Luonan Chen

Luonan Chen

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Luonan Chen

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Single-sample landscape entropy reveals the imminent phase transition during disease progression.

Bioinformatics 2019 Oct 9. Epub 2019 Oct 9.

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/bioinformatics/btz758DOI Listing
October 2019

Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers.

J Mol Cell Biol 2019 Aug;11(8):649-664

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/jmcb/mjy059DOI Listing
August 2019

Dynamic edge-based biomarker non-invasively predicts hepatocellular carcinoma with hepatitis B virus infection for individual patients based on blood testing.

J Mol Cell Biol 2019 Aug;11(8):665-677

Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.

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http://dx.doi.org/10.1093/jmcb/mjz025DOI Listing
August 2019

Hierarchical graphical model reveals HFR1 bridging circadian rhythm and flower development in .

NPJ Syst Biol Appl 2019 12;5:28. Epub 2019 Aug 12.

1CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190 China.

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http://dx.doi.org/10.1038/s41540-019-0106-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6690920PMC
August 2019

Computational systems biology for omics data analysis.

Authors:
Luonan Chen

J Mol Cell Biol 2019 Aug;11(8):631-632

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/jmcb/mjz095DOI Listing
August 2019

Targeted genetic screening in mice through haploid embryonic stem cells identifies critical genes in bone development.

PLoS Biol 2019 Jul 2;17(7):e3000350. Epub 2019 Jul 2.

State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1371/journal.pbio.3000350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629148PMC
July 2019

Branched-Chain Amino Acid Metabolic Reprogramming Orchestrates Drug Resistance to EGFR Tyrosine Kinase Inhibitors.

Cell Rep 2019 Jul;28(2):512-525.e6

State Key Laboratory of Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 200120, China; University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.06.026DOI Listing
July 2019

Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model.

Bioinformatics 2019 Jul 26. Epub 2019 Jul 26.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/bioinformatics/btz542DOI Listing
July 2019

The onset mechanism of Parkinson's beta oscillations: A theoretical analysis.

J Theor Biol 2019 Jun 8;470:1-16. Epub 2019 Mar 8.

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2019.03.008DOI Listing
June 2019

Cell-specific network constructed by single-cell RNA sequencing data.

Nucleic Acids Res 2019 Jun;47(11):e62

Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1093/nar/gkz172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582408PMC
June 2019

A vitamin-C-derived DNA modification catalysed by an algal TET homologue.

Nature 2019 May 1;569(7757):581-585. Epub 2019 May 1.

State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.

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http://www.nature.com/articles/s41586-019-1160-0
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http://dx.doi.org/10.1038/s41586-019-1160-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628258PMC
May 2019

Erratum: Lina Lu et al.; Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers. 2017, , 268.

Genes (Basel) 2019 05 2;10(5). Epub 2019 May 2.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.3390/genes10050335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562478PMC
May 2019

Systems biology intertwines with single cell and AI.

BMC Bioinformatics 2019 May 1;20(Suppl 7):204. Epub 2019 May 1.

Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1186/s12859-019-2731-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509840PMC
May 2019

Predicting protein-ligand interactions based on bow-pharmacological space and Bayesian additive regression trees.

Sci Rep 2019 May 22;9(1):7703. Epub 2019 May 22.

College of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.

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http://dx.doi.org/10.1038/s41598-019-43125-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6531441PMC
May 2019

Competitive endogenous RNA is an intrinsic component of EMT regulatory circuits and modulates EMT.

Nat Commun 2019 04 9;10(1):1637. Epub 2019 Apr 9.

Laboratory of Systems Biology, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 200031, Shanghai, China.

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http://www.nature.com/articles/s41467-019-09649-1
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http://dx.doi.org/10.1038/s41467-019-09649-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456586PMC
April 2019

High-Order Correlation Integration for Single-Cell or Bulk RNA-seq Data Analysis.

Front Genet 2019 26;10:371. Epub 2019 Apr 26.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.3389/fgene.2019.00371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497731PMC
April 2019

Cullin5 deficiency promotes small-cell lung cancer metastasis by stabilizing integrin β1.

J Clin Invest 2019 Mar 28;129(3):972-987. Epub 2019 Jan 28.

State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China.

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https://www.jci.org/articles/view/122779
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http://dx.doi.org/10.1172/JCI122779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391098PMC
March 2019

Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity.

Proc Natl Acad Sci U S A 2019 02 11;116(9):3646-3655. Epub 2019 Feb 11.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China;

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http://dx.doi.org/10.1073/pnas.1816086116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397529PMC
February 2019

A Semisupervised Classification Approach for Multidomain Networks With Domain Selection.

IEEE Trans Neural Netw Learn Syst 2019 01 14;30(1):269-283. Epub 2018 Jun 14.

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http://dx.doi.org/10.1109/TNNLS.2018.2837166DOI Listing
January 2019

Detecting early-warning signals of influenza outbreak based on dynamic network marker.

J Cell Mol Med 2019 Jan 19;23(1):395-404. Epub 2018 Oct 19.

School of Mathematics, South China University of technology, Guangzhou, China.

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http://doi.wiley.com/10.1111/jcmm.13943
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http://dx.doi.org/10.1111/jcmm.13943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307766PMC
January 2019

Victors: a web-based knowledge base of virulence factors in human and animal pathogens.

Nucleic Acids Res 2019 Jan;47(D1):D693-D700

Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

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https://academic.oup.com/nar/advance-article/doi/10.1093/nar
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http://dx.doi.org/10.1093/nar/gky999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324020PMC
January 2019

Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis.

BMC Plant Biol 2019 Jan 7;19(1):11. Epub 2019 Jan 7.

Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.

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https://bmcplantbiol.biomedcentral.com/articles/10.1186/s128
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http://dx.doi.org/10.1186/s12870-018-1589-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323737PMC
January 2019

Single cell clustering based on cell-pair differentiability correlation and variance analysis.

Bioinformatics 2018 11;34(21):3684-3694

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/bioinformatics/bty390DOI Listing
November 2018

Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures.

Brief Bioinform 2018 Oct 5. Epub 2018 Oct 5.

School of Mathematical Sciences, Peking University, Beijing, China.

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http://dx.doi.org/10.1093/bib/bby093DOI Listing
October 2018

Randomly distributed embedding making short-term high-dimensional data predictable.

Proc Natl Acad Sci U S A 2018 10 8;115(43):E9994-E10002. Epub 2018 Oct 8.

Key Laboratory of Systems Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China;

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http://dx.doi.org/10.1073/pnas.1802987115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205453PMC
October 2018

PWCDA: Path Weighted Method for Predicting circRNA-Disease Associations.

Int J Mol Sci 2018 Oct 31;19(11). Epub 2018 Oct 31.

Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada.

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http://dx.doi.org/10.3390/ijms19113410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6274797PMC
October 2018

The oscillatory boundary conditions of different frequency bands in Parkinson's disease.

J Theor Biol 2018 08 1;451:67-79. Epub 2018 May 1.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2018.04.040DOI Listing
August 2018

Discovering personalized driver mutation profiles of single samples in cancer by network control strategy.

Bioinformatics 2018 06;34(11):1893-1903

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, University of Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1093/bioinformatics/bty006DOI Listing
June 2018

Quantifying direct dependencies in biological networks by multiscale association analysis.

IEEE/ACM Trans Comput Biol Bioinform 2018 Jun 12. Epub 2018 Jun 12.

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http://dx.doi.org/10.1109/TCBB.2018.2846648DOI Listing
June 2018

Unravelling miRNA regulation in yield of rice (Oryza sativa) based on differential network model.

Sci Rep 2018 05 31;8(1):8498. Epub 2018 May 31.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.

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http://dx.doi.org/10.1038/s41598-018-26438-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5981461PMC
May 2018

In vivo CRISPR screening unveils histone demethylase UTX as an important epigenetic regulator in lung tumorigenesis.

Proc Natl Acad Sci U S A 2018 04 9;115(17):E3978-E3986. Epub 2018 Apr 9.

State Key Laboratory of Cell Biology, Innovation Center for Cell Signaling Network, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China;

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http://dx.doi.org/10.1073/pnas.1716589115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924887PMC
April 2018

Integrating data- and model-driven strategies in systems biology.

BMC Syst Biol 2018 04 24;12(Suppl 4):38. Epub 2018 Apr 24.

Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1186/s12918-018-0562-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998873PMC
April 2018

Improved flower pollination algorithm for identifying essential proteins.

BMC Syst Biol 2018 04 24;12(Suppl 4):46. Epub 2018 Apr 24.

Key Laboratory of Systems Biology, CAS center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1186/s12918-018-0573-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5998882PMC
April 2018

Efficient Mining Multi-mers in a Variety of Biological Sequences.

IEEE/ACM Trans Comput Biol Bioinform 2018 Apr 19. Epub 2018 Apr 19.

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http://dx.doi.org/10.1109/TCBB.2018.2828313DOI Listing
April 2018

The generation mechanism of spike-and-slow wave discharges appearing on thalamic relay nuclei.

Sci Rep 2018 03 21;8(1):4953. Epub 2018 Mar 21.

Key Laboratory of Systems Biology, CAS center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1038/s41598-018-23280-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862852PMC
March 2018

Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma.

Nat Commun 2018 02 14;9(1):678. Epub 2018 Feb 14.

Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.

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http://dx.doi.org/10.1038/s41467-018-03024-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813207PMC
February 2018

Impaired Functional Criticality of Human Brain during Alzheimer's Disease Progression.

Sci Rep 2018 01 22;8(1):1324. Epub 2018 Jan 22.

Department of Neurology, XuanWu Hospital of Capital Medical University, Beijing, 100053, China.

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http://dx.doi.org/10.1038/s41598-018-19674-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778032PMC
January 2018

A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.

BMC Genomics 2018 01 19;19(Suppl 1):924. Epub 2018 Jan 19.

Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710072, China.

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http://dx.doi.org/10.1186/s12864-017-4332-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780855PMC
January 2018

Dysfunction of PLA2G6 and CYP2C44-associated network signals imminent carcinogenesis from chronic inflammation to hepatocellular carcinoma.

J Mol Cell Biol 2017 12;9(6):489-503

Key Laboratory of Systems Biology, CAS center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1093/jmcb/mjx021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907842PMC
December 2017

Detecting causality from short time-series data based on prediction of topologically equivalent attractors.

BMC Syst Biol 2017 12 21;11(Suppl 7):128. Epub 2017 Dec 21.

Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20031, China.

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http://dx.doi.org/10.1186/s12918-017-0512-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763311PMC
December 2017

Data-driven systems biology approaches.

Authors:
Luonan Chen

J Mol Cell Biol 2017 12;9(6):435

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http://dx.doi.org/10.1093/jmcb/mjy004DOI Listing
December 2017

Individual-specific edge-network analysis for disease prediction.

Nucleic Acids Res 2017 Nov;45(20):e170

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Chinese Academy Science, Shanghai 200031, China.

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http://dx.doi.org/10.1093/nar/gkx787DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714249PMC
November 2017

Low-Grade Dysplastic Nodules Revealed as the Tipping Point during Multistep Hepatocarcinogenesis by Dynamic Network Biomarkers.

Genes (Basel) 2017 Oct 13;8(10). Epub 2017 Oct 13.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.3390/genes8100268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664118PMC
October 2017

Detecting the tipping points in a three-state model of complex diseases by temporal differential networks.

J Transl Med 2017 10 26;15(1):217. Epub 2017 Oct 26.

Collaborative Research Center for Innovative Mathematical Modelling, University of Tokyo, Tokyo, 153-8505, Japan.

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http://dx.doi.org/10.1186/s12967-017-1320-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5658963PMC
October 2017

Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data.

Bioinformatics 2017 Sep;33(17):2706-2714

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China.

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http://dx.doi.org/10.1093/bioinformatics/btx176DOI Listing
September 2017

Understanding biological systems through the lens of data.

BMC Syst Biol 2017 Sep 21;11(Suppl 4):77. Epub 2017 Sep 21.

Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918
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http://dx.doi.org/10.1186/s12918-017-0450-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5615238PMC
September 2017

Quantifying critical states of complex diseases using single-sample dynamic network biomarkers.

PLoS Comput Biol 2017 Jul 5;13(7):e1005633. Epub 2017 Jul 5.

Institute of Industrial Science, the University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1371/journal.pcbi.1005633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517040PMC
July 2017

Local network component analysis for quantifying transcription factor activities.

Methods 2017 07 12;124:25-35. Epub 2017 Jul 12.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, China. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2017.06.018DOI Listing
July 2017

Comparative network stratification analysis for identifying functional interpretable network biomarkers.

BMC Bioinformatics 2017 Mar 14;18(Suppl 3):48. Epub 2017 Mar 14.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1186/s12859-017-1462-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374559PMC
March 2017

Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth.

Oncotarget 2017 Feb;8(7):12093-12107

Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.

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http://dx.doi.org/10.18632/oncotarget.14517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355328PMC
February 2017

Uncovering Driver DNA Methylation Events in Nonsmoking Early Stage Lung Adenocarcinoma.

Biomed Res Int 2016 17;2016:2090286. Epub 2016 Aug 17.

Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Institute of Industrial Science, University of Tokyo, Tokyo 153-8505, Japan; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

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http://dx.doi.org/10.1155/2016/2090286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5005773PMC
January 2017

Personalized characterization of diseases using sample-specific networks.

Nucleic Acids Res 2016 12 4;44(22):e164. Epub 2016 Sep 4.

Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

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http://dx.doi.org/10.1093/nar/gkw772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5159538PMC
December 2016

Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers.

Sci Rep 2016 12 21;6:39663. Epub 2016 Dec 21.

Center for Systems Biology, Soochow University, Suzhou, 215006, China.

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http://dx.doi.org/10.1038/srep39663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5175196PMC
December 2016

CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data.

BMC Bioinformatics 2016 Dec 23;17(Suppl 17):535. Epub 2016 Dec 23.

CAS Key Laboratory of Computational Biology and State Key Laboratory of Hybrid Rice, CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 20031, China.

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http://dx.doi.org/10.1186/s12859-016-1324-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5260056PMC
December 2016

Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors.

Curr Top Med Chem 2016 ;16(6):604-15

Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, P.R. China.

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http://dx.doi.org/10.2174/1568026615666150819110703DOI Listing
August 2016

Inference of Gene Regulatory Network Based on Local Bayesian Networks.

PLoS Comput Biol 2016 08 1;12(8):e1005024. Epub 2016 Aug 1.

Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, China.

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http://dx.doi.org/10.1371/journal.pcbi.1005024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968793PMC
August 2016

Interferon-microRNA signalling drives liver precancerous lesion formation and hepatocarcinogenesis.

Gut 2016 07 9;65(7):1186-201. Epub 2016 Feb 9.

International Co-operation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China National Center for Liver Cancer, Shanghai, China State Key Laboratory for Oncogenes and Related Genes, Cancer Institute of RenJi Hospital, Shanghai JiaoTong University, Shanghai, China.

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http://dx.doi.org/10.1136/gutjnl-2015-310318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624432PMC
July 2016

Detecting critical state before phase transition of complex biological systems by hidden Markov model.

Bioinformatics 2016 07 19;32(14):2143-50. Epub 2016 Mar 19.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China Collaborative Research Center for Innovative Mathematical Modelling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw154DOI Listing
July 2016

Discovering a critical transition state from nonalcoholic hepatosteatosis to nonalcoholic steatohepatitis by lipidomics and dynamical network biomarkers.

J Mol Cell Biol 2016 06 18;8(3):195-206. Epub 2016 Mar 18.

Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai 200031, China University of the Chinese Academy of Sciences, CAS, Beijing 100049, China School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China Key Laboratory of Food Safety Risk Assessment, Ministry of Health, Beijing 100021, China

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http://dx.doi.org/10.1093/jmcb/mjw016DOI Listing
June 2016

Identifying joint biomarker panel from multiple level dataset by an optimization model.

Biomark Med 2016 06 12;10(6):567-75. Epub 2016 May 12.

National Center for Mathematics & Interdisciplinary Sciences, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China.

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http://dx.doi.org/10.2217/bmm-2015-0022DOI Listing
June 2016

Modelling biochemical reaction systems by stochastic differential equations with reflection.

J Theor Biol 2016 May 23;396:90-104. Epub 2016 Feb 23.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, China. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.02.010DOI Listing
May 2016

Corrigendum for "Modelling biochemical reaction systems by stochastic differential equations with reflection".

J Theor Biol 2016 May 23;396:207-9. Epub 2016 Mar 23.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, China. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.03.023DOI Listing
May 2016

Part mutual information for quantifying direct associations in networks.

Proc Natl Acad Sci U S A 2016 May 18;113(18):5130-5. Epub 2016 Apr 18.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of the Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China; Collaborative Research Center for Innovative Mathematical Modelling, Institute of Industrial Science, University of Tokyo, Tokyo 113-8654, Japan

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http://dx.doi.org/10.1073/pnas.1522586113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4983806PMC
May 2016

Network stratification analysis for identifying function-specific network layers.

Mol Biosyst 2016 Apr 16;12(4):1232-40. Epub 2016 Feb 16.

School of Computer, Wuhan University, Wuhan 430072, China.

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http://dx.doi.org/10.1039/c5mb00782hDOI Listing
April 2016

Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster.

Metallomics 2016 Mar;8(3):354-65

Key Laboratory of Food Safety Research, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China. and Key Laboratory of Food Safety Risk Assessment Ministry of Health, Beijing, China.

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http://dx.doi.org/10.1039/c5mt00134jDOI Listing
March 2016

Towards a critical transition theory under different temporal scales and noise strengths.

Phys Rev E 2016 Mar 21;93(3):032137. Epub 2016 Mar 21.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, and Chinese Academy of Sciences, Shanghai 200031, China; Institute of Industrial Science, University of Tokyo, Tokyo 153-8505, Japan.

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http://dx.doi.org/10.1103/PhysRevE.93.032137DOI Listing
March 2016

PPIM: A Protein-Protein Interaction Database for Maize.

Plant Physiol 2016 Feb 30;170(2):618-26. Epub 2015 Nov 30.

Department of Computer Science and Technology, Tongji University, Shanghai 201804, China (G.Z., P.-P.X., J.W., X.-M.Z.);Key Laboratory of Food Safety Research, Institute for Nutritional Sciences (A.W.), and Key Laboratory of Systems Biology (L.C.), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China;Department of Mathematics, Shanghai University, Shanghai 200444, China (X.-J.X.); andMonsanto Company, St. Louis, Missouri 63167 (L.L., J.L., Y.C.)

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http://dx.doi.org/10.1104/pp.15.01821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4734591PMC
February 2016

Multiscale modeling biological systems.

IET Syst Biol 2016 Feb;10(1)

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http://dx.doi.org/10.1049/iet-syb.2016.0002DOI Listing
February 2016

Transcriptomic analysis of the effects of Toll-like receptor 4 and its ligands on the gene expression network of hepatic stellate cells.

Fibrogenesis Tissue Repair 2016 18;9. Epub 2016 Feb 18.

Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., Room 11-70C, New York, 10029-6574 NY USA.

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http://dx.doi.org/10.1186/s13069-016-0039-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759739PMC
February 2016

Comparison of Chromosome 4 gene expression profile between lung telocytes and other local cell types.

J Cell Mol Med 2016 Jan 17;20(1):71-80. Epub 2015 Dec 17.

Zhongshan Hospital, Fudan University Center for Clinical Bioinformatics, Shanghai Institute of Clinical Bioinformatics, Shanghai, China.

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http://dx.doi.org/10.1111/jcmm.12746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4717865PMC
January 2016

Identifying early-warning signals of critical transitions with strong noise by dynamical network markers.

Sci Rep 2015 Dec 9;5:17501. Epub 2015 Dec 9.

Collaborative Research Center for Innovative Mathematical Modelling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505, Japan.

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http://dx.doi.org/10.1038/srep17501DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673532PMC
December 2015

Single amino acid changes in naked mole rat may reveal new anti-cancer mechanisms in mammals.

Gene 2015 Nov 3;572(1):101-107. Epub 2015 Jul 3.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China; Collaborative Research Centre for Innovative Mathematical Modelling, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2015.07.004DOI Listing
November 2015

Identifying critical differentiation state of MCF-7 cells for breast cancer by dynamical network biomarkers.

Front Genet 2015 28;6:252. Epub 2015 Jul 28.

Collaborative Research Center for Innovative Mathematical Modelling, University of Tokyo Tokyo, Japan.

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http://dx.doi.org/10.3389/fgene.2015.00252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4516973PMC
August 2015

A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors.

Methods 2015 Jul 15;83:3-17. Epub 2015 May 15.

National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.05.011DOI Listing
July 2015

Detecting disease genes of non-small lung cancer based on consistently differential interactions.

Cancer Metastasis Rev 2015 Jun;34(2):195-208

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1007/s10555-015-9561-5DOI Listing
June 2015

Unravelling personalized dysfunctional gene network of complex diseases based on differential network model.

J Transl Med 2015 Jun 13;13:189. Epub 2015 Jun 13.

Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

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http://dx.doi.org/10.1186/s12967-015-0546-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467679PMC
June 2015

Bio-network medicine.

J Mol Cell Biol 2015 Jun 15;7(3):185-6. Epub 2015 Jun 15.

Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China E-mail:

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http://dx.doi.org/10.1093/jmcb/mjv038DOI Listing
June 2015