**2024**

R. Laubenbacher, F. Adler, G. An, F. Castiglione, S. Eubank, L. L. Fonseca, J. Glazier, T. Helikar, M. Jett-Tilton, D. Kirschner, P. Macklin, B. Mehrad, B. Moore, V. Pasour, I. Shmulevich, A. Smith, I. Voigt, T. E. Yankeelov, T. Ziemssen, “Forum on immune digital twins: a meeting report,” *npj Systems Biology and Applications*, Vol. 10, No. 19, 2024.

Y. Zhang, G. Qin, B. Aguilar, N. Rappaport, J. Yurkovich, L. Pflieger, S. Huang, L. Hood, I. Shmulevich, “A framework towards digital twins for type 2 diabetes,” *Frontiers in Digital Health*, Vol. 6, 2024.

**2023**

V. Nikolić, M. Echlin, B. Aguilar, I. Shmulevich, “Computational capabilities of a multicellular reservoir computing system,” *PLoS ONE*, Vol. 18, No. 4, e0282122, 2023.

M. Echlin, B. Aguilar, I. Shmulevich, “Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model,” *Entropy*, Vol. 25, No. 319, 2023.

**2022**

B. Tercan, G. Qin, T-K. Kim, B. Aguilar, J. Phan, W. Longabaugh, D. Pot, C. J. Kemp, N. Chambwe, I. Shmulevich, “SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery,” *F1000Research*, Vol. 11, No. 493, 2022.

R. Moser, K. E. Gurley, O. Nikolova, G. Qin, R. Joshi, E. Mendez, I. Shmulevich, A. Ashley, C. Grandori, C. J. Kemp, “Synthetic lethal kinases in Ras/p53 mutant squamous cell carcinoma,” *Oncogene*, Vol 41, No. 24, pp. 3355-3369, 2022.

E. A. Stahlberg, M. Abdel-Rahman, B. Aguilar, A. Asadpoure, R. A. Beckman, L. L. Borkon, J. Bryan, C. Cebulla, Y. H. Chang, A. Chatterjee, J. Deng, S. Dolatshahi, O. Gevaert, E. J. Greenspan, W. Hao, T. Hernandez-Boussard, P. R. Jackson, M. Kuijjer, A. Lee, P. Macklin, S. Madhavan, M. D. McCoy, N. M. Mirzaei, T. Razzaghi, H. Rocha, L. Shahriyari, I. Shmulevich, D. G. Stover, Y. Sun, T. Syeda-Mahmood, J. Wang, Q. Wang, and I. Zervantonakis, “Exploring approaches for Predictive cancer patient digital twins: Opportunities for collaboration and Innovation,” *Frontiers in Digital Health*, vol. 4, 2022.

B. Tercan, B. Aguilar, S. Huang, E. R. Dougherty, I. Shmulevich, “Probabilistic Boolean Networks Predict Transcription Factor Targets to Induce Transdifferentiation,” *iScience*, Vol. 25, No. 9, 104951, 2022.

G. Qin, T. A. Knijnenburg, D. L. Gibbs, R. Moser, R. J. Monnat Jr., C. J. Kemp, I. Shmulevich, “A functional module states framework reveals transcriptional states for drug and target prediction,” *Cell **Reports*, Vol. 38, No. 3, 110269, 2022.

**2021**

T. Hernandez-Boussard, P. Macklin, E. J. Greenspan, A. L. Gryshuk, E. Stahlberg, T. Syeda-Mahmood, I. Shmulevich, “Digital Twins for predictive oncology will be a paradigm shift for precision cancer care,” *Nature Medicine*, (PMID: 34824458), 2021.

D. L. Gibbs, B. Aguilar, V. Thorsson, A. V. Ratushny, I. Shmulevich, “Patient-specific cell communication networks associate with disease progression in cancer,” *Frontiers in Genetics*, Vol. 12, 667382, 2021.

Y. H. Lo, K. Kolahi, Y. Du, C. Y. Chang, A. Krokhotin, A. Nair, W. Sobba, K. Karlsson, S. Jones, T. Longacre, A. Mah, B. Tercan, A. Sockell, H. Xu, J. Seoane, J. Chen, I. Shmulevich, J. Weissman, C. Curtis, A. Califano, H. Fu, G. Crabtree, C. J. Kuo, “A CRISPR/Cas9-engineered ARID1A-deficient human gastric cancer organoid model reveals essential and non-essential modes of oncogenic transformation,” *Cancer Discovery*, Vol. 11, No. 6, pp. 1562-1581, 2021.

A. Fedorov, W. J. R. Longabaugh, D. Pot, D. A. Clunie, S. Pieper, H. J. W. L. Aerts, A. Homeyer, R. Lewis, A. Akbarzadeh, D. Bontempi, W. Clifford, M. D. Herrmann, H. Höfener, I. Octaviano, C. Osborne, S. Paquette, J. Petts, D. Punzo, M. Reyes, D. P. Schacherer, M. Tian, G. White, E. Ziegler, I. Shmulevich, T. Pihl, U. Wagner, K. Farahani, and R. Kikinis, “NCI imaging Data Commons,” *Cancer Research*, Vol. 81, No. 16, pp. 4188–4193, 2021.

**2020**

S. Cao, D. C. Zhou, C. Oh, R. G. Jayasinghe, Y. Zhao, C. J. Yoon, M. A. Wyczalkowski, M. H. Bailey, T. Tsou, Q. Gao, A. Malone, S. Reynolds, I. Shmulevich, M. C. Wendl, F. Chen, L. Ding, “Discovery of driver non-coding splice-site-creating mutations in cancer,” *Nature **Communications*, Vol. 11, No. 1, 5573, 2020.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, “Pan-cancer analysis of whole genomes,” *Nature*, Vol. 578, No. 7793, pp. 82-93, 2020.

S. Cao, D. C. Zhou, C. Oh, R. G. Jayasinghe, Y. Zhao, C. J. Yoon, M. A. Wyczalkowski, M. H. Bailey, T. Tsou, Q. Gao, A. Malone, S. Reynolds, I. Shmulevich, M. C. Wendl, F. Chen, L. Ding, “Discovery of driver non-coding splice-site-creating mutations in cancer,” *Nature Communications*, Vol. 11, No. 1, 5573, 2020.

J. A. Eddy, V. Thorsson, A. E. Lamb, D. L. Gibbs, C. Heimann, J. X. Yu, V. Chung, Y. Chae, K. Dang, B. G. Vincent, I. Shmulevich, J. Guinney, “CRI iAtlas: an interactive portal for immuno-oncology research,” *F1000Research*, Vol. 9, 1028, 2020.

B. Aguilar, D. L. Gibbs, D. L. Reiss, M. McConnell, S. A. Danziger, A. Dervan, M. Trotter, D. Bassett, R. Hershberg, A. V. Ratushny, I. Shmulevich, “A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma,” *GigaScience*, Vol. 9, No. 7, giaa075, 2020.

I. Shmulevich, “On the Lyapunov Exponent of Monotone Boolean Networks,” *Mathematics*, Vol. 8, 1035, 2020.

J. B. Xavier, V. B. Young, J. Skufca, F. Ginty, T. Testerman, A. T. Pearson, P. Macklin, A. Mitchell, I. Shmulevich, L. Xie, J. G. Caporaso, K. A. Crandall, N. L. Simone, F. Godoy-Vitorino, T. J. Griffin, K. L. Whiteson, H. H. Gustafson, D. J. Slade, T. M. Schmidt, M. R. S. Walther-Antonio, T. Korem, B. M. Webb-Robertson, M. P. Styczynski, W. E. Johnson, C. Jobin, J. M. Ridlon, A. Y. Koh, M. Yu, L. Kelly, J. A. Wargo, “The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View,” *Trends in Cancer*, Vol. 6, No. 3, pp. 192-204, 2020.

E.J.R. Peterson, A. A. Abidi, M. L. Arrieta-Ortiz, B. Aguilar, J. T. Yurkovich, A. Kaur, M. Pan, V. Srinivas, I. Shmulevich, N. S. Baliga, “Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis,” *Cell Reports*, Vol. 31, No. 4, 107577, 2020.

**2019**

T. A. Knijnenburg, J. G. Vockley, N. Chambwe, D. L. Gibbs, C. Humphries, K. C. Huddleston, E. Klein, P. Kothiyal, R. Tasseff, V. Dhankani, D. L. Bodian, W. S. W. Wong, G. Glusman, D. E. Mauldin, M. Miller, J. Slagel, S. Elasady, J. C. Roach, R. Kramer, K. Leinonen, J. Linthorst, R. Baveja, R. Baker, B. D. Solomon, G. Eley, R. K. Iyer, G. L. Maxwell, B. Bernard, I. Shmulevich, L. Hood, J. E. Niederhuber, “Genomic and molecular characterization of preterm birth,” *Proceedings of the National Academy of Sciences of the USA*, 201716314, 2019.

S. A. Danziger, D. L. Gibbs, I. Shmulevich, M. McConnell, M. W. B. Trotter, F. Schmitz, D. J. Reiss, A. V. Ratushny, “ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells,” *PLoS ONE*, Vol. 14, No. 11, e0224693, 2019.

**2018**

M. Echlin, B. Aguilar, M. Notarangelo, D. L. Gibbs, I. Shmulevich, “Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters,” *Entropy*, Vol. 20, No. 12, 954, 2018.

C. Kang, B. Aguilar and I. Shmulevich, “Emergence of diversity in homogeneous coupled Boolean networks“, *Physical Review E*, Vol. 97, No. 5, 2018.

J. Orozco, T. Knijnenburg, A. Manughian-Peter, M. Salomon, G. Barkhoudarian, J. Jalas, J. Wilmott, P. Hothi, X. Wang, Y. Takasumi, M. Buckland, J. Thompson, G. Long, C. Cobbs, I. Shmulevich, D. Kelly, R. Scolyer, D. Hoon, D. Marzese, “Epigenetic profiling for the molecular classification of metastatic brain tumors,” *Nature Communications*, Vol. 9, No. 4627, 2018.

V. Thorsson, D. Gibbs, S. Brown, D. Wolf, D. Bortone, T. Ou Yang, E. Porta-Pardo, G. Gao, C. Plaisier, J. Eddy, E. Ziv, A. Culhane, E. Paull, I. Sivakumar, A. Gentles, R. Malhotra, F. Farshidfar, A. Colaprico, J. Parker, L. Mose, N. Vo, J. Liu, Y. Liu, J. Rader, V. Dhankani, S. Reynolds, R. Bowlby, A. Califano, A. Cherniack, D. Anastassiou, D. Bedognetti, A. Rao, K. Chen, A. Krasnitz, H. Hu, T. Malta, H. Noushmehr, C. Pedamallu, S. Bullman, A. Ojesina, A. Lamb, W. Zhou, H. Shen, T. Choueiri, J. Weinstein, J. Guinney, J. Saltz, R. Holt, C. Rabkin, Cancer Genome Atlas Research Network, A. Lazar, J. Serody, E. Demicco, M. Disis, B. Vincent, l. Shmulevich, “The Immune Landscape of Cancer“, *Immunity*, Vol. 48, No. 4, pp. 812-830.e14, 2018.

K. Huang, R. Mashl, Y. Wu, D. Ritter, J. Wang, C. Oh, M. Paczkowska, S. Reynolds, M. Wyczalkowski, N. Oak, A. Scott, M. Krassowski, A. Cherniack, K. Houlahan, R. Jayasinghe, L. Wang, D. Zhou, D. Liu, S. Cao, Y. Kim, A. Koire, J. McMichael, V. Hucthagowder, T. Kim, A. Hahn, C. Wang, M. McLellan, F. Al-Mulla, K. Johnson, O. Cancer Genome Atlas Research Network, Lichtarge, P. Boutros, B. Raphael, A. Lazar, W. Zhang, M. Wendl, R. Govindan, S. Jain, D. Wheeler, S. Kulkarni, J. Dipersio, J. Reimand, F. Meric-Bernstam, K. Chen, I. Shmulevich, S. Plon, F. Chen, L. Ding, “Pathogenic Germline Variants in 10,389 Adult Cancers“, *Cell*, vol. 173, no. 2, pp. 355-370.e14, 2018.

F. Sanchez-Vega, M. Mina, J. Armenia, W. Chatila, A. Luna, K. La, S. Dimitriadoy, D. Liu, H. Kantheti, S. Saghafinia, D. Chakravarty, F. Daian, Q. Gao, M. Bailey, W. Liang, S. Foltz, I. Shmulevich, L. Ding, Z. Heins, A. Ochoa, B. Gross, J. Gao, H. Zhang, R. Kundra, C. Kandoth, I. Bahceci, L. Dervishi, U. Dogrusoz, W. Zhou, H. Shen, P. Laird, G. Way, C. Greene, H. Liang, Y. Xiao, C. Wang, A. Iavarone, A. Berger, T. Bivona, A. Lazar, G. Hammer, T. Giordano, L. Kwong, G. McArthur, C. Huang, A. Tward, M. Frederick, F. McCormick, M. Meyerson, Cancer Genome Atlas Research Network, E. Van Allen, A. Cherniack, G. Ciriello, C. Sander, N. Schultz, S. “Oncogenic Signaling Pathways in The Cancer Genome Atlas“, *Cell*, Vol. 173, No. 2, pp. 321-337.e10, 2018.

L. Ding, M. Bailey, E. Porta-Pardo, V. Thorsson, A. Colaprico, D. Bertrand, D. Gibbs, A. Weerasinghe, K. Huang, C. Tokheim, I. Cortés-Ciriano, R. Jayasinghe, F. Chen, L. Yu, S. Sun, C. Olsen, J. Kim, A. Taylor, A. Cherniack, R. Akbani, C. Suphavilai, N. Nagarajan, J. Stuart, G. Mills, M. Wyczalkowski, B. Vincent, C. Hutter, J. Zenklusen, K. Hoadley, M. Wendl, l. Shmulevich, A. Lazar, D. Wheeler, G. Getz, Cancer Genome Atlas Research Network, “Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics“, *Cell*, Vol. 173, No. 2, pp. 305-320.e10, 2018.

R. Jayasinghe, S. Cao, Q. Gao, M. Wendl, N. Vo, S. Reynolds, Y. Zhao, H. Climente-González, S. Chai, F. Wang, R. Varghese, M. Huang, W. Liang, M. Wyczalkowski, S. Sengupta, Z. Li, S. Payne, D. Fenyö, J. Miner, M. Walter, Cancer Genome Atlas Research Network, B. Vincent, E. Eyras, K. Chen, I. Shmulevich, F. Chen, L. Ding, “Systematic Analysis of Splice-Site-Creating Mutations in Cancer“, *Cell Reports*, Vol. 23, No. 1, pp. 270-281.e3, 2018.

T. Knijnenburg, L. Wang, M. Zimmermann, N. Chambwe, G. Gao, A. Cherniack, H. Fan, H. Shen, G. Way, C. Greene, Y. Liu, R. Akbani, B. Feng, L. Donehower, C. Miller, Y. Shen, M. Karimi, H. Chen, P. Kim, P. Jia, E. Shinbrot, S. Zhang, J. Liu, H. Hu, M. Bailey, C. Yau, D. Wolf, Z. Zhao, J. Weinstein, L. Li, L. Ding, G. Mills, P. Laird, D. Wheeler, I. Shmulevich, Cancer Genome Atlas Research Network, R. Monnat, Y. Xiao, C. Wang, “Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas“, *Cell Reports*, Vol. 23, No. 1, pp. 239-254.e6, 2018.

Q. Gao, W. Liang, S. Foltz, G. Mutharasu, R. Jayasinghe, S. Cao, W. Liao, S. Reynolds, M. Wyczalkowski, L. Yao, L. Yu, S. Sun, K. Chen, A. Lazar, R. Fields, M. Wendl, B. Van Tine, R. Vij, F. Chen, M. Nykter, I. Shmulevich, L. Ding, Cancer Genome Atlas Research Network, “Driver Fusions and Their Implications in the Development and Treatment of Human Cancers“, *Cell Reports*, Vol. 23, No. 1, pp. 227-238.e3, 2018.

J. Saltz, R. Gupta, L. Hou, T. Kurc, P. Singh, V. Nguyen, D. Samaras, K. Shroyer, T. Zhao, R. Batiste, J. Van Arnam, Cancer Genome Atlas Research Network, I. Shmulevich, A. Rao, A. Lazar, A. Sharma, V. Thorsson, “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images“, *Cell Reports*, Vol. 23, No. 1, pp. 181-193.e7, 2018.

B. Aguilar, A. Ghaffarizadeh, C. D. Johnson, G. J. Podgorski, I. Shmulevich, N. S. Flann, “Cell death as a trigger for morphogenesis,” *PLoS ONE* Vol. 13, No. 3, e0191089, 2018.

**2017**

The Cancer Genome Atlas Research Network, “Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas,” *Cell*, Vol. 171, No. 4, pp. 950–965.e28, 2017.

The Cancer Genome Atlas Research Network, “Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma,” *Cell*, Vol. 169, No. 7, pp. 1327–1341.e23, 2017.

V. Kytola, U. Topaloglu, L. D. Miller, R. L. Bitting, M. M. Goodman, J. D. Agostino RB, R. J. Desnoyers, C. Albright, G. Yacoub, S. A. Qasem, B. DeYoung, V. Thorsson, I. Shmulevich, M. Yang, A. Shcherban, M. Pagni, L. Liu, M. Nykter, K. Chen, G. A. Hawkins, S. C. Grant, W. J. Petty, A. T. Alistar, E. A. Levine, E. D. Staren, C. D. Langefeld, V. Miller, G. Singal, R. M. Petro, M. Robinson, W. Blackstock, B. L. Powell, L. I. Wagner, K. L. Foley, E. Abraham, B. Pasche, and W. Zhang, “Mutational Landscapes of Smoking-Related Cancers in Caucasians and African Americans: Precision Oncology Perspectives at Wake Forest Baptist Comprehensive Cancer Center,” *Theranostics*, Vol. 7, pp. 2914-2923, 2017.

W. Poole, K. Leinonen, I. Shmulevich, T. Knijnenburg, B. Bernard, “Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression,” *PLoS Computational Biology*, Vol. 13, No. 2, e1005347, 2017.

The Cancer Genome Atlas Research Network, “Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma,” *Cancer Cell*, Vol. 31, No. 2, pp.181-193, 2017.

The Cancer Genome Atlas Research Network, “Integrated genomic characterization of oesophageal carcinoma,” *Nature*, Vol. 541, pp. 169–175, 2017.

The Cancer Genome Atlas Research Network, “Integrated genomic and molecular characterization of cervical cancer,” *Nature*, Vol. 543, pp. 387-384, 2017.

Y. Sun, P. Ji, T. Chen, X. Zhou, D. Yang, Y. Guo, Y. Liu, L. Hu, D. Xia, Y. Liu, A. S. Multani, I. Shmulevich, R. Kucherlapati, S. Kopetz, A. K. Sood, S. R. Hamilton, B. Sun, and W. Zhang, “MIIP haploinsufficiency induces chromosomal instability and promotes tumour progression in colorectal cancer,” *The Journal of Pathology*, Vol. 241, No. 1, pp. 67–79, 2017.

D. Gibbs, I. Shmulevich, “Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle,” *PLoS Computational Biology*, Vol. 13, No. 6, e1005591, 2017.

S. M. Reynolds, M. Miller, P. Lee, K. Leinonen, S. M. Paquette, Z. Rodebaugh, A. Hahn, D. L. Gibbs, J. Slagel, W. J. Longabaugh, V. Dhankani, M. Reyes, T. Pihl, M. Backus, M. Bookman, N. Deflaux, J. Bingham, D. Pot, I. Shmulevich, “The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research,” *Cancer Research*, Vol. 77, No. 21, e7-e10, 2017.

H. T. Yang, J. H. Ju, Y. T. Wong, I. Shmulevich, J.H. Chiang, “Literature-based discovery of new candidates for drug repurposing,” *Briefings in Bioinformatics*, Vol. 18, No. 3, pp. 488-497, 2017.

**2016**

T. A. Knijnenburg, G. W. Klau, F. Iorio, M. J. Garnett, U. McDermott, I. Shmulevich, L. F. A. Wessels, “Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy,” *Scientific Reports*, Vol. 6, 36812, 2016.

W. Poole, D. L. Gibbs, I. Shmulevich, B. Bernard, T. A. Knijnenburg, “Combining dependent P-values with an empirical adaptation of Brown’s method,” *Bioinformatics*, Vol. 32, No. 17, pp. i430-i436, 2016.

V. Dhankani, D. L. Gibbs, T. Knijnenburg, R. Kramer, J. Vockley, J. Niederhuber, I. Shmulevich, B. Bernard, “Using incomplete trios to boost confidence in family based association studies,” *Frontiers in Genetics*, Vol. 7, No. 34, 2016.

The Cancer Genome Atlas Research Network, “Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma,” *Cancer Cell*, Vol. 29, No. 5, pp. 723-736, 2016.

**2015**

T. Knijnenburg, T. Bismeijer, L. Wessels, I. Shmulevich, “A multilevel pan-cancer map links gene mutations to cancer hallmarks,” *Chinese Journal of Cancer*, Vol. 34, 48, 2015.

The Cancer Genome Atlas Research Network, “Genomic Classification of Cutaneous Melanoma,” *Cell*, Vol. 161, No. 7, pp. 1681–1696, 2015.

The Cancer Genome Atlas Research Network, “The Molecular Taxonomy of Primary Prostate Cancer,” *Cell*, Vol. 163 , No. 4 , pp. 1011-1025, 2015.

The Cancer Genome Atlas Research Network, “Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas,” *The New England Journal of Medicine*, Vol. 372, pp. 2481-2498, 2015.

Y. Liu, M. Yasukawa, K. Chen, L. Hu, R. R. Broaddus, L. Ding, E. R. Mardis, P. Spellman, D. A. Levine, G. B. Mills, I. Shmulevich, A. K. Sood, W. Zhang, “Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma,” *JAMA Oncology*, Vol. 1, No. 4, pp. 486-494, 2015.

Y. Sun, F. Guo, M. Bagnoli, F.-X. Xue, B.-C. Sun, I. Shmulevich, D. Mezzanzanica, K.-X. Chen, A. Sood, D. Yang, W. Zhang, “Key nodes of a microRNA network associated with the integrated mesenchymal subtype of high-grade serous ovarian cancer,” *Chinese Journal of Cancer*, Vol. 34, No. 1, pp. 28-40, 2015.

G. Liu, D. Yang, R. Rupaimoole, C. V. Pecot, Y. Sun, L. S. Mangala, X. Li, P. Ji, D. Cogdell, L. Hu, Y. Wang, C. Rodriguez-Aguayo, G. Lopez-Berestein, I. Shmulevich, L. De Cecco, K. Chen, D. Mezzanzanica, F. Xue, A. K. Sood, W. Zhang, “Augmentation of Response to Chemotherapy by microRNA-506 Through Regulation of RAD51 in Serous Ovarian Cancers,” *Journal of the National Cancer Institute*, Vol. 107, No. 7, djv108, 2015.

R. Bressler, R. B. Kreisberg, B. Bernard, J. E. Niederhuber, J. G. Vockley, I. Shmulevich, T. A. Knijnenburg, “CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data,” *PLoS ONE*, Vol. 10, No. 12, e0144820, 2015.

G. Glusman, A. Severson, V. Dhankani, M. Robinson, T. Farrah, D. Mauldin, A. B. Stittrich, S. A. Ament, J. Roach, M. Brunkow, D. Bodian, J. Vockley, I. Shmulevich, J. Niederhuber, L. Hood, “Identification of copy number variants in whole-genome data using Reference Coverage Profiles,” *Frontiers in Genetics*, Vol 6, No. 45, 2015.

K. M. Turner, Y. Sun, P. Ji, K. J. Granberg, B. Bernard, L. Hu, D. E. Cogdell, X. Zhou, O. Yli-Harja, M. Nykter, I. Shmulevich, W. K. Yung, G. N. Fuller, W. Zhang, “Genomically amplified Akt3 activates DNA repair pathway and promotes glioma progression,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 112, No. 11, pp. 3421-3426, 2015.

**2014**

The Cancer Genome Atlas Research Network, “Integrated Genomic Characterization of Papillary Thyroid Carcinoma,” *Cell*, Vol. 159, No. 3, pp. 676–690, 2014.

The Cancer Genome Atlas Research Network, “Comprehensive Molecular Characterization of Gastric Adenocarcinoma,” *Nature*, Vol. 513, pp. 202–209, 2014.

J. Ashworth, B. Bernard, S. Reynolds, C. L. Plaisier, I. Shmulevich, N. S. Baliga, “Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers,” *Nucleic Acids Research*, Vol. 42, No. 21, pp. 12973-12983, 2014.

C. J. Kemp, J. M. Moore, R. Moser, B. Bernard, M. Teater, L. E. Smith, N. Rabaia, K. E. Gurley, J. Guinney, S. E. Busch, R. Shaknovich, V. V. Lobanenkov, D. Liggitt, I. Shmulevich, A. Melnick, G. N. Filippova, “CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer,” *Cell Reports*, Vol. 7, No. 4, pp. 1020-1029, 2014.

X. Li, Y. Liu, K. J. Granberg, Q. Wang, L. M. Moore, P. Ji, J. Gumin, E. P. Sulman, G. A. Calin, H. Haapasalo, M. Nykter, I. Shmulevich, G. N. Fuller, F. F. Lang, W. Zhang, “Two mature products of MIR-491 coordinate to suppress key cancer hallmarks in glioblastoma,” *Oncogene*, Vol. 34, pp. 1619-1628, 2014.

The Cancer Genome Atlas Research Network, “Comprehensive molecular characterization of urothelial bladder carcinoma,” *Nature*, Vol. 507, pp. 315–322, 2014.

G. Liu, Y. Sun, P. Ji, X. Li, D. Cogdell, D. Yang, B. C. Parker-Kerrigan, I. Shmulevich, K. Chen, A. K. Sood, F. Xue, W. Zhang, “MiR-506 Suppresses Proliferation and Induces Senescence by Directly Targeting the CDK4/6-FOXM1 Axis in Ovarian Cancer,” *The Journal of Pathology*, Vol. 233, No. 3, pp. 308-318, 2014.

Y. Liu , L. Patel , G. B. Mills, K. H. Lu , A. K. Sood , L. Ding, R. Kucherlapati , E. Mardis, D. A. Levine, I. Shmulevich, R. R. Broaddus, W. Zhang, “Clinical Significance of CTNNB1 Mutation and Wnt Pathway Activation in Endometrioid Endometrial Carcinoma,” *Journal of the National Cancer Institute*, Vol. 106, No. 9, 2014.

F. Guo, B. C. Parker, D. Yang, L. Hu, I. Shmulevich, A. K. Sood, F. Xue, W. Zhang, “Post-Transcriptional Regulatory Network of Epithelial-to-Mesenchymal and Mesenchymal-to-Epithelial Transitions,” *Journal of Hematology & Oncology*, Vol. 7, No. 19, 2014.

S. Kang, S. Kahan, J. McDermott, N. Flann, I. Shmulevich, “Biocellion: Accelerating Computer Simulation of Multicellular Biological System Models,” *Bioinformatics*, Vol. 30, No. 21, pp. 3101-3108, 2014.

T. A. Knijnenburg, S. A. Ramsey, B. P. Berman, K. A. Kennedy, A.F.A. Smit, L. F.A. Wessels, P. W. Laird, A. Aderem, I. Shmulevich, “Multiscale representation of genomic signals,” *Nature Methods, *Vol. 11, pp. 689–694, 2014.

P. Ruusuvuori, Jake Lin, A. C. Scott, Z. Tan, S. Sorsa, A. Kallio, M. Nykter, O. Yli-Harja, I. Shmulevich, A. M. Dudley, “Quantitative analysis of colony morphology in yeast,” *BioTechniques*, Vol. 56, No. 1, pp. 18–27, 2014.

**2013**

J. Lin, R. Kreisberg, A. Kallio, A. M. Dudley, M. Nykter, I. Shmulevich, P. May, R. Autio, “POMO – Plotting Omics analysis results for Multiple Organisms,” *BMC Genomics*, Vol. 14, No. 1, 918, 2013.

C. W. Brennan, R.G.W. Verhaak, A. McKenna, B. Campos, H. Noushmehr, S. R. Salama, S. Zheng, D. Chakravarty, J. Z. Sanborn, S. H. Berman, R. Beroukhim, B. Bernard, C.J. Wu, G. Genovese, I. Shmulevich, J. Barnholtz-Sloan, L. Zou, R. Vegesna, S. A. Shukla, G. Ciriello, W.K. Yung, W. Zhang, C. Sougnez, T. Mikkelsen, K. Aldape, D. D. Bigner, E. G. Van Meir, M. Prados, A. Sloan, K. L. Black, J. Eschbacher, G. Finocchiaro, W. Friedman, D. W. Andrews, A. Guha, M. Iacocca, B. P. O’Neill, G. Foltz, J. Myers, D. J. Weisenberger, R. Penny, R. Kucherlapati, C. M. Perou, D. N. Hayes, R. Gibbs, M. Marra, G. B. Mills, E. Lander, P. Spellman, R. Wilson, C. Sander, J. Weinstein, M. Meyerson, S. Gabriel, P. W. Laird, D. Haussler, G. Getz, L. Chin, TCGA Research Network, “The Somatic Genomic Landscape of Glioblastoma,” *Cell*, Vol. 155, No. 2, pp. 462-477, 2013.

The Cancer Genome Atlas Research Network, John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart, “The Cancer Genome Atlas Pan-Cancer analysis project,” *Nature Genetics*, Vol. 45, No. 10, pp. 1113-1120, 2013.

The Cancer Genome Atlas Research Network, “Integrated genomic characterization of endometrial carcinoma,” *Nature*, Vol. 497, pp. 67–73, 2013.

D. Yang, Y. Sun, L. Hu, H. Zheng, P. Ji, C. V. Pecot, Y. Zhao, S. Reynolds, H. Cheng, R. Rupaimoole, D. Cogdell, M. Nykter, R. Broaddus, C. Rodriguez-Aguayo, G. Lopez-Berestein, J. Liu, I. Shmulevich, A. K. Sood, K. Chen, W. Zhang, “Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer,” *Cancer Cell*, Vol. 23, No. 2, pp. 186-199, 2013.

L. M. Moore, V. Kivinen, Y. Liu, M. Annala, D. Cogdell, X. Liu, C.G. Liu, R. Sawaya, O. Yli-Harja, I. Shmulevich, G.N. Fuller, W. Zhang, M. Nykter, “Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma,” *The Journal of Pathology*, Vol. 229, No. 3, pp. 449-459, 2013.

M. Heinäniemi, M. Nykter, R. Kramer, A. Wienecke-Baldacchino, L. Sinkkonen, J. X. Zhou, R. Kreisberg, S. A. Kauffman, S. Huang, I. Shmulevich, “Gene-pair expression signatures reveal lineage control,” *Nature Methods*, Vol. 10, No. 6, pp. 577-583, 2013.

A. Larjo, I. Shmulevich, H. Lähdesmäki, “Structure learning for Bayesian networks as models of biological networks,” *Methods in Molecular Biology*, Vol. 939, pp. 35-45, 2013.

A. Sadot, S. Sarbu, J. Kesseli, H. Amir-Kroll, W. Zhang, M. Nykter, I. Shmulevich, “Information-Theoretic Analysis of the Dynamics of an Executable Biological Model,” *PLoS ONE*, Vol. 8, No. 3, e59303, 2013.

H. Mirzaei, T. A. Knijnenburg, B. Kim, M. Robinson, P. Picotti, G. W. Carter, S. Li, D. J. Dilworth, J. K. Eng, J. D. Aitchison, I. Shmulevich, T. Galitski, R. Aebersold, J. Ranish, “Systematic measurement of transcription factor-DNA interactions by SRM mass spectrometry identifies candidate gene regulatory proteins,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 110, No. 9, pp. 3645-3650, 2013.

**2012**

R. Bressler, J. Lin, A. Eakin, T. Robinson, R. Kreisberg, H. Rovira, T. Knijnenburg, J. Boyle, I. Shmulevich, “Fastbreak: a tool for analysis and visualization of structural variations in genomic data,” *EURASIP Journal on Bioinformatics and Systems Biology*, Vol. 2012(1), No. 15, 2012.

B. Bernard, V. Thorsson, H. Rovira, I. Shmulevich, “Increasing coverage of transcription factor position weight matrices through domain-level homology,” *PLoS ONE*, Vol. 7, No. 8, e42779, 2012.

The Cancer Genome Atlas Network, “Comprehensive Molecular Characterization of Human Colon and Rectal Cancer,” *Nature*, Vol. 487, No. 7407, pp. 330-337, 2012.

Y. Liu, Y. Sun, R. Broaddus, J. Liu, A. K. Sood, I. Shmulevich, Wei Zhang, “Integrated Analysis of Gene Expression and Tumor Nuclear Image Profiles Associated with Chemotherapy Response in Serous Ovarian Carcinoma,” *PLoS ONE*, Vol. 7, No. 5, e36383, 2012.

The Cancer Genome Atlas Network, “Comprehensive Molecular Portraits of Human Breast Tumors,” *Nature*, Vol. 490, No. 7418, pp. 61–70, 2012.

E. R. Dougherty, I. Shmulevich, “On the Limitations of Biological Knowledge,” *Current Genomics*, Vol. 13, No. 7, pp. 574-587, 2012.

G. Liu, D. Yang, Y. Sun, I. Shmulevich, F. Xue, A.K. Sood, W. Zhang, “Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer,” *Pharmacogenomics*, Vol. 13, No. 13, pp. 1523-1535, 2012.

**2011**

D. Yang, S. Khan, Y. Sun, K. Hess, I. Shmulevich, A. K. Sood, W. Zhang, “Association of BRCA1 and BRCA2 Mutations With Survival, Chemotherapy Sensitivity, and Gene Mutator Phenotype in Patients With Ovarian Cancer,” *JAMA*, Vol. 306, No. 14, pp. 1557-1565, 2011.

T. A. Knijnenburg, J. Lin, H. Rovira, J. Boyle, I. Shmulevich, “EPEPT: A web service for enhanced P-value estimation in permutation tests,” *BMC Bioinformatics*, Vol. 12, No. 411, 2011.

T. Knijnenburg, O. Roda, Y. Wan, G. Nolan, J. Aitchison, I. Shmulevich, “A regression model approach to enable cell morphology correction in high-throughput flow cytometry,” *Molecular Systems Biology*, Vol. 7, No. 531, 2011.

A. V. Ratushny, I. Shmulevich, J. D. Aitchison, “Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues,” *PLoS Computational Biology*, Vol. 7, No. 6, e1002091, 2011.

D. Falconnet, A. Niemistö, R. J. Taylor, M. Ricicova, T. Galitski, I. Shmulevich, C. L. Hansen, “High-throughput tracking of single yeast cells in a microfluidic imaging matrix,” *Lab on a Chip*, Vol. 11, pp. 466-473, 2011.

**2010**

D. B. Burdick, C. Cavnor, J. Handcock, S. Killcoyne, J. Lin, B. Marzolf, S. A. Ramsey, H. Rovira, I. Shmulevich, J. Boyle, “SEQADAPT: An adaptable system for the tracking, storage and analysis of high throughput sequencing experiments,” *BMC Bioinformatics*, Vol. 11, No. 377, 2010.

T. Erkkilä, S. Lehmusvaara, P. Ruusuvuori, T. Visakorpi, I. Shmulevich, H. Lähdesmäki, “Probabilistic analysis of gene expression measurements from heterogeneous tissues,” *Bioinformatics*, Vol. 26, No. 20, pp. 2571-2577, 2010.

D. Yang, A. Ylipää, J. Yang, K. Hunt, R. Pollock, J. Trent, O. Yli-Harja, I. Shmulevich, M. Nykter, W. Zhang, “An integrated study of aberrant gene copy number and gene expression in GIST and LMS,” *Technology in Cancer Research and Treatment*, Vol. 9, No. 2, pp. 171-178, 2010.

S. A. Ramsey, T. A. Knijnenburg, K. A. Kennedy, D. E. Zak, M. Gilchrist, E. S. Gold, C. D. Johnson, A. Lampano, V. Litvak, G. Navarro, T. Stolyar, A. Aderem, I. Shmulevich, “Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites,” *Bioinformatics*, Vol. 26, No. 17, pp. 2071-2075, 2010.

D. J. Galas, M. Nykter, G. W. Carter, N. D. Price, I. Shmulevich, “Biological information as set-based complexity,” *IEEE Transactions on Information Theory*, Vol. 56, No. 2, pp. 667-677, 2010.

R. A. Saleem, R. Long-O’Donnell, D. J. Dilworth, A. M. Armstrong, A. P. Jamakhandi, Y. Wan, T. A. Knijnenburg, A. Niemistö, J. Boyle, R. A. Rachubinski, I. Shmulevich, J. D. Aitchison, “Genome-Wide Analysis of Effectors of Peroxisome Biogenesis,” PLoS ONE, Vol. 5, No. 8, e11953, 2010.

**2009**

I. Shmulevich and E. R. Dougherty, *Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks*, SIAM Press, 2009.

V. Litvak, S. Ramsey, A. Rust, D. Zak, K. Kennedy, A. Lampano, M. Nykter, I. Shmulevich, A. Aderem, “Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals,” *Nature Immunology*, Vol. 10, No. 4, pp. 437-43, 2009.

M. Nykter, H. Lähdesmäki, A. Rust, V. Thorsson, I. Shmulevich, “A data integration framework for prediction of transcription factor targets: a BCL6 case study,” *Annals of the New York Academy of Sciences*, Vol. 1158, pp. 205-214, 2009.

L. Hu, W. Hittelman, T. Lu, P. Ji, R. Arlinghaus, I. Shmulevich, S. R. Hamilton, W. Zhang, “NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells,” *Laboratory Investigation*, Vol. 89, pp. 531–548, 2009.

I. Shmulevich, J. D. Aitchison, “Deterministic and stochastic models of genetic regulatory networks,” *Methods in Enzymology*, Vol. 467, pp. 335-356, 2009.

A. C. Huang, L. Hu, S.A. Kauffman, W. Zhang, I. Shmulevich, “Using Cell Fate Attractors to Uncover Transcriptional Regulation of HL60 Neutrophil Differentiation,” *BMC Systems Biology*, Vol. 3, No. 20, 2009.

T. A. Knijnenburg, L. F. A. Wessels, M. J. T. Reinders, I. Shmulevich, “Fewer permutations, more accurate P-values,” *Bioinformatics*, Vol. 25, No. 12, pp. i161-i168, 2009.

M. Nykter, J. Kesseli, and I. Shmulevich, “Dynamical systems analysis of stack filters,” in I. Tabus, K. Egiazarian, and M. Gabbouj, editors, *Festschrift in honor of Jaakko Astola on the occasion of his 60th Birthday*, pp. 169-181, Tampere International Center of Signal Processing, 2009.

J. Selinummi, P. Ruusuvuori, I. Podolsky, A. Ozinsky, E. Gold, O. Yli-Harja, A. Aderem, I. Shmulevich, “Bright Field Microscopy as an Alternative to Whole Cell Fluorescence in Automated Analysis of Macrophage Images ,” *PLoS ONE*, Vol. 4, No. 10, 2009.

R. J. Taylor, D. Falconnet, A. Niemistö, S. A. Ramsey, S. Prinz, I. Shmulevich, T. Galitski, C. L. Hansen, “Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 106, No. 10, pp. 3758-3763, 2009.

J. Boyle, H. Rovira, C. Cavnor, D. Burdick, S. Killcoyne, I. Shmulevich, “Adaptable Data Management for Systems Biology Investigations,” *BMC Bioinformatics*, Vol. 10, No. 79, 2009.

**2008**

W. Liu, H. Lähdesmäki, E. R. Dougherty, I. Shmulevich, “Inference of Boolean Networks using Sensitivity Regularization,” *EURASIP Journal on Bioinformatics and Systems Biology*, Vol. 2008, Article ID 780541, 12 pages, 2008.

S. A. Ramsey, S. L. Klemm, D. E. Zak, K. A. Kennedy, V. Thorsson, B. Li, M. Gilchrist, E. Gold, C. D. Johnson, V. Litvak, G. Navarro, J. C. Roach, C. M. Rosenberger, A. G. Rust, N. Yudkovsky, A. Aderem, I. Shmulevich, “Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics,” *PLoS Computational Biology*, Vol. 4, No. 3, e1000021, 2008.

H. Lähdesmäki, A. G. Rust, I. Shmulevich, “Probabilistic inference of transcription factor binding from multiple data sources,” *PLoS ONE*, Vol. 3, No. 3, e1820, 2008.

H. Lähdesmäki, I. Shmulevich, “Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements,” *Machine Learning*, Vol. 71, pp.185-217, 2008

E. Balleza, E. Alvarez-Buylla, A. Chaos, S. A. Kauffman, I. Shmulevich, M. Aldana, “Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms,” *PLoS ONE*, Vol. 3, No. 6, e2456, 2008.

M. Korb, A. G. Rust, V. Thorsson, C. Battail, B. Li, D. Hwang, K. Kennedy, J. C. Roach, C. M. Rosenberger, M. Gilchrist, D. Zak, C. Johnson, B. Marzolf, A. Aderem, I. Shmulevich, H. Bolouri, “The Innate Immune Database (IIDB),” *BMC Immunology*, Vol. 9, No. 7, 2008.

M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, I. Shmulevich, “Critical networks exhibit maximal information diversity in structure-dynamics relationships,” *Physical Review Letters*, Vol. 100, 058702, 2008.

M. Nykter, N. D. Price , M. Aldana, S. A. Ramsey, S. A. Kauffman, L. Hood, O. Yli-Harja, I. Shmulevich, “Gene Expression Dynamics in the Macrophage Exhibit Criticality,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 105, No. 6, pp. 1897-1900, 2008.

W. W. Lee, D. Cui, M. Czesnikiewicz-Guzik, R.Z. Vencio, I. Shmulevich, A. Aderem, C.M. Weyand, J.J. Goronzy, “Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling,” Rejuvenation Research, Vol. 11, No. 6, pp. 1001-1011, 2008.

J. Boyle, C. Cavnor, S. Killcoyne, I. Shmulevich, “Systems biology driven software design for the research enterprise,” *BMC Bioinformatics*, Vol. 9, No. 295, 2008.

**2007**

N. D. Price, I. Shmulevich, “Biochemical and statistical network models for systems biology,” *Current Opinion in Biotechnology*, Vol. 18, pp. 365-370, 2007.

P. Krawitz, I. Shmulevich, “Entropy of complex relevant components in Boolean networks,” *Physical Review E*, Vol. 76, 036115, 2007.

P. Krawitz, I. Shmulevich, “Basin Entropy in Boolean Network Ensembles,” *Physical Review Letters*, Vol. 98, No. 15, pp. 158701, 2007.

R. Vêncio, I. Shmulevich, “ProbCD: enrichment analysis accounting for categorization uncertainty,” *BMC Bioinformatics*, Vol. 8, No. 383, 2007.

R. Vêncio, L. Varuzza, C. Pereira, H. Brentani, I. Shmulevich, “Simcluster: clustering enumeration gene expression data on the simplex space,” *BMC Bioinformatics*, Vol. 8, No. 246, 2007.

M. Ahdesmäki , H. Lähdesmäki, A. Gracey , I. Shmulevich and O. Yli-Harja, “Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data,” *BMC Bioinformatics*, Vol. 8, No. 233, 2007.

N. D. Price, J. Trent, A. K. El-Naggar, D. Cogdell, E. Taylor, K. K. Hunt, R. E. Pollock, L. Hood, I. Shmulevich, W. Zhang, “Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 104, No. 9, pp- 3414-3419, 2007.

J. Selinummi, A. Niemistö, R. Saleem, G. W. Carter, J. Aitchison, O. Yli-Harja, I. Shmulevich, and J. Boyle, “A Case Study on 3-D Reconstruction and Shape Description of Peroxisomes in Yeast, ” *IEEE International Conference on Signal Processing and Communication (ICSPC07)*, Dubai, United Arab Emirates (UAE), November 24-27, 2007.

A. Niemistö, T. Korpelainen, R. Saleem, O. Yli-Harja, J. Aitchison, I. Shmulevich, “A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy,” *29th International Conference of the IEEE Engineering in Medicine and Biology Society*, Lyon, France, August 23-26, 2007.

S. A. Kauffman, R. K. Logan, R. Este, R. Goebel, D. Hobill, I. Shmulevich, “Propagating Organization: An Enquiry,” *Biology and Philosophy*, Vol. 23, No. 1, pp. 27-45, 2007.

**2006**

A. Niemistö, J. Selinummi, R. Saleem, I. Shmulevich, J. Aitchison, O. Yli-Harja, “Extraction of the number of peroxisomes in yeast cells by automated image analysis,” *The 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society*, New York, New York, August 30 – September 3, 2006.

C. Gershenson, S. A. Kauffman, and I. Shmulevich, “The Role of Redundancy in the Robustness of Random Boolean Networks,” in Rocha, L. M., L. S. Yaeger, M. A. Bedau, D. Floreano, R. L. Goldstone, and A. Vespignani (Eds.), *Artificial Life X, Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems*, pp. 35-42. MIT Press, 2006.

H. Lähdesmäki, S. Hautaniemi, I. Shmulevich, O. Yli-Harja, “Relationships Between Probabilistic Boolean Networks and Dynamic Bayesian Networks as Models of Gene Regulatory Networks,” *Signal Processing*, Vol. 86, No. 4, pp. 814-834, 2006.

M. Nykter, K. K. Hunt, R. E. Pollock, A. K. El-Naggar, E. Taylor, I. Shmulevich, O. Yli-Harja, W. Zhang, “Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies,” *Technology in Cancer Research and Treatment*, Vol. 5, No. 2, pp. 177-182, 2006.

R. Jiang, C. Mircean, I. Shmulevich, D. Cogdell, Y. Jia, I. Tabus, K. Aldape, R. Sawaya, J. M. Bruner, G. N. Fuller, W. Zhang, “Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays,” *Proteomics*, Vol. 6, pp. 2964-2971, 2006.

I. Tabus, A. Hategan, C. Mircean, J. Rissanen, I. Shmulevich, W. Zhang, J. Astola, “Nonlinear modeling of protein expressions in protein arrays,” *IEEE Transactions on Signal Processing*, Vol. 54, No. 6, pp. 2394-2407, 2006.

**2005**

M. Brun, E. R. Dougherty, I. Shmulevich, “Steady-State Probabilities for Attractors in Probabilistic Boolean Networks,” *Signal Processing*, Vol. 85, No. 4, pp. 1993-2013, 2005.

T. Toulouse, P. Ao, I. Shmulevich, S. A. Kauffman, “Noise in a Small Genetic Circuit that Undergoes Bifurcation,” *Complexity*, Vol. 11, No. 1, pp. 45-51, 2005.

I. Shmulevich, S. A. Kauffman, M. Aldana, “Eukaryotic cells are dynamically ordered or critical but not chaotic,” *Proceedings of the National Academy of Sciences of the USA,* Vol. 102, No. 38, pp. 13439-13444, 2005

C. Mircean, I. Shmulevich, D. Cogdell, W. Choi, Y. Jia, I. Tabus, S. R. Hamilton, W. Zhang, “Robust estimation of protein expression ratios with lysate microarray technology,” *Bioinformatics*, Vol. 21, No. 9, pp. 1935-1942, 2005.

H. Lähdesmäki, I. Shmulevich, V. Dunmire, O. Yli-Harja, W. Zhang, “In Silico Microdissection of Microarray Data from Heterogeneous Cell Populations,” *BMC Bioinformatics* 6:54, 2005.

G. N. Fuller, C. Mircean, I. Tabus, E. Taylor, R. Sawaya, J. M. Bruner, I. Shmulevich, W. Zhang, “Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression,” *Oncology Reports*, Vol. 14, pp. 651-656, 2005.

E. Lee, C. Mircean, I. Shmulevich, H. Wang, J. Liu, A. Niemistö, J. Kavanagh, JH Lee, W. Zhang, “Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion,” *Molecular Cancer*, Vol. 4, No. 7, 2005.

A. Niemistö, V. Dunmire, O. Yli-Harja, W. Zhang, I. Shmulevich, “Robust quantification of in vitro angiogenesis through image analysis,” *IEEE Transactions on Medical Imaging*, Vol. 24, No. 4, pp. 549-553, 2005.

A. Niemistö, V. Dunmire, O. Yli-Harja, W. Zhang, I. Shmulevich, “Analysis of angiogenesis using in vitro experiments and stochastic growth models,” *Physical Review E*, Vol. 72, 062902, 2005.

**2004**

I. Shmulevich, S. A. Kauffman, “Activities and Sensitivities in Boolean Network Models,” *Physical Review Letters*, Vol. 93, No. 4, pp. 048701(1-4), 2004.

W. Just, I. Shmulevich, J. Konvalina, “The number and probability of canalizing functions,” *Physica D*, Vol. 197, pp. 211-221, 2004.

E. R. Dougherty, I. Shmulevich, M. L. Bittner, “Genomic Signal Processing: The Salient Issues,” *EURASIP Journal on Applied Signal Processing*, Vol. 2004, No. 1, pp. 146-153, 2004.

H. Lähdesmäki, X. Hao, B. Sun, L. Hu, O. Yli-Harja, I. Shmulevich, and W. Zhang, “Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis,” *International Journal of Oncology*, Vol. 24, No. 6, pp. 1589–1596, June 2004.

X. Hao, B. Sun, L. Hu, H. Lähdesmäki, V. Dunmire, Y. Feng, S.-W. Zhang, H. Wang, C. Wu, H. Wang, G. N. Fuller, W. F. Symmans, I. Shmulevich, and W. Zhang, “Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis,” *Cancer*, Vol. 100, No. 6, pp. 1110-1122, 2004.

C. Mircean, I. Tabus, T. Kobayashi, M. Yamaguchi, H. Shiku, I. Shmulevich, W. Zhang, “Pathway Analysis of Informative Genes from Microarray Data Reveals that Metabolism and Signal Transduction Genes Distinguish Different Subtypes of Lymphomas,” *International Journal of Oncology*, Vol. 24, No. 3, pp. 497-504, 2004.

R. F. Hashimoto, S. Kim, I. Shmulevich, W. Zhang, M. L. Bittner, E. R. Dougherty, “Growing genetic regulatory networks from seed genes,” Bioinformatics, Vol. 20, No. 8, pp. 1241-1247, 2004.

I. Shmulevich, H. Lähdesmäki, and K. Egiazarian “Spectral Methods for Testing Membership in Certain Post Classes and the Class of Forcing Functions,” *IEEE Signal Processing Letters*, Vol. 11, No. 2, pp. 289-292, 2004.

**2003**

I. Shmulevich, I. Gluhovsky, R. Hashimoto, E. R. Dougherty, and W. Zhang, “Steady-State Analysis of Genetic Regulatory Networks Modeled by Probabilistic Boolean Networks,” *Comparative and Functional Genomics*, Vol. 4, No. 6, pp. 601-608, 2003.

I. Shmulevich, “Model Selection in Genomics,” Guest Editorial in Toxicogenomics Section of *Environmental Health Perspectives*, Vol. 111, No. 6, pp. A328-A329, May 2003.

I. Shmulevich, H. Lähdesmäki, E. R. Dougherty, J. Astola, W. Zhang, “The role of certain Post classes in Boolean network models of genetic networks,” *Proceedings of the National Academy of Sciences of the USA*, Vol. 100, No. 19, pp. 10734-10739, 2003.

I. Shmulevich, J. Astola, D. Cogdell, S. R. Hamilton, and W. Zhang, “Data Extraction From Composite Oligonucleotide Microarrays,” *Nucleic Acids Research*, Vol. 31, No. 7, e36, 2003.

E. R. Dougherty and I. Shmulevich, “Mappings Between Probabilistic Boolean Networks,” *Signal Processing*, Vol. 83, No. 4, pp. 799-809, 2003.

H. Lähdesmäki, I. Shmulevich, and O. Yli-Harja, “On Learning Gene Regulatory Networks Under the Boolean Network Model,” *Machine Learning*, Vol. 52, pp. 147-167, 2003.

J. Morikawa, H. Li, S. Kim, K. Nishi, S. Ueno, E. Suh, E. Dougherty, I. Shmulevich, H. Shiku, W. Zhang, and T. Kobayashi, “Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARa),” *International Journal of Oncology*, Vol. 23, No. 3, pp. 617-625, 2003.

T. Kobayashi, M. Yamaguchi, S. Kim, J. Morikawa, S. Ogawa, S. Ueno, E. Suh, E. Dougherty, I. Shmulevich, H. Shiku, W. Zhang, “Microarray Reveals Differences in Both Tumors and Vascular Specific Gene Expression in De Novo CD5+ and CD5- Diffuse Large B-cell Lymphomas,” *Cancer Research*, vol. 63, pp. 60-66, January 2003.

**2002**

I. Shmulevich, W. Zhang, “Binary Analysis and Optimization-Based Normalization of Gene Expression Data,” *Bioinformatics*, Vol. 18, No. 4, pp. 555-565, 2002.

I. Shmulevich, E.R. Dougherty, and W. Zhang, “From Boolean to probabilistic Boolean networks as models of genetic regulatory networks,” *Proceedings of the IEEE*, Vol. 90, No. 11, pp. 1778-1792, 2002.

I. Shmulevich, E. R. Dougherty, W. Zhang, “Gene Perturbation and Intervention in Probabilistic Boolean Networks,” *Bioinformatics*, Vol. 18, No. 10, pp. 1319-1331, 2002.

I. Shmulevich, E.R. Dougherty, and W. Zhang, “Control of stationary behavior in Probabilistic Boolean Networks by means of structural intervention,” *Journal of Biological Systems*, Vol. 10, No. 4, pp. 431-445, 2002.

I. Shmulevich, E. R. Dougherty, S. Kim, W. Zhang, “Probabilistic Boolean Networks: A Rule-based Uncertainty Model for Gene Regulatory Networks,” *Bioinformatics*, Vol. 18, No. 2, pp. 261-274, 2002.

S. Kim, E. R. Dougherty, I. Shmulevich, K. R. Hess, S. R. Hamilton, J. M. Trent, G. N. Fuller, W. Zhang, “Identification of Combination Gene Sets for Glioma Classification,” *Molecular Cancer Therapeutics*, vol. 1, pp. 1229-1236, November 2002.

I. Shmulevich, K. Hunt, A. El-Naggar, E. Taylor, L. Ramdas, P. Labordé, K. R. Hess, R. Pollock, W. Zhang, “Tumor Specific Gene Expression Profiles in Human Leiomyosarcoma: an Evaluation of Intra-Tumor Heterogeneity,” *Cancer*, Vol. 94, No. 7, pp. 2069-2075, 2002.

I. Shmulevich, A. van der Ven, “An Inhibition-Based Stochastic Countable-Time Decision Model,” *British Journal of Mathematical and Statistical Psychology*, Vol. 55, pp. 17-25, 2002.

I. Shmulevich, O. Yli-Harja, J. Astola, A. Korshunov, “On the Robustness of the Class of Stack Filters,” *IEEE Transactions on Signal Processing*, Vol. 50, No. 7, pp. 1640-1649, July 2002.

I. Gluhovsky, V. Melnik, I. Shmulevich, “Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications,” *Journal of Mathematical Imaging and Vision*, Vol. 16, pp. 237-249, 2002.

A. D. Korshunov, I. Shmulevich, “On the Distribution of the Number of Monotone Boolean Functions Relative to the Number of Lower Units,” *Discrete Mathematics*, Vol. 257, pp. 463-479, 2002.

V. Katkovnik, I. Shmulevich, “Kernel Density Estimation with Varying Data-Driven Bandwidth,” *Pattern Recognition Letters*, Vol. 23, pp. 1641-1648, 2002.

**2001**

I. Shmulevich and G. R. Arce, “Spectral design of weighted median filters admitting negative weights,” *IEEE Signal Processing Letters*, Vol. 8, No. 12, pp. 313-316, 2001.