associated Gene Expression Matrices.
Bioinformatics, Vol.18(3):389-394, 2002.
- 280
-
Winston Patrick Kuo, Tor-Kristian Jenssen, Atul J. Butte, Lucila Ohno-Machado,
and Isaac S. Kohane .
Analysis of matched mRNA measurements from two different microarray
technologies.
Bioinformatics, Vol.18(3):405-412, 2002.
- 281
-
Kurt Fellenberg, Nicole C. Hauser, Benedikt Brors, Jörg D. Hoheisel, and
Martin Vingron.
Microarray Data Warehouse Allowing for Inclusion of Experiment
Annotations in Statistical Analysis.
Bioinformatics, Vol.18(3):423-433, 2002.
- 282
-
Wolfram Liebermeister.
Linear Modes of Gene Expression Determined by Independent Component
Analysis.
Bioinformatics, Vol.18(1):51-60, 2002.
- 283
-
R. Sasik, N. Iranfar, T. Hwa, and W. F. Loomis.
Extracting Transcriptional Events from Temporal Gene Expression
Patterns During Dictyostelium Development.
Bioinformatics, Vol.18(1):61-66, 2002.
- 284
-
Christophe Ambroise, and Geoffrey J. McLachlan.
Selection Bias in Gene Extraction on the Basis of Microarray
Gene-Expression Data.
Proc. Natl. Acad. Sci. USA, Vol.99(10):6562-6566, May 2002.
- 285
-
Hidde De Jong.
Modeling and Simulation of Genetic Regulatory Systems: A Literature
Review.
Journal of Computational Biology, Vol.9(1):67-103, 2002.
- 286
-
Amir Ben-Dor, Nir Friedman, and Zohar Yakhini.
Scoring Genes for Relevance.
Technical Report AGL-2000-13, Agilent Laboratories, 2000.
- 287
-
R. Sharan, R. Elkon and R. Shamir.
Cluster Analysis and its Applications to Gene Expression Data.
To appear in Proceedings of the Ernst Schering workshop on
Bioinformatics and Genome Analysis Springer Verlag, 2002.
- 288
-
Jenny Bryan, Katherine S. Pollard, and Mark J. van der Laan.
Paired and Unpaired Comparison and Clustering with Gene Expression
Data.
University of British Columbia, 2002.
- 289
-
Ziv Bar-Joseph Georg Gerber David K. Gifford Tommi S. Jaakkola.
A New Approach to Analyzing Gene Expression Time Series Data.
In RECOMB 2002: Proceedings of the Sixth Annual International
Conference on Computational Biology. ACM Press, 2002.
- 290
-
Ingrid Lyonnstedt and Terry Speed.
Replicated Microarray Data.
Department of Mathematics, Uppsala University, 2001.
- 291
-
Amir Ben-Dor, Ron Shamir, and Zohar Yakhini.
Clustering Gene Expression Patterns, 1999.
- 292
-
David B. Finkelstein, Jeremy Gollub, Rob Ewing, Fredrik Sterky, Shauna
Somerville, J. Michae Cherry.
Iterative Linear Regression by Sector: Renormalization of cDNA
Microarray Data and Cluster Analysis Weighted by Cross Homology.
In CAMDA 00, Duke University, Durham, N.C., December 2000.
- 293
-
Mayi Arcellana-Panlilio and Stephen M. Robbins.
Cutting-edge Technology I. Global Gene Expression Profiling Using
Dna Microarrays.
Am J Physiol Gastrointest Liver Physiol, Vol. 282:397-402,
2002.
- 294
-
Siyoung Park, Daewoo Choi, and Chi-Hyuck Jun.
A Clustering Method for Discovering Patterns Using Gene Regulatory
Processes.
Genome Informatics, Vol. 12:249-251, 2001.
- 295
-
Mitsuteru Nakao, Hidemasa Bono, Shuichi Kawashima, Tomomi Kamiya, Kazushige
Sato, Susumu Goto, and Minoru Kanehisa.
Genome-scale Gene Expression Analysis and Pathway Reconstruction in
KEGG, 2000.
- 296
-
Johanna Hardin, David M.Rocke, and David L.Woodru .
Robust Model-Based Clustering of Genes in Microarray Data: Are there
Gene Clusters?, December 2000.
- 297
-
A.Chilingaryan, N.Gevorgyan, A.Vardanyan, D.Jones, and A.Szabo.
Multivariate approach for selecting sets of differentially
Expressioned Genes.
Mathematical Biosciences, Vol.176:59-72, 2002.
- 298
-
Yidong Chen, Zohar Yakhini, Amir Ben-Dor, Edward Dougherty, Jeffrey M. Trent,
and Michael Bittne.
Analysis of Expression Patterns: The Scope of the Problem, the
Problem of Scope.
Disease Markers, Vol.17:59-65, 2001.
- 299
-
Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju, and
Eric P Hoffman.
Sources of Variability and Effect of Experimental Approach on
Expression Profiling Data Interpretation.
BMC Bioinformatics, Vol. 3(4):1-29, 2002.
- 300
-
Margaret A. Shipp, Ken N. Ross, Pablo Tamayo, Andrew P. Weng, Jeffery L.
Kutok, Ricardo C. T. Aguiar, Michelle Gaasenbeek, Michael Angelo, Michael
Reich, Geraldine S. Pinkus, Tane S. Ray, Margaret A. Koval, Kim W. Last,
Andrew Norton, T. Andrew Lister, Jill Mesirov, Donna S. Neuberg, Eric S.
Lander, Jon C. Aster, and Todd R. Golub.
Supplementary Information for: Diffuse Large B-Cell Lymphoma Outcome
Prediction by Gene Expression Profiling and Supervised Machine Learning,
December 2001.
- 301
-
M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M.
Radmacher, R. Simon, Z. Yakhinik, A. Ben-Dor, N. Sampas, E. Dougherty, E.
Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, J.
Carpten, E. Gillanders, D. Leja, K. Dietrich, C. Beaudry, M. Berens, D.
Alberts, V. Sondak, N. Hayward, and J. Trent.
Molecular Classification of Cutaneous Malignant Melanoma by Gene
Expression Profiling.
Nature, Vol. 406(3):536-540, August 2001.
- 302
-
DR Goldstein, E Conlon, D Ghosh.
Statistical Issues in The Clustering of Gene Expression Data.
Statistica Sinica, 12(1):to appear, 2002.
- 303
-
Danh V. Nguyen and David M. Rocke.
Multi-Class Cancer Classfication Via Partial Least Squares With Gene
Expression Profiles.
Department of Statistics Texas A&M University, College Station, TX
77843, February 2002.
- 304
-
Werner Dubitzky, Martin Granzow, Daniel Berrar.
Data Mining and Machine Learning Methods for Microarray Analysis.
Methods of Microarray Data Analysis, pages 5-22, 2002.
- 305
-
Marcel Dettling and Peter B uhlmann.
How to Use Boosting for Tumor Classification with Gene Expression
Data.
Seminar fur Statistik ETH Zurich CH-8092 Switzerland, February 2002.
- 306
-
Hui-Rong Qian.
ANOVA Analysis of cDNA Microarray Data to Identify Differentially
Expressed Genes, 2001.
- 307
-
Sorin Draghici.
Statistical Intelligence: Effective Analysis of High-Density
Microarray Data.
Wayne State University, Detroit, MI 48202, April 2002.
- 308
-
Chris H.Q. Ding.
Analysis of Gene Expression Profiles: Class Discovery and Leaf
Ordering.
Proc. RECOMB 2002, pages 127-136, April 2002.
- 309
-
Chris H.Q. Ding.
Unsupervised Feature Selection in Gene Expression Analysis:
Bootstrap Via Two-Way Ordering.
NERSC Division, Lawrence Berkeley National Laboratory, 2002.
- 310
-
Sandrine Dudoit, Jane Fridlyand, and Terence P. Speed.
Comparison of Discrimination Methods for the Classi cation of Tumors
Using Gene Expression Data.
Journal of the American Statistical Association, Vol.
97(457):77-87, March 2002.
- 311
-
Yee Hwa Yang, Sandrine Dudoit, Percy Luu, David M. Lin, Vivian Peng, John
Ngai, and Terence P. Speed .
Normalization for cDNA Microarray Data: A Robust Composite Method
Addressing Single and Multiple Slide Systematic Variation.
Nucleic Acids Research, Vol. 30(4):e15, 2002.
- 312
-
Peter Adorjan, Jurgen Distler, Evelyne Lipscher, Fabian Model, Jurgen Muller,
Cecile Pelet, Aron Braun, Andrea R. Florl, David Gutig, Gabi Grabs, Andre
Howe, Mischo Kursar, Ralf Lesche, Erik Leu, Andre Lewin, Sabine Maier, Volker
Muller, Thomas Otto, Christian Scholz, Wolfgang A. Schulz, Hans-Helge
Seifert, Ina Schwope, Heike Ziebarth, Kurt Berlin, Christian Piepenbrock, and
Alexander Olek.
Tumour Class Prediction and Discovery by Microarray-Based DNA
Methylation Analysis.
Nucleic Acids Research, Vol. 30(5):e21, 2002.
- 313
-
Paul Pavlidis, Christopher Tang, and William Stafford Noble.
Classification of Genes Using Probabilistic Models of Microarray
Expression Profiles.
BIOKDD01: Workshop on Data Mining in Bioinformatics (with
SIGKDD01 Conference), pages 1-7, 2001.
- 314
-
Gary S. Firestein and David S. Pisetsky.
Editorial: DNA Microarrays: Boundless Technology or Bound By
Technology? Guidelines for Studies Using Microarray Technology.
Arthritis & Rheumatism, Vol. 46(4):859-861, April 2002.
- 315
-
Finny G. Kuruvilla, Peter J. Park, and Stuart L. Schreiber.
Vector Algebra in the Analysis of Genome-Wide Expression Data.
Genome Biology, Vol. 3(3):research0011.1-0011.11, February
2002.
- 316
-
D. Ghosh.
Singular Value Decomposition Regression Models for Classification of
Tumors from Microarray Experiments.
PSB 2003, 2002.
- 317
-
Erez Hartuv and Armin Schmitt and Jorg Lange and Sebastian Meier-Ewert and
Hans Lehrachs and Ron Shamir.
An Algorithm for Clustering cDNAs for Gene Expression Analysis.
In RECOMB 1999, pages 188-197, 1999.
- 318
-
Jie Cheng, Christos Hatzis, Hisashi Hayashi, Mark-A. Krogel, Shinichi
Morishita, David Page, and Jun Sese.
KDD Cup 2001 Report.
SIGKDD Explorations, 3(2):1-17, January 2002.
ACM SIGKDD.
- 319
-
Pollard, K. S. and Lann, M. J.
Statistical Inference for Simultaneous Clustering for Gene
Expression Data.
Div. of Biostatistics, University of California, 2001.
- 320
-
Goutham Kurra, Wen Niu and Raj Bhatnagar.
Mining Microarray Expression Data for Classifier Gene-Cores.
BIOKDD01: Workshop on Data Mining in Bioinformatics (with
SIGKDD01 Conference), pages 8-14, 2001.
- 321
-
John N. Weinstein, Uwe Scherf, Jae K. Lee, Satoshi Nishizuka, Fuad Gwadry,
Ajay, Kim Bussey, S. Kim, Lawrence H. Smith, Lorraine Tanabe, Samuel Richman,
Jessie Alexander, Hosein Kouros-Mehr, Alika Maunakea, and William C.
Reinhold.
The Bioinformatics of Microarray Gene Expression Profiling.
Cytometry, Vol. 47:46-49, 2001.
- 322
-
Roded Sharan and Ron Shamir.
CLICK: A Clustering Algorithm with Applications to Gene Expression
Analysis.
Department of Computer Science, Tel-Aviv University, 2000.
- 323
-
Leping Li, Lee G. Pedersen, Thomas A. Darden, and Clarice R. Weinberg.
Class Prediction and Discovery based on Gene Expression Data.
Biostatistics Branch and 2 Laboratory of Structural Biology, National
Institute of Environmental Health Sciences, Research Triangle Park, North
Carolina, 2002.
- 324
-
Efron B, Tibshirani R, Goss V, and Chu G.
Microarrays and Their Use in a Comparative Experiment.
Stanford University, October 2001.
- 325
-
Scott L. Pomeroy, Pablo Tamayo, Michelle Gaasenbeek, Lisa M. Sturla, Michael
Angelo, Margaret E. McLaughlin, John Y. H. Kim, Liliana C. Goumnerovak, Peter
M. Blackk, Ching Lau, Jeffrey C. Allen, David Zagzag, James M. Olson, Tom
Curran, Cynthia Wetmore, Jaclyn A. Biegel, Tomaso Poggio, Shayan Mukherjee,
Ryan Rifkin, Andrea Califano, Gustavo Stolovitzky, David N. Louis, Jill P.
Mesirov, Eric S. Lander, and Todd R. Golub.
Prediction of Central Nervous System Embryonal Tumour Outcome Based
on Gene Expression.
Nature, Vol. 415(24):436-442, January 2001.
- 326
-
Frank De Smet, Janick Mathys, Kathleen Marchal, Gert Thijs, Bart De Moor, and
Yves Moreau .
Adaptive Quality-Based Clustering of Gene Expression Profiles.
Bioinformatics, Vol. 18(5):735-746, 2002.
- 327
-
David M. Rocke, and Blythe Durbin.
A Model for Measurement Error for Gene Expression Arrays.
Journal of Computational Biology, Vol. 8(6):557-569, 2001.
- 328
-
Pavlidis, P., Lewis, D.P., and Noble, W.S.
Exploring Gene Expression Data With Class Scores.
PSB: Proceedings of the Pacific Symposium on Biocomputing,
pages 7-18, 2002.
- 329
-
Raymond T. Ng, Jorg Sander, and Monica C. Sleumer.
Hierarchical Cluster Analysis of Sage Data for Cancer Profiling.
BIOKDD01: Workshop on Data Mining in Bioinformatics (with
SIGKDD01 Conference), pages 65-72, 2001.
- 330
-
Giovanni Parmigiani, Elizabeth S. Garrett, Ramaswamy Anbazhagan, and Edward
Gabrielson.
A Statistical Framework for Expression Based Molecular
Classification in Cancer.
Johns Hopkins University, Baltimore, 2001.
- 331
-
Xuegong Zhang, Wing H. Wong,.
Recursive Sample Classification and Gene Selection Based on SVM:
Method and Software Description.
Department of Biostatistics, Harvard School of Public Health, 2001.
- 332
-
M. Rattray, N. Morrison, D.Hoyle, and A. Brass.
DNA Microarray Normalisation, PCA and a Related Latent Variable
Model.
University of Manchester, Manchester, UK., November 2001.
- 333
-
Alexander Zien, Juliane Fluck, Ralf Zimmer, and Thomas Lengauer.
Microarrays: How Many Do You Need?
In RECOMB 2002: Proceedings of the Sixth Annual International
Conference on Computational Biology. ACM Press, 2002.
- 334
-
Jobst Landgrebe, Wolfgang Wurst, and Gerhard Welzl.
Permutation-Validated Principal Components Analysis of Microarray
Data.
Genome Biology, Vol. 3(4):0019.1-0019.11, March 2002.
- 335
-
Felix Naef Coleen R. Hacker, Nila Patil, and Marcelo Magnasco.
Empirical Characterization of The Expression Ratio Noise Structure
in High-Density Oligonucleotide Arrays.
Genome Biology, Vol. 3(4):0018.1-0018.11, March 2002.
- 336
-
Wei Pan, Jizhen Lin, and Chap T. Le.
Model-Based Cluster Analysis of Microarray Gene-Expression Data.
Genome Biology, Vol. 3(2):0009.1-0009.8, January 2002.
- 337
-
Trond Hellem Bo and Inge Jonassen.
New Feature Subset Selection Procedures for Classification of
Expression Profiles.
Genome Biology, Vol. 3(4):0017.1-0027.11, March 2002.
- 338
-
Ka Yee Yeung, Walter L. Ruzzo.
Details of the Adjusted Rand index and Clustering algorithms
Supplement to the paper An empirical study on Principal Component Analysis
for clustering gene expression data.
Bioinformatics, May 2001.
- 339
-
Sunduz Keles, Mark van der Lann, and Michael B Eisen.
Identification of Regulatory Elements Using a Feature Selection
Method.
University of California, Berkeley, February 2002.
- 340
-
K. Y. Yeung and W. L. Ruzzo.
Principal Component Analysis for Clustering Gene Expression Data.
Bioinformatics, Vol. 17(9):763-774, 2001.
- 341
-
Vladimir Pavlovic, Ashutosh Garg, and Simon Kasif`.
A Bayesian Framework for Combining Gene Predictions.
Bioinformatics, Vol. 18(1):19-27, 2002.
- 342
-
Ursula Rost and Erich Bornberg-Bauer.
TreeWiz: Interactive Exploration of Huge Trees.
Bioinformatics, Vol. 18(1):109-114, 2002.
- 343
-
Ying Xu, Victor Olman, and Dong Xu.
Clustering Gene Expression Data Using A Graph-Theoretic Approach: an
Application of Minimum Spanning Trees.
Bioinformatics, Vol. 18(4):536-545, 2002.
- 344
-
Wei Pan.
A Comparative Review of Statistical Methods for Discovering
Differentially Expressed Genes in Replicated Microarray Experiments.
Bioinformatics, Vol. 18(4):546-554, 2002.
- 345
-
Ilya Shmulevich and Wei Zhang.
Binary Analysis and Optimization-Based Normalization of Gene
Expression Data.
Bioinformatics, Vol. 18(4):555-565, 2002.
- 346
-
David C. Hoyle, Magnus Rattray, Ray Jupp, and Andrew Brass.
Making Sense of Microarray Data Distributions.
Bioinformatics, Vol. 18(4):576-584, 2002.
- 347
-
Jinyan Li and Limsoon Wong.
Identifying Good Diagnostic Gene Groups from Gene Expression
Profiles Using The Concept of Emerging Patterns.
Bioinformatics, Vol. 18(5):725-734, 2002.
Li Zhang
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