Orly Alter - Publications in Genetics
Orly Alter - Publications in Physics





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).
Mention: Among the most shared Applied Physics Letters (APL) Bioengineering research as of 2021, APL Bioengineering (October 30, 2021).




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.




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.
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).
Mention: Among the top 10 most downloaded Applied Physics Letters (APL) Bioengineering articles as of 2019, APL Bioengineering (May 14, 2019).




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.




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




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.
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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.
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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 the top 10% most cited Public Library of Science (PLoS) One articles as of 2017, PLoS One (June 30, 2017).
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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.
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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.
Press Release: B. Rische, "Mathematical Modeling Correctly Predicts Previously Unknown Biological Mechanism of Regulation," American Association for the Advancement of Science (AAAS) EurekAlert! (October 13, 2009).
Recommendation: M. Méchali, Faculty Opinions recommendation 1728974 (February 2010).
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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.




O. Alter, "Genomic Signal Processing: From Matrix Algebra to Genetic Networks." In: M. J. Korenberg, editor, Microarray Data Analysis: Methods and Applications. Berlin, Germany: Springer Nature, Methods in Molecular Biology (MIMB), vol. 377, pp. 17–59 (May 2007); doi: 10.1007/978-1-59745-390-5_2.




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.




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.




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 (November 2005); doi: 10.1073/pnas.0509033102.




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.




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: J. Wixon and J. Ashurst, "Genome Informatics," Comparative and Functional Genomics 4 (5), pp. 509–514 (October 2003).
Feature: M. E. Kilmer and C. D. Moravitz Martin, "Decomposing a Tensor," Society for Industrial and Applied Mathematics (SIAM) News 37 (9), (November 2004).³




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.
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).




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.




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.
Feature: National Research Council, Mathematics and 21st Century Biology. Washington, DC: National Academies Press (July 2005), 149 pp.
Mention: 7th most cited Proceedings of the National Academy of Sciences (PNAS) USA paper of the year 2000 and 45th most cited PNAS paper of all time, Google Scholar (February 11, 2024).