Journal Papers

  1. S. P. Ponnapalli, M. A. Saunders, G. H. Golub and O. Alter, "A Higher-Order Generalized Singular Value Decomposition for Comparative Analysis of Large-Scale Datasets," submitted.
  2. L. Omberg, G. H. Golub and O. Alter, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies," Proceedings of the National Academy of Sciences 104 (47), pp. 18371–18376 (November 2007) (supplemental material at http://www.bme.utexas.edu/research/orly/HOSVD/).
  3. O. Alter and G. H. Golub, "Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening," Proceedings of the National Academy of Sciences 103 (32), pp. 11828 – 11833 (August 2006) (supplemental material at http://www.bme.utexas.edu/research/orly/harmonic_oscillator/).
  4. O. Alter and G. H. Golub, "Reconstructing the Pathways of a Cellular System from Genome-Scale Signals Using Matrix and Tensor Computations," Proceedings of the National Academy of Sciences 102 (49), pp. 17559–17564 (December 2005) (supplemental material at http://www.bme.utexas.edu/research/orly/network_decomposition/).
  5. O. Alter and G. H. Golub, "Integrative Analysis of Genome-Scale Data Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication and RNA Transcription," Proceedings of the National Academy of Sciences 101 (47), pp. 16577–16582 (November 2004) (supplemental material at http://www.bme.utexas.edu/research/orly/pseudoinverse/).
  6. O. Alter, P. O. Brown and D. Botstein, "Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms," Proceedings of the National Academy of Sciences 100 (6), pp. 3351–3356 (March 2003) (supplemental material at http://genome-www.stanford.edu/GSVD/ and at http://www.bme.utexas.edu/research/orly/GSVD/).
  7. S. P. Bohen, O. G. Troyanskaya, O. Alter, R. Warnke, D. Botstein, P. O. Brown and R. Levy, "Variation in Gene Expression Patterns in Follicular Lymphoma and the Response to Rituximab," Proceedings of the National Academy of Sciences 100 (4), pp. 1926–1930 (February 2003).
  8. T. Nielsen, R. B. West, S. C. Linn, O. Alter, M. A. Knowling, J. O'Connell, S. Zhu, M. Fero, G. Sherlock, J. R. Pollack, P. O. Brown, D. Botstein and M. van de Rijn, "Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study," Lancet 359 (9314), pp. 1301–1307 (April 2002) (supplemental material at http://genome-www.stanford.edu/sarcoma/).
  9. O. Alter, P. O. Brown and D. Botstein, "Singular Value Decomposition For Genome-Wide Expression Data Processing and Modeling," Proceedings of the National Academy of Sciences 97 (18), pp. 10101–10106 (August 2000) (supplemental material at http://genome-www.stanford.edu/SVD/ and at http://www.bme.utexas.edu/research/orly/SVD/PNAS_2000/).

Commentaries

  1. O. Alter, "Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data," Proceedings of the National Academy of Sciences 103 (44), pp. 16063–16064 (October 2006).

Book Chapters

  1. O. Alter, "Genomic Signal Processing: From Matrix Algebra to Genetic Networks," in Microarray Data Analysis: Methods and Applications, edited by M. J. Korenberg (Humana Press, Totowa, 2007), pp. 17–59.
  2. O. Alter, P. O. Brown and D. Botstein, "Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition," in Microarrays: Optical Technologies and Informatics, edited by M. L. Bittner, Y. Chen, A. N. Dorsel and E. R. Dougherty (International Society for Optical Engineering, Bellingham, 2001), vol. 4266, pp. 171–186 (supplemental material at http://genome-www.stanford.edu/SVD/ and at http://www.bme.utexas.edu/research/orly/SVD/SPIE_2001/).

Technical Reports

  1. O. Alter, G. H. Golub, P. O. Brown and D. Botstein, "Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models," in the Proceedings of the Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer, edited by M. P. Deutscher, S. Black, P. E. Boehmer, G. D'Urso, T. Fletcher, F. Huijing, A. Marshall, B. Pulverer, B. Renault, J. D. Rosenblatt, J. M. Slingerland and W. J. Whelan (University of Miami School of Medicine, Miami, 2004) vol. 15, http://www.med.miami.edu/mnbws/documents/Alter-.pdf.

Plenary, Keynote and Invited Talks and Tutorials

  1. O. Alter, "Mathematical Modeling of DNA Microarray Data: From Discovery of Patterns to Discovery of Molecular Biological Mechanisms," scheduled for the 2008 SIAM Annual Meeting (San Diego, California, July 7–11, 2008), invited talk.
  2. O. Alter, "Tensor Computations for Modeling Large-Scale Molecular Biological Data: From Discovery of Patterns to Discovery of Principles of Nature," Croucher Advanced Study Institute on Mathematical and Algorithmic Challenges for Modeling and Analyzing Modern Data Sets (Hong Kong, April 21–25, 2008), invited lecture.
  3. C. Muralidhara, R. R. Gutell, G. H. Golub and O. Alter, "Matrix Decompositions for Identifying Patterns of Evolution in RNA Sequences," scheduled for the 2008 SIAM Annual Meeting (San Diego, California, July 7–11, 2008), invited talk.
  4. L. Omberg, G. H. Golub and O. Alter, "Integrating DNA Microarray Data From Different Studies Using Higher-Order Singular Value Decompositions," scheduled for the 2008 SIAM Annual Meeting (San Diego, California, July 7–11, 2008), invited talk.
  5. S. P. Ponnapalli, M. A. Saunders, G. H. Golub and O. Alter, "A Novel Higher-Order Generalized Singular Value Decomposition for Comparative Analysis of DNA Microarray Data From Different Organisms," scheduled for the 2008 SIAM Annual Meeting (San Diego, California, July 7–11, 2008), invited talk.
  6. O. Alter, "Integrative and Comparative Analyses of DNA Microarray Data from Different Studies of the Cell Division Cycle," Heraeus International Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany, July 16–28, 2007), invited tutorials and computational laboratory sessions.
  7. O. Alter, "Tensor Computations for Genomic Signal Processing," 6th International Congress on Industrial and Applied Mathematics (Zürich, Switzerland, July 16–20, 2007), invited talk.
  8. O. Alter, "Discovery of Principles of Nature From Matrix and Tensor Modeling of DNA Microarray Data," 2007 SIAM Conference on Data Mining (Minneapolis, Minnesota, April 26–28, 2007), invited talk.
  9. O. Alter, "Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data," Argonne National Laboratory and University of Chicago Symposium on Mathematics for Systems Biology (Chicago, Illinois, February 22, 2007), plenary talk.
  10. O. Alter, "Uncovering the Biological and Physical Principles that Govern Activities of DNA and RNA With Mathematical Modeling of DNA Microarray Data," RIKEN International Workshop on Recent Advances in Biological Control (Nagoya, Japan, July 29–30, 2006), invited talk.
  11. O. Alter and G. H. Golub, "Matrix and Tensor Computations for Reconstructing the Pathways of a Cellular System from Genome-Scale Signals," 17th International Symposium on the Mathematical Theory of Networks and Systems (MTNS) (Kyoto, Japan, July 24–28, 2006), invited talk.
  12. O. Alter, "Matrix and Tensor Computations for Reconstructing the Pathways of a Cellular System from Genome-Scale Signals," Stanford/Yahoo! Workshop on Algorithms for Modern Massive Data Sets (Stanford, California, June 21–24, 2006), plenary talk.
  13. O. Alter, "Uncovering the Molecular Biological Principles that Govern Cellular Systems With Blind Source Separation Models," 6th International Conference on Independent Component Analysis and Blind Source Separation (Charleston, South Carolina, March 5–8, 2006), keynote talk.
  14. O. Alter, "Genomic Signal Processing: From Matrix and Tensor Computations to Genetic Networks," Institute for Operations Research and the Management Science Conference on Optimization and Health Care (San Antonio, Texas, February 3–5, 2006), invited talk.
  15. O. Alter, "Linear Algebra and its Applications Lecture of the International Linear Algebra Society: From Matrix Algebra to Genetic Networks,"12th International Linear Algebra Society (ILAS) Meeting (Regina, Saskatchewan, Canada, June 26–29, 2005), plenary talk.
  16. O. Alter, "Genomic Signal Processing: Predicting Basic Molecular Biological Principles," 2005 March Meeting of the American Physical Society (Los Angeles, California, March 21–26, 2005), invited talk L7.00003.
  17. O. Alter, "Genomic Signal Processing: Large-Scale Data, Matrix (and Tensor) Algebra and Basic Biological Principles," 2005 Haifa Matrix Theory Conference (Haifa, Israel, January 3–7, 2005), invited talk.
  18. O. Alter, "Genomic Signal Processing: Large-Scale Data, Matrix (and Tensor) Algebra and Basic Biological Principles," American Institute of Mathematics Workshop on Tensor Decomposition (Palo Alto, California, July 19–23, 2004), plenary talk.
  19. O. Alter, "Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms Using Generalized Singular Value Decomposition," 3rd Australian Microarray Meeting (Couran Cove, South Stradbroke Island, Queensland, Australia, July 23–26, 2003), keynote talk.
  20. O. Alter, "Modeling Genome-Scale mRNA Expression Datasets: From Matrix Algebra to Genetic Networks," 2003 March Meeting of the American Physical Society (Austin, Texas, March 3–7, 2003), invited talk S10.002.
  21. O. Alter, "SVD and GSVD for Modeling Genome-Scale mRNA Expression Data," 2nd International Workshop on Parallel Matrix Algorithms and Applications (PMMA 2002) (Neuchâtel, Switzerland, November 9–10, 2002), invited talk.
  22. O. Alter, "Genome-Wide Expression Data Analysis: From Tools to Predictive Models," Bat Sheva Interdisciplinary Workshop on Global Information in Biological Systems: Emergence of Functional Organization (Dead Sea, Israel, October 9–11, 2002), invited talk.
  23. O. Alter, "Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition," At the Interface of Biology, Mathematics and Physics (Tucson, Arizona, March 9–10, 2001), invited talk.
  24. O. Alter, P. O. Brown and D. Botstein, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling," Mathematical Sciences Research Institute Short Course on Mathematical and Computational Challenges in Molecular and Cell Biology (Berkeley, California, June 12–23, 2000), invited tutorial.
  25. O. Alter, "Singular Value Decomposition for Gene Expression Data Processing and Modeling," 5th After the Genome Conference (ATGC) (Jackson Hole, Wyoming, October 6–10, 1999), invited talk.

Contributed Talks and Posters

  1. S. P. Ponnapalli, G. H. Golub and O. Alter, "A Novel Higher-Order Generalized Singular Value Decomposition for Comparative Analysis of Multiple Genome-Scale Datasets From Different Organisms," Croucher Advanced Study Institute on Mathematical and Algorithmic Challenges for Modeling and Analyzing Modern Data Sets (Hong Kong, April 21–25, 2008), contributed talk.
  2. C. Muralidhara, A. M. Gross, R. R. Gutell and O. Alter, "Singular Value Decomposition Analysis of 16S rRNA Sequence Alignments Reveals Phylogenetic Subgroups and Corresponding Characteristic Sites," scheduled for the 20th Cold Spring Harbor Laboratory Annual Meeting on the Biology of Genomes (Cold Spring Harbor, New York, May 6–10, 2008), contributed poster.
  3. L. Omberg and O. Alter, "Integrative Analysis of Genome-Scale Expression Data From Yeast Cell Cycle Time Courses Under Different Oxidative Stress Conditions," scheduled for the 20th Cold Spring Harbor Laboratory Annual Meeting on the Biology of Genomes (Cold Spring Harbor, New York, May 6–10, 2008), contributed poster.
  4. L. Omberg, G. H. Golub and O. Alter, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies," 7th Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics (Cold Spring Harbor, New York, November 1–5, 2007), contributed poster.
  5. C. Muralidhara, R. R. Gutell, G. H. Golub and O. Alter, "Analysis of Sequence Alignments Using Singular Value Decomposition," Heraeus International Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany, July 16–28, 2007), contributed talk.
  6. L. Omberg, G. H. Golub and O. Alter, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data From Different Studies," Heraeus International Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany, July 16–28, 2007), contributed talk.
  7. S. P. Ponnapalli, G. H. Golub and O. Alter, "A Novel Higher-Order Generalized Singular Value Decomposition for Comparative Analysis of Multiple Genome-Scale Datasets From Different Organisms," Heraeus International Summer School on Statistical Physics of Gene Regulation – From Networks to Expression Data and Back (Bremen, Germany, July 16–28, 2007), contributed talk.
  8. C. Muralidhara, R. R. Gutell, G. H. Golub and O. Alter, "Exploring Phylogenetic Relationships in Sequence Alignments Through Singular Value Decomposition," Stanford/Yahoo! Workshop on Algorithms for Modern Massive Data Sets (Stanford, California, June 21–24, 2006), contributed poster.
  9. L. Omberg, G. H. Golub and O. Alter, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data," Stanford/Yahoo! Workshop on Algorithms for Modern Massive Data Sets (Stanford, California, June 21–24, 2006), contributed poster.
  10. S. P. Ponnapalli, G. H. Golub and O. Alter, "A Novel Higher-Order Generalized Singular Value Decomposition for Comparative Analysis of Multiple Genome-Scale Datasets," Stanford/Yahoo! Workshop on Algorithms for Modern Massive Data Sets (Stanford, California, June 21–24, 2006), contributed poster.
  11. O. Alter, G. H. Golub, P. O. Brown and D. Botstein, "Integrative Data-Driven Mathematical Models Predict Novel Genome-Scale Correlation Between DNA Replication Initiation and RNA Transcription During the Cell Cycle in Yeast," 2004 Annual Meeting of the American Institute of Chemical Engineers (AIChE) (Austin, Texas, November 7–12, 2004), contributed talk.
  12. O. Alter and G. H. Golub, "Integrative Analysis of Genome-Scale Data Using Pseudoinverse Projection Predicts Novel Correlation Between DNA Replication Initiation and RNA Transcription in Yeast," 4th Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics (Cambridge, United Kingdom, September 22–26, 2004), contributed talk.
  13. O. Alter and G. H. Golub, "Network Decomposition: From Systems to Pathways," 4th Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics (Cambridge, United Kingdom, September 22–26, 2004), contributed poster.
  14. O. Alter, G. H. Golub, P. O. Brown and D. Botstein, "Data-Driven Models Predict a Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast," Biology of Genomes (Cold Spring Harbor, New York, May 12–16, 2004), contributed poster.
  15. O. Alter, G. H. Golub, P. O. Brown and D. Botstein, "Novel Genome-Scale Correlation Between DNA Replication and RNA Transcription During the Cell Cycle in Yeast is Predicted by Data-Driven Models," Miami Nature Biotechnology Winter Symposium on the Cell Cycle, Chromosomes and Cancer (Miami Beach, Florida, January 31–February 4, 2004), contributed poster.
  16. O. Alter, P. O. Brown and D. Botstein, "Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms Using Generalized Singular Value Decomposition," 2nd Cold Spring Harbor Laboratory/Wellcome Trust Conference on Genome Informatics (Cambridge, United Kingdom, September 4–8, 2002), contributed talk.
  17. O. Alter, P. O. Brown and D. Botstein, "On Singular Value Decomposition for Processing and Modeling Genome-Wide Expression Data," 2001 March Meeting of the American Physical Society (Seattle, Washington, March 12–16, 2001), contributed talk E23.002.
  18. O. Alter, P. O. Brown and D. Botstein, "Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition," International Biomedical Optics Symposium (BIOS 2001) (San Jose, California, January 20–26, 2001), contributed talk 4266-24.
  19. O. Alter, P. O. Brown and D. Botstein, "Singular Value Decomposition for Gene Expression Data Processing and Modeling," International Symposium on Quantitative Challenges in the Post-Genomic Era (LJIS 2000) (San Diego, CA, January 13–15, 2000), contributed talk.