Ilya Shmulevich, PhD

Professor

Ilya Shmulevich

Ilya Shmulevich received his Ph.D. in Electrical and Computer Engineering from Purdue University, West Lafayette, IN, in 1997. His graduate research was in the area of nonlinear signal processing, with a focus on the theory and design of nonlinear digital filters, Boolean algebra, lattice theory, and applications to music pattern recognition. From 1997-1998, he was a postdoctoral researcher at the Nijmegen Institute for Cognition and Information at the University of Nijmegen (now Radboud University) and National Research Institute for Mathematics and Computer Science at the University of Amsterdam in The Netherlands, where he studied computational models of music perception and recognition, focusing on tonality induction and rhythm complexity. In 1998-2000, he worked as a senior researcher at the Tampere International Center for Signal Processing at the Signal Processing Laboratory in Tampere University of Technology, Tampere, Finland. While in Tampere, he did research in nonlinear systems, image recognition and classification, image correspondence, computational learning theory, multiscale and spectral methods, and statistical signal processing.

This background proved to be fruitful for undertaking problems in computational biology at a time when genomic technologies were beginning to produce large amounts of data. In 2001, he joined the Department of Pathology at The University of Texas M. D. Anderson Cancer Center as an Assistant Professor and held an adjunct faculty appointment in the Department of Statistics in Rice University. He and his colleagues developed statistical approaches for cancer classification, diagnosis, and prognosis, and applied them to the study of metastasis, cancer progression, and tumor heterogeneity for multiple different cancer types. He co-developed the model class of probabilistic Boolean networks (PBNs), which has been applied to the study of gene regulatory networks in cancer.

Dr. Shmulevich joined the ISB faculty in 2005 where he is currently a Professor. Dr. Shmulevich directed a Genome Data Analysis Center within The Cancer Genome Atlas (TCGA) consortium. He also directed one of three NCI Cancer Genomics Cloud Pilots, which is now operating as an NCI Cancer Genomics Cloud Resource (isb-cgc.org).

Dr. Shmulevich’s research interests include theoretical studies of complex systems, including information theoretic approaches, as well as the application of image processing and analysis to high-throughput cellular imaging. His main research interest is multiscale modeling for cancer therapy.

Dr. Shmulevich is a co-author or co-editor of six books in the areas of computational biology. He holds Affiliate Professor appointments in the Departments of Bioengineering and Electrical Engineering at the University of Washington and has held affiliate appointments in the Department of Signal Processing in Tampere University of Technology, Finland and in the Department of Electronic and Electrical Engineering in Strathclyde University, Glasgow, UK.

  • Computational Systems Biology
  • Cancer Research, Immuno-oncology
  • Signal and Image Processing
  • Complex Systems Theory
  • Computational Learning Theory, Machine Learning
  • Multiscale Theory and Analysis
  • Complexity of Algorithms
  • Music Pattern Recognition
  • Cognition, Perception, and Mathematical Psychology

PhD, Electrical and Computer Engineering, Purdue University, 1997

Xavier, Joao B., Vincent B. Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T. Pearson, Paul Macklin, et al. 2020. “The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.” Trends in Cancer 6 (3): 192–204. https://doi.org/10.1016/j.trecan.2020.01.004. Cite Download
Peterson, Eliza J. R., Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, and Nitin S. Baliga. 2020. “Intricate Genetic Programs Controlling Dormancy in Mycobacterium Tuberculosis.” Cell Reports 31 (4): 107577. https://doi.org/10.1016/j.celrep.2020.107577. Cite Download
Aguilar, Boris, David L. Gibbs, David J. Reiss, Mark McConnell, Samuel A. Danziger, Andrew Dervan, Matthew Trotter, et al. 2020. “A Generalizable Data-Driven Multicellular Model of Pancreatic Ductal Adenocarcinoma.” GigaScience 9 (7). https://doi.org/10.1093/gigascience/giaa075. Cite Download
Cao, Song, Daniel Cui Zhou, Clara Oh, Reyka G. Jayasinghe, Yanyan Zhao, Christopher J. Yoon, Matthew A. Wyczalkowski, et al. 2020. “Discovery of Driver Non-Coding Splice-Site-Creating Mutations in Cancer.” Nature Communications 11 (1): 5573. https://doi.org/10.1038/s41467-020-19307-6. Cite Download
Danziger, Samuel A., David L. Gibbs, Ilya Shmulevich, Mark McConnell, Matthew W. B. Trotter, Frank Schmitz, David J. Reiss, and Alexander V. Ratushny. 2019. “ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells.” PloS One 14 (11): e0224693. https://doi.org/10.1371/journal.pone.0224693. Cite Download
Knijnenburg, Theo A., Joseph G. Vockley, Nyasha Chambwe, David L. Gibbs, Crystal Humphries, Kathi C. Huddleston, Elisabeth Klein, et al. 2019. “Genomic and Molecular Characterization of Preterm Birth.” Proceedings of the National Academy of Sciences of the United States of America 116 (12): 5819–27. https://doi.org/10.1073/pnas.1716314116. Cite Download
Thorsson, Vésteinn, David L. Gibbs, Scott D. Brown, Denise Wolf, Dante S. Bortone, Tai-Hsien Ou Yang, Eduard Porta-Pardo, et al. 2018. “The Immune Landscape of Cancer.” Immunity 48 (4): 812-830.e14. https://doi.org/10.1016/j.immuni.2018.03.023. Cite Download
Orozco, Javier I. J., Theo A. Knijnenburg, Ayla O. Manughian-Peter, Matthew P. Salomon, Garni Barkhoudarian, John R. Jalas, James S. Wilmott, et al. 2018. “Epigenetic Profiling for the Molecular Classification of Metastatic Brain Tumors.” Nature Communications 9 (1): 4627. https://doi.org/10.1038/s41467-018-06715-y. Cite Download
Kang, Chris, Boris Aguilar, and Ilya Shmulevich. 2018. “Emergence of Diversity in Homogeneous Coupled Boolean Networks.” Physical Review. E 97 (5–1): 052415. https://doi.org/10.1103/PhysRevE.97.052415. Cite
Saltz, Joel, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, Vu Nguyen, Dimitris Samaras, et al. 2018. “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.” Cell Reports 23 (1): 181-193.e7. https://doi.org/10.1016/j.celrep.2018.03.086. Cite Download
Sanchez-Vega, Francisco, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, Konnor C. La, Sofia Dimitriadoy, et al. 2018. “Oncogenic Signaling Pathways in The Cancer Genome Atlas.” Cell 173 (2): 321-337.e10. https://doi.org/10.1016/j.cell.2018.03.035. Cite
Gao, Qingsong, Wen-Wei Liang, Steven M. Foltz, Gnanavel Mutharasu, Reyka G. Jayasinghe, Song Cao, Wen-Wei Liao, et al. 2018. “Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.” Cell Reports 23 (1): 227-238.e3. https://doi.org/10.1016/j.celrep.2018.03.050. Cite
Knijnenburg, Theo A., Linghua Wang, Michael T. Zimmermann, Nyasha Chambwe, Galen F. Gao, Andrew D. Cherniack, Huihui Fan, et al. 2018. “Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas.” Cell Reports 23 (1): 239-254.e6. https://doi.org/10.1016/j.celrep.2018.03.076. Cite
Jayasinghe, Reyka G., Song Cao, Qingsong Gao, Michael C. Wendl, Nam Sy Vo, Sheila M. Reynolds, Yanyan Zhao, et al. 2018. “Systematic Analysis of Splice-Site-Creating Mutations in Cancer.” Cell Reports 23 (1): 270-281.e3. https://doi.org/10.1016/j.celrep.2018.03.052. Cite
Huang, Kuan-Lin, R. Jay Mashl, Yige Wu, Deborah I. Ritter, Jiayin Wang, Clara Oh, Marta Paczkowska, et al. 2018. “Pathogenic Germline Variants in 10,389 Adult Cancers.” Cell 173 (2): 355-370.e14. https://doi.org/10.1016/j.cell.2018.03.039. Cite
Ding, Li, Matthew H. Bailey, Eduard Porta-Pardo, Vesteinn Thorsson, Antonio Colaprico, Denis Bertrand, David L. Gibbs, et al. 2018. “Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics.” Cell 173 (2): 305-320.e10. https://doi.org/10.1016/j.cell.2018.03.033. Cite
Aguilar, Boris, Ahmadreza Ghaffarizadeh, Christopher D. Johnson, Gregory J. Podgorski, Ilya Shmulevich, and Nicholas S. Flann. 2018. “Cell Death as a Trigger for Morphogenesis.” PloS One 13 (3): e0191089. https://doi.org/10.1371/journal.pone.0191089. Cite
Reynolds, Sheila M., Michael Miller, Phyliss Lee, Kalle Leinonen, Suzanne M. Paquette, Zack Rodebaugh, Abigail Hahn, et al. 2017. “The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research.” Cancer Research 77 (21): e7–10. https://doi.org/10.1158/0008-5472.CAN-17-0617. Cite
Gibbs, David L., and Ilya Shmulevich. 2017. “Solving the Influence Maximization Problem Reveals Regulatory Organization of the Yeast Cell Cycle.” PLoS Computational Biology 13 (6): e1005591. https://doi.org/10.1371/journal.pcbi.1005591. Cite
Kytola, Ville, Umit Topaloglu, Lance D. Miller, Rhonda L. Bitting, Michael M. Goodman, Ralph B. D Agostino, Rodwige J. Desnoyers, et al. 2017. “Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center.” Theranostics 7 (11): 2914–23. https://doi.org/10.7150/thno.20355. Cite
Sun, Yan, Ping Ji, Tao Chen, Xinhui Zhou, Da Yang, Yuhong Guo, Yuexin Liu, et al. 2017. “MIIP Haploinsufficiency Induces Chromosomal Instability and Promotes Tumour Progression in Colorectal Cancer.” The Journal of Pathology 241 (1): 67–79. https://doi.org/10.1002/path.4823. Cite
Poole, William, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, and Brady Bernard. 2017. “Multiscale Mutation Clustering Algorithm Identifies Pan-Cancer Mutational Clusters Associated with Pathway-Level Changes in Gene Expression.” PLoS Computational Biology 13 (2): e1005347. https://doi.org/10.1371/journal.pcbi.1005347. Cite
Knijnenburg, Theo A., Gunnar W. Klau, Francesco Iorio, Mathew J. Garnett, Ultan McDermott, Ilya Shmulevich, and Lodewyk F. A. Wessels. 2016. “Logic Models to Predict Continuous Outputs Based on Binary Inputs with an Application to Personalized Cancer Therapy.” Scientific Reports 6: 36812. https://doi.org/10.1038/srep36812. Cite
Poole, William, David L. Gibbs, Ilya Shmulevich, Brady Bernard, and Theo A. Knijnenburg. 2016. “Combining Dependent P-Values with an Empirical Adaptation of Brown’s Method.” Bioinformatics (Oxford, England) 32 (17): i430–36. https://doi.org/10.1093/bioinformatics/btw438. Cite
Sun, Yan, Ping Ji, Tao Chen, Xinhui Zhou, Da Yang, Yuhong Guo, Yuexin Liu, et al. 2016. “MIIP Haploinsufficiency Induces Chromosomal Instability and Promotes Tumour Progression in Colorectal Cancer.” The Journal of Pathology. https://doi.org/10.1002/path.4823. Cite
Dhankani, Varsha, David L. Gibbs, Theo Knijnenburg, Roger Kramer, Joseph Vockley, John Niederhuber, Ilya Shmulevich, and Brady Bernard. 2016. “Using Incomplete Trios to Boost Confidence in Family Based Association Studies.” Frontiers in Genetics 7: 34. https://doi.org/10.3389/fgene.2016.00034. Cite
Yang, Hsih-Te, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, and Jung-Hsien Chiang. 2016. “Literature-Based Discovery of New Candidates for Drug Repurposing.” Briefings in Bioinformatics. https://doi.org/10.1093/bib/bbw030. Cite
Liu, Y., M. Yasukawa, K. Chen, L. Hu, R. R. Broaddus, L. Ding, E. R. Mardis, et al. 2015. “Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma.” JAMA Oncology 1 (July): 486–94. https://doi.org/10.1001/jamaoncol.2015.1432. Cite
Liu, Guoyan, Da Yang, Rajesha Rupaimoole, Chad V. Pecot, Yan Sun, Lingegowda S. Mangala, Xia Li, et al. 2015. “Augmentation of Response to Chemotherapy by MicroRNA-506 Through Regulation of RAD51 in Serous Ovarian Cancers.” J Natl Cancer Inst 107 (July). https://doi.org/10.1093/jnci/djv108. Cite
Cancer Genome Atlas Research Network, Daniel J. Brat, Roel G. W. Verhaak, Kenneth D. Aldape, W. K. Alfred Yung, Sofie R. Salama, Lee A. D. Cooper, et al. 2015. “Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.” The New England Journal of Medicine 372 (26): 2481–98. https://doi.org/10.1056/NEJMoa1402121. Cite
Li, X., Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, et al. 2015. “Two Mature Products of MIR-491 Coordinate to Suppress Key Cancer Hallmarks in Glioblastoma.” Oncogene 34 (March): 1619–28. https://doi.org/10.1038/onc.2014.98. Cite
Turner, K. M., Y. Sun, P. Ji, K. J. Granberg, B. Bernard, L. Hu, D. E. Cogdell, et al. 2015. “Genomically Amplified Akt3 Activates DNA Repair Pathway and Promotes Glioma Progression.” Proceedings of the National Academy of Sciences of the United States of America 112 (11): 3421–26. Cite
Knijnenburg, T. A., T. Bismeijer, L. F. Wessels, and I. Shmulevich. 2015. “A Multilevel Pan-Cancer Map Links Gene Mutations to Cancer Hallmarks.” Chinese Journal of Cancer 34 (March): 48. https://doi.org/10.1186/s40880-015-0050-6. Cite
Glusman, G., A. Severson, V. Dhankani, M. Robinson, T. Farrah, D. E. Mauldin, A. B. Stittrich, et al. 2015. “Identification of Copy Number Variants in Whole-Genome Data Using Reference Coverage Profiles.” Frontiers in Genetics 6: 45. Cite
Bressler, R., R. B. Kreisberg, B. Bernard, J. E. Niederhuber, J. G. Vockley, I. Shmulevich, and T. A. Knijnenburg. 2015. “CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.” PloS One 10: e0144820. https://doi.org/10.1371/journal.pone.0144820. Cite
Kang, Seunghwa, Simon Kahan, Jason McDermott, Nicholas Flann, and Ilya Shmulevich. 2014. “Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models.” Bioinformatics (Oxford, England) 30 (21): 3101–8. https://doi.org/10.1093/bioinformatics/btu498. Cite
Liu, Yuexin, Lalit Patel, Gordon B. Mills, Karen H. Lu, Anil K. Sood, Li Ding, Raju Kucherlapati, et al. 2014. “Clinical Significance of CTNNB1 Mutation and Wnt Pathway Activation in Endometrioid Endometrial Carcinoma.” Journal of the National Cancer Institute 106 (9). https://doi.org/10.1093/jnci/dju245. Cite
Liu, Guoyan, Yan Sun, Ping Ji, Xia Li, David Cogdell, Da Yang, Brittany C. Parker Kerrigan, et al. 2014. “MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer.” The Journal of Pathology 233 (3): 308–18. https://doi.org/10.1002/path.4348. Cite
Knijnenburg, Theo A., Stephen A. Ramsey, Benjamin P. Berman, Kathleen A. Kennedy, Arian F. A. Smit, Lodewyk F. A. Wessels, Peter W. Laird, Alan Aderem, and Ilya Shmulevich. 2014. “Multiscale Representation of Genomic Signals.” Nature Methods 11 (6): 689–94. https://doi.org/10.1038/nmeth.2924. Cite
Kemp, Christopher J., James M. Moore, Russell Moser, Brady Bernard, Matt Teater, Leslie E. Smith, Natalia A. Rabaia, et al. 2014. “CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer.” Cell Reports 7 (4): 1020–29. https://doi.org/10.1016/j.celrep.2014.04.004. Cite
Ruusuvuori, P., J. Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, and A. M. Dudley. 2014. “Quantitative Analysis of Colony Morphology in Yeast.” BioTechniques 56 (1): 18–27. Cite
Guo, Fei, Brittany C. Parker Kerrigan, Da Yang, Limei Hu, Ilya Shmulevich, Anil K. Sood, Fengxia Xue, and Wei Zhang. 2014. “Post-Transcriptional Regulatory Network of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions.” J Hematol Oncol 7: 19. https://doi.org/10.1186/1756-8722-7-19. Cite
Brennan, Cameron W., Roel G. W. Verhaak, Aaron McKenna, Benito Campos, Houtan Noushmehr, Sofie R. Salama, Siyuan Zheng, et al. 2013. “The Somatic Genomic Landscape of Glioblastoma.” Cell 155 (October): 462–77. https://doi.org/10.1016/j.cell.2013.09.034. Cite
Heinäniemi, Merja, Matti Nykter, Roger Kramer, Anke Wienecke-Baldacchino, Lasse Sinkkonen, Joseph Xu Zhou, Richard Kreisberg, Stuart A. Kauffman, S. Huang, and Ilya Shmulevich. 2013. “Gene-Pair Expression Signatures Reveal Lineage Control.” Nat Methods 10 (June): 577–83. https://doi.org/10.1038/nmeth.2445. Cite
Mirzaei, H., T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, et al. 2013. “Systematic Measurement of Transcription Factor-DNA Interactions by Targeted Mass Spectrometry Identifies Candidate Gene Regulatory Proteins.” Proceedings of the National Academy of Sciences of the United States of America 110 (9): 3645–50. Cite
Yang, D., Y. Sun, L. Hu, H. Zheng, P. Ji, C. V. Pecot, Y. Zhao, et al. 2013. “Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer.” Cancer Cell 23 (2): 186–99. Cite
Lin, Jake, Richard Kreisberg, Aleksi Kallio, Aimée M. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, and Reija Autio. 2013. “POMO–Plotting Omics Analysis Results for Multiple Organisms.” BMC Genomics 14: 918. https://doi.org/10.1186/1471-2164-14-918. Cite
Sadot, A., S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, and I. Shmulevich. 2013. “Information-Theoretic Analysis of the Dynamics of an Executable Biological Model.” PLoS One 8 (3): e59303. Cite
Larjo, A., I. Shmulevich, and H. Lahdesmaki. 2013. “Structure Learning for Bayesian Networks as Models of Biological Networks.” Methods in Molecular Biology 939: 35–45. Cite
Bressler, R., J. Lin, A. Eakin, T. Robinson, R. Kreisberg, H. Rovira, T. Knijnenburg, J. Boyle, and I. Shmulevich. 2012. “Fastbreak: A Tool for Analysis and Visualization of Structural Variations in Genomic Data.” EURASIP Journal on Bioinformatics & Systems Biology 2012 (1): 15. Cite