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.
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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).
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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).
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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)
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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)
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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)
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