Publications

Books

• Joseph L. Hellerstein, Yixin Diao, Sujah Parekh, and Dawn M. Tilbury. Feedback Control of Computing Systems. John Wiley & Sons. 2004.

• Joseph L. Hellerstein, David A. Klein, and Keith R. Milliken. Expert Systems In Data Processing. John Wiley & Sons. 1989.

Representative Publications

I have published over 200 peer-reviewed articles. Below are publications that are representative of the scope of my research.

Systems Biology

• Adel Heydarabadipour, Lucian Smith, Joseph L. Hellerstein, and Herbert M. Sauro. SBMLNetwork: a framework for standards-based visualization of biochemical models. To appear in PLOS Computational Biology, 2025.

• Herbert M Sauro, Eran Agmon, Michael L Blinov, John H Gennari, Joseph L Hellerstein, et al. From FAIR to CURE: Guidelines for Computational Models of Biological Systems. In submission, 2025.

• Lucian Smith, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning Hermjakob, Jonathan Kar, Bilal Shaikh, Logan Drescher, Ion I. Moraru, James C. Schaff, Eran Agmon, Alexander A. Patrie, Michael L. Blinov, Joseph L. Hellerstein, Elebeoba E. May, David P. Nickerson, John H. Gennari, Herbert M. Sauro. Verification and reproducible curation of the BioModels repository. In submission, 2025.

• Joseph L Hellerstein, Lucian P Smith, Lillian T. Tatka,  Steven S. Andrews, Michael A. Kochen and Herbert M. Sauro. Discovering Subnetworks in SBML Models. To appear in Oxford Bioinformatics, 2025.

• Michael A Kochen, Joseph L Hellerstein, Herbert M Sauro. First-order ulrasensitivity in phosphorylation cycles. Interface Focus. Febuary, 2024.

• Tatka LT, Smith LP, Hellerstein JL, Sauro HM. Adapting modeling and simulation credibility standards to computational systems biology. J Transl Med. 2023 Jul 26;21(1):501.

• Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein and Herbert M. Sauro. VSCode-Antimony: A Source Editor for Building, Analyzing, and Translating Antimony Models. Oxford Bioinformatics. https://doi.org/10.1093/bioinformatics/btad753, 2023.

• Joseph L. Hellerstein. An Oscillating Reaction Network With an Exact Closed Form Solution in the Time Domain.  BMC Bioinformatics.  (24) 466. 2023.

• Tatka LT, Luk W, Elston TC, Hellerstein JL, Sauro HM. Cesium: A public database of evolved oscillatory reaction networks. Biosystems. 2023.

• Woosub Shin, John H Gennari, Joseph L Hellerstein, Herbert M Sauro.  An Automated Model Annotation System (AMAS) for SBML Models. Oxford Bioinformatics. 2023.

• J Kyle Medley, Sung Sik Woo, Jonathan Teo, Joseph Hellerstein, Rahul Sarpeshkar, and Herbert M Sauro. A compiler for biological networks on silicon chips. PLOS Computational Biology. 2020.

• Woosub Shin and Joseph L. Hellerstein. Isolating Structural Errors in Reaction Networks in Systems Biology. Oxford BioInformatics, 2020.

• J. Kyle Medley, Joseph L. Hellerstein, and Herbert M. Sauro. libsbmljs—Enabling web-based SBML tools. Biosystems. Volume 195. July, 2020.

• Joseph L. Hellerstein, Stanley Gu, Kiri Chou, and Herbert M. Sauro. Recent Advances in Building Biomedical Models: A Manifesto For Model Engineering. F1000Research, March 2019.

• J Kyle Medley, Kiri Choi, Matthias Konig, Lucian Smith, Stanley Gu, Joseph Hellerstein, Stuart C. Sealfon, Herbert M Sauro. Tellurium Notebooks - An Environment for Reproducible Dynamical Modeling in Systems Biology. PLOS Computational Biology. 2018.

Computing Systems and Applications

• Andrew J Connolly, Joseph L Hellerstein, Naomi Alterman, David AC Beck, Rob Fatland, Edward D. Lazowska, Vani Mandava, and Sarah A Stone. Software Engineering Practices In Academia: Promoting the 3Rs - Readability, Resilience, and Reuse. Isue 5.2. Spring, 2023.

• A Clark and JL Hellerstein. SciSheets: Providing the Power of Programming with the Simplicity of Spreadsheets. Scientific Computing With Python, 2017 (video). DOI 10.25080/shinma-7f4c6e7-007.

• Q Zhang, MF Zani, R Boutaba, JL Hellerstein. Dynamic Heterogeneity-Aware Resource Provisioning in the Cloud. IEEE Transactions on Cloud Computing. Volume: 2, Issue: 1, Jan.-March 2014.

• JL Hellerstein, KJ Kohlkoff, DM Konerding. Science in the Cloud: Accelerating Discovery in the 21st Century. IEEE Internet Computing. Volume: 16, Issue: 4, July-Aug. 2012.

• A Misra, JL Hellerstein, W Cirne, CR Das. Towards Characterizing Cloud Backend Workloads: Insights from Google Compute Clusters. ACM Sigmetrics, 2010.

• Y Diao, JL Hellerstein, S Parekh, R Griffith, G Kaiser,  D Phung. A Control Theory Foundation for Self-Managing Computing Systems. IEEE Journal on Selected Areas in Communications. Volume: 23, Issue: 12, Dec. 2005.

• Y Diao, N Ghandi, JL Hellerstein, S Parekh, and DM Tilbury. Using MIMO Feedback Control to Enforce Policies for Interrelated Metrics with Application to the Apache Web Server. Network Operations and Management, 2002.

• S Ma and JL Hellerstein. Mining Partially Periodic Event Patterns with Unknown Periods. IEEE International Conference Data Engineering. 2001.

• JL Hellerstein. Constructing Quantitative Models Using Monotone Relationships. IEEE Transactions on Knowledge and Data Engineering, Volume: 7, Issue: 2, Apr 1995.

• JL Hellerstein. Achieving Service Rate Objectives with Decay Usage Scheduling. IEEE Transactions on Software Engineering. Volume: 19, Issue: 8, Aug 1993 .

• WW Chu and JL Hellerstein. The Exclusive-Writer Approach to Updating Replicated Files in Distributed Processing Systems. IEEE Transactions on Computers. Volume: C-34, Issue: 6, June 1985.