Bio

Professional Education


  • Doctor of Philosophy, Peking University (2010)
  • Bachelor of Mathematics, Peking University (2005)

Stanford Advisors


Research & Scholarship

Lab Affiliations


Publications

Journal Articles


  • Identifying critical transitions of complex diseases based on a single sample. Bioinformatics Liu, R., Yu, X., Liu, X., Xu, D., Aihara, K., Chen, L. 2014; 30 (11): 1579-1586

    Abstract

    Unlike traditional diagnosis of an existing disease state, detecting the pre-disease state just before the serious deterioration of a disease is a challenging task, because the state of the system may show little apparent change or symptoms before this critical transition during disease progression. By exploring the rich interaction information provided by high-throughput data, the dynamical network biomarker (DNB) can identify the pre-disease state, but this requires multiple samples to reach a correct diagnosis for one individual, thereby restricting its clinical application.In this article, we have developed a novel computational approach based on the DNB theory and differential distributions between the expressions of DNB and non-DNB molecules, which can detect the pre-disease state reliably even from a single sample taken from one individual, by compensating insufficient samples with existing datasets from population studies. Our approach has been validated by the successful identification of pre-disease samples from subjects or individuals before the emergence of disease symptoms for acute lung injury, influenza and breast cancer.

    View details for DOI 10.1093/bioinformatics/btu084

    View details for PubMedID 24519381

  • Early Diagnosis of Complex Diseases by Molecular Biomarkers, Network Biomarkers, and Dynamical Network Biomarkers MEDICINAL RESEARCH REVIEWS Liu, R., Wang, X., Aihara, K., Chen, L. 2014; 34 (3): 455-478

    Abstract

    Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high-throughput data (or big data). Detailed comparisons of various types of biomarkers as well as their applications are also discussed.

    View details for DOI 10.1002/med.21293

    View details for Web of Science ID 000333677600001

    View details for PubMedID 23775602

  • Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis BRIEFINGS IN BIOINFORMATICS Li, M., Zeng, T., Liu, R., Chen, L. 2014; 15 (2): 229-243

    Abstract

    Identifying early warning signals of critical transitions during disease progression is a key to achieving early diagnosis of complex diseases. By exploiting rich information of high-throughput data, a novel model-free method has been developed to detect early warning signals of diseases. Its theoretical foundation is based on dynamical network biomarker (DNB), which is also called as the driver (or leading) network of the disease because components or molecules in DNB actually drive the whole system from one state (e.g. normal state) to another (e.g. disease state). In this article, we first reviewed the concept and main results of DNB theory, and then applied the new method to the analysis of type 2 diabetes mellitus (T2DM). Specifically, based on the temporal-spatial gene expression data of T2DM, we identified tissue-specific DNBs corresponding to the critical transitions occurring in liver, adipose and muscle during T2DM development and progression. Actually, we found that there are two different critical states during T2DM development characterized as responses to insulin resistance and serious inflammation, respectively. Interestingly, a new T2DM-associated function, i.e. steroid hormone biosynthesis, was discovered, and those related genes were significantly dysregulated in liver and adipose at the first critical transition during T2DM deterioration. Moreover, the dysfunction of genes related to responding hormone was also detected in muscle at the similar period. Based on the functional and network analysis on pathogenic molecular mechanism of T2DM, we showed that most of DNB genes, in particular the core ones, tended to be located at the upstream of biological pathways, which implied that DNB genes act as the causal factors rather than the consequence to drive the downstream molecules to change their transcriptional activities. This also validated our theoretical prediction of DNB as the driver network. As shown in this study, DNB can not only signal the emergence of the critical transitions for early diagnosis of diseases, but can also provide the causal network of the transitions for revealing molecular mechanisms of disease initiation and progression at a network level.

    View details for DOI 10.1093/bib/bbt027

    View details for Web of Science ID 000333249500008

    View details for PubMedID 23620135

  • Deciphering early development of complex diseases by progressive module network. Methods (San Diego, Calif.) Zeng, T., Zhang, C. C., Zhang, W., Liu, R., Liu, J., Chen, L. 2014; 67 (3): 334-43

    Abstract

    There is no effective cure nowadays for many complex diseases, and thus it is crucial to detect and further treat diseases in earlier stages. Generally, the development and progression of complex diseases include three stages: normal stage, pre-disease stage, and disease stage. For diagnosis and treatment, it is necessary to reveal dynamical organizations of molecular modules during the early development of the disease from the pre-disease stage to the disease stage. Thus, we develop a new framework, i.e. we identify the modules presenting at the pre-disease stage (pre-disease module) based on dynamical network biomarkers (DNBs), detect the modules observed at the advanced stage (disease-responsive module) by cross-tissue gene expression analysis, and finally find the modules related to early development (progressive module) by progressive module network (PMN). As an application example, we used this new method to analyze the gene expression data for NOD mouse model of Type 1 diabetes mellitus (T1DM). After the comprehensive comparison with the previously reported milestone molecules, we found by PMN: (1) the critical transition point was identified and confirmed by the tissue-specific modules or DNBs relevant to the pre-disease stage, which is considered as an earlier event during disease development and progression; (2) several key tissues-common modules related to the disease stage were significantly enriched on known T1DM associated genes with the rewired association networks, which are marks of later events during T1DM development and progression; (3) the tissue-specific modules associated with early development revealed several common essential progressive genes, and a few of pathways representing the effect of environmental factors during the early T1DM development. Totally, we developed a new method to detect the critical stage and the key modules during the disease occurrence and progression, and show that the pre-disease modules can serve as warning signals for the pre-disease state (e.g. T1DM early diagnosis) whereas the progressive modules can be used as the therapy targets for the disease state (e.g. advanced T1DM), which were also validated by experimental data.

    View details for DOI 10.1016/j.ymeth.2014.01.021

    View details for PubMedID 24561825

  • Detecting early-warning signals of type 1 diabetes and its leading biomolecular networks by dynamical network biomarkers BMC MEDICAL GENOMICS Liu, X., Liu, R., Zhao, X., Chen, L. 2013; 6

    Abstract

    Type 1 diabetes (T1D) is a complex disease and harmful to human health, and most of the existing biomarkers are mainly to measure the disease phenotype after the disease onset (or drastic deterioration). Until now, there is no effective biomarker which can predict the upcoming disease (or pre-disease state) before disease onset or disease deterioration. Further, the detail molecular mechanism for such deterioration of the disease, e.g., driver genes or causal network of the disease, is still unclear.In this study, we detected early-warning signals of T1D and its leading biomolecular networks based on serial gene expression profiles of NOD (non-obese diabetic) mice by identifying a new type of biomarker, i.e., dynamical network biomarker (DNB) which forms a specific module for marking the time period just before the drastic deterioration of T1D.Two dynamical network biomarkers were obtained to signal the emergence of two critical deteriorations for the disease, and could be used to predict the upcoming sudden changes during the disease progression. We found that the two critical transitions led to peri-insulitis and hyperglycemia in NOD mice, which are consistent with other independent experimental results from literature.The identified dynamical network biomarkers can be used to detect the early-warning signals of T1D and predict upcoming disease onset before the drastic deterioration. In addition, we also demonstrated that the leading biomolecular networks are causally related to the initiation and progression of T1D, and provided the biological insight into the molecular mechanism of T1D. Experimental data from literature and functional analysis on DNBs validated the computational results.

    View details for DOI 10.1186/1755-8794-6-S2-S8

    View details for Web of Science ID 000318871600009

    View details for PubMedID 23819540

  • SOME COMMON EXPRESSIONS AND NEW BIFURCATION PHENOMENA FOR NONLINEAR WAVES IN A GENERALIZED mKdV EQUATION INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS Liu, R., Yan, W. 2013; 23 (3)
  • THE EXPLICIT NONLINEAR WAVE SOLUTIONS OF THE GENERALIZED b-EQUATION COMMUNICATIONS ON PURE AND APPLIED ANALYSIS Rui, L. 2013; 12 (2): 1029-1047
  • Existence and Asymptotic Behavior of Traveling Wave Fronts for a Time-Delayed Degenerate Diffusion Equation ABSTRACT AND APPLIED ANALYSIS Yan, W., Liu, R. 2013
  • Some Explicit Expressions and Interesting Bifurcation Phenomena for Nonlinear Waves in Generalized Zakharov Equations ABSTRACT AND APPLIED ANALYSIS Li, S., Liu, R. 2013
  • Identifying critical transitions and their leading biomolecular networks in complex diseases SCIENTIFIC REPORTS Liu, R., Li, M., Liu, Z., Wu, J., Chen, L., Aihara, K. 2012; 2

    Abstract

    Identifying a critical transition and its leading biomolecular network during the initiation and progression of a complex disease is a challenging task, but holds the key to early diagnosis and further elucidation of the essential mechanisms of disease deterioration at the network level. In this study, we developed a novel computational method for identifying early-warning signals of the critical transition and its leading network during a disease progression, based on high-throughput data using a small number of samples. The leading network makes the first move from the normal state toward the disease state during a transition, and thus is causally related with disease-driving genes or networks. Specifically, we first define a state-transition-based local network entropy (SNE), and prove that SNE can serve as a general early-warning indicator of any imminent transitions, regardless of specific differences among systems. The effectiveness of this method was validated by functional analysis and experimental data.

    View details for DOI 10.1038/srep00813

    View details for Web of Science ID 000312254500001

    View details for PubMedID 23230504

  • Existence and critical speed of traveling wave fronts in a modified vector disease model with distributed delay JOURNAL OF DYNAMICAL AND CONTROL SYSTEMS Yan, W., Liu, R. 2012; 18 (3): 355-378
  • Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers SCIENTIFIC REPORTS Chen, L., Liu, R., Liu, Z., Li, M., Aihara, K. 2012; 2

    Abstract

    Considerable evidence suggests that during the progression of complex diseases, the deteriorations are not necessarily smooth but are abrupt, and may cause a critical transition from one state to another at a tipping point. Here, we develop a model-free method to detect early-warning signals of such critical transitions, even with only a small number of samples. Specifically, we theoretically derive an index based on a dynamical network biomarker (DNB) that serves as a general early-warning signal indicating an imminent bifurcation or sudden deterioration before the critical transition occurs. Based on theoretical analyses, we show that predicting a sudden transition from small samples is achievable provided that there are a large number of measurements for each sample, e.g., high-throughput data. We employ microarray data of three diseases to demonstrate the effectiveness of our method. The relevance of DNBs with the diseases was also validated by related experimental data and functional analysis.

    View details for DOI 10.1038/srep00342

    View details for Web of Science ID 000302127600001

    View details for PubMedID 22461973

  • COEXISTENCE OF MULTIFARIOUS EXACT NONLINEAR WAVE SOLUTIONS FOR GENERALIZED b-EQUATION INTERNATIONAL JOURNAL OF BIFURCATION AND CHAOS Liu, R. 2010; 20 (10): 3193-3208
  • SEVERAL NEW TYPES OF SOLITARY WAVE SOLUTIONS FOR THE GENERALIZED CAMASSA-HOLM-DEGASPERIS-PROCESI EQUATION COMMUNICATIONS ON PURE AND APPLIED ANALYSIS Liu, R. 2010; 9 (1): 77-90

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