ORLY ALTER portrait
  • Adjunct Associate Professor, Human Genetics
  • Utah Science, Technology, and Research (USTAR) Associate Professor, Scientific Computing and Imaging (SCI) Institute
  • Investigator, and Member of the Cancer Control and Population Sciences Program, Huntsman Cancer Institute (HCI)
  • Co-Founder and Chief Technology Officer (CTO), Eigengene, Inc.
  • Associate Professor, Biomedical Engineering
(801) 585-7738
https://alterlab.org/

Publications

  • S. P. Ponnapalli, M. W. Bradley, K. Devine, J. Bowen, S. E. Coppens, K. M. Leraas, B. A. Milash, F. Li, H. Luo, S. Qiu, K. Wu, H. Yang, C. T. Wittwer, C. A. Palmer, R. L. Jensen, J. M. Gastier-Foster, H. A. Hanson, J. S. Barnholtz-Sloan and O. Alter, "Retrospective Clinical Trial Experimentally Validates Glioblastoma Genome-Wide Pattern of DNA Copy-Number Alterations Predictor of Survival," Applied Physics Letters (APL) Bioengineering 4 (2), article 026106 (May 2020); doi: 10.1063/1.5142559. Press Release: J. Kiefer, "Genome-Wide Pattern Found in Tumors from Brain Cancer Patients Predicts Life Expectancy," American Association for the Advancement of Science (AAAS) EurekAlert! (May 15, 2020). Published, 05/2020.
  • M. W. Bradley, K. A. Aiello, S. P. Ponnapalli,* H. A. Hanson* and O. Alter, "GSVD- and Tensor GSVD-Uncovered Patterns of DNA Copy-Number Alterations Predict Adenocarcinomas Survival in General and in Response to Platinum," Applied Physics Letters (APL) Bioengineering 3 (3), article 036104 (August 2019); doi: 10.1063/1.5099268. Published, 08/2019.
  • K. A. Aiello, S. P. Ponnapalli and O. Alter, "Mathematically Universal and Biologically Consistent Astrocytoma Genotype Encodes for Transformation and Predicts Survival Phenotype," Applied Physics Letters (APL) Bioengineering 2 (3), Special Topic: Bioengineering of Cancer invited article 031909 (September 2018); doi: 10.1063/1.5037882. Mention: Among the top 10 most downloaded Applied Physics Letters (APL) Bioengineering articles of 2018. Feature: A. J. Engler and D. E. Discher, "Rationally Engineered Advances in Cancer Research," Applied Physics Letters (APL) Bioengineering 2 (3), Special Topic: Bioengineering of Cancer preface 031601 (September 2018). Published, 09/2018.
  • K. A. Aiello, S. P. Ponnapalli and O. Alter, "Mathematically Universal and Biologically Consistent Astrocytoma Genotype Encodes for Transformation and Predicts Survival Phenotype," 2018 American Association for Cancer Research (AACR) Annual Meeting (Chicago, IL, April 14–18, 2018). Philadelphia, PA: AACR (July 2018); doi: 10.1158/1538-7445.AM2018-4262. Published, 07/2018.
  • K. A. Aiello, C. A. Maughan, T. E. Schomay, S. P. Ponnapalli, H. A. Hanson and O. Alter, "Patterns of DNA Copy-Number Alterations Revealed by the GSVD and Tensor GSVD Encode for Cell Transformation and Predict Survival and Response to Platinum in Adenocarcinomas," 2018 American Association for Cancer Research (AACR) Annual Meeting (Chicago, IL, April 14–18, 2018). Philadelphia, PA: AACR (July 2018); doi: 10.1158/1538-7445.AM2018-4267. Published, 07/2018.
  • 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. Published, 10/2016.
  • 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. Published, 01/2016.
  • 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. Published, 04/2015.
  • 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. Published, 11/2013.
  • 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. Published, 01/2012.
  • 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. Mention: Among 10% Most Cited in PLoS One. Highlight. Published, 12/2011.
  • 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. Published, 04/2011.
  • 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 recommendation 1728974 (February 2010). Highlight. Published, 10/2009.
  • 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) USA104 (47), pp. 18371–18376 (November 2007); doi: 10.1073/pnas.0709146104. Published, 11/2007.
  • 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. Published, 05/2007.
  • 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. Published, 10/2006.
  • 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. Published, 08/2006.
  • 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).3. Published, 06/2006.
  • 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. Published, 12/2005.
  • 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. Published, 11/2004.
  • 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). Published, 01/31/2004.
    http://www.med.miami.edu/mnbws/documents/Alter-.pd...
  • 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," SIAM News 37 (9), (November 2004). Feature: J. Wixon and J. Ashurst, "Genome Informatics," Computational Functional Genomics 4 (5), pp. 509–514 (October 2003). Published, 03/2003.
  • 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). Published, 04/2002.
  • O. Alter and Y. Yamamoto, Quantum Measurement of a Single System. New York, NY: Wiley-Interscience (May 2001), 136 pp.; doi: 10.1002/9783527617128. Ph.D. Dissertation Slides. Published, 05/2001.
  • 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. Published, 01/21/2001.
  • 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. Published, 08/2000.
  • O. Alter and Y. Yamamoto, "Fundamental Quantum Limit to External Force Detection via Monitoring a Single Harmonic Oscillator or Free Mass," Physics Letters A 263 (4–6), pp. 226–231 (December 1999); doi: 10.1016/S0375-9601(99)00743-4. Published, 12/1999.
  • O. Alter and Y. Yamamoto, "Impossibility of Determining the Unknown Wavefunction of a Single Quantum System: Quantum Non-Demolition Measurements, Measurements without Entanglement and Adiabatic Measurements," Fortschritte der Physik 46 (6–8), pp. 817–827 (November 1998). Published, 11/1998.
  • O. Alter and Y. Yamamoto, "Reply to the Comment on 'Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State,' " Physical Review A 56 (1), pp. 1057–1059 (July 1997); doi: 10.1103/PhysRevA.56.1057. Published, 07/1997.
  • O. Alter and Y. Yamamoto, "Quantum Zeno Effect and the Impossibility of Determining the Quantum State of a Single System," Physical Review A Rapid Communications 55 (4), pp. R2499–R2502 (April 1997); doi: 10.1103/PhysRevA.55.R2499. Published, 04/1997.
  • O. Alter and Y. Yamamoto, "Inhibition of the Measurement of the Wavefunction of a Single Quantum System and the Projection Postulate." In: M. Namiki, I. Ohba, K. Maeda and Y. Aizawa, editors, Quantum Physics, Chaos Theory and Cosmology. New York, NY: American Institute of Physics, pp. 151–172 (October 1996). Published, 10/1996.
  • O. Alter and Y. Yamamoto, "The Quantum Zeno Effect of a Single System is Equivalent to the Indetermination of the Quantum State of a Single System. In: F. De Martini, G. Denardo and Y. Shih, editors, Quantum Interferometry. Weinheim, Germany: Wiley-VCH, pp. 539–544 (October 1996). Published, 10/1996.
  • O. Alter and Y. Yamamoto, "Protective Measurement of the Wave Function of a Single Squeezed Harmonic Oscillator State," Physical Review A Rapid Communications 53 (5), R2911–R2914 (May 1996); doi: 10.1103/PhysRevA.53.R2911. Published, 05/1996.
  • O. Alter and Y. Yamamoto, "The Unknown Wavefunction of a Single System Cannot Be Inferred Using Repeated Quantum Measurements." In: K. Fujikawa and Y. A. Ono, editors, Quantum Coherence and Decoherence. Amsterdam, Netherlands: Elsevier Science, pp. 31–34 (May 1996). Published, 05/1996.
  • O. Alter and Y. Yamamoto, "Inhibition of the Measurement of the Wave Function of a Single Quantum System in Repeated Weak Quantum Nondemolition Measurements," Physical Review Letters 74 (21), pp. 4106–4109 (May 1995); doi: 10.1103/PhysRevLett.74.4106. Published, 05/1995.
  • O. Alter and Y. Yamamoto, "Can We Measure the Wave Function of a Single Wave Packet of Light?: Brownian Motion and Continuous Wave Packet Collapse in Repeated Weak Quantum Non-Demolition Measurements." In: D. M. Greenberger and A. Zeilinger, editors, Fundamental Problems in Quantum Theory. New York, NY: New York Academy of Sciences, vol. 755, pp. 103–109 (April 1995). Published, 04/1995.

Research Statement

Orly Alter's Google Scholar Citations

NCI U01 CA-202144: Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics

In the Genomic Signal Processing Lab, we invented the "eigengene,"1,2,3  and pioneered the matrix4,5,6  and tensor7,8,9  modeling of large-scale molecular biological data, which, as we demonstrated, can correctly predict previously unknown physical,10,11,12  cellular,13,14,15,16  and evolutionary17,18  mechanisms.19,20,21

Now, supported by a five-year, three million-dollar National Cancer Institute (NCI) Physical Sciences in Oncology U01 project grant,22,23  we formulate and develop novel, multi-tensor24,25,26,27 generalizations of the singular value decomposition, and use them in the comparisons of, e.g., brain,28,29,30,31,32,33  lung,34,35  ovarian,36,37,38,39,40,41,42  and uterine cancer and normal genomes. We uncover genome-scale patterns of DNA copy-number alterations that predict survival and response to treatment, statistically better than, and independent of, the best indicators in clinical use and existing laboratory tests. Our recent retrospective clinical trial experimentally validates the brain cancer pattern.43,44  Recurring alterations have been recognized as a hallmark of cancer for over a century, and observed in these cancers' genomes for decades; however, copy-number subtypes predictive of patients' outcomes were not identified before. The data had been publicly available, but the patterns remained unknown until the data were modeled by using the multi-tensor decompositions. This demonstrates that the decompositions underlie a mathematically universal description of the genotype-phenotype relationships in cancer that other machine learning methods miss.

Amazon Web Services (AWS) Education Research Webinar (January 30, 2020), hosted by M. L. Collinson.

Stanford University Institute for Computational and Mathematical Engineering Seminar (Stanford, CA, January 16, 2020), hosted by M. A. Saunders; Slides.

Presentations

  • O. Alter, “Retrospective Clinical Trial Experimentally Validates Glioblastoma Genome-Wide Pattern of DNA Copy-Number Alterations Predictor of Survival,“ National Cancer Institute (NCI) Physical Sciences in Oncology Virtual Symposium (September 21–23, 2020). Invited Talk/Keynote, Accepted, 08/2020.
  • O. Alter, “Discovering Genome-Scale Predictors of Survival and Response to Treatment with Multi-Tensor Decompositions,” 2020 American Association for Cancer Research (AACR) Virtual Annual Meeting II (June 22–24, 2020). Invited Talk/Keynote, Presented, 06/2020.
    https://www.abstractsonline.com/pp8/#!/9045/presen...
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Amazon Web Services (AWS) Research Seminar Series (January 30, 2020). Invited Talk/Keynote, Presented, 01/2020.
    https://youtu.be/s4ezu0OHKAs
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Stanford University Institute for Computational and Mathematical Engineering Seminar (Stanford, CA, January 16, 2020), hosted by M. A. Saunders; https://alterlab.org/announcements/Alter_Stanford_ICME_2020_Seminar.pdf. Invited Talk/Keynote, Presented, 01/2020.
    https://youtu.be/opiYfUKDJ2U
  • O. Alter, “Retrospective Clinical Trial Revalidates Glioblastoma DNA Copy-Number Genotype Predictor of Survival Phenotype,“ NCI Physical Sciences in Oncology Symposium (Minneapolis, MN, September 18–20, 2019). Invited Talk/Keynote, Presented, 09/2019.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Los Alamos National Laboratory, Sandia National Laboratories, NSF, and University of California San Diego Workshop on Artificial Intelligence and Tensor Factorizations for Physical, Chemical, and Biological Systems (Santa Fe, NM, September 17–20, 2019). Invited Talk/Keynote, Presented, 09/2019.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” International Congress on Industrial and Applied Mathematics (ICIAM) 2019 (Valencia, Spain, July 15–19, 2019). Invited Talk/Keynote, Presented, 07/2019.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Northwestern University Chemistry of Life Processes Institute Seminar (Evanston, IL, June 5, 2019), hosted by T. V. O'Halloran. Invited Talk/Keynote, Presented, 06/2019.
  • S. P. Ponnapalli and O. Alter, “Tensor and Higher-Order Generalizations of the GSVD with Applications to Personalized Cancer Medicine,” European Organization for Nuclear Research (CERN) Seminar of the Large Hadron Collider (LHC) Inter-Experimental Machine Learning (IML) Working Group (Geneva, Switzerland, April 15, 2019), hosted by S. Schramm. Invited Talk/Keynote, Presented, 04/2019.
  • S. P. Ponnapalli and O. Alter, “Tensor and Higher-Order Generalizations of the GSVD with Applications to Personalized Cancer Medicine,” Stanford University ICME Seminar on Linear Algebra and Optimization (Stanford, CA, December 6, 2018), hosted by M. A. Saunders. Invited Talk/Keynote, Presented, 12/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2018 Biomedical Engineering Society (BMES) Annual Meeting (Atlanta, GA, October 27–20, 2018). Invited Talk/Keynote, Presented, 10/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” NCI Joint Meeting of the Cancer Systems Biology Consortium (CSBC) and the Physical Sciences in Oncology Network (PS-ON) (Bethesda, MD, September 25–28, 2018). Invited Talk/Keynote, Presented, 09/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” European Association for Signal Processing (EURASIP) Summer School on Tensors in Medicine (Leuven, Belgium, August 27–31, 2018). Invited Talk/Keynote, Presented, 08/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2018 Society for Industrial and Applied Mathematics (SIAM) Annual Meeting (Portland, OR, July 9–13, 2018). Invited Talk/Keynote, Presented, 07/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 14th International Conference on Latent Variable Analysis and Signal Separation (LVA ICA) (Guildford, United Kingdom, July 2–6, 2018). Invited Talk/Keynote, Presented, 07/2018.
    https://cvssp.org/events/lva-ica-2018//keynotes/#o...
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 9th Multidisciplinary Conference on Three-Way Methods in Chemistry and Psychology (TRICAP) (Angel Fire, NM, June 10–15, 2018). Invited Talk/Keynote, Presented, 06/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 3rd Nordic Institute for Theoretical Physics (NORDITA) Meeting on Quantitative Perspectives on Cancer (Stockholm, Sweden, May 28 – June 1, 2018). Invited Talk/Keynote, Presented, 05/2018.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Beijing Genomics Institute (BGI) and China National GeneBank Seminar (Shenzhen, China, May 9, 2018), hosted by K. Wu. Invited Talk/Keynote, Presented, 05/2018.
  • S. P. Ponnapalli and O. Alter, “Tensor and Higher-Order Generalizations of the GSVD with Applications to Personalized Cancer Medicine,” BGI and China National GeneBank Seminar (Shenzhen, China, May 9, 2018), hosted by K. Wu. Invited Talk/Keynote, Presented, 05/2018.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2018 SIAM Conference on Applied Linear Algebra (SIAM-ALA18) (Hong Kong, China, May 4–8, 2018). Invited Talk/Keynote, Presented, 05/2018.
    http://www.math.hkbu.edu.hk/siam-ala18/Invited.htm...
  • S. P. Ponnapalli, H. A. Hanson and O. Alter, “Patterns of DNA Copy-Number Alterations Revealed by the GSVD and Tensor GSVD Encode for Cell Transformation and Predict Survival and Response to Platinum in Adenocarcinomas,” 2018 SIAM Conference on Applied Linear Algebra (Hong Kong, China, May 4–8, 2018). Invited Talk/Keynote, Presented, 05/2018.
    https://alterlab.org/announcements/SIAM-ALA_2018_D...
  • S. P. Ponnapalli and O. Alter, “Mathematically Universal and Biologically Consistent Astrocytoma Genotype Encodes for Transformation and Predicts Survival Phenotype,” 2018 Society for Industrial and Applied Mathematics (SIAM) Conference on Applied Linear Algebra (Hong Kong, China, May 4–8, 2018). Invited Talk/Keynote, Presented, 05/2018.
    https://alterlab.org/announcements/SIAM-ALA_2018_D...
  • S. P. Ponnapalli and O. Alter, “Tensor Higher-Order GSVD: A Comparative Spectral Decomposition of Multiple Column-Matched but Row-Independent Large-Scale High-Dimensional Datasets,” 2018 SIAM Conference on Applied Linear Algebra (Hong Kong, China, May 4–8, 2018). Invited Talk/Keynote, Presented, 05/2018.
    https://alterlab.org/announcements/SIAM-ALA_2018_D...
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Georgia Institute of Technology Computational Science and Engineering Seminar (Atlanta, GA, March 29, 2018), hosted by S. Aluru. Invited Talk/Keynote, Presented, 03/2018.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Michigan State University Science at the Edge Seminar (East Lansing, MI, October 13, 2017), hosted by C. Piermarocchi. Invited Talk/Keynote, Presented, 10/2017.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2017 SIAM Conference on Applied Algebraic Geometry (Atlanta, GA, July 31 – August 4, 2017). Invited Talk/Keynote, Presented, 07/2017.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” University of Oxford Mathematical Institute Seminar on the Mathematics of Data Science (Oxford, United Kingdom, July 3, 2017), hosted by U. L. Tillmann. Invited Talk/Keynote, Presented, 07/2017.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” International High-Performance Computing (HPC) Summer School 2017 on HPC Challenges in Computational Sciences (Boulder, CO, June 25 – June 30, 2017). Invited Talk/Keynote, Presented, 06/2017.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Boston University Systems Biology Seminar (Boston, MA, March 16, 2017), hosted by S. Kasif and E. D. Kolaczyk. Invited Talk/Keynote, Presented, 03/2017.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics” University of Pennsylvania Physical Sciences in Oncology Center Seminar (Philadelphia, PA, March 13, 2017), hosted by D. E. Discher. Invited Talk/Keynote, Presented, 03/2017.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 1st Gordon Research Conference on the Physics of Cancer (Galveston, TX, February 5–10, 2017). Invited Talk/Keynote, Presented, 02/2017.
  • O. Alter, "Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics," Australian Mathematical Sciences Institute (AMSI) BioInfoSummer 2016 (Adelaide, SA, Australia, November 28 – December 2, 2016). Invited Talk/Keynote, Presented, 11/2016.
  • O. Alter, "Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics," NCI Joint Meeting of the CSBC and the PS-ON (Rockville, MD, August 29–31, 2016). Invited Talk/Keynote, Presented, 08/2016.
  • K. A. Aiello and O. Alter, “Cancer Diagnostics and Prognostics from Comparative Spectral Decompositions of Patient-Matched Genomic Profiles,” 20th International Linear Algebra Society (ILAS) Meeting (Leuven, Belgium, July 11–15, 2016). Invited Talk/Keynote, Presented, 07/2016.
  • O. Alter, "Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics," 2016 SIAM Annual Meeting (Boston, MA, July 11–14, 2016). Invited Talk/Keynote, Presented, 07/2016.
  • O. Alter, "Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics," International HPC Summer School 2016 on HPC Challenges in Computational Sciences (Ljubljana, Slovenia, June 26 – July 1, 2016). Invited Talk/Keynote, Presented, 07/2016.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” NCI Physical Sciences in Oncology Symposium (Rockville, MD, February 2–3, 2016). Invited Talk/Keynote, Presented, 02/2016.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2016 Tensor Decompositions and Applications (TDA) Workshop (Leuven, Belgium, January 18–22, 2016). Invited Talk/Keynote, Presented, 01/2016.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 2015 Joint Statistical Meetings (JSM) (Seattle, WA, August 8–13, 2015). Invited Talk/Keynote, Presented, 08/2015.
  • O. Alter, “Multi-Tensor Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,“ Jošef Stefan Institute Colloquium (Ljubljana, Slovenia, June 29, 2016), hosted by P. Ziherl and A. Studen. Invited Talk/Keynote, Presented, 06/2016.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” International HPC Summer School 2015 on HPC Challenges in Computational Sciences (Toronto, Canada, June 21–26, 2015). Invited Talk/Keynote, Presented, 06/2015.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” Joint Applied Mathematics, Modeling and Computational Science and Canadian Applied and Industrial Mathematics Society (AMMCS-CAIMS) Congress (Waterloo, Canada, June 7–12, 2015). Invited Talk/Keynote, Presented, 06/2015.
  • O. Alter, “Comparative Spectral Decompositions for Personalized Cancer Diagnostics, Prognostics, and Therapeutics,” 8th Multidisciplinary Conference on Three-Way Methods in Chemistry and Psychology (TRICAP) (Zoldo Alto, Italy, May 31 – June 5, 2015). Invited Talk/Keynote, Presented, 06/2015.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” Genentech, Inc. Research Seminar (South San Francisco, CA, November 6, 2014), hosted by M. J. Brauer. Invited Talk/Keynote, Presented, 11/2014.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” 48th Annual Asilomar Conference on Signals, Systems, and Computers (Pacific Grove, CA, November 2–5, 2014). Invited Talk/Keynote, Presented, 11/2014.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” 5th Association for Computing Machinery (ACM) Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB) (Newport Beach, CA, September 20–23, 2014). Invited Talk/Keynote, Presented, 09/2014.
    https://cse.buffalo.edu/ACM-BCB2014/panel.html
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” 2014 American Association of Physicists in Medicine (AAPM) Annual Meeting Science Council Session on the Physics of Cancer (Austin, TX, July 20–24, 2014). Invited Talk/Keynote, Presented, 07/2014.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” 2014 SIAM Annual Meeting (Chicago, IL, July 7–11, 2014). Invited Talk/Keynote, Presented, 07/2014.
    http://meetings.siam.org/sess/dsp_talk.cfm?p=63691
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” International HPC Summer School 2014 on HPC Challenges in Computational Sciences (Budapest, Hungary, June 1–6, 2014). Invited Talk/Keynote, Presented, 06/2014.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” Distinguished Speaker Lectures at Bloomberg L.P. (New York, NY, May 5, 2014), hosted by S. P. Ponnapalli. Invited Talk/Keynote, Presented, 05/2014.
    https://alterlab.org/teaching/Bloomberg_L.P./
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” University of Washington eScience Seminar (Seattle, WA, October 1, 2013), hosted by C. R. Aragon. Invited Talk/Keynote, Presented, 10/2013.
  • O. Alter, “Discovery of Principles of Nature from Matrix and Tensor Modeling of Large-Scale Molecular Biological Data,” 2013 BMES Annual Meeting (Seattle, WA, September 25–28, 2013). Invited Talk/Keynote, Presented, 09/2013.
    https://alterlab.org/announcements/BMES_2013_Bioin...

Languages

  • English, fluent.
  • Hebrew, fluent.

Grants, Contracts & Research Gifts

  • National Cancer Institute (NCI) U01 CA-202144 Physical Sciences in Oncology Project: Multi-Tensor Decompositions for Personalized Cancer Diagnostics and Prognostics. PI: O. Alter. http://physics.cancer.gov/network/UniversityofUtah... National Cancer Institute (NCI), 09/23/2015 - 09/22/2021. Total project budget to date: $3,395,986.00
  • Cancer Research (CR) UK Project: Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression. PI: O. Alter. CR UK, 03/27/2007 - present. Total project budget to date: $7,500.00
  • NCI K07 CA-230150 Mentored Cancer Prevention, Control, Behavioral and Population Sciences Career Development Award: Subtyping Bladder Cancer, a Multi-Omic, Exposure-Informed, Genealogical Approach. PI: H. A. Hanson. NCI, 07/01/2018 - 06/30/2023. Total project budget to date: $747,520.00
  • National Human Genome Research Institute (NHGRI) T32 HG-008962 Training Grant: The University of Utah Health Sciences (UUHS) Training Program in Genomic Medicine. PI: L. B. Jorde. NHGRI, 06/01/2016 - 05/31/2021. Total project budget to date: $1,366,000.00
  • National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) T32 DK-110966 Training Grant: University of Utah Program in Bioinformatics and Diabetes, Obesity, and Metabolic Disease. PI: W. W. Chapman and S. J. Fisher. NIDDK, 07/01/2016 - 06/30/2021. Total project budget to date: $1,043,208.00
  • NHGRI R25 HG-009886 Genomics Summer Research for Minorities: A Pathway to Promote Diversity in Science Research. PI: H. J. Yost. NHGRI, 09/2018 - 06/2023. Total project budget to date: $1,311,390.00
  • NSF Division of Mathematical Sciences (DMS) 0847173 CAREER Award: Integrative and Comparative Tensor Algebra Models of DNA Microarray Data from Different Studies of the Cell Cycle. PI: O. Alter. http://nsf.gov/awardsearch/showAward.do?AwardNumbe... NSF DMS, 08/01/2009 - 07/31/2015. Total project budget to date: $400,053.00
  • NHGRI R01 HG-004302: Tensor Computations for Modeling Large-Scale Molecular Biological Data, from Discovery of Patterns to Discovery of Principles of Nature. PI: O. Alter. NHGRI, 08/23/2007 - 05/31/2015. Total project budget to date: $1,768,525.00
  • NHGRI K01 HG-000038 Individual Mentored Research Scientist Development Award in Genomic Research and Analysis: Mathematical Tools for Genome-Wide Expression Data Analysis. PI: O. Alter. NHGRI, 04/01/2000 - 03/31/2005. Total project budget to date: $527,367.00
  • Sloan Foundation/DOE Postdoctoral Fellowship in Computational Molecular Biology FG03-99ER62836: Analytical and Computational Tools for Genome-Wide Gene Expression Data Analysis. PI: O. Alter. Sloan Foundation/DOE, 09/01/1999 - 08/31/2003. Total project budget to date: $100,000.00
  • National Center for Advancing Translational Sciences (NCATS) UL1 TR-001067 University of Utah Center for Clinical and Translational Science. PI: W. H. Dere, C. L. Byington, D. A. McClain. NCATS, 09/2013 - 04/2018. Total project budget to date: $4,104,882.00

Patents

  • “Genetic Alterations in Glioblastoma,” European Patent EP 2773777 A4. Status: Issued. Inventors: O. Alter. File date 10/2012; Issue date 05/2020. Assignee: National Institutes of Health (NIH).
  • “Genetic Alterations in Glioma,” United States Patent US 10202643 B2. Status: Issued. Inventors: O. Alter. File date 10/2012; Issue date 02/2019. Assignee: NIH.
  • “Advanced Tensor Decompositions for Computational Assessment and Prediction from Data,“ United States Nationalized Patent Cooperation Treaty (PCT) US 20180301223 A1. Status: Published. Inventors: O. Alter. File date 04/2014. Assignee: NIH.
  • “Genetic Alterations in Ovarian Cancer,“ United States Nationalized PCT US 20180122507 A1. Status: Published. Inventors: O. Alter. File date 04/2014. Assignee: NIH.
  • “Genomic Tensor Analysis for Medical Assessment and Prediction,“ United States Nationalized PCT US 20140249762 A1. Status: Published. Inventors: O. Alter. File date 03/2014. Assignee: NIH.
  • “Genomic Tensor Analysis for Medical Assessment and Prediction,“ European Nationalized PCT EP 2754077 A4. Status: Published. Inventors: O. Alter. File date 09/2012. Assignee: NIH.

Software Titles

  • Retrospective Clinical Trial Experimentally Validates Glioblastoma Genome-Wide Pattern of DNA Copy-Number Alterations Predictor of Survival. https://alterlab.org/GBM_retrospective_clinical_trial/. Release Date: 05/2020. Inventors: © S. P. Ponnapalli and O. Alter.
  • GSVD- and Tensor GSVD-Uncovered Patterns of DNA Copy-Number Alterations Predict Adenocarcinomas Survival in General and in Response to Platinum. https://alterlab.org/adenocarcinomas_genotype-phenotype/. Release Date: 08/2019. Inventors: © M. W. Bradley, S. P. Ponnapalli, H. A. Hanson and O. Alter.
  • Mathematically Universal and Biologically Consistent Astrocytoma Genotype Encodes for Transformation and Predicts Survival Phenotype. https://alterlab.org/astrocytoma_genotype-phenotype/. Release Date: 09/2018. Inventors: © K. A. Aiello, Sri Priya Ponnapalli 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. https://alterlab.org/astrocytoma_prognosis/. Release Date: 10/2016. Inventors: © 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. https://alterlab.org/OV_prognosis/. Release Date: 04/2015. Inventors: © P. Sankaranarayanan, T. E. Schomay, K. A. Aiello and O. Alter.
  • SVD Identifies Transcript Length Distribution Functions from DNA Microarray Data and Reveals Evolutionary Forces Globally Affecting GBM Metabolism. https://alterlab.org/GBM_metabolism/. Release Date: 11/2013. Inventors: © N. M. Bertagnolli, J. A. Drake and O. Alter.
  • GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival. https://alterlab.org/GBM_prognosis/. Release Date: 01/2012. Inventors: © B. O. Alpert and O. Alter.
  • A Higher-Order Generalized Singular Value Decomposition for Comparison of Global mRNA Expression from Multiple Organisms. https://alterlab.org/HO_GSVD/. Release Date: 12/2011. Inventors: © S. P. Ponnapalli and O. Alter.
  • Tensor Decomposition Reveals Concurrent Evolutionary Convergences and Divergences and Correlations with Structural Motifs in Ribosomal RNA. https://alterlab.org/rRNA/. Release Date: 04/2011. Inventors: © A. M. Gross and O. Alter 2011.
  • Global Effects of DNA Replication and DNA Replication Origin Activity on Eukaryotic Gene Expression. https://alterlab.org/verification_of_prediction/. Release Date: 10/2009. Inventors: © O. Alter 2009.
  • A Tensor Higher-Order Singular Value Decomposition for Integrative Analysis of DNA Microarray Data from Different Studies. https://alterlab.org/HOSVD/. Release Date: 11/2007. Inventors: © O. Alter 2007.
  • Singular Value Decomposition of Genome-Scale mRNA Lengths Distribution Reveals Asymmetry in RNA Gel Electrophoresis Band Broadening. https://alterlab.org/harmonic_oscillator/. Release Date: 08/2006. Inventors: © O. Alter.
  • Reconstructing the Pathways of a Cellular System from Genome-Scale Signals by Using Matrix and Tensor Computations. https://alterlab.org/network_decomposition/. Release Date: 12/2005. Inventors: © O. Alter.
  • Integrative Analysis of Genome-Scale Data by Using Pseudoinverse Projection Predicts Novel Correlation between DNA Replication and RNA Transcription. https://alterlab.org/pseudoinverse/. Release Date: 11/2004. Inventors: © O. Alter.
  • Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms. https://alterlab.org/GSVD/. Release Date: 03/2003. Inventors: © O. Alter.
  • Processing and Modeling Genome-Wide Expression Data Using Singular Value Decomposition. https://alterlab.org/SVD/. Release Date: 01/2001. Inventors: © O. Alter.
  • Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling. https://alterlab.org/singular_value_decomposition/. Release Date: 09/2000. Inventors: © O. Alter.