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Orly Alter, Ph.D. - Publications

Affiliations: 
1991-1998 Applied Physics Stanford University, Palo Alto, CA 
 1998-2004 Genetics Stanford University, Palo Alto, CA 
 2004-2010 Biomedical Engineering, & Cellular & Molecular Biology University of Texas at Austin, Austin, Texas, U.S.A. 
 2010- Bioengineering, & Scientific Computing & Imaging University of Utah, Salt Lake City, UT 
 2010-2016 Mathematics University of Texas at Austin, Austin, Texas, U.S.A. 
 2011- Human Genetics University of Utah, Salt Lake City, UT 
 2016- Huntsman Cancer University of Utah, Salt Lake City, UT 
Area:
genetics, mathematics, physics
Website:
https://alterlab.org/orly/biography.html
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Ponnapalli SP, Bradley MW, Devine K, Bowen J, Coppens SE, Leraas KM, Milash BA, Li F, Luo H, Qiu S, Wu K, Yang H, Wittwer CT, Palmer CA, Jensen RL, ... ... Alter O, et al. Retrospective clinical trial experimentally validates glioblastoma genome-wide pattern of DNA copy-number alterations predictor of survival. Apl Bioengineering. 4: 026106. PMID 32478280 DOI: 10.1063/1.5142559  0.76
2019 Bradley MW, Aiello KA, Ponnapalli SP, Hanson HA, Alter O. GSVD- and tensor GSVD-uncovered patterns of DNA copy-number alterations predict adenocarcinomas survival in general and in response to platinum. Apl Bioengineering. 3: 036104. PMID 31463421 DOI: 10.1063/1.5099268  0.776
2019 Alter O, Yamamoto Y. Protective measurement of the wave function of a single squeezed harmonic-oscillator state. Physical Review. a, Atomic, Molecular, and Optical Physics. 53: R2911-R2914. PMID 9913322 DOI: 10.1103/Physreva.53.R2911  0.467
2018 Aiello KA, Ponnapalli SP, Alter O. Mathematically universal and biologically consistent astrocytoma genotype encodes for transformation and predicts survival phenotype. Apl Bioengineering. 2. PMID 30397684 DOI: 10.1063/1.5037882  0.791
2018 Aiello KA, Maughan CA, Schomay TE, Ponnapalli SP, Hanson HA, Alter O. Abstract 4267: 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 Cancer Research. 78: 4267-4267. DOI: 10.1158/1538-7445.Am2018-4267  0.497
2016 Aiello KA, Alter O. 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. Plos One. 11: e0164546. PMID 27798635 DOI: 10.1371/Journal.Pone.0164546  0.536
2016 Alter O. Abstract A60: 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. Clinical Cancer Research. 22. DOI: 10.1158/1557-3265.Ovca15-A60  0.485
2015 Sankaranarayanan P, Schomay TE, Aiello KA, Alter O. 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. Plos One. 10: e0121396. PMID 25875127 DOI: 10.1371/Journal.Pone.0121396  0.51
2013 Bertagnolli NM, Drake JA, Tennessen JM, Alter O. SVD identifies transcript length distribution functions from DNA microarray data and reveals evolutionary forces globally affecting GBM metabolism. Plos One. 8: e78913. PMID 24282503 DOI: 10.1371/Journal.Pone.0078913  0.728
2012 Lee CH, Alpert BO, Sankaranarayanan P, Alter O. GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival. Plos One. 7: e30098. PMID 22291905 DOI: 10.1371/Journal.Pone.0030098  0.506
2011 Ponnapalli SP, Saunders MA, Van Loan CF, Alter O. A higher-order generalized singular value decomposition for comparison of global mRNA expression from multiple organisms. Plos One. 6: e28072. PMID 22216090 DOI: 10.1371/Journal.Pone.0028072  0.738
2011 Muralidhara C, Gross AM, Gutell RR, Alter O. Tensor decomposition reveals concurrent evolutionary convergences and divergences and correlations with structural motifs in ribosomal RNA. Plos One. 6: e18768. PMID 21625625 DOI: 10.1371/Journal.Pone.0018768  0.694
2009 Omberg L, Meyerson JR, Kobayashi K, Drury LS, Diffley JF, Alter O. Global effects of DNA replication and DNA replication origin activity on eukaryotic gene expression. Molecular Systems Biology. 5: 312. PMID 19888207 DOI: 10.1038/Msb.2009.70  0.718
2007 Omberg L, Golub GH, Alter O. A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies. Proceedings of the National Academy of Sciences of the United States of America. 104: 18371-6. PMID 18003902 DOI: 10.1073/Pnas.0709146104  0.788
2007 Alter O. Genomic signal processing: from matrix algebra to genetic networks. Methods in Molecular Biology (Clifton, N.J.). 377: 17-60. PMID 17634608 DOI: 10.1007/978-1-59745-390-5_2  0.526
2006 Alter O. Discovery of principles of nature from mathematical modeling of DNA microarray data. Proceedings of the National Academy of Sciences of the United States of America. 103: 16063-4. PMID 17060616 DOI: 10.1073/Pnas.0607650103  0.529
2006 Alter O, Golub GH. Singular value decomposition of genome-scale mRNA lengths distribution reveals asymmetry in RNA gel electrophoresis band broadening. Proceedings of the National Academy of Sciences of the United States of America. 103: 11828-33. PMID 16877539 DOI: 10.1073/Pnas.0604756103  0.661
2005 Alter O, Golub GH. Reconstructing the pathways of a cellular system from genome-scale signals by using matrix and tensor computations. Proceedings of the National Academy of Sciences of the United States of America. 102: 17559-64. PMID 16314560 DOI: 10.1073/Pnas.0509033102  0.61
2004 Alter O, Golub GH. 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 of the United States of America. 101: 16577-82. PMID 15545604 DOI: 10.1073/Pnas.0406767101  0.662
2004 Alter O, Golub GH, Brown PO, Botstein D. Integrative data-driven mathematical models predict novel genome-scale correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast Aiche Annual Meeting, Conference Proceedings. 1007-1008.  0.772
2004 Alter O, Golub GH, Brown PO, Botstein D. Integrative data-driven mathematical models predict novel genomescale correlation between DNA replication initiation and RNA transcription during the cell cycle in yeast Aiche Annual Meeting, Conference Proceedings. 8303-8304.  0.761
2003 Alter O, Brown PO, Botstein D. Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms. Proceedings of the National Academy of Sciences of the United States of America. 100: 3351-6. PMID 12631705 DOI: 10.1073/Pnas.0530258100  0.725
2003 Bohen SP, Troyanskaya OG, Alter O, Warnke R, Botstein D, Brown PO, Levy R. Variation in gene expression patterns in follicular lymphoma and the response to rituximab. Proceedings of the National Academy of Sciences of the United States of America. 100: 1926-30. PMID 12571354 DOI: 10.1073/Pnas.0437875100  0.764
2002 Nielsen TO, West RB, Linn SC, Alter O, Knowling MA, O'Connell JX, Zhu S, Fero M, Sherlock G, Pollack JR, Brown PO, Botstein D, van de Rijn M. Molecular characterisation of soft tissue tumours: a gene expression study. Lancet (London, England). 359: 1301-7. PMID 11965276 DOI: 10.1016/S0140-6736(02)08270-3  0.765
2001 Alter O, Brown PO, Botstein D. Processing and modeling genome-wide expression data using singular value decomposition Proceedings of Spie - the International Society For Optical Engineering. 4266: 171-186. DOI: 10.1117/12.427986  0.697
2001 Alter O, Yamamoto Y. Quantum Measurement of a Single System New York, Ny: Wiley. DOI: 10.1002/9783527617128  0.227
2000 Alter O, Brown PO, Botstein D. Singular value decomposition for genome-Wide expression data processing and modeling Proceedings of the National Academy of Sciences of the United States of America. 97: 10101-10106. PMID 10963673 DOI: 10.1073/Pnas.97.18.10101  0.746
1999 Alter O, Yamamoto Y. Fundamental quantum limit to external force detection via monitoring a single harmonic oscillator or free mass Physics Letters A. 263: 226-231. DOI: 10.1016/S0375-9601(99)00743-4  0.467
1999 Alter O, Yamamoto Y. Fundamental quantum limit to external force detection via monitoring a single harmonic oscillator or free mass Physics Letters, Section a: General, Atomic and Solid State Physics. 263: 226-231.  0.236
1998 Alter O, Yamamoto Y. Impossibility of determining the unknown quantum wavefunction of a single system: Quantum non-demolition measurements, measurements without entanglement and adiabatic measurements Fortschritte Der Physik. 46: 817-827. DOI: 10.1002/(Sici)1521-3978(199811)46:6/8<817::Aid-Prop817>3.0.Co;2-Y  0.342
1997 Alter O, Yamamoto Y. Reply to ''Comment on 'Protective measurement of the wave function of a single squeezed harmonic-oscillator state' '' Physical Review A. 56: 1057-1059. DOI: 10.1103/Physreva.56.1057  0.469
1997 Alter O, Yamamoto Y. Quantum Zeno effect and the impossibility of determining the quantum state of a single system Physical Review A. 55: R2499-R2502. DOI: 10.1103/Physreva.55.R2499  0.478
1997 Alter O, Yamamoto Y. Quantum Zeno effect and the impossibility of determining the quantum state of a single system Physical Review a - Atomic, Molecular, and Optical Physics. 55.  0.25
1997 Alter O, Yamamoto Y. Reply to "comment on 'protective measurement of the wave function of a single squeezed harmonic-oscillator state' " Physical Review a - Atomic, Molecular, and Optical Physics. 56: 1057-1059.  0.232
1996 Alter O, Yamamoto Y. Inhibition of the Measurement of the Wavefunction of a Single Quantum System and the Projection Postulate M. Namiki, I. Ohba, K. Maeda and Y. Aizawa, Editors, Quantum Physics, Chaos Theory and Cosmology. New York, Ny: American Institute of Physics. 151-172. DOI: https://ui.adsabs.harvard.edu/abs/1996qpct.conf..151A/abstract  0.228
1996 Alter O, Yamamoto Y. The Quantum Zeno Effect of a Single System is Equivalent to the Indetermination of the Quantum State of a Single System F. De Martini, G. Denardo and Y. Shih, Editors, Quantum Interferometry. New York, Ny: Wiley. 539-544. DOI: https://pi.lib.uchicago.edu/1001/cat/bib/2611343#toc  0.226
1996 Alter O, Yamamoto Y. The Unknown Wavefunction of a Single System Cannot Be Inferred Using a Series of Quantum Measurements K. Fujikawa and Y. a. Ono, Editors, Quantum Coherence and Decoherence. Amsterdam, Netherlands: Elsevier Science. 31-34. DOI: https://pi.lib.uchicago.edu/1001/cat/bib/2611342#toc  0.238
1996 Alter O, Yamamoto Y. Protective measurement of the wave function of a single squeezed harmonic-oscillator state Physical Review a - Atomic, Molecular, and Optical Physics. 53.  0.231
1995 ALTER O, YAMAMOTO Y. Can We Measure the Wave Function of a Single Wave Packet of Light? Annals of the New York Academy of Sciences. 755: 103-109. DOI: 10.1111/J.1749-6632.1995.Tb38960.X  0.437
1995 Alter O, Yamamoto Y. Inhibition of the measurement of the wave function of a single quantum system in repeated weak quantum nondemolition measurements Physical Review Letters. 74: 4106-4109. DOI: 10.1103/Physrevlett.74.4106  0.47
1991 Zachar O, Alter O. Interpretation of the curious results of the new quantum formalism of pre- and post-selected systems Foundations of Physics. 21: 803-820. DOI: 10.1007/Bf00733346  0.365
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