Leming Shi

Leming Shi

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Leming Shi

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Optimized CRISPR guide RNA design for two high-fidelity Cas9 variants by deep learning.

Nat Commun 2019 Sep 19;10(1):4284. Epub 2019 Sep 19.

State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200432, China.

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http://dx.doi.org/10.1038/s41467-019-12281-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753114PMC
September 2019

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

Sci China Life Sci 2019 Jul 20;62(7):895-904. 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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612563PMC
July 2019

MicroRNA-302d promotes the proliferation of human pluripotent stem cell-derived cardiomyocytes by inhibiting in the Hippo pathway.

Clin Sci (Lond) 2019 Jul 2;133(13):1387-1399. Epub 2019 Jul 2.

Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China

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http://dx.doi.org/10.1042/CS20190099DOI Listing
July 2019

Integrative Analysis of Somatic Mutations in Non-coding Regions Altering RNA Secondary Structures in Cancer Genomes.

Sci Rep 2019 Jun 3;9(1):8205. Epub 2019 Jun 3.

Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China.

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http://dx.doi.org/10.1038/s41598-019-44489-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546760PMC
June 2019

Correction to: Similarities and differences between variants called with human reference genome HG19 or HG38.

BMC Bioinformatics 2019 May 15;20(1):252. Epub 2019 May 15.

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

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http://dx.doi.org/10.1186/s12859-019-2776-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6521484PMC
May 2019

Alcohol Intake Interacts with Functional Genetic Polymorphisms of Aldehyde Dehydrogenase (ALDH2) and Alcohol Dehydrogenase (ADH) to Increase Esophageal Squamous Cell Cancer Risk.

J Thorac Oncol 2019 04 9;14(4):712-725. Epub 2019 Jan 9.

Fudan University Taizhou Institute of Health Sciences, Taizhou, People's Republic of China; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

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https://linkinghub.elsevier.com/retrieve/pii/S15560864193001
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http://dx.doi.org/10.1016/j.jtho.2018.12.023DOI Listing
April 2019

Similarities and differences between variants called with human reference genome HG19 or HG38.

BMC Bioinformatics 2019 Mar 14;20(Suppl 2):101. Epub 2019 Mar 14.

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

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http://dx.doi.org/10.1186/s12859-019-2620-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419332PMC
March 2019

PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs.

Nucleic Acids Res 2019 Jan;47(D1):D1090-D1101

State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai 200438, China.

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http://dx.doi.org/10.1093/nar/gky1042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324052PMC
January 2019

A Comprehensive Analysis of Gene Expression of Xenobiotic and Endogenous Metabolizing Enzymes and Transporters in Rat Multiple Organs.

Curr Pharm Biotechnol 2018 ;19(3):240-249

Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai 200438, China.

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http://dx.doi.org/10.2174/1389201019666180525113727DOI Listing
October 2018

Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients.

Biol Direct 2018 07 16;13(1):14. Epub 2018 Jul 16.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, Nobels vag 12A, Karolinska Institutet, 171 77, Stockholm, PO, Sweden.

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http://dx.doi.org/10.1186/s13062-018-0218-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048860PMC
July 2018

ArrayTrack: An FDA and Public Genomic Tool.

Methods Mol Biol 2017 ;1613:333-353

Division of Systems Toxicology, National Center for Toxicological Research (NCTR), FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA.

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http://dx.doi.org/10.1007/978-1-4939-7027-8_13DOI Listing
May 2018

Mitochondrial dysfunction induced by leflunomide and its active metabolite.

Toxicology 2018 03 8;396-397:33-45. Epub 2018 Feb 8.

School of Pharmacy and School of Life Sciences, Fudan University, Shanghai 200438, China. Electronic address:

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http://dx.doi.org/10.1016/j.tox.2018.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909954PMC
March 2018

A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models.

FEBS Open Bio 2018 03 25;8(3):481-490. Epub 2018 Jan 25.

State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology Collaborative Innovation Center for Genetics and Development School of Life Sciences and Institutes of Biomedical Sciences Fudan University Shanghai China.

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http://dx.doi.org/10.1002/2211-5463.12343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832988PMC
March 2018

A genomic characterization of the influence of silver nanoparticles on bone differentiation in MC3T3-E1 cells.

J Appl Toxicol 2018 Feb 4;38(2):172-179. Epub 2017 Oct 4.

Center for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, Little Rock, AR, 72204, USA.

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http://dx.doi.org/10.1002/jat.3528DOI Listing
February 2018

Endoplasmic reticulum stress and MAPK signaling pathway activation underlie leflunomide-induced toxicity in HepG2 Cells.

Toxicology 2017 12 5;392:11-21. Epub 2017 Oct 5.

Division of Biochemical Toxicology, National Center for Toxicological Research/U.S. FDA, Jefferson, AR 72079, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tox.2017.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736314PMC
December 2017

The international MAQC Society launches to enhance reproducibility of high-throughput technologies.

Nat Biotechnol 2017 12;35(12):1127-1128

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

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http://dx.doi.org/10.1038/nbt.4029DOI Listing
December 2017

[Expression, purification and immunoreactivity characterization of extracellular antigenic domains of NMDAR1 protein].

Sheng Wu Gong Cheng Xue Bao 2017 Dec;33(12):1979-1988

School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China.

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http://dx.doi.org/10.13345/j.cjb.170422DOI Listing
December 2017

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

Proceedings of the 1st International Conference for Cancer Metabolism and Therapy, October 14-17, 2016, Dalian, China.

Pancreas 2017 08;46(7):953-963

From the *School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian, China; †Department of Medicine, Creighton University Medical Center, Omaha, NE; ‡Second Military Medical University, Shanghai, China; §National Key Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; ‖Xiangya Medical College, Chinese Southern University, Changsha, China; ¶Biomedical Mass Spectrometry and Metabolomics Core at Harbor-UCLA, LABiomedical Research Institute, David Geffen School of Medicine at UCLA, Torrance, CA; #Departments of Neuro-Oncology and Molecular/Cellular Oncology, MD Anderson Cancer Center, Houston, TX; **Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA; ††School of Life Sciences, University of Science and Technology of China, Hefei, China; ‡‡Protein Quality Control and Diseases Laboratory, School of Life Sciences, Wenzhou Medical University, Wenzhou, China; §§Institute of Genomic Medicine, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; ‖‖School of Life Sciences, Fudan University, Shanghai, China; and ¶¶UCLA Agi Hirshberg Center for Pancreatic Diseases, David Geffen School of Medicine, Los Angeles, CA.

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http://Insights.ovid.com/crossref?an=00006676-201708000-0001
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http://dx.doi.org/10.1097/MPA.0000000000000854DOI Listing
August 2017

Advances in single-cell RNA sequencing and its applications in cancer research.

Oncotarget 2017 Aug 16;8(32):53763-53779. Epub 2017 May 16.

Center for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, 200438, China.

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http://dx.doi.org/10.18632/oncotarget.17893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581148PMC
August 2017

Somatic mutations in ZFHX4 gene are associated with poor overall survival of Chinese esophageal squamous cell carcinoma patients.

Sci Rep 2017 07 10;7(1):4951. Epub 2017 Jul 10.

Center for Pharmacogenomics, School of Pharmacy and Shanghai Cancer Center, Fudan University, Shanghai, China.

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http://dx.doi.org/10.1038/s41598-017-04221-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5504002PMC
July 2017

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq.

Sci Rep 2017 06 23;7(1):4200. Epub 2017 Jun 23.

Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, 200438, China.

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http://dx.doi.org/10.1038/s41598-017-04520-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482823PMC
June 2017

Exploring functions of long noncoding RNAs across multiple cancers through co-expression network.

Sci Rep 2017 04 7;7(1):754. Epub 2017 Apr 7.

College of Chemistry, Sichuan University, Chengdu, 610064, China.

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http://dx.doi.org/10.1038/s41598-017-00856-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429718PMC
April 2017

Activation of the Nrf2 signaling pathway in usnic acid-induced toxicity in HepG2 cells.

Arch Toxicol 2017 Mar 1;91(3):1293-1307. Epub 2016 Jul 1.

Division of Biochemical Toxicology, National Center for Toxicological Research (NCTR)/U.S. Food and Drug Administration (FDA), HFT-110, 3900 NCTR Road, Jefferson, AR, 72079, USA.

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http://dx.doi.org/10.1007/s00204-016-1775-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5727582PMC
March 2017

Dynamic transcriptomes identify biogenic amines and insect-like hormonal regulation for mediating reproduction in Schistosoma japonicum.

Nat Commun 2017 03 13;8:14693. Epub 2017 Mar 13.

State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China.

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http://dx.doi.org/10.1038/ncomms14693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355954PMC
March 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

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

HLADR: a database system for enhancing the discovery of biomarkers for predicting human leukocyte antigen-mediated idiosyncratic adverse drug reactions.

Biomark Med 2015 26;9(11):1079-93. Epub 2015 Oct 26.

Center for Pharmacogenomics & State Key Laboratory of Genetic Engineering, School of Life Sciences & School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.

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http://dx.doi.org/10.2217/bmm.15.98DOI Listing
August 2016

Standardization efforts enabling next-generation sequencing and microarray based biomarkers for precision medicine.

Biomark Med 2015 26;9(11):1265-72. Epub 2015 Oct 26.

Center for Pharmacogenomics & Department of Clinical Pharmacy, School of Pharmacy, Fudan University, Shanghai, China.

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http://dx.doi.org/10.2217/bmm.15.99DOI Listing
August 2016

Assessment of pharmacogenomic agreement.

F1000Res 2016 9;5:825. Epub 2016 May 9.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada.

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http://dx.doi.org/10.12688/f1000research.8705.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926729PMC
July 2016

Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.

Sci Rep 2016 06 22;6:28400. Epub 2016 Jun 22.

Center for Pharmacogenomics, School of Pharmacy, and State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 201203, China.

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http://dx.doi.org/10.1038/srep28400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916594PMC
June 2016

Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.

Sci Data 2014 26;1:140020. Epub 2014 Aug 26.

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA ; State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China.

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http://dx.doi.org/10.1038/sdata.2014.20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322577PMC
December 2015

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.

Sci Data 2014 26;1:140021. Epub 2014 Aug 26.

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1038/sdata.2014.21DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322565PMC
December 2015

Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.

Sci Data 2014 24;1:140013. Epub 2014 Jun 24.

Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China ; National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA ; Fudan-Zhangjiang Center for Clinical Genomics and Zhanjiang Center for Translational Medicine , Shanghai, 201203, China.

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http://dx.doi.org/10.1038/sdata.2014.13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381750PMC
November 2015

Molecular docking to identify associations between drugs and class I human leukocyte antigens for predicting idiosyncratic drug reactions.

Comb Chem High Throughput Screen 2015 ;18(3):296-304

National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581727PMC
http://dx.doi.org/10.2174/1386207318666150305144015DOI Listing
October 2015

Machine Learning Methods for Predicting HLA-Peptide Binding Activity.

Bioinform Biol Insights 2015 11;9(Suppl 3):21-9. Epub 2015 Oct 11.

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

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http://dx.doi.org/10.4137/BBI.S29466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603527PMC
October 2015

Integrated microRNA, mRNA, and protein expression profiling reveals microRNA regulatory networks in rat kidney treated with a carcinogenic dose of aristolochic acid.

BMC Genomics 2015 May 8;16:365. Epub 2015 May 8.

Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.

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http://dx.doi.org/10.1186/s12864-015-1516-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456708PMC
May 2015

Toxicogenomics and cancer susceptibility: advances with next-generation sequencing.

J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 2014 ;32(2):121-58

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

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http://dx.doi.org/10.1080/10590501.2014.907460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712441PMC
January 2015

Targeted RNA-sequencing with competitive multiplex-PCR amplicon libraries.

PLoS One 2013 13;8(11):e79120. Epub 2013 Nov 13.

Department of Medicine, University of Toledo Health Sciences Campus, Toledo, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079120PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827295PMC
September 2014

Detecting and correcting systematic variation in large-scale RNA sequencing data.

Nat Biotechnol 2014 Sep 24;32(9):888-95. Epub 2014 Aug 24.

1] Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA. [2] The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA. [3] The Feil Family Brain and Mind Research Institute, New York, New York, USA.

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http://www.nature.com/articles/nbt.3000
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http://dx.doi.org/10.1038/nbt.3000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160374PMC
September 2014

Enhancing reproducibility in cancer drug screening: how do we move forward?

Cancer Res 2014 Aug 11;74(15):4016-23. Epub 2014 Jul 11.

Princess Margaret Cancer Centre, University Health Network; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada;

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http://dx.doi.org/10.1158/0008-5472.CAN-14-0725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119520PMC
August 2014

DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome.

Nucleic Acids Res 2014 Jul 29;42(Web Server issue):W46-52. Epub 2014 May 29.

Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, China

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http://academic.oup.com/nar/article/42/W1/W46/2437493/DDICPI
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http://dx.doi.org/10.1093/nar/gku433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086096PMC
July 2014

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model.

Arch Toxicol 2014 Jul 11;88(7):1439-49. Epub 2014 Jun 11.

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA.

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http://dx.doi.org/10.1007/s00204-014-1276-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753582PMC
July 2014

Estimating relative noise to signal in DNA microarray data.

Int J Bioinform Res Appl 2013 ;9(5):433-48

Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1504/IJBRA.2013.056085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983989PMC
March 2014

Next-generation sequencing in the clinic: promises and challenges.

Cancer Lett 2013 Nov 19;340(2):284-95. Epub 2012 Nov 19.

School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China; National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1016/j.canlet.2012.11.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739311PMC
November 2013

Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

PLoS One 2013 23;8(4):e60368. Epub 2013 Apr 23.

Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0060368PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634068PMC
November 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

Utilization of gene expression signature for quality control of traditional Chinese medicine formula Si-Wu-Tang.

AAPS J 2013 Jul 24;15(3):884-92. Epub 2013 May 24.

School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.

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http://dx.doi.org/10.1208/s12248-013-9491-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691416PMC
July 2013

Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine.

Sci China Life Sci 2013 Feb 8;56(2):110-8. Epub 2013 Feb 8.

Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.

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http://link.springer.com/content/pdf/10.1007/s11427-013-4439
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http://link.springer.com/10.1007/s11427-013-4439-7
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http://dx.doi.org/10.1007/s11427-013-4439-7DOI Listing
February 2013

Studies on abacavir-induced hypersensitivity reaction: a successful example of translation of pharmacogenetics to personalized medicine.

Sci China Life Sci 2013 Feb 8;56(2):119-24. Epub 2013 Feb 8.

Division of Systems Biology, National Center for Toxicological Research, the US Food and Drug Administration, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1007/s11427-013-4438-8DOI Listing
February 2013

mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies.

Sci China Life Sci 2013 Feb 8;56(2):134-42. Epub 2013 Feb 8.

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

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http://link.springer.com/content/pdf/10.1007/s11427-013-4437
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http://link.springer.com/10.1007/s11427-013-4437-9
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http://dx.doi.org/10.1007/s11427-013-4437-9DOI Listing
February 2013

Inhalation Anesthesia-Induced Neuronal Damage and Gene Expression Changes in Developing Rat Brain.

Syst Pharmacol 2013 1;1:1-9. Epub 2013 Jan 1.

Division of Neurotoxicology, National Center for Toxicological Research, U.S. Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079 USA.

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http://dx.doi.org/10.2478/sph-2012-0001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755976PMC
January 2013

Transcriptional profiling of Chinese medicinal formula Si-Wu-Tang on breast cancer cells reveals phytoestrogenic activity.

BMC Complement Altern Med 2013 Jan 10;13:11. Epub 2013 Jan 10.

Department of Pharmaceutical Sciences and Center for Advancement of Drug Research, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.

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http://dx.doi.org/10.1186/1472-6882-13-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637310PMC
January 2013

Sex Differences in the Expression of Drug-Metabolizing and Transporter Genes in Human Liver.

J Drug Metab Toxicol 2012 10;3(3):1000119. Epub 2012 Jul 10.

Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.4172/2157-7609.1000119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5699760PMC
July 2012

Cytotoxicity and inhibitory effects of low-concentration triclosan on adipogenic differentiation of human mesenchymal stem cells.

Toxicol Appl Pharmacol 2012 Jul 1;262(2):117-23. Epub 2012 May 1.

Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1016/j.taap.2012.04.024DOI Listing
July 2012

Shifting from population-wide to personalized cancer prognosis with microarrays.

PLoS One 2012 25;7(1):e29534. Epub 2012 Jan 25.

Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029534PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266237PMC
June 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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028318PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227660PMC
April 2012

Methysticin and 7,8-dihydromethysticin are two major kavalactones in kava extract to induce CYP1A1.

Toxicol Sci 2011 Dec 9;124(2):388-99. Epub 2011 Sep 9.

Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1093/toxsci/kfr235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736320PMC
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://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-12-590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3288009PMC
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://dx.doi.org/10.1186/1471-2164-12-S5-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287499PMC
December 2011

Selecting a single model or combining multiple models for microarray-based classifier development?--a comparative analysis based on large and diverse datasets generated from the MAQC-II project.

BMC Bioinformatics 2011 Oct 18;12 Suppl 10:S3. Epub 2011 Oct 18.

Center for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas, USA.

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http://dx.doi.org/10.1186/1471-2105-12-S10-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236846PMC
October 2011

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys.

Chem Res Toxicol 2011 Sep 23;24(9):1486-93. Epub 2011 Aug 23.

ICF International at FDA's National Center for Toxicological Research, 3900 NCTR Road, Jefferson, Arkansas 72079, USA.

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http://dx.doi.org/10.1021/tx200103bDOI Listing
September 2011

DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemical-protein interactome.

Nucleic Acids Res 2011 Jul 10;39(Web Server issue):W492-8. Epub 2011 May 10.

Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.

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http://dx.doi.org/10.1093/nar/gkr299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125745PMC
July 2011

Next-generation sequencing and its applications in molecular diagnostics.

Expert Rev Mol Diagn 2011 Apr;11(3):333-43

Z-Tech, an ICF International Company at US FDA's National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1586/erm.11.3DOI Listing
April 2011

Similarities and differences in the expression of drug-metabolizing enzymes between human hepatic cell lines and primary human hepatocytes.

Drug Metab Dispos 2011 Mar 13;39(3):528-38. Epub 2010 Dec 13.

Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1124/dmd.110.035873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061558PMC
March 2011

Exploring off-targets and off-systems for adverse drug reactions via chemical-protein interactome--clozapine-induced agranulocytosis as a case study.

PLoS Comput Biol 2011 Mar 31;7(3):e1002016. Epub 2011 Mar 31.

Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.

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https://dx.plos.org/10.1371/journal.pcbi.1002016
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http://dx.doi.org/10.1371/journal.pcbi.1002016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068927PMC
March 2011

Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples.

BMC Bioinformatics 2010 Oct 7;11 Suppl 6:S10. Epub 2010 Oct 7.

Division of Systems Biology, National Center for Toxicological Research (NCTR), US Food and Drug Administration (FDA), 3900 NCTR Road, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S6-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026357PMC
October 2010

The EDKB: an established knowledge base for endocrine disrupting chemicals.

BMC Bioinformatics 2010 Oct 7;11 Suppl 6:S5. Epub 2010 Oct 7.

Division of Bioinformatics, Z-Tech Corporation, ICF International Company at NCTR/FDA, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1186/1471-2105-11-S6-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3026379PMC
October 2010

Genomic analysis of microRNA time-course expression in liver of mice treated with genotoxic carcinogen N-ethyl-N-nitrosourea.

BMC Genomics 2010 Oct 28;11:609. Epub 2010 Oct 28.

Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1186/1471-2164-11-609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091750PMC
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://dx.doi.org/10.1038/nbt.1665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

Molecular biomarkers: a US FDA effort.

Biomark Med 2010 Apr;4(2):215-25

Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US FDA 3900 NCTR Road, Jefferson, AR, USA.

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http://dx.doi.org/10.2217/bmm.09.81DOI Listing
April 2010

Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies.

J Genet 2010 Apr;89(1):55-64

Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.

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http://dx.doi.org/10.1007/s12041-010-0011-4DOI Listing
April 2010

Identifying unexpected therapeutic targets via chemical-protein interactome.

PLoS One 2010 Mar 8;5(3):e9568. Epub 2010 Mar 8.

Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009568PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2833192PMC
March 2010