Research Interests

Human Microbiome and Community Ecology. 
Human-associated microbes form a very complex and dynamic ecosystem, which can be altered by drastic diet change, medical interventions, and many other factors. The alterability of our microbiome offers a promising future for a variety of microbiome-based therapies such as ingesting probiotics or prebiotics, and fecal microbiota transplantation, in treating diseases associated with disrupted microbiota. Despite successful cases for each strategy, we still lack a complete understanding of which strategy works best for a given individual, and whether there are long-term safety issues. Indeed, the complex topology and dynamics of the ecological network underlying the human gut microbiota render the quantitative study of microbiome-based therapies extremely difficult. The future of microbiome-based therapies will be bright only if we fully understand the structure and dynamics of our gut microbial ecosystems. Our long-term objective is to construct a modeling framework based on community ecology and dynamical systems to better design microbiome-based therapies.

Selected Publications/Preprints:

  1. Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, Liu Y-YUniversality of Human Microbial Dynamics. Nature 2016;534:259-262.
  2. Gibson TE, Bashan A, Cao H-T, Weiss ST, Liu Y-YOn the Origins and Control of Community Types in the Human Microbiome. PLOS Computational Biology (highlighted in the journal's homepage) 2016;12(2):e1004688.
  3. McGeachie MJ, Sordillo JE, Gibson T, Weinstock GM, Liu Y-Y, Gold DR, Weiss ST, Litonjua A. Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks. Scientific Reports 2016;6:20369.
  4. Cao H-T, Gibson T, Bashan A, Liu Y-YPitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data. BioEssays 2017;39(2):1600188.
  5. Yan G, Martinez ND, Liu Y-YStability of Degree Heterogeneous Ecological Networks. Journal of the Royal Society Interface 2017;14(131):20170189. 
  6. Xiao Y, Angulo MT, Friedman J, Waldor MK, Weiss ST, Liu Y-YMapping the ecological networks of microbial communitiesNature Communications  2017;8:2042.
  7. Chen Y, Angulo MT, Liu Y-YRevealing complex ecological dynamics via symbolic regression. bioRxiv's Version
  8. Angulo MT, Moog CH, Liu Y-YControlling microbial communities: a theoretical framework. bioRxiv's Version
  9. Tian L, Wu A-K, Friedman J, Waldor MK, Weiss ST, Liu Y-YDeciphering Functional Redundancy in the Human MicrobiomebioRxiv's Version
  10. Gibson TE, Carey V, Bashan A, Hohmann EL, Weiss ST, Liu Y-YOn the Stability Landscape of the Human Gut Microbiome: Implications for Microbiome-based TherapiesbioRxiv's Version
  11. Fan Y, Xiao Y, Momeni B, Liu Y-YHorizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial SystemsbioRxiv's Version
  12. Li P, Zhang T, Xiao Y, Tian L, Cui B, Ji G, Liu Y-Y, Zhang F. When to start the second fecal microbiota transplantation for patients with active Crohns disease: a pragmatic study,. Submitted.
  13. Sonawane AR, Tian L, Chu C, Qiu X, Wang L, Holden-Wiltse J, Grier A, Gill SR, Caserta MT, Walsh EE, Mariani TJ, Weiss ST, Silverman EK, Glass K, Liu Y-YNetwork-based Integrative Analysis of Nasal Microbiome, Host CD4 T Cell Transcriptome, and Clinical Outcomes in Infants with Respiratory Syncytial Virus Infection. In Preparation;
Control Principles of Complex Systems. 
A reflection of our ultimate understanding of a complex networked system is our ability to control its behavior. Typically, control has multiple prerequisites: it requires an accurate map of the network that governs the interactions between the system’s components, a quantitative description of the dynamical laws that govern the temporal behavior of each component, and an ability to influence the state and temporal behavior of a selected subset of the components. With deep roots in dynamical systems and control theory, notions of control and controllability have taken a new life recently in the study of complex networks, inspiring several fundamental questions: What are the control principles of complex systems? How do networks organize themselves to balance control with functionality? Uncovering the control principles of complex networked systems can help us explore and ultimately understand the fundamental laws that govern their behavior.

Selected Publications/Preprints:

  1. Liu Y-Y, Slotine J-J, Barabási A-L. Controllability of complex networks. Nature (featured as a cover story) 2011;473:167–173.
  2. Slotine J-J, Liu Y-YComplex networks: The missing link. Nature Physics 2012;8:512–513.
  3. Liu Y-Y, Slotine J-J, Barabási A-L. Control Centrality and Hierarchical Structure in Complex Networks. PLOS ONE 2012;7:e44459.
  4. Liu Y-Y, Slotine J-J, Barabási A-L. Observability of complex systemsPNAS (featured as a cover story) 2013;110:2460–2465.
  5. Pósfai M, Liu Y-Y, Slotine J-J, Barabási A-L. Effect of correlations on network controllability. Scientific Reports 2013;3:1067
  6. Jia T, Liu Y-Y, Csóka E, Pósfai M, Slotine J-J, Barabási A-L. Emergence of bimodality in controlling complex networks. Nature Communications 2013;4:2002.
  7. Gao J, Liu Y-Y, D’Souza R, Barabási A-L. Target Control of Complex Networks. Nature Communications 2014;5:5415.
  8. Yan G, Tsekenis G, Barzel B, Slotine J-J, Liu Y-Y, Barabási A-L. Spectrum of Controlling and Observing Complex Networks. Nature Physics 2015;11:779-786.
  9. Zhao C, Wang W-X, Liu Y-Y, Slotine J-J. Individual dynamics induces symmetry in network controllability. Scientific Reports 2015;5(8422):1-5. 
  10. Basler G, Nikoloski Z, Larhlimi A, Barabási A-L, Liu Y-YControl of Fluxes in Metabolic Networks. Genome Research (featured as a cover story) 2016;26:956-968.
  11. Vinayagam A, Gibson TE, Lee H-J, Yilmazel B, Roesel C, Hu Y, Kwon Y, Sharma A, Liu Y-Y, Perrimon N, Barabási A-L. Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets. PNAS 2016;113(18):4976-4981.
  12. Liu Y-Y, Barabási A-L. Control Principles of Complex Systems. Reviews of Modern Physics 2016;88(3):053006.
  13. Li A, Cornelius S, Liu Y-Y, Wang L, Barabási A-L. The Fundamental Advantages of Temporal Networks. Science 2017;358(6366):1042-1046.
  14. Li A, Cornelius S, Liu Y-Y, Wang L, Barabási A-L. Control energy scaling in temporal networks. arXiv's Version 
  15. Sharma A, Halu A, Decano JL, Menche J, Liu Y-Y, Fadista J, Santolini M, Padi M, Weiss ST, Vidal M, Silverman EK, Aikawa M, Barabási A-L, Groop L, Loscalzo J. Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genesbioRxiv's Version

 

Complex Networks: Structure and Dynamics.
We are interested in the intricate interplay between the structure and dynamics of complex networks. In particular, using tools from statistical physics and graph theory, we studied various percolation transitions on complex networks, revealing their implications in dynamical processes on networked systems. We explored the origins of network motifs --- the overrepresented interconnection patterns observed in various real-world networks, finding that network motifs naturally emerge from interconnection patterns that favor stability. We also studied the fundamental limitations in reconstructing networks from measured temporal data of complex dynamical systems. Counterintuitively, we find that reconstructing any property of the interaction matrix is generically as difficult as reconstructing the interaction matrix itself, requiring equally informative temporal data. 

Selected Publications/Preprints:

  1. Liu Y-Y, Csóka E, Zhou H, Pósfai M. Core percolation on complex networks. Physical Review Letters. 2012;109:205703.
  2. Zhao J-H, Zhou H-J, Liu Y-YInducing effect on the percolation transition in complex networks. Nature Communications 2013;4:2412.
  3. Angulo MT, Liu Y-Y, Slotine J-J. Network motifs emerge from interconnections that favor stability. Nature Physics 2015;11:848-852.
  4. Barzel B, Liu Y-Y, Barabási A-L. Constructing minimal models for complex system dynamics. Nature Communications 2015;6:7186.
  5. Tian L, Bashan A, Shi D-N, Liu Y-YArticulation Points in Complex Networks. Nature Communications 2017;8:14223.
  6. Cao H-T, Gibson TE, Mou S, Liu Y-YImpacts of Network Topology on the Performance of a Distributed Algorithm Solving Linear Equations. Proceedings of the 55th IEEE Conference on Decision and Control (CDC), 2016; arXiv's Version
  7. Angulo MT, Moreno JA, Barabási A-L, Liu Y-YFundamental limitations of network reconstruction. Journal of the Royal Society Interface 2017;14(127):20160966.
  8. Wu A-K, Tian L, Liu Y-YBridges in Complex Networks. Physical Review E 2018;97:012307.
  9. Coutinho BC, Zhou H-J, Liu Y-YPercolations on HypergraphsarXiv Version
  10. Angulo MT, Lippner G, Liu Y-Y, Barabási A-L. Sensitivity of Complex NetworksarXiv Version
  11. Wu M, Zhang Y, He S, Chen J, Sun Y, Liu Y-YA General Framework of Studying Eigenvector Multicentrality in Multilayer Networks. arXiv's Version

 

Bioinformatics and Machine Learning.

The exponential growth of the amount of biological data available today prompts us to adopt and develop machine techniques to transform all these heterogeneous data into biological knowledge and testable models. We have been working biomedical data analysis using various machine learning techniques, e.g., hidden Markov modeling, network-based clustering, Bayesian network, consensus clustering, echo state networks. We are genearlly interested in integrative analysis of multi-omics data. Currently, we are interested in exploring the impact of network structure of artificial neural networks on their performance.   

ECC

Selected Publications/Preprints:

  1. Liu Y, Park J, Dahmen KA, Chemla YR, Ha T. A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis. The Journal of Physical Chemistry B 2010;114:5386–5403.
  2. McDonald M-L, Mattheisen M, Cho M, Liu Y-Y, Harshfield B, Hersh C, Bakke P, Gulsvik A, Lange C, Beaty T, Silverman E. Beyond GWAS in COPD: Probing the Landscape between Gene-Set Associations, Genome-Wide Associations and Protein-Protein Interaction Networks. Human Heredity 2014;78(3):131-139.
  3. McGeachie MJ, Sordillo JE, Gibson T, Weinstock GM, Liu Y-Y, Gold DR, Weiss ST, Litonjua A. Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks. Scientific Reports 2016;6:20369.
  4. Chang Y, Glass K, Liu Y-Y, Silverman EK, Crapo J, Tal-Singer R, Bowler RP, Dy J, Cho MH, Castaldi PJ. COPD Subtypes Identified by Network-Based Clustering of Blood Gene Expression. Genomics (featured as a cover story) 2016;107(2-3):51-58.
  5. Liu H, Zhao R, Fang H, Cheng F, Fu Y, Liu Y-YA Novel Clustering Method for Patient Stratification. Bioinformatics 2017;btx167:1-8.
  6. Chen Y, Angulo MT, Liu Y-YRevealing complex ecological dynamics via symbolic regression. bioRxiv's Version
  7. Aceituno PV, Yan G, Liu Y-YTailoring Artificial Neural Networks for Optimal LearningarXiv's Version
  8. Wang X-W, Chen Y, Liu Y-YLink Prediction through Deep Learning. bioRxiv's Version