Books

  1. O. Alter, Genomic Signal Processing: Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data. New York, NY: Wiley-Interscience, in preparation.
  2. Journal Papers

  3. K. A. Aiello and O. Alter, "Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition," Public Library of Science (PLoS) One 11 (10), article e0164546 (October 2016); doi: 10.1371/journal.pone.0164546.
  4. P. Sankaranarayanan,* T. E. Schomay,* K. A. Aiello and O. Alter, "Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival," Public Library of Science (PLoS) One 10 (4), article e0121396 (April 2015); doi: 10.1371/journal.pone.0121396.
    Press Release: J. Kiefer, "New Method Increases Accuracy of Ovarian Cancer Prognosis and Diagnosis," American Association for the Advancement of Science (AAAS) EurekAlert! (April 15, 2015).
    Feature: R. Atkins, "Calculating Cancer Cures," National Academy of Engineering (NAE) Innovation Podcast and Radio Series (April 19, 2015).1
    Feature: F. Pavlou, "Big Data, Hidden Knowledge," The Pathologist (June 15, 2015).2
  5. N. M. Bertagnolli, J. A. Drake, J. M. Tennessen and O. Alter, "SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism," Public Library of Science (PLoS) One 8 (11), article e78913 (November 2013); doi: 10.1371/journal.pone.0078913.
    Highlight.
  6. C. H. Lee,* B. O. Alpert,* P. Sankaranarayanan and O. Alter, "GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival," Public Library of Science (PLoS) One 7 (1), article e30098 (January 2012); doi: 10.1371/journal.pone.0030098.
    Highlight.
  7. S. P. Ponnapalli, M. A. Saunders, C. F. Van Loan and O. Alter, "A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms," Public Library of Science (PLoS) One 6 (12), article e28072 (December 2011); doi: 10.1371/journal.pone.0028072.
    Highlight.
  8. C. Muralidhara, A. M. Gross, R. R. Gutell and O. Alter, "Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA," Public Library of Science (PLoS) One 6 (4), article e18768 (April 2011); doi: 10.1371/journal.pone.0018768.
    Highlight.
  9. L. Omberg, J. R. Meyerson, K. Kobayashi, L. S. Drury, J. F. X. Diffley and O. Alter, "Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression," Molecular Systems Biology (MSB) 5, article 312 (October 2009); doi: 10.1038/msb.2009.70.
    Review: M. Méchali, Faculty of 1000 evaluation 1728974 (February 2010).
    Highlight.
  10. 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 (PNAS) USA 104 (47), pp. 18371–18376 (November 2007); doi: 10.1073/pnas.0709146104.
  11. 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 (PNAS) USA 103 (32), pp. 11828–11833 (August 2006); doi: 10.1073/pnas.0604756103.
  12. O. Alter and G. H. Golub, "Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations," Proceedings of the National Academy of Sciences (PNAS) USA 102 (49), pp. 17559–17564 (December 2005); doi: 10.1073/pnas.0509033102.
  13. O. Alter and G. H. Golub, "Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation between DNA Replication and RNA Transcription," Proceedings of the National Academy of Sciences (PNAS) USA 101 (47), pp. 16577–16582 (November 2004); doi: 10.1073/pnas.0406767101.
  14. 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 (PNAS) USA 100 (6), pp. 3351–3356 (March 2003); doi: 10.1073/pnas.0530258100.
    Feature: M. E. Kilmer and C. D. Moravitz Martin, "Decomposing a Tensor," Society for Industrial and Applied Mathematics (SIAM) News 37 (9), (November 2004).
    Feature: J. Wixon and J. Ashurst, "Genome Informatics," Computational Functional Genomics 4 (5), pp. 509–514 (October 2003).
  15. 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 (PNAS) USA 100 (4), pp. 1926–1930 (February 2003); doi: 10.1073/pnas.0437875100.
  16. 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); doi: 10.1016/S0140-6736(02)08270-3.
    Invited Commentary: L. Y. Dirix and A. T. van Oosterom, "Gene-Expression Profiling to Classify Soft-Tissue Sarcomas," Lancet 359 (9314), pp. 1263–1264 (April 2002).
  17. 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 (PNAS) USA 97 (18), pp. 10101–10106 (August 2000); doi: 10.1073/pnas.97.18.10101.
  18. Commentaries

  19. O. Alter, "Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data," Proceedings of the National Academy of Sciences (PNAS) USA 103 (44), pp. 16063–16064 (October 2006); doi: 10.1073/pnas.0607650103.
  20. Book Chapters

  21. O. Alter, "Genomic Signal Processing: From Matrix Algebra to Genetic Networks." In: M. J. Korenberg, editor, Microarray Data Analysis: Methods and Applications. Totowa, NJ: Humana Press, Methods in Molecular Biology, vol. 377, pp. 17–59 (May 2007); doi: 10.1007/978-1-59745-390-5_2.
  22. O. Alter, P. O. Brown and D. Botstein, "Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition." In: M. L. Bittner, Y. Chen, A. N. Dorsel and E. R. Dougherty, editors, Microarrays: Optical Technologies and Informatics. Bellingham, WA: International Society for Optics and Photonics (SPIE), vol. 4266, pp. 171–186 (January 21, 2001); doi: 10.1117/12.427986.
  23. Technical Reports

  24. O. Alter, "DNA Copy-Number Alterations in Primary Ovarian Serous Cystadenocarcinoma Encoding for Cell Transformation and Predicting Survival and Response to Platinum Therapy Throughout the Course of the Disease," American Association for Cancer Research (AACR) Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities (Orlando, FL, October 17–20, 2015). Philadelphia, PA: AACR (January 2016); doi: 10.1158/1557-3265.OVCA15-A60.
  25. 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," Workshop on Algorithms for Modern Massive Datasets (MMDS). Stanford, CA: Stanford University and Yahoo! Research (June 21–24, 2006).
  26. 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: 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, editors, Miami Nature Biotechnology Winter Symposium: Cell Cycle, Chromosomes and Cancer. Miami Beach, FL: University of Miami School of Medicine, vol. 15 (January 31 – February 4, 2004); http://www.med.miami.edu/mnbws/documents/Alter-.pdf.
  27. Patents

  28. O. Alter, "Advanced Tensor Decompositions for Computational Assessment and Prediction from Data," International Patent Filed under the Patent Cooperation Treaty (PCT) US 16/27642.
  29. O. Alter, "Genetic Alterations in Ovarian Cancer," International Patent Filed under PCT US 16/27641.
  30. O. Alter, "Genomic Tensor Analysis for Medical Assessment and Prediction," Utility Patents Pending US 14/201739 and Europe 12830209.8.
  31. O. Alter, "Genetic Alterations in Gliomas," Utility Patents Pending US 14/354543 and Europe 12846126.6.

    Copyrighted Software

  1. © K. A. Aiello and O. Alter 2016, "Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition;" http://www.alterlab.org/astrocytoma_prognosis/.
  2. © P. Sankaranarayanan, T. E. Schomay, K. A. Aiello and O. Alter 2015, "Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival;" http://www.alterlab.org/OV_prognosis/.
  3. © N. M. Bertagnolli, J. A. Drake and O. Alter 2013, "SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism;" http://www.alterlab.org/GBM_metabolism/.
  4. © B. O. Alpert and O. Alter 2012, "GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival;" http://www.alterlab.org/GBM_prognosis/.
  5. © S. P. Ponnapalli and O. Alter 2011, "A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms;" http://www.alterlab.org/HO_GSVD/.
  6. © A. M. Gross and O. Alter 2011, "Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA;" http://www.alterlab.org/rRNA/.
  7. © O. Alter 2009, "Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression;" http://www.alterlab.org/verification_of_prediction/.
  8. © O. Alter 2007, "A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data from Different Studies;" http://www.alterlab.org/HOSVD/.
  9. © O. Alter 2006, "Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening;" http://www.alterlab.org/harmonic_oscillator/.
  10. © O. Alter 2005, "Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations;" http://www.alterlab.org/network_decomposition/.
  11. © O. Alter 2004, "Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation between DNA Replication and RNA Transcription;" http://www.alterlab.org/pseudoinverse/.
  12. © O. Alter 2003, "Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms;" http://www.alterlab.org/GSVD/.
  13. © O. Alter 2001, "Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition;" http://www.alterlab.org/SVD/.
  14. © O. Alter 2000, "Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling;" http://www.alterlab.org/singular_value_decomposition/.

    Recent Plenary and Keynote Lectures and Invited Talks and Tutorials at International Meetings

    O. Alter, "Cancer Diagnostics and Prognostics from Comparative Spectral Decompositions of Patient-Matched Genomic Profiles"

  1. 2018 Society for Industrial and Applied Mathematics (SIAM) Conference on Applied Linear Algebra (Hong Kong, China, May 4–8, 2018).
  2. 2017 SIAM Conference on Applied Algebraic Geometry (Atlanta, GA, July 31 – August 4, 2017).
  3. 1st Gordon Research Conference on the Physics of Cancer (Galveston, TX, February 5–10, 2017).
  4. Australian Mathematical Sciences Institute (AMSI) BioInfoSummer 2016 (Adelaide, SA, Australia, November 28 – December 2, 2016).
    Slides.
  5. National Cancer Institute (NCI) Joint Meeting of the Cancer Systems Biology Consortium and the Physical Sciences in Oncology Network (Rockville, MD, August 29–31, 2016).
  6. 20th International Linear Algebra Society (ILAS) Meeting (Leuven, Belgium, July 11–15, 2016).
  7. 2016 SIAM Annual Meeting (Boston, MA, July 11–14, 2016).
  8. International High-Performance Computing (HPC) Summer School 2016 on HPC Challenges in Computational Sciences (Ljubljana, Slovenia, June 26 – July 1, 2016).
  9. NCI Physical Sciences in Oncology Symposium (Rockville, MD, February 2–3, 2016).
  10. 2016 Tensor Decompositions and Applications (TDA) Workshop (Leuven, Belgium, January 18–22, 2016).
  11. 2015 Joint Statistical Meetings (JSM) (Seattle, WA, August 8–13, 2015).
  12. International HPC Summer School 2015 on HPC Challenges in Computational Sciences (Toronto, Canada, June 21–26, 2015).
  13. Joint Applied Mathematics, Modeling and Computational Science and Canadian Applied and Industrial Mathematics Society (AMMCS-CAIMS) Congress (Waterloo, Canada, June 7–12, 2015).
  14. 8th Multidisciplinary Conference on Three-Way Methods in Chemistry and Psychology (TRICAP) (Zoldo Alto, Italy, May 31 – June 5, 2015).

  15. O. Alter, "Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data"

  16. 48th Annual Asilomar Conference on Signals, Systems, and Computers (Pacific Grove, CA, November 2–5, 2014).
  17. 5th Association for Computing Machinery (ACM) Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB) (Newport Beach, CA, September 20–23, 2014).
  18. 2014 American Association of Physicists in Medicine (AAPM) Annual Meeting Science Council Session on the Physics of Cancer (Austin, TX, July 20–24, 2014).
  19. 2014 SIAM Annual Meeting (Chicago, IL, July 7–11, 2014).
  20. International HPC Summer School 2014 on HPC Challenges in Computational Sciences (Budapest, Hungary, June 1–6, 2014).
  21. 2013 Biomedical Engineering Society (BMES) Annual Meeting (Seattle, WA, September 25–28, 2013).
  22. NSF-Statistical and Applied Mathematical Sciences Institute (SAMSI)/Foundations of Data and Visual Analytics (FODAVA) Program Workshop on Interactive Visualization and Analysis of Massive Data (Research Triangle Park, NC, December 10–12, 2012).
  23. 16th Haifa Matrix Theory Conference (Haifa, Israel, November 12–15, 2012).
  24. 2012 BMES Annual Meeting (Atlanta, GA, October 24–27, 2012).
  25. International Conference on Stochastic Processes in Systems Biology, Genetics and Evolution (Houston, TX, August 21–25, 2012).
  26. 7th Multidisciplinary Conference on Three-Way Methods in Chemistry and Psychology (TRICAP) (Bruges, Belgium, June 2–7, 2012).
  27. 43rd Symposium on the Interface: Future of Statistical Computing (Houston, TX, May 16–18, 2012).
  28. Leibniz Center for Informatics Joint Session of the Seminars on Data Mining, Networks and Dynamics and Analysis of Dynamic Technological and Social Networks (Schloss Dagstuhl, Germany, November 6–11, 2011).
  29. Mathematical and Computational Approaches in High-Throughput Genomics Program of the NSF Institute for Pure and Applied Mathematics (IPAM): Transcriptomics and Epigenomics (Los Angeles, CA, October 25–28, 2011).
  30. NSF-Rensselaer Polytechnic Institute (RPI) Data Science Research Center Workshop on Data Driven Multiscale Modeling of Complex Systems (Troy, NY, September 12–14, 2011).
  31. Society for Industrial and Applied Mathematics (SIAM) Conference on Applications of Dynamical Systems (Snowbird, UT, May 22–26, 2011).
  32. 2nd World DNA and Genome Day (Dalian, China, April 25–30, 2011).
  33. Recent Invited Presentations at Other Institutions

    O. Alter, "Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics"

  34. Boston University Systems Biology Seminar (Boston, MA, March 16, 2017), hosted by S. Kasif and E. D. Kolaczyk.
  35. University of Pennsylvania Physical Sciences in Oncology Center Seminar (Philadelphia, PA, March 13, 2017), hosted by D. E. Discher.
  36. Jošef Stefan Institute Colloquium (Ljubljana, Slovenia, June 29, 2016), hosted by P. Ziherl and A. Studen.

  37. O. Alter, "Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data"

  38. Genentech, Inc. Research Seminar (South San Francisco, CA, November 6, 2014), hosted by M. J. Brauer.
  39. Distinguished Speaker Lectures at Bloomberg L.P. (New York, NY, May 5, 2014), hosted by S. P. Ponnapalli.
  40. Slides.
  41. University of Washington eScience Seminar (Seattle, WA, October 1, 2013), hosted by C. R. Aragon.
  42. Electrical Engineering Seminar at KU Leuven (Leuven, Belgium, June 8, 2012), hosted by S. Van Huffel.
  43. Agilent Research Center Biosciences Seminar (Tel Aviv, Israel, November 28, 2011), hosted by Z. Yakhini.
  44. Seminar of the Wellcome Trust/Cancer Research UK Gurdon Institute at the University of Cambridge (Cambridge, UK, November 17, 2011), hosted by P. A. Zegerman.
  45. Rockefeller University Center for Studies in Physics and Biology Seminar (New York, NY, September 16, 2011), hosted by J. E. Cohen.
  46. National Cancer Institute (NCI) Cell Cycle and Cancer Genomics Seminar (Bethesda, MD, March 24, 2011), hosted by M. I. Aladjem.
  47. University of California at Irvine Center for Complex Biological Systems Seminar (Irvine, CA, February 7, 2011), hosted by Q. Nie.