Ruoshi Yuan (袁若石)
Ph.D.
Supervisor : Prof. Ping AO.
Office : Room C207 Systems Biomedicine Building, Shanghai Jiao Tong University
Email : rsyuan.acm06 AT gmail.com
Education
2016 now, Postdoc, Department of Systems Biology, Harvard Medical School.
20122016, Ph.D., Department of Biomedical Engineering, Shanghai Jiao Tong University.
Thesis title: Endogenous network hypothesis for cancer and its foundation on nonlinear stochastic dynamics.
20102012, M.S., Department of Computer Science, Shanghai Jiao Tong University
20082011, B.S., Department of Physics, Shanghai Jiao Tong University
20062010, B.S., ACM Honored Class, Department of Computer Science, Shanghai Jiao Tong University
Research
My research interest includes: stochastic and nonlinear dynamics, statistical physics, and mathematical modeling of biological phenomena.

We have worked out several explicit constructions of potential functions in dynamical systems with multiple fixed points, limit cycle, and even chaotic attractor.

Meanwhile, we developed a new stochastic interpretation for stochastic differential equations different from traditional Ito's or Stratonovich's with a clear physical meaning and a correspondence with the deterministic counterpart.

We construct endogenous molecularcellular networks for various cancers. The network dynamics can be written as a set of nonlinear ordinary differential equations or stochastic differential equations. The attractors are understood as different functional states, including normal states and abnormal states such as cancer. Within this model the genesis and progression of cancer may be viewed as stochastic transitions between different attractors.

I create and develop a calculation platform for biological networks including automatically generated network graphs, calculation of attractors of the corresponding Boolean network, and searching stable states of ODEs with multiCPU acceleration. The software will be put online soon.
I am concerning on how to construct the network from the insufficient and noisy biological knowledge and data. Can we find or prove the existence of a robust topological structure inside the biological network based on the current knowledge? Or more generally, is there something that organisms learn to use in the long process of evolution? I think there is; the question is how to describe them mathematically. Our network hypothesis may be a candidate.
Publications
1. Journal Papers:

Yuan, R.S.; Zhu, X.M.; Wang, G.W.; Li, S.T. & Ao, P., Cancer as robust intrinsic state shaped by evolution: a key issues review, Reports on Progress in Physics, 2017, 80 (4), 121

Yuan, R.S.; Tang, Y. & Ao, P., On Uniqueness of "SDE Decomposition" in Atype Stochastic Integration (Comment to P. Zhou and T. Li, J. Chem. Phys. 144, 094109, 2016), The Journal of Chemical Physics, 2016, 145 (14), 147104

Chen, Y.C.; Yuan, R.S.; Ao, P.; Xu, M.J. & Zhu, X.M., Towards Stable Kinetics of Large Metabolic Networks: Nonequilibrium Potential Function Approach, Physical Review E, 2016, 93, 062409

Yuan, R.S.; Zhu, X.M.; Radich, J. P. & Ao, P., From Molecular Interaction to Acute Promyelocytic Leukemia: Calculating Leukemogenesis and Remission from Endogenous MolecularCellular Network, Scientific Reports, 2016, 6, 24307

Wang, G.W.; Su, H.; Yu, H.L.; Yuan, R.S.; Zhu, X.M. & Ao, P., Endogenous Network States Predict Gain or Loss of Functions for Genetic Mutations in Hepatocellular Carcinoma, Journal of the Royal Society Interface, 2016, 13, 20151115

Yuan, R.S.; Ma, S.F.; Zhu, X.M.; Li, J.; Liang, Y.H.; Liu, T.; Zhu, Y.X.; Zhang, B.B.; Tan, S.; Guo, H.J. ; Guan, S.G.; Ao, P. & Zhou G.Q., Core Level Regulatory Network of Osteoblast as Molecular Mechanism for Osteoporosis and Treatment, Oncotarget, 2016, 6923

Tang, Y.; Yuan, R.S. & Ao, P., Anomalous Free Energy Changes Induced by Topology, Physical Review E, 2015, 92, 062129

Tang, Y.; Yuan, R.S.; Chen, J.H. & Ao, P., Work Relations Connecting Nonequilibrium Steady States without Detailed Balance, Physical Review E, 2015, 91, 042108

Zhu, X.M.; Yuan, R.S.; Hood, L. & Ao, P., Endogenous MolecularCellular Hierarchical Modeling of Prostate Carcinogenesis Uncovers Robust Structure, Progress in Biophysics and Molecular Biology, 2015, 117(1): 3042 (Corresponding author)

Tang, Y.; Yuan, R.S.; Chen, J.H. & Ao, P., Controlling SymmetryBreaking States by a Hidden Quantity in Multiplicative Noise, Physical Review E, 2014, 90, 052121

Tang, Y.; Yuan, R.S. & Ao, P., Summing over Trajectories of Stochastic Dynamics with Multiplicative Noise, The Journal of Chemical Physics, 2014, 141 (4), 044125

Tang, Y.; Yuan, R.S. & Ao, P., Nonequilibrium Work Relation Beyond the BoltzmannGibbs Distribution, Physical Review E, 2014, 89, 062112

Hu, J.; Zhu, X.M.; Wang, X.A.; Yuan, R.S.; Zheng, W.; Xu, M.J. & Ao, P., Two Programmed Replicative Lifespans of Saccharomyces cerevisiae Formed by Endogenous MolecularCellular Network, Journal of Theoretical Biology, 2014, in press

Ma, Y.A.; Tan, Q.J.; Yuan, R.S.; Yuan, B. & Ao, P., Potential Function in a Continuous Dissipative Chaotic System: Decomposition Scheme and Role of Strange Attractor, International Journal of Bifurcation and Chaos, 2014, 24 (2), 1450015 (Arxiv preprint arXiv:1208.1654)

Yuan, R.S.; Ma, Y.A.; Yuan, B. & Ao, P., Lyapunov Function as Potential Function: A Dynamical Equivalence, Chinese Physics B. 2014, 23 (1): 010505 (Arxiv preprint arXiv:1012.2721)

Yuan, R.S.; Wang, X.A.; Ma, Y.A.; Yuan, B. & Ao, P., Exploring a Noisy van der Pol Type Oscillator with a Stochastic Approach, Physical Review E, 2013, 87 (6), 062109 (Arxiv preprint arXiv:1210.7284)

Tang, Y.; Yuan, R.S. & Ma, Y.A., Dynamical Behaviors Determined by the Lyapunov Function in Competitive LotkaVolterra Systems, Physical Review E, 2013, 87 (1), 012708 (Cofirst author, Arxiv preprint arXiv:1210.7662)

Yuan, R.S. & Ao, P., Beyond Itô versus Stratonovich, Journal of Statistical Mechanics: Theory and Experiment, 2012, P07010 (Arxiv preprint arXiv:1203.6600)

Shi, J.H.; Chen, T.Q.; Yuan, R.S.; Yuan, B. & Ao, P., Relation of a New Interpretation of Stochastic Differential Equations to Ito Process, Journal of Statistical Physics, 2012, 148 (3), 579590 (Arxiv preprint arXiv:1111.2987)

Sun, T.Z.; Yuan, R.S.; Xu, W.; Zhu, F. & Shen, P.P., Exploring a Minimal Twocomponent p53 Model, Physical Biology, 2010, 7 (3), 036008
2. Conference:

Wang, X.A.; Yuan, R.S.; Yuan, B. & Ao, P., A New Numerical Method to Construct Global Lyapunov Function for Complex Attractors, Proceedings of the 32th Chinese Control Conference, 2013, accepted

Yuan, R.S.; Ma, Y.A.; Yuan, B. & Ao, P., Potential Function in Dynamical Systems and the Relation with Lyapunov Function, Proceedings of the 30th Chinese Control Conference, 2011, 6573  6580
3. Preprints:

Ma, Y.A.; Yuan, R.S.; Yuan, B. & Ao, P., Lyapunov Functions in Piecewise Linear Systems: From Fixed Point to Limit Cycle, Arxiv preprint arXiv:1306.6880, 2013

Yuan, R.S. & Ao, P., Zero Mass Limit and Its Experimental Test, Arxiv preprint arXiv:1202.5765, 2012
Talks and Posters

Gordon Research Conference: Stochastic Physics in Biology, Jan. 11st16th 2015, Ventura Beach, CA, USA, Poster

Chinese Physical Society Fall Meeting, Sept. 13rd15th 2013, Xiamen China, Talk (Setp. 15th, 9:30~9:45) and Poster

Small System Nonequilibrium Fluctuations, Dynamics and Stochastics, and Anomalous Behavior, Friday July 12nd 2013, KITPC Beijing China, Talk

The International Conference on Noise and Fluctuations, June 24th28th, 2013, Montpellier (France), Poster1, Poster2
Research Experience
20142015, Visiting Scholar, Department of Systems Biology, Harvard Medical School, advised by Prof. Johan Paulsson.
2009present, Research Assistant, Systems Biology Lab, advised by Prof. Ping Ao.
20092012, Research Assistant, Biocomputing and Bioinformatics Lab, advised by Prof. Bo Yuan.
2009, Research Assistant, Microsoft Research Asia, advised by Researcher Bin Gao.
20082009, Research Assistant, APEX Lab, advised by Prof. Yong Yu.