Tieliu Shi

Tieliu Shi

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Tieliu Shi

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Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.

Sci China Life Sci 2019 May 20. Epub 2019 May 20.

National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA.

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http://dx.doi.org/10.1007/s11427-018-9479-5DOI Listing
May 2019

Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma.

Cell Commun Signal 2019 May 22;17(1):48. Epub 2019 May 22.

Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1186/s12964-019-0363-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532229PMC
May 2019

QuaPra: efficient transcript assembly and quantification using quadratic programming with Apriori algorithm.

Sci China Life Sci 2019 May 22. Epub 2019 May 22.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-018-9433-3DOI Listing
May 2019

Natural variations of growth thermo-responsiveness determined by SAUR26/27/28 proteins in Arabidopsis thaliana.

New Phytol 2019 May 25. Epub 2019 May 25.

School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA.

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http://dx.doi.org/10.1111/nph.15956DOI Listing
May 2019

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis.

Front Genet 2019 5;10:317. Epub 2019 Apr 5.

Center for Bioinformatics and Computational Biology, and Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.

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http://dx.doi.org/10.3389/fgene.2019.00317DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460256PMC
April 2019

A region-resolved mucosa proteome of the human stomach.

Nat Commun 2019 01 3;10(1):39. Epub 2019 Jan 3.

State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of lifeomics, Beijing, 102206, China.

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http://www.nature.com/articles/s41467-018-07960-x
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http://dx.doi.org/10.1038/s41467-018-07960-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318339PMC
January 2019

Integrative analysis identifies potential DNA methylation biomarkers for pan-cancer diagnosis and prognosis.

Epigenetics 2019 01 29;14(1):67-80. Epub 2019 Jan 29.

a Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai , China.

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https://www.tandfonline.com/doi/full/10.1080/15592294.2019.1
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http://dx.doi.org/10.1080/15592294.2019.1568178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380428PMC
January 2019

RDAD: A Machine Learning System to Support Phenotype-Based Rare Disease Diagnosis.

Front Genet 2018 4;9:587. Epub 2018 Dec 4.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

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http://dx.doi.org/10.3389/fgene.2018.00587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288202PMC
December 2018

Whole-Genome Sequencing Identifies a Novel Variation of Gene Coordinating With Heterozygous Germline Mutation of to Enhance Hepatoblastoma Oncogenesis.

Front Genet 2018 19;9:668. Epub 2018 Dec 19.

Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.

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http://dx.doi.org/10.3389/fgene.2018.00668DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305990PMC
December 2018

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma.

Front Genet 2018 18;9:477. Epub 2018 Oct 18.

Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China.

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http://dx.doi.org/10.3389/fgene.2018.00477DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6201709PMC
October 2018

Coordinate regulation of Ustilago maydis ammonium transporters and genes involved in mating and pathogenicity.

Fungal Biol 2018 07 31;122(7):639-650. Epub 2018 Mar 31.

Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.funbio.2018.03.011DOI Listing
July 2018

Application of genome analysis strategies in the clinical testing for pediatric diseases.

Pediatr Investig 2018 Jul;2(2):72-81

Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.

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http://dx.doi.org/10.1002/ped4.12044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6089540PMC
July 2018

SUMO suppresses and MYC amplifies transcription globally by regulating CDK9 sumoylation.

Cell Res 2018 Jun 27;28(6):670-685. Epub 2018 Mar 27.

Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital-ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1038/s41422-018-0023-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993822PMC
June 2018

Lack of correlation between aristolochic acid exposure and hepatocellular carcinoma.

Sci China Life Sci 2018 06 20;61(6):727-728. Epub 2018 Apr 20.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-018-9288-1DOI Listing
June 2018

Biological data processing based on bio-processor unit (BPU), a new concept for next generation computational biology.

Sci China Life Sci 2018 05 12;61(5):597-598. Epub 2018 Mar 12.

State Key Laboratory of Mathematical Engineering and Advanced Computation, Wuxi, 214122, China.

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http://link.springer.com/10.1007/s11427-018-9278-3
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http://dx.doi.org/10.1007/s11427-018-9278-3DOI Listing
May 2018

Author Correction: A proteomic landscape of diffuse-type gastric cancer.

Nat Commun 2018 05 8;9(1):1850. Epub 2018 May 8.

The Joint Laboratory of Translational Medicine, National Center for Protein Sciences (Beijing) and Peking University Cancer Hospital, State Key Laboratory of Proteomics, Institute of Lifeomics, 102206, Beijing, China.

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http://dx.doi.org/10.1038/s41467-018-04166-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5940851PMC
May 2018

A proteomic landscape of diffuse-type gastric cancer.

Nat Commun 2018 03 8;9(1):1012. Epub 2018 Mar 8.

The Joint Laboratory of Translational Medicine, National Center for Protein Sciences (Beijing) and Peking University Cancer Hospital, State Key Laboratory of Proteomics, Institute of Lifeomics, Beijing, 102206, China.

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http://dx.doi.org/10.1038/s41467-018-03121-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5843664PMC
March 2018

eRAM: encyclopedia of rare disease annotations for precision medicine.

Nucleic Acids Res 2018 Jan;46(D1):D937-D943

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1093/nar/gkx1062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753383PMC
January 2018

TCMID 2.0: a comprehensive resource for TCM.

Nucleic Acids Res 2018 Jan;46(D1):D1117-D1120

TCM Clinical Basis Institute, Zhejiang Chinese Medicine University, Zhejiang 310000, China.

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http://academic.oup.com/nar/article/46/D1/D1117/4584630
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http://dx.doi.org/10.1093/nar/gkx1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753259PMC
January 2018

PedAM: a database for Pediatric Disease Annotation and Medicine.

Nucleic Acids Res 2018 Jan;46(D1):D977-D983

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1093/nar/gkx1049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753298PMC
January 2018

Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data.

PLoS One 2013 18;8(6):e66521. Epub 2013 Jun 18.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066521PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3688907PMC
October 2017

MicroRNA hsa-miR-370-3p suppresses the expression and induction of CYP2D6 by facilitating mRNA degradation.

Biochem Pharmacol 2017 09 26;140:139-149. Epub 2017 May 26.

National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bcp.2017.05.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687086PMC
September 2017

Class I histone deacetylases are major histone decrotonylases: evidence for critical and broad function of histone crotonylation in transcription.

Cell Res 2017 Jul 12;27(7):898-915. Epub 2017 May 12.

Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://www.nature.com/doifinder/10.1038/cr.2017.68
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http://dx.doi.org/10.1038/cr.2017.68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5518989PMC
July 2017

Error-prone DNA polymerase and oxidative stress increase the incidences of A to G mutations in tumors.

Oncotarget 2017 Jul;8(28):45154-45163

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.18632/oncotarget.13293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5542174PMC
July 2017

The challenge and promise of rare disease diagnosis in China.

Authors:
Xin Ni Tieliu Shi

Sci China Life Sci 2017 07 14;60(7):681-685. Epub 2017 Jun 14.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://link.springer.com/10.1007/s11427-017-9100-1
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http://dx.doi.org/10.1007/s11427-017-9100-1DOI Listing
July 2017

Towards efficiency in rare disease research: what is distinctive and important?

Sci China Life Sci 2017 Jul 16;60(7):686-691. Epub 2017 Jun 16.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-017-9099-3DOI Listing
July 2017

Identifying and Characterizing the Circular RNAs during the Lifespan of Arabidopsis Leaves.

Front Plant Sci 2017 20;8:1278. Epub 2017 Jul 20.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal UniversityShanghai, China.

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http://dx.doi.org/10.3389/fpls.2017.01278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5517402PMC
July 2017

Erratum to: Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins.

Sci China Life Sci 2017 06;60(6):680

Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-017-9025-9DOI Listing
June 2017

Phosphoproteome of crab-eating macaque cerebral cortex characterized through multidimensional reversed-phase liquid chromatography/mass spectrometry with tandem anion/cation exchange columns.

J Chromatogr A 2017 May 22;1498:196-206. Epub 2017 Jan 22.

Department of Chemistry, The University of Hong Kong, Hong Kong, China. Electronic address:

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http://dx.doi.org/10.1016/j.chroma.2017.01.048DOI Listing
May 2017

Firmiana: towards a one-stop proteomic cloud platform for data processing and analysis.

Nat Biotechnol 2017 05;35(5):409-412

State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China.

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http://www.nature.com/doifinder/10.1038/nbt.3825
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http://dx.doi.org/10.1038/nbt.3825DOI Listing
May 2017

MOF as an evolutionarily conserved histone crotonyltransferase and transcriptional activation by histone acetyltransferase-deficient and crotonyltransferase-competent CBP/p300.

Cell Discov 2017 23;3:17016. Epub 2017 May 23.

Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.

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http://dx.doi.org/10.1038/celldisc.2017.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441097PMC
May 2017

Proof-of-Concept Workflow for Establishing Reference Intervals of Human Urine Proteome for Monitoring Physiological and Pathological Changes.

EBioMedicine 2017 Apr 22;18:300-310. Epub 2017 Mar 22.

State Key Laboratory of Proteomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing Proteome Research Center, Beijing 102206, China; Joint Center for Translational Medicine, Tianjin Baodi Hospital, Tianjin 301800, China; Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ebiom.2017.03.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405183PMC
April 2017

Characterizing and annotating the genome using RNA-seq data.

Sci China Life Sci 2017 Feb 13;60(2):116-125. Epub 2016 Jun 13.

Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.

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http://dx.doi.org/10.1007/s11427-015-0349-4DOI Listing
February 2017

Significant variations in alternative splicing patterns and expression profiles between human-mouse orthologs in early embryos.

Sci China Life Sci 2017 Feb 4;60(2):178-188. Epub 2016 Jul 4.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-015-0348-5DOI Listing
February 2017

Interplay of transcription factors and microRNAs during embryonic hematopoiesis.

Sci China Life Sci 2017 Feb 9;60(2):168-177. Epub 2016 Nov 9.

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-016-0168-0DOI Listing
February 2017

Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins.

Sci China Life Sci 2017 02 13;60(2):138-151. Epub 2017 Feb 13.

Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-016-0413-3DOI Listing
February 2017

Ten years of achievements in biological and medical sciences.

Sci China Life Sci 2017 02 18;60(2):111-115. Epub 2017 Feb 18.

Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s11427-017-9003-3DOI Listing
February 2017

AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis.

Nucleic Acids Res 2017 01 28;45(D1):D1060-D1063. Epub 2016 Nov 28.

Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China

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http://dx.doi.org/10.1093/nar/gkw1029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210528PMC
January 2017

dbSAP: single amino-acid polymorphism database for protein variation detection.

Nucleic Acids Res 2017 01 29;45(D1):D827-D832. Epub 2016 Nov 29.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China

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http://dx.doi.org/10.1093/nar/gkw1096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210569PMC
January 2017

Identifying and annotating human bifunctional RNAs reveals their versatile functions.

Sci China Life Sci 2016 Oct 20;59(10):981-992. Epub 2016 Sep 20.

Center for Pharmacogenomics, School of Pharmacy and School of Life Sciences, Fudan University, Shanghai, 201203, China.

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http://dx.doi.org/10.1007/s11427-016-0054-1DOI Listing
October 2016

Multidimensional Proteomics Reveals a Role of UHRF2 in the Regulation of Epithelial-Mesenchymal Transition (EMT).

Mol Cell Proteomics 2016 07 25;15(7):2263-78. Epub 2016 Apr 25.

From the ‡State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (Beijing); National Engineering Research Center for Protein Drugs, Beijing 102206, China; ‖Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030

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http://dx.doi.org/10.1074/mcp.M115.057448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937503PMC
July 2016

Ligand cluster-based protein network and ePlatton, a multi-target ligand finder.

Authors:
Yu Du Tieliu Shi

J Cheminform 2016 30;8:23. Epub 2016 Apr 30.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China.

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http://dx.doi.org/10.1186/s13321-016-0135-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853874PMC
May 2016

Deciphering the Potential Pharmaceutical Mechanism of Chinese Traditional Medicine (Gui-Zhi-Shao-Yao-Zhi-Mu) on Rheumatoid Arthritis.

Sci Rep 2016 Mar 3;6:22602. Epub 2016 Mar 3.

TCM Clinical Basis Institute, Zhejiang Chinese Medicine University, 548 Binwen Road, Hangzhou, Zhejiang, 310000, China.

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http://dx.doi.org/10.1038/srep22602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4776278PMC
March 2016

The REGγ-proteasome forms a regulatory circuit with IκBɛ and NFκB in experimental colitis.

Nat Commun 2016 Feb 22;7:10761. Epub 2016 Feb 22.

Shanghai Key Laboratory of Regulatory Biology, Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), Institute of Biomedical Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1038/ncomms10761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764899PMC
February 2016

A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration.

Sci Rep 2015 Nov 12;5:16401. Epub 2015 Nov 12.

TCM Clinical Basis Institute, Zhejiang Chinese Medicine University, 548 Binwen Road, Hangzhou, Zhejiang, 310000, China.

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http://dx.doi.org/10.1038/srep16401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642335PMC
November 2015

Genome-wide protein-protein interactions and protein function exploration in cyanobacteria.

Sci Rep 2015 Oct 22;5:15519. Epub 2015 Oct 22.

Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.

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http://dx.doi.org/10.1038/srep15519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614683PMC
October 2015

Non-germ Line Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells.

J Biol Chem 2015 May 21;290(22):14181-91. Epub 2015 Apr 21.

From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241 and the Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China

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http://www.jbc.org/lookup/doi/10.1074/jbc.M114.626697
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http://dx.doi.org/10.1074/jbc.M114.626697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4447987PMC
May 2015

Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses.

Sci Rep 2015 Mar 30;5:9453. Epub 2015 Mar 30.

The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1038/srep09453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377585PMC
March 2015

PubAngioGen: a database and knowledge for angiogenesis and related diseases.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D963-7. Epub 2014 Nov 11.

The center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China

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http://dx.doi.org/10.1093/nar/gku1139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383947PMC
January 2015

Evaluating the pharmacological mechanism of Chinese medicine Si-Wu-Tang through multi-level data integration.

PLoS One 2013 4;8(11):e72334. Epub 2013 Nov 4.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Science, East China Normal University, Shanghai, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072334PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817162PMC
August 2014

Regulatory network rewiring for secondary metabolism in Arabidopsis thaliana under various conditions.

BMC Plant Biol 2014 Jul 4;14:180. Epub 2014 Jul 4.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Science, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1186/1471-2229-14-180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105546PMC
July 2014

Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach.

Bioinformatics 2014 Mar 5;30(6):823-30. Epub 2013 Nov 5.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1093/bioinformatics/btt596DOI Listing
March 2014

Proteomic evidence for genetic epistasis: ClpR4 mutations switch leaf variegation to virescence in Arabidopsis.

Plant J 2013 Dec 12;76(6):943-56. Epub 2013 Nov 12.

National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.

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http://dx.doi.org/10.1111/tpj.12344DOI Listing
December 2013

GPR116, an adhesion G-protein-coupled receptor, promotes breast cancer metastasis via the Gαq-p63RhoGEF-Rho GTPase pathway.

Cancer Res 2013 Oct 5;73(20):6206-18. Epub 2013 Sep 5.

Authors' Affiliations: East China Normal University and Shanghai Changzheng Hospital Joint Research Center for Orthopedic Oncology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China; and Center for Cancer and Stem Cell Biology, Alkek Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas.

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October 2013

HDAM: a resource of human disease associated mutations from next generation sequencing studies.

BMC Med Genomics 2013 23;6 Suppl 1:S16. Epub 2013 Jan 23.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Science, East China Normal University, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552701PMC
August 2013

Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis.

BMC Med Genomics 2013 23;6 Suppl 1:S17. Epub 2013 Jan 23.

Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552677PMC
August 2013

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches.

Hum Genet 2013 Aug 10;132(8):899-911. Epub 2013 Apr 10.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, China.

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http://dx.doi.org/10.1007/s00439-013-1300-9DOI Listing
August 2013

Ligand binding site similarity identification based on chemical and geometric similarity.

Authors:
Haibo Tu Tieliu Shi

Protein J 2013 Jun;32(5):373-85

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s10930-013-9494-1DOI Listing
June 2013

Replacements of rare herbs and simplifications of traditional chinese medicine formulae based on attribute similarities and pathway enrichment analysis.

Evid Based Complement Alternat Med 2013 21;2013:136732. Epub 2013 Feb 21.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1155/2013/136732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594946PMC
March 2013

Next-generation sequencing technologies for personalized medicine: promising but challenging.

Sci China Life Sci 2013 Feb 8;56(2):101-3. Epub 2013 Feb 8.

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February 2013

Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq.

Sci China Life Sci 2013 Feb 8;56(2):143-55. Epub 2013 Feb 8.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

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February 2013

Inhibition of breast cancer metastases by a novel inhibitor of TGFβ receptor 1.

J Natl Cancer Inst 2013 Jan 24;105(1):47-58. Epub 2012 Nov 24.

Institute of Biomedical Sciences, East China Normal University, 500 Dongchuan Rd, Shanghai, China.

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January 2013

TCMID: Traditional Chinese Medicine integrative database for herb molecular mechanism analysis.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D1089-95. Epub 2012 Nov 29.

Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Science, East China Normal University, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531123PMC
January 2013

Exploring virus relationships based on virus-host protein-protein interaction network.

BMC Syst Biol 2011 23;5 Suppl 3:S11. Epub 2011 Dec 23.

The Center for Bioinformatics and Computational Biology and Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai, 200241, China.

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http://dx.doi.org/10.1186/1752-0509-5-S3-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287566PMC
November 2012

A transcriptional dynamic network during Arabidopsis thaliana pollen development.

BMC Syst Biol 2011 23;5 Suppl 3:S8. Epub 2011 Dec 23.

College of Life Sciences, Northeast Forestry University, Heilongjiang, Harbin 150040, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287576PMC
November 2012

Blood-based gene expression profiles models for classification of subsyndromal symptomatic depression and major depressive disorder.

PLoS One 2012 13;7(2):e31283. Epub 2012 Feb 13.

Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3278427PMC
July 2012

Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.

PLoS One 2011 30;6(11):e28318. Epub 2011 Nov 30.

Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227660PMC
April 2012

REGγ is associated with multiple oncogenic pathways in human cancers.

BMC Cancer 2012 Feb 23;12:75. Epub 2012 Feb 23.

Institute of Biomedical Sciences, East China Normal University, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3350384PMC
February 2012

Prognostic significance of vascular endothelial growth factor expression in gastric carcinoma: a meta-analysis.

J Cancer Res Clin Oncol 2011 Dec 15;137(12):1799-812. Epub 2011 Sep 15.

The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China.

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http://dx.doi.org/10.1007/s00432-011-1057-2DOI Listing
December 2011

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq.

BMC Genomics 2011 Dec 2;12:590. Epub 2011 Dec 2.

Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288009PMC
December 2011

Overview of available methods for diverse RNA-Seq data analyses.

Sci China Life Sci 2011 Dec 7;54(12):1121-8. Epub 2012 Jan 7.

Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai 200241, China.

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December 2011

De novo transcriptome assembly of RNA-Seq reads with different strategies.

Sci China Life Sci 2011 Dec 7;54(12):1129-33. Epub 2012 Jan 7.

Center for Bioinformatics and Computational Biology, Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai 200241, China.

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December 2011

Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile.

BMC Genomics 2011 Dec 23;12 Suppl 5:S3. Epub 2011 Dec 23.

The Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287499PMC
December 2011

Maximizing biomarker discovery by minimizing gene signatures.

BMC Genomics 2011 Dec 23;12 Suppl 5:S6. Epub 2011 Dec 23.

The Center for Bioinformatics and Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287502PMC
December 2011

A comprehensive analysis of the dynamic biological networks in HCV induced hepatocarcinogenesis.

PLoS One 2011 Apr 19;6(4):e18516. Epub 2011 Apr 19.

Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences, School of Life Science, East China Normal University, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079719PMC
April 2011

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis.

Nucleic Acids Res 2011 Jan 29;39(Database issue):D1130-3. Epub 2010 Oct 29.

Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.

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http://dx.doi.org/10.1093/nar/gkq959DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013798PMC
January 2011

Integrative identification of Arabidopsis mitochondrial proteome and its function exploitation through protein interaction network.

PLoS One 2011 Jan 31;6(1):e16022. Epub 2011 Jan 31.

College of Life Sciences, Center for Bioinformatics and Institute of Biomedical Sciences, East China Normal University, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3031521PMC
January 2011

Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana.

BMC Genomics 2010 Nov 2;11 Suppl 2:S2. Epub 2010 Nov 2.

College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975419PMC
November 2010

Nucleosome structure incorporated histone acetylation site prediction in Arabidopsis thaliana.

BMC Genomics 2010 Nov 2;11 Suppl 2:S7. Epub 2010 Nov 2.

Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2975415PMC
November 2010

Systematical detection of significant genes in microarray data by incorporating gene interaction relationship in biological systems.

PLoS One 2010 Oct 29;5(10):e13721. Epub 2010 Oct 29.

The Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences, The School of Life Sciences, East China Normal University, Shanghai, China.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2966410PMC
October 2010

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

Nat Biotechnol 2010 Aug 30;28(8):827-38. Epub 2010 Jul 30.

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

HCCNet: an integrated network database of hepatocellular carcinoma.

Cell Res 2010 Jun 18;20(6):732-4. Epub 2010 May 18.

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http://dx.doi.org/10.1038/cr.2010.67DOI Listing
June 2010

HLungDB: an integrated database of human lung cancer research.

Nucleic Acids Res 2010 Jan 9;38(Database issue):D665-9. Epub 2009 Nov 9.

Center for Bioinformatics and Computational Biology, and The Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai 200241, China.

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http://dx.doi.org/10.1093/nar/gkp945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808962PMC
January 2010

Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain.

Genome Biol 2007 ;8(11):R244

School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

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http://dx.doi.org/10.1186/gb-2007-8-11-r244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2258200PMC
August 2008

Exploration of gene-gene interaction effects using entropy-based methods.

Eur J Hum Genet 2008 Feb 31;16(2):229-35. Epub 2007 Oct 31.

Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1038/sj.ejhg.5201921DOI Listing
February 2008

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.

Nucleic Acids Res 2008 Jan 25;36(Database issue):D999-1008. Epub 2007 Oct 25.

College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, China.

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http://dx.doi.org/10.1093/nar/gkm844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238993PMC
January 2008

InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.

BMC Bioinformatics 2007 Oct 26;8:414. Epub 2007 Oct 26.

Virginia Institute for Psychiatric and Behavioral Genetics and Department of Psychiatry, Virginia Commonwealth University, Richmond, VA 23298, USA.

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http://dx.doi.org/10.1186/1471-2105-8-414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238723PMC
October 2007

Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family.

Biochem Biophys Res Commun 2006 Nov 29;350(3):648-56. Epub 2006 Sep 29.

School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 201101, China.

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November 2006