Bing LIU Personal Particulars Tel: (412) 799-3756 ; (412) 648-7775 Office: 3085 BST3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA. E-mail: liubing@pitt.edu Web: http://www.pitt.edu/~liubing Research Interests My research area centers on computational systems biology. I develop computational modeling, simulation and analysis techniques to study the dynamics of biological systems. As an integral part of my research, I collaborate with biologists and model a variety of biological systems crucial to human immunity and cancer. I also leverage high-performance computing, model checking and machine learning techniques to enable the analysis of multi-scale biological systems. Employment University of Pittsburgh Jan 2014 - Present Research Associate Department of Computational & Systems Biology • Advisor: Ivet Bahar Carnegie Mellon University Jun 2012 - Dec 2013 Post-Doctoral Fellow Computer Science Department • Advisor: Edmund M. Clarke (Turing Award laureate) National University of Singapore Jun 2011 - May 2012 Post-Doctoral Fellow Computer Science Department • Advisor: P.S. Thiagarajan Education National University of Singapore Aug 2006 - May 2011 Ph.D. in Computational Systems Biology, NUS Graduate School for Integrative Sciences and Engineering • Thesis title: “Probabilistic Approximation and Analysis Techniques for Bio-Pathway Models” • Advisors: P.S. Thiagarajan and David Hsu (Computer Science Department) • Committee: Limsoon Wong (National University of Singapore), Saturo Miyano (The University of Tokyo) and Marta Kwiatkowska (University of Oxford ) National University of Singapore Aug 2002 - Jul 2006 Bachelor of Computer Science, Department of Computer Science Publications Peer-reviewed Journal Papers 1. V E. Kagan, G Mao, F Qu, J P F Angeli, S Doll, C S Croix, H Dar, Bing Liu, V A Tyurin, V B Ritov, O A Kapralov, A A Amoscato, J Jiang, T Anthonymuthu, D Mohammadyani, Q Yang, J Klein-Seetharaman, S Watkins, I Bahar, J Greenberger, R Mallampalli, B R Stockwell, Y Y Tyurina, M Conrad, H Bayir. Oxidized Arachidonic/Adrenic Phosphatidylethanolamines Navigate Cells to Ferroptosis. Nature Chemical Biology, in revision. 2. Bing Liu, Q Liu, S Palaniappan, I Bahar, P S Thiagarajana and J L Ding. TLR3-TLR7 Pathway Crosstalk Confers Innate Immune Memory and Homeostasis. Science Signaling, in press. 1 3. Bing Liu, D Bhatt, Z N Oltvai, J S Greenberger, I Bahar. Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies. Scientific Reports, Nature Publishing Group 4:6245 (2014). 4. H Zhou, S Gao, N N Nguyen, M Fan, J Jin, Bing Liu, L Zhao, G Xiong, M Tan, S Li, L Wong. Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv proteinprotein interactions. Biology Direct, 9(5):1-52 (2014). 5. A Hagiescu, Bing Liu, Z Cui, B Chattopadhyay, P S Thiagarajan and W F Wong. GPU code generation for ODE-based applications with phased shared-data access patterns. ACM Transactions on Architecture and Code Optimization, 10(4):55 (2013). 6. Bing Liu, A Hagiescu, S K Palaniappan, B Chattopadhyay, Z Cui, W F Wong, P S Thiagarajan. Approximate Probabilistic Analysis of Biopathway Dynamics. Bioinformatics, 28(11):1508-1516 (2012). 7. S K Palaniappan, S Akshay, Bing Liu, B Genest, P S Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5):1352-1365 (2012). 8. Bing Liu, P S Thiagarajan. Modeling and Analysis of Biopathways Dynamics. Journal of Bioinformatics and Computational Biology, 10(4):1231001 (2012). 9. Bing Liu, J Zhang, P Y Tan, D Hsu, A M Blom, B Leong, S Sethi, B Ho, J L Ding, P S Thiagarajan. A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System. PLoS Computational Biology, 7(1):e1001059 (2011). 10. Bing Liu, D Hsu, P S Thiagarajan. Probabilistic Approximations of ODEs based Bio-Pathway Dynamics. Theoretical Computer Science, 412(21):2188-2206 (2011). 11. T Zhu, P Korshunov, Bing Liu, W T Ooi. Plasma: A Scripting Language for Processing Media Streams. ACM/SPIE Multimedia Computing and Networking (MMCN), Proceedings of SPIE:6504, pp. 65040Q (2007). Peer-reviewed Conference Proceedings 12. Q Wang, N Miskov-Zivanov, Bing Liu, J R Faeder, M Lotze, E M Clarke. A Multicellular Model of Pancreatic Cancer Microenvironment. Computer Aided Verification (CAV), in revision. 13. B Gyori, Bing Liu, S Paul, R Ramanathan and P S Thiagarajan. Probabilistic Approximation and Analysis of Hybrid Systems. Hybrid Systems Biology (HSB), Springer, LNCS:9271, pp. 1-15 (2015). 14. Bing Liu, S Kong, S Gao, P Zuliani and E M Clarke. Towards Personalized Prostate Cancer Therapy Using Delta-Reachability Analysis. Hybrid Systems: Computation and Control (HSCC), ACM New York, pp. 227-232 (2015). 15. Bing Liu, S Kong, S Gao, P Zuliani and E M Clarke. Parameter Synthesis for Cardiac Cell Hybrid Models Using Delta-Decisions. Computational Methods in Systems Biology (CMSB), Springer, LNCS:8859, pp. 99-113 (2014). 16. S K Palaniappan, B Gyori, Bing Liu, D Hsu, and P S Thiagarajan. Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models. Computational Methods in Systems Biology (CMSB), Springer, LNCS:8130, pp 120-134 (2013). 17. Bing Liu, P S Thiagarajan, D Hsu. Probabilistic Approximations of Signaling Pathway Dynamics. Computational Methods in Systems Biology (CMSB), Springer, LNCS:5688, pp. 251-265 (2009). 18. Bing Liu and W T Ooi. SLIME: A Tool for Composing Live and Stored Media. In Proc. of the 11th NUROP Congress, Singapore (2006). 2 Books 19. Bing Liu. Computational Modeling of Biological Pathways: Probabilistic Approximation and Analysis Techniques. LAP LAMBERT Academic Publishing, ISBN-10: 3847372114, 2012. Other Publications 20. Bing Liu, S Kong, S Gao, and E M Clarke. Parameter Identification Using Delta-Decisions for Biological Hybrid Systems. CMU SCS Technical Report, CMU-CS-13-136 (2013). 21. Bing Liu. Statistical analysis of partially calibrated bio-pathway models. HPC E-newsletter Issue No. 24. 2009. (HPC Challenge 2009 Winning Project) Manuscripts In Preparation 22. Bing Liu, Hulya Bayir, Gary Silverman, Stephan Pak, Zoltan N. Oltvai, Daivd Perlmutter and Ivet Bahar. Cell Fate Decision between Autophagy and Apoptosis: Insights from Quantitative Modeling. 23. Bing Liu, Gary Silverman, Stephan Pak, Zoltan N. Oltvai, Daivd Perlmutter and Ivet Bahar. Computational Modeling Reveals Polypharmacological Strategies for Regulating Alpha1Antitrypsin Z Mutant Protein Disposal. 24. Bing Liu, Zongda Che and Ivet Bahar. Mathematical Modeling of Cell Fate Decision between Necroptosis and Apoptosis. 25. Bing Liu, Indira Shrivastava, Jinming Zhao, Sally E. Wenzel and Ivet Bahar. A Multiscale Approach Reveals the Mechanism of Lipoxygenase-PEBP1 Interaction that Regulates Mucociliary Clearance in Type 2 Asthma. 26. Bing Liu, She Zhang, Hulya Bayir, Valerian E. Kagan, James R. Faeder, and Ivet Bahar. Cardiolipin Spatiotemporal Dynamics Confers Cell Decision in Response to Mitochondrial Damage. 27. Bing Liu, Cihan Kaya, Mary B. Kennedy and Ivet Bahar. Stochastic Modeling Reveals the Significance of CamKII Dynamics in Synaptic Plasticity. Published Abstracts 28. C Kaya, B Liu, JR Faeder, I Bahar. Unified Model of Synaptic Transmission. Biophysical Journal 108 (2), 155a (2015). 29. B Liu, T A Wall, I Bahar. Stochastic Modeling of Apoptosis-Autophagy Crosstalk. Gorden Research Conference: Stochastic Physics in Biology, Ventura, US (2015). 30. B Liu, D Bhatt, Z N Oltvai, J S Greenberger, I Bahar. Modeling of p53-Mediated Apoptosis Pathways Reveals Polypharmacological Strategies for Radiomitigation. Science - Sustain It, Pittsburgh, US (2014). 31. C Kaya, B Liu, J R Faeder, I Bahar. Spatiotemporal Modeling of Chemical Synapse. Biophysical Society Thematic Meeting - Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations, Istanbul, Turkey (2014). 32. B Liu, Q Liu, S Palaniappan, I Bahar, P S Thiagarajan, J L Ding. Mathematical Modeling Reveals a Synergistic Mechanism of Toll-like Receptor Pathways. The 8th q-bio Conference on Advancing Predictive Modeling of Cellular Regulation (q-bio), Santa Fe, US (2014). 33. A Hagiescu, B Liu, R. Ramanathan, S K Palaniappan, Z Cui, B Chattopadhyay, W F Wong, P S Thiagarajan. GPU Code Generation for Parallel Computation with Phased Shared-data Access Patterns. The 9th International Conference on High-Performance and Embedded Architectures and Compilers (HiPEAC), Vienna, Austria (2014). 3 34. B Liu, D Hsu, P S Thiagarajan. Probabilistic Approximations of Bio-pathway Dynamics. The 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Tucson, US (2009). Honors and Awards Best Poster Presentation Award, UPPDA, 2015 Postdoc of the Year, University of Pittsburgh, 2015 Silver Award of High Performance Computing Challenge, National University of Singapore, 2009 First Prize Winner of NGS Challenge, National University of Singapore, 2007 Dean’s List, School of Computing, National University of Singapore, 2005 Second Prize of National Mathematical Olympiad, Chinese Mathematical Society, 2000 First Prize of National Chemical Olympiad, Chinese Chemical Society, 1998 Grants and Scholarships Professional Activities Grant from Google Inc. for open-source software development 2010 NGS Scholarship 2006 - 2010 Singapore Ministry of Education Scholarship 2001 - 2006 Editorial Board Member Computers in Biology and Medicine Journal of Bioinformatics, Computational and Systems Biology Austin Journal of Lung Cancer Research Conference Program Committee Member/Organizer The 11th International Conference on Artificial Intelligence Applications and Innovations (AIAI’15), Bayonne/Biarritz, France, 2015. The 3rd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Singapore, 2011. The 2nd NGS Student Symposium, Singapore, 2009. The 1st NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Singapore, 2008. Reviewer of Journals Bioinformatics Nature Scientific Reports PLoS One Chaos: An Interdisciplinary Journal of Nonlinear Science Journal of Theoretical Biology BioMed Research International Computers in Biology and Medicine Journal of Bioinformatics and Computational Biology Theoretical Computer Science International Journal of Biomedical Science ACM Transactions on Modeling and Computer Simulation LNCS Transactions on Petri Nets and Other Models of Concurrency International Journal on Software Tools for Technology Transfer Journal of Clinical Diagnosis and Research American Journal of Medical and Biological Research Austin Journal of Proteomics, Bioinformatics & Genomics Reviewer of Conference Proceedings ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB) International Conference on Computational Methods in Systems Biology (CMSB) 4 International Conference on Computer Aided Verification (CAV) ACM/IEEE Symposium on Logic in Computer Science (LICS) International Workshop on Biological Processes and Petri Nets (BioPPN) International Conference on Genome Informatics (GIW) International Conference on Artificial Intelligence Applications and Innovations (AIAI) International Conference on Biomedical Engineering and Biotechnology (ICBEB) International Conference on Systems Biology (ISB) Translational Bioinformatics Conference (TSB) Invited Talks Model Checking Biology Systems UPPDA P2P, Pittsburgh, US, Oct 2015. Towards Prostate Personalized Cancer Therapy Using Delta-Reachability Analysis. The 18th ACM International Conference on Hybrid Systems: Computation and Control (HSCC), Seattle, US, Apr 2015. Computational Modeling of the Crosstalk Between Autophagy and Apoptosis. Biophysical Theory Club, Pittsburgh, US, Mar 2015. Parameter Identification using Model Checking for Systems Biology. Clarke Symposium, Pittsburgh, US, Sep 2014. Parameter Identification using Delta-Decisions for Hybrid Models in Biology. CMACS/AVAC Joint Workshop, Pittsburgh, United States, Nov 2013. Approximation and Verification Techniques for Biological Pathway Modeling. National Heart, Lung, and Blood Institute, NIH, Washington DC, United States, Nov 2013. Probabilistic Modeling and Analysis of Biopathways. Biophysical Theory Club, University of Pittsburgh, Pittsburgh, United States, Oct 2012. Approximating Biopathway Models. French Institute for Research in Computer Science and Control (INRIA), Paris, France, Apr 2012. Probabilistic Approximation Techniques for Biopathway Modeling. Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Singapore, Feb 2012. A Platform-aware GPU Realization of A Systems Biology Application. The 3nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Singapore, Apr 2011. A Computational and Experimental Study of the Complement System. The 2nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Tokyo, Japan, Feb 2010. Statistical Analysis of Partially Calibrated Bio-pathways Models. High Performance Computing Challenge Ceremony, Singapore, Nov 2009. Stochastic Approximations of Signaling Pathway Dynamics. The 1st NUS-U.Tokyo Joint Workshop on Computational Systems Biology, Singapore, Sep 2008. Teaching Experience Carnegie Mellon University 18-669 Special Topics In Cad I: Computing and Biology: Theory and Practice (Lecturer) 2015 Fall 15-817 Graduate Verification Seminar (Lecturer) 2013 Spring National University of Singapore CS6280 Computational Systems Biology (Teaching Assistant & Lecturer) CS1101S Programming Concepts and Data Structure (Teaching Assistant) 5 2007 - 2010 2005 Student Supervision Zongda Che (2015), accepted by Princeton University Bipasa Chattopadhyay (2010), now a PhD student at University of North Carolina at Chapel Hill. Luo Weiwei (2009), now a PhD student at Mechanobiology Institute. (Best Thesis Award) Anushka Singh (2008), now a graduate student at Johns Hopkins University. (Best Thesis Award) 6