Bing Liu
Research Assistant Professor
Computational & Systems Biology Department
School of Medicine, University of Pittsburgh
Address: BST3 3085, 3501 Fifth Ave, Pittsburgh, PA 15213
Phone: (412) 648-7775
Email: liubing[AT]cs.cmu.edu
About
I received Bachelor and PhD in Computer Science under the supervision of Profs P.S. Thiagarajan and David Hsu from National University of Singapore. Previously, I have been working with Prof Edmund M. Clarke (Turing Award 2007) as a Postdoctoral Fellow in Department of Computer Science, Carnegie Mellon University, and with Prof Ivet Bahar as a Research Associate in the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh. Currently, I am Research Assistant Professor in the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh. [CV]
Research
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 a number of biologists and clinicians to study a variety of crucial biological processes related to human immunity and cancer. I also leverage high-performance computing, formal verification, and machine learning techniques to enable the analysis of multi-scale multi-cellular systems. Furthermore, I am applying the techniques I have been developing to analyze cyber-physical systems that are ubiquitous in safety-critical applications. [More]
Publications
- B Liu, Z Oltvai, H Bayir, G Silverman, S Pak, D Perlmutter, I Bahar. Quantitative Assessment of Cell Fate Decision between Autophagy and Apoptosis, Nature Scientific Reports, 7:17605 (2017).
PDF - J Steinman, M Epperly, Wen Hou, J Willis, H Wang, R Fisher, B Liu, I Bahar, T McCaw, V Kagan, H Bayir, J Yu, P Wipf, S Li, M S Huq, J S Greenberger. Improved Total Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways. Radiation Research,189(1):68-83 (2017). doi: 10.1667/RR14787.1
PDF - V E Kagan, G Mao, F Qu, J P F Angeli, S Doll, C S Croix, H Dar, B 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 and Adrenic PEs Navigate Cells to Ferroptosis, Nature Chemical Biology, 13:81-90 (2017). doi:10.1038/nchembio.2238.
PDF - B Liu, J R Faeder. Parameter Estimation of Rule-based Models Using Statistical Model Checking, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China (2016). IEEE, pp. 1458-1464.
PDF - Q Wang, N Miskov-Zivanov, B Liu, J R Faeder, M Lotze, E M Clarke. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment, Computational Methods in Systems Biology (CMSB), Cambridge, UK (2016). Springer, LNCS:9859, pp. 289-305.
PDF - B Liu, Q Liu, S Palaniappan, L Yang, I Bahar, P S Thiagarajan, J L Ding. Innate Immune Memory and Homeostasis May Be Conferred Through crosstalk between TLR3 and TLR7 Pathways, Science Signaling, 9(436) ra70 (2016).
PDF - B Gyori, B Liu, S Paul, R Ramanathan, and P S Thiagarajan. Approximate Probabilistic Verification of Hybrid Systems. Hybrid Systems Biology (HSB), Madrid, Spain (2015). Springer, LNCS:9271, pp. 96-116.
PDF - C Kaya, B Liu, J R Faeder, I Bahar. Unified Model of Synaptic Transmission. Biophysical Journal, 108(2) 155a (2015).
PDF - G F Cooper, I Bahar, M J Becich, P V Benos, J Berg, J U Espino, C Glymour, R C Jacobson, M Kienholz, A V Lee, X Lu, R Scheines, Center for Causal Discovery team. The center for causal discovery of biomedical knowledge from big data Journal of the American Medical Informatics Association, 22(6):1132-1136 (2015).
PDF - B Liu, S Kong, S Gao, P Zuliani and E M Clarke. Towards Personalized Cancer Therapy Using Delta-Reachability Analysis. Hybrid Systems: Computation and Control (HSCC), Seattle, USA (2015). ACM, pp. 227-232.
PDF Supplementary Website - B 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. Nature Scientific Reports, 4:6245 (2014).
PDF Supplementary Website - B 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), Manchester, UK (2014). Springer, LNCS:8859, pp. 99-113.
PDF Supplementary Website - H Zhou, S Gao, N N Nguyen, M Fan, J Jin, B Liu, L Zhao, G Xiong, M Tan, S Li, L Wong. Stringent Homology-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions. Biology Direct, 9(5):1-52 (2014).
PDF - A Hagiescu, B Liu, R. Ramanathan, S K Palaniappan, Z Cui, B Chattopadhyay, W F Wong, P S Thiagarajan. GPU Code Generation for ODE-Based Applications with Phased Shared-data Access Patterns. ACM Transactions on Architecture and Code Optimization, 10(4):551-5519 (2013).
PDF - S Palaniappan, B Gyori, B Liu, D Hsu, P S Thiagarajan and E M Clarke. Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models. Computational Methods in Systems Biology (CMSB), Klosterneuburg, Austria (2013). Springer, LNCS:8130, pp 120-134.
PDF - B 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).
PDF - B 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).
PDF Supplementary Website - S K Palaniappan, S Akshay, B 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).
PDF Supplementary Website - B Liu, P S Thiagarajan. Modeling and Analysis of Biopathways Dynamics. Journal of Bioinformatics and Computational Biology, 10(4):1231001 (2012).
PDF - B 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).
PDF News@NGS Website - B Liu, D Hsu, P S Thiagarajan. Probabilistic Approximations of ODEs based Bio-Pathway Dynamics. Theoretical Computer Science, 412(21):2188-2206 (2011).
PDF Supplementary Website - B Liu, P S Thiagarajan, D Hsu. Probabilistic Approximations of Signaling Pathway Dynamics. Computational Methods in Systems Biology (CMSB) , Bologna, Italy (2009). Springer, LNCS:5688, pp. 251-265.
PDF Supplementary Website - B Liu. Statistical analysis of partially calibrated bio-pathway models. HPC E-newsletter Issue No. 24. (HPC Challenge 2009 Winning Project) (2009).
PDF - T Zhu, P Korshunov, B Liu, W T Ooi. Plasma: A Scripting Language for Processing Media Streams. ACM/SPIE Multimedia Computing and Networking (MMCN), San Jose, US (2007). Proceedings of SPIE:6504, pp. 65040Q.
PDF - B Liu, W T Ooi. SLIME: A Tool for Composing Live and Stored Media. In Proc. of the 11th NUROP Congress, Singapore (2006).
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In Preparation
Conference Abstracts/Posters
- B Liu, P S Thiagarajan, J L Ding, I Bahar Systems-level Insights into Immune Regulation from Quantitative Modeling. Computational & Systems Biology and Immunology Joint Retreat, Pittsburgh, US. (2017)
PDF - B Liu, J Garcia-Olivares, S M Underhill, S G Amara, I Bahar. Computational Modeling of Amphetamine-stimulated Dopamine Dynamics. Brain Day, Pittsburgh, US (2016).
PDF - B Liu, Q Liu, S Palaniappan, I Bahar, P S Thiagarajan, J L Ding. TLR3-TLR7 Pathway Crosstalk Confers Innate Immune Memory and Homeostasis. Integrative Systems Biology Symposium, Pittsburgh, US (2015).
PDF - C Kaya, B Liu, J R Faeder, I Bahar. Unified Model of Synaptic Transmission. Biophysical Society 59th Annual Meeting, Baltimore, Maryland (2015).
PDF - B Liu, T A Wall, I Bahar. Stochastic Modeling of Apoptosis-Autophagy Crosstalk. Gorden Research Conference: Stochastic Physics in Biology, Ventura, US (2015).
PDF - 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).
PDF - 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).
PDF - 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).
PDF - 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).
PDF - B Liu, D Hsu, P S Thiagarajan. Probabilistic Approximations of Bio-pathway Dynamics. In the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB) Poster Book, Tucson, US (2009).
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Book
- B Liu. Computational Modeling of Biological Pathways: Probabilistic Approximation and Analysis Techniques. LAP LAMBERT Academic Publishing, ISBN-10: 3847372114, Jan 2012. (176 pages)
Theses
- B Liu. Probabilistic Approximation and Analysis Techniques for Bio-Pathway Models. PhD Thesis (2011).
PDF - B Liu. Computational Modeling and Analysis of Biological Pathways. Bachelor's Thesis (2006).
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Software
PADA: a PAthway Dynamics Approximator, which can approximate the dynamics of ODE-based biopathway models using dynamic Bayesian networks. It supports System Biology Mark-up Language (SBML) format and multiple platforms.
PADA-GPU: a GPU-based implementation of PADA. It supports the NIVIDA Tesla 2.0 (Fermi) platform.
SLIME: a Stored and LIve Media Editor written in Tcl/Tk.
Talks
- Systems-level Insights into Cell Death from Quantitative Modeling. CMCR Seminar, October 2017, Pittsburgh, US.
- Decipher Biological Machinery . Sun Yat-sen University University, June 2017, Zhuhai, China.
- Model Checking, Systems Biology, and Better Therapeutics. Fudan University, December 2016, Shanghai, China.
- Model Checking, Systems Biology, and Better Therapeutics. Soochow University, December 2016, Suzhou, China.
- Parameter Estimation of Rule-based Models Using Statistical Model Checking. IEEE International Conference on Bioinformatics and Biomedicine (BIBM),, December 2016, Shenzhen, China.
- Systems-level Insights into Cellular Regulation from Quantitative Modeling. National Institute of Mental Health, August 2016, Washington DC, US.
- Model Checking Biology Systems. UPPDA P2P, October 2015, Pittsburgh, US.
- Towards Prostate Personalized Cancer Therapy Using Delta-Reachability Analysis. The 18th ACM International Conference on Hybrid Systems: Computation and Control (HSCC), April 2015, Seattle, US.
- Computational Modeling of the Crosstalk Between Autophagy and Apoptosis. Biophysical Theory Club, March 2015, Pittsburgh, US.
- Mathematical Modeling of TLR3-TLR7 Signaling Crosstalk. CSB-Squared, December 2014, Pittsburgh, US.
- Parameter Identification using Model Checking for Systems Biology. Clarke Symposium, September 2014, Pittsburgh, US.
- Parameter Identification using Delta-Decisions for Hybrid Systems in Biology. CMACS/AVACS Workshop, November 2013, Pittsburgh, US.
- Approximation and Verification Techniques for Biology Pathway Modeling. National Heart, Lung, and Blood Institute, NIH, November 2013, Washington DC, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. CMACS Seminar, November 2012, Pittsburgh, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. Biophysical Theory Club, October 2012, Pittsburgh, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. INRIA Contraintes Seminar, April 2012, Paris, France.
- Probabilistic Approximation Techniques for Biopathway Modeling. Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, February 2012, Singapore.
- A Platform-aware GPU Realization of A Systems Biology Application. The 3nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, April 2011, Singapore.
- Computational and Experimental Study of Complement System. The 2nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, February 2010, Tokyo, Japan.
- Probabilistic Approximations of ODE-based Bio-Pathway Dynamics. Applied and Computational Math Seminar, February 2010, Singapore.
- Statistical Analysis of Partially Calibrated Bio-pathways Models. High Performance Computing Challenge Ceremony, November 2009, Singapore.
- Probabilistic Approximations of Signaling Pathway Dynamics. the 7th International Conference on Computational Methods in Systems Biology (CMSB), September 2009, Bologna, Italy.
- Probabilistic Approximations of Signaling Pathway Dynamics. The 1st NGS Student Symposium, February 2009, Singapore.
- Stochastic Approximations of Signaling Pathway Dynamics. The 1st NUS-U.Tokyo Joint Workshop on Computational Systems Biology, September 2008, Singapore.
Professional Services
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 :
International Conference on Computational Chemistry and Biology (ICCCB'17), Barcelona, Spain, 2017.
Computational & Systems Biology-Immunology Joint Retreat (CSBIR'17), Pittsburgh, US, 2017.
IEEE International Conference on Bioinformatics and Biomedicine (BIBM'16) FMBBS Workshop, Shenzhen, China, 2016.
The 14th conference on Computational Methods in Systems Biology (CMSB'16), University of Cambridge, UK, 2016.
The 11th International Conference on Artificial Intelligence Applications and Innovations (AIAI'15), Bayonne/Biarritz, France, 2015.
Workshop on Signal Processing, Image Processing and Pattern Recognition (SIPR'15), Kochi, India, 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
Integrative Biology
PLoS One
BMC Systems Biology
Chaos: An Interdisciplinary Journal of Nonlinear Science
Journal of Theoretical Biology
BioSystems
Mathematical Biosciences
International Journal of Computer Assisted Radiology and Surgery
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)
International Conference on Computer Aided Verification (CAV)
ACM/IEEE Symposium on Logic in Computer Science (LICS)
International Symposium on Automated Technology for Verification and Analysis (ATVA)
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)
Education
- 2006 - 2011, PhD Computational Systems Biology, National University of Singapore
- 2002 - 2006, Bachelor of Computer Science, National University of Singapore
Misc
My Erdös number is 4.
➚ David Hsu ➙ Rajeev Motwani ➙ Yoshiharu Kohayakawa ➘
Bing Liu ➙ Edmund M. Clarke ➙ Robert P. Kurshan ➙ Andrew M. Odlyzko ➙ Paul Erdös
➘ P.S. Thiagarajan ➙ Rohit J. Parikh ➙ Melvyn B. Nathanson ➚