Ilya Shmulevich, PhD


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 (

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

Qin, Guangrong, Jin Dai, Sylvia Chien, Timothy J. Martins, Brenda Loera, Quy H. Nguyen, Melanie L. Oakes, et al. 2024. “Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia.” Clinical Cancer Research, April, OF1–13. Cite Download
Qin, Guangrong, Jin Dai, Sylvia Chien, Timothy J. Martins, Brenda Loera, Quy H. Nguyen, Melanie L. Oakes, et al. 2024. “Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia.” Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, April, OF1–13. Cite
Laubenbacher, R., B. Mehrad, I. Shmulevich, and N. Trayanova. 2024. “Digital Twins in Medicine.” Nature Computational Science 4 (3): 184–91. Cite Download
Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Forum on Immune Digital Twins: A Meeting Report.” NPJ Systems Biology and Applications 10 (1): 19. Cite Download
Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Toward Mechanistic Medical Digital Twins: Some Use Cases in Immunology.” Frontiers in Digital Health 6: 1349595. Cite Download
Zhang, Yue, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, and Ilya Shmulevich. 2024. “A Framework towards Digital Twins for Type 2 Diabetes.” Frontiers in Digital Health 6: 1336050. Cite Download
Nikolić, Vladimir, Moriah Echlin, Boris Aguilar, and Ilya Shmulevich. 2023. “Computational Capabilities of a Multicellular Reservoir Computing System.” PloS One 18 (4): e0282122. Cite Download
Echlin, Moriah, Boris Aguilar, and Ilya Shmulevich. 2023. “Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.” Entropy (Basel, Switzerland) 25 (2): 319. Cite Download
Stahlberg, Eric A., Mohamed Abdel-Rahman, Boris Aguilar, Alireza Asadpoure, Robert A. Beckman, Lynn L. Borkon, Jeffrey N. Bryan, et al. 2022. “Exploring Approaches for Predictive Cancer Patient Digital Twins: Opportunities for Collaboration and Innovation.” Frontiers in Digital Health 4: 1007784. Cite Download
Tercan, Bahar, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J. Kemp, Nyasha Chambwe, and Ilya Shmulevich. 2022. “SL-Cloud: A Cloud-Based Resource to Support Synthetic Lethal Interaction Discovery.” F1000Research 11: 493. Cite Download
Thorsson, Vésteinn, Carolina Heimann, Andrew Lamb, David Gibbs, Dante Bortone, Sarah Dexheimer, Steven Vensko, et al. 2022. “927 Streamlining Cancer Immunotherapy Research with the CRI IAtlas Data Resource and Web Portal.” Journal for ImmunoTherapy of Cancer 10 (Suppl 2). Cite Download
Nikolić, Vladimir, Moriah Echlin, Boris Aguilar, and Ilya Shmulevich. 2022. “Multicellular Reservoir Computing.” bioRxiv. Cite Download
Silverstein, Arthur, Anton Dudaev, Maria Studneva, John Aitken, Sofya Blokh, Andrew David Miller, Sofia Tanasova, et al. 2022. “Evolution of Biomarker Research in Autoimmunity Conditions for Health Professionals and Clinical Practice.” In , 219–76. Elsevier. Cite
Tercan, Bahar, Boris Aguilar, Sui Huang, Edward R. Dougherty, and Ilya Shmulevich. 2022. “Probabilistic Boolean Networks Predict Transcription Factor Targets to Induce Transdifferentiation.” IScience 25 (9). Cite Download
Moser, Russell, Kay E. Gurley, Olga Nikolova, Guangrong Qin, Rashmi Joshi, Eduardo Mendez, Ilya Shmulevich, Amanda Ashley, Carla Grandori, and Christopher J. Kemp. 2022. “Synthetic Lethal Kinases in Ras/P53 Mutant Squamous Cell Carcinoma.” Oncogene. Cite
Qin, Guangrong, Theo A. Knijnenburg, David L. Gibbs, Russell Moser, Raymond J. Monnat, Christopher J. Kemp, and Ilya Shmulevich. 2022. “A Functional Module States Framework Reveals Transcriptional States for Drug and Target Prediction.” Cell Reports 38 (3): 110269. Cite Download
Hernandez-Boussard, Tina, Paul Macklin, Emily J. Greenspan, Amy L. Gryshuk, Eric Stahlberg, Tanveer Syeda-Mahmood, and Ilya Shmulevich. 2021. “Digital Twins for Predictive Oncology Will Be a Paradigm Shift for Precision Cancer Care.” Nature Medicine. Cite
Fedorov, Andrey, William J. R. Longabaugh, David Pot, David A. Clunie, Steve Pieper, Hugo J. W. L. Aerts, André Homeyer, et al. 2021. “NCI Imaging Data Commons.” Cancer Research 81 (16): 4188–93. Cite Download
Gibbs, David L., Boris Aguilar, Vésteinn Thorsson, Alexander V. Ratushny, and Ilya Shmulevich. 2021. “Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer.” Frontiers in Genetics 12: 667382. Cite Download
Lo, Yuan-Hung, Kevin S. Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D. Sobba, et al. 2021. “A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Non-Essential Modes of Oncogenic Transformation.” Cancer Discovery. Cite Download
Eddy, James A., Vésteinn Thorsson, Andrew E. Lamb, David L. Gibbs, Carolina Heimann, Jia Xin Yu, Verena Chung, et al. 2020. “CRI IAtlas: An Interactive Portal for Immuno-Oncology Research.” F1000Research 9: 1028. Cite Download
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. 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. 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). 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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). Cite