Lei Liu

Summary

Affiliation: Shanghai Institutes for Biological Sciences
Country: China

Publications

  1. pmc MetaBinG: using GPUs to accelerate metagenomic sequence classification
    Peng Jia
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e25353. 2011
  2. pmc An integrated pharmacokinetics ontology and corpus for text mining
    Heng yi Wu
    Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
    BMC Bioinformatics 14:35. 2013
  3. ncbi request reprint MicroRNA mediated network and DNA methylation in colorectal cancer
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, China
    Protein Pept Lett 20:352-63. 2013
  4. pmc Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example
    Ru Dong Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Syst Biol 6:S11. 2012
  5. pmc An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis
    Ru Dong Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Syst Biol 5:S12. 2011
  6. doi request reprint The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Int J Comput Biol Drug Des 4:5-18. 2011
  7. doi request reprint Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells
    Lei Liu
    The State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nat Cell Biol 14:177-85. 2012
  8. pmc Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e33393. 2012
  9. doi request reprint A novel variant of Oct3/4 gene in mouse embryonic stem cells
    Chang long Guo
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Stem Cell Res 9:69-76. 2012
  10. pmc Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms
    Kang Tu
    Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, PR China
    Nucleic Acids Res 37:5969-80. 2009

Collaborators

Detail Information

Publications19

  1. pmc MetaBinG: using GPUs to accelerate metagenomic sequence classification
    Peng Jia
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 6:e25353. 2011
    ..MetaBinG is publicly available at http://cbb.sjtu.edu.cn/~ccwei/pub/software/MetaBinG/MetaBinG.php...
  2. pmc An integrated pharmacokinetics ontology and corpus for text mining
    Heng yi Wu
    Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
    BMC Bioinformatics 14:35. 2013
    ....
  3. ncbi request reprint MicroRNA mediated network and DNA methylation in colorectal cancer
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, China
    Protein Pept Lett 20:352-63. 2013
    ..This study sheds lights on the regulatory mechanisms in CRC and we provide some insights on the epigenetic of CRC...
  4. pmc Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example
    Ru Dong Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Syst Biol 6:S11. 2012
    ..Also, the manner of individual sensitivity analysis in most flux-analysis approaches cannot reveal the simultaneous impacts on collateral components as well as the overall impact on the system, thus lacking in system-level perspective...
  5. pmc An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis
    Ru Dong Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Syst Biol 5:S12. 2011
    ..But this model did not integrate the metabolic regulatory effects of transcriptional control and other complex factors. It also left out the information of some key intermediates (e.g. butyryl-phosphate)...
  6. doi request reprint The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Int J Comput Biol Drug Des 4:5-18. 2011
    ..Then, the relationship between dysfunctional networks and HCV infection was analysed. Our results may help understand the mechanisms of HCV-induced malignant transformation and provide clues to cirrhosis and HCC therapy or prevention...
  7. doi request reprint Mitochondrial outer-membrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells
    Lei Liu
    The State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nat Cell Biol 14:177-85. 2012
    ..Mechanistic studies further revealed that hypoxia induced dephosphorylation of FUNDC1 and enhanced its interaction with LC3 for selective mitophagy. Our findings thus offer insights into mitochondrial quality control in mammalian cells...
  8. pmc Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e33393. 2012
    ..It has not escaped our notice that the method can be applied to identify the genes of other diseases as well...
  9. doi request reprint A novel variant of Oct3/4 gene in mouse embryonic stem cells
    Chang long Guo
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Stem Cell Res 9:69-76. 2012
    ..These findings will be important for further analysis of the epigenetic mechanisms of reprogramming and highlight the necessity of discriminating Oct4 isoforms in future stem cell research...
  10. pmc Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms
    Kang Tu
    Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, PR China
    Nucleic Acids Res 37:5969-80. 2009
    ..Our results reinforce the growing awareness that non-coding RNAs may play key roles in the transcription regulatory network. Our strategy could be applied to reveal conditional regulatory pathways in many more cellular contexts...
  11. pmc TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
    Qi Liu
    School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
    BMC Bioinformatics 11:S5. 2010
    ..However, the low overlap between binding targets of a TF and the affected genes of the TF knockout limits the power of those methods...
  12. pmc Role of operon aaoSo-mutT in antioxidant defense in Streptococcus oligofermentans
    Peng Zhou
    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
    PLoS ONE 7:e38133. 2012
    ..In this way, we were able to determine the role of the aao(So)-mutT operon in antioxidant defense in S. oligofermentans...
  13. doi request reprint Rapid conversion of human ESCs into mouse ESC-like pluripotent state by optimizing culture conditions
    Qi Gu
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Protein Cell 3:71-9. 2012
    ..Thus the rapid conversion established a naïve pluripotency in human ESCs like mouse ESCs, and provided a new model to study the regulation of pluripotency...
  14. doi request reprint Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes
    Zhen Wang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Mol Biol Evol 28:1131-40. 2011
    ..Our results imply that phosphorylation may have an essential role in the evolution of vertebrates...
  15. pmc Function of the pyruvate oxidase-lactate oxidase cascade in interspecies competition between Streptococcus oligofermentans and Streptococcus mutans
    Lei Liu
    State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
    Appl Environ Microbiol 78:2120-7. 2012
    ..oligofermentans failed to inhibit S. mutans even though lox was active. In summary, S. oligofermentans develops a Pox-Lox synergy strategy to maximize its H(2)O(2) formation so as to win the interspecies competition...
  16. pmc Direct reprogramming of Sertoli cells into multipotent neural stem cells by defined factors
    Chao Sheng
    State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Cell Res 22:208-18. 2012
    ..In addition, iNSCs can survive and generate synapses following transplantation into the dentate gyrus. Generation of iNSCs may have important implications for disease modeling and regenerative medicine...
  17. pmc Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment
    Jie Wang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    BMC Evol Biol 11:161. 2011
    ..The mechanisms used by plants to coordinate the expression of such transferred genes, as well as other genes in the host nuclear genome, are still poorly understood...
  18. pmc Superoxide flashes: early mitochondrial signals for oxidative stress-induced apoptosis
    Qi Ma
    Joint Laboratory of Apoptosis and Cancer Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    J Biol Chem 286:27573-81. 2011
    ....
  19. pmc Modeling the effects of cell cycle M-phase transcriptional inhibition on circadian oscillation
    Bin Kang
    Laboratory of Systems Biology corrected Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS Comput Biol 4:e1000019. 2008
    ....