Wiki source for JunfeiZhao
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====== Junfei Zhao======
Postdoc Research Fellow
Department of Systems Biology
Department of Biomedical Informatics
Columbia University College of Physicians & Surgeons
ICRC Building 8th Floor, Office 811
1130 St. Nicholas Ave ยท New York, NY 10032
Email : [[jz2835(at)cumc.columbia.edu]]
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=== {{color c="blue" text=" Educational Background "}} ===
~- PhD Major in Operational Research & Bioinformatics(PhD-direct student), Academy of Mathematics & System Sciences, CAS, 2009.9 - 2014.07
~- Bachelor Major in Information and Computing Science, Changsha University of science & technology, 2005.09 - 2009.06
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=== {{color c="blue" text="Research Areas and Interests"}} ===
Bioinformatics; System Biology.
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=== {{color c="blue" text="Publications"}} ===
~1) **Zhao J**, Cheng F, Zhao Z. ---**[[http://cancerres.aacrjournals.org/content/early/2017/03/31/0008-5472.CAN-16-2460 Tissue-specific signaling networks rewired by major somatic mutations in human cancer revealed by proteome-wide discovery.]]**--- Cancer Research (2017). doi: 10.1158/0008-5472.CAN-16-2460.
~1) Pora Kim, **Junfei Zhao**, Pinyi Lu, and Zhongming Zhao . ---**[[https://academic.oup.com/nar/article/45/D1/D256/2770660/mutLBSgeneDB-mutated-ligand-binding-site-gene mutLBSgeneDB: mutated Ligand Binding Site gene DataBase.]]**--- Nucleic Acids Research (2017) 45 (D1): D256-D263.
~1) Peilin Jia, Guangchun Han, **Junfei Zhao**, Pinyi Lu, and Zhongming Zhao. ---**[[https://academic.oup.com/nar/article/45/D1/D915/2770658/SZGR-2-0-a-one-stop-shop-of-schizophrenia SZGR 2.0: a one-stop shop of schizophrenia candidate genes.]]**--- Nucleic Acids Research (2017) 45 (D1): D915-D924.
~1) Feixiong Cheng, **Junfei Zhao** (co-first author), Ariella B. Hanker, Monica Red Brewer, Carlos L. Arteaga, Zhongming Zhao. ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27771839 Transcriptome and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CAH1047R in HER2/ER-positive breast cancer.]]**--- Breast Cancer Res Treat. 2016 Dec;160(3):457-474.
~1) Cheng, Feixiong, **Junfei Zhao**, Michaela Fooksa, and Zhongming Zhao . ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27026610 A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.]]**--- J Am Med Inform Assoc. 2016 Jul;23(4):681-91.
~1) Pora Kim, Feixiong Cheng, **Junfei Zhao** (co-first author), and Zhongming Zhao. ---**[[http://nar.oxfordjournals.org/content/early/2015/10/29/nar.gkv1128.abstract ccmGDB: a database for cancer cell metabolism genes.]]**--- Nucleic acids research 44.D1 (2016): D959-D968.
~1) **Zhao J**, Cheng F, Wang Y, Arteaga CL, Zhao Z. ---**[[http://www.mcponline.org/content/15/2/642.long Systematic prioritization of druggable mutations in ~5,000 genomes across 16 cancer types using a structural genomics-based approach.]]**--- Molecular & Cellular Proteomics (2015): mcp-M115.
~1) Cheng F, **Zhao J**, Zhao Z. ---**[[http://bib.oxfordjournals.org/content/early/2015/08/24/bib.bbv068.full.pdf+html Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.]]**--- Brief Bioinform (2015) doi: 10.1093/bib/bbv068.
~1) Feixiong Cheng, Chuang Liu, Chen-Ching Lin, **Junfei Zhao**, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao. ---**[[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004497 A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.]]**--- PLOS Computational Biology (2015). DOI: 10.1371/journal.pcbi.1004497.
~1) Zhao M, Kim P, Mitra R, **Zhao J**, Zhao Z. ---**[[http://nar.oxfordjournals.org/content/44/D1/D1023.long TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.]]**--- Nucleic acids research (2015): gkv1268.
~1) **Junfei Zhao**,Xiang-Sun Zhang, Shihua Zhang.---**[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944117/ Predicting cooperative drug effects by the quantitative cellular profiling of response to individual drugs.]] **---CPT Pharmacometrics Syst. Pharmacol (2014) 3, e1; doi:10.1038/psp.2013.79.
~1) James C Costello et al. (**Junfei Zhao** is listed as one co-author).---**[[http://www.nature.com/nbt/journal/v32/n12/pdf/nbt.2877.pdf The challenge of drug sensitivity prediction: an assessment of methods through collaborative competition.]] **---Nature Biotechnology (2014), doi: 10.1038/nbt.2877..
~1) Mukesh Bansal et al. (**Junfei Zhao** is listed as one co-author).---**[[http://www.nature.com/nbt/journal/v32/n12/pdf/nbt.3052.pdf A community computational challenge to predict the activity of pairs of compounds.]] **---Nature biotechnology 32.12 (2014): 1213-1222.
~1) **Junfei Zhao**, Shihua Zhang, Ling-Yun Wu, and Xiang-Sun Zhang.---**[[http://bioinformatics.oxfordjournals.org/content/early/2012/09/14/bioinformatics.bts564.abstract?keytype=ref&ijkey=jTZqXD6CglnPsUI Efficient methods for identifying mutated driver pathways in cancer.]] **---//Bioinformatics//, doi: 10.1093/bioinformatics/bts564, 2012.
~1) Shihua Zhang, **Junfei Zhao**, Xiang-Sun Zhang.---**[[http://pre.aps.org/abstract/PRE/v85/i5/e056110 Common community structure in time-varying networks.]] **---//Physical Review E//, 85, 056110, 2012.
~1) Chen Chen, **Junfei Zhao**, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang.---**[[http://www.biomedcentral.com/1752-0509/6/S1/S7 Inferring domain-domain interactions from protein-protein interactions in the complex network conformation]].**---BMC Systems Biology (2012), 6(Suppl 1):S7.
~1) **Junfei Zhao**, Jiguang Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F15.pdf A SVC-based Method to Detect Multi-scalar Noisy Communities in Complex Networks.]] **---ISORA 2011, pp. 133-143.
~1) Junhua Zhang, Shihua Zhang, Yong Wang, **Junfei Zhao**, Xiang-Sun Zhang. ---**[[http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?tp=&arnumber=6314154&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6314154 Identifying Mutated Core Modules in Glioblastoma by Integrative Network Analysis.]]**--- 2012 IEEE International Conference on Systems Biology (ISB), pp. 304-309.
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=== {{color c="blue" text="Links"}} ===
~- [[http://www.nature.com Nature]]
~- [[http://www.plos.org PLoS]]
~- [[http://www.sciencemag.org Science]]
~- [[http://www.pnas.org PNAS]]
~- [[http://www.ctex.org CTEX]]
""<a href="http://www.clustrmaps.com/map/zhangroup.aporc.org/JunfeiZhao" title="Visitor Map for zhangroup.aporc.org/JunfeiZhao"><img src="//www.clustrmaps.com/map_v2.png?u=kkpr&d=u9PujgO0Xl9556aBY5EWr1QA5ICOxWQcuiZDaaud7iM" /></a>""
====== Junfei Zhao======
Postdoc Research Fellow
Department of Systems Biology
Department of Biomedical Informatics
Columbia University College of Physicians & Surgeons
ICRC Building 8th Floor, Office 811
1130 St. Nicholas Ave ยท New York, NY 10032
Email : [[jz2835(at)cumc.columbia.edu]]
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
=== {{color c="blue" text=" Educational Background "}} ===
~- PhD Major in Operational Research & Bioinformatics(PhD-direct student), Academy of Mathematics & System Sciences, CAS, 2009.9 - 2014.07
~- Bachelor Major in Information and Computing Science, Changsha University of science & technology, 2005.09 - 2009.06
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=== {{color c="blue" text="Research Areas and Interests"}} ===
Bioinformatics; System Biology.
--------------------------------------------------------------------------------
=== {{color c="blue" text="Publications"}} ===
~1) **Zhao J**, Cheng F, Zhao Z. ---**[[http://cancerres.aacrjournals.org/content/early/2017/03/31/0008-5472.CAN-16-2460 Tissue-specific signaling networks rewired by major somatic mutations in human cancer revealed by proteome-wide discovery.]]**--- Cancer Research (2017). doi: 10.1158/0008-5472.CAN-16-2460.
~1) Pora Kim, **Junfei Zhao**, Pinyi Lu, and Zhongming Zhao . ---**[[https://academic.oup.com/nar/article/45/D1/D256/2770660/mutLBSgeneDB-mutated-ligand-binding-site-gene mutLBSgeneDB: mutated Ligand Binding Site gene DataBase.]]**--- Nucleic Acids Research (2017) 45 (D1): D256-D263.
~1) Peilin Jia, Guangchun Han, **Junfei Zhao**, Pinyi Lu, and Zhongming Zhao. ---**[[https://academic.oup.com/nar/article/45/D1/D915/2770658/SZGR-2-0-a-one-stop-shop-of-schizophrenia SZGR 2.0: a one-stop shop of schizophrenia candidate genes.]]**--- Nucleic Acids Research (2017) 45 (D1): D915-D924.
~1) Feixiong Cheng, **Junfei Zhao** (co-first author), Ariella B. Hanker, Monica Red Brewer, Carlos L. Arteaga, Zhongming Zhao. ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27771839 Transcriptome and proteome-oriented identification of dysregulated eIF4G, STAT3, and Hippo pathways altered by PIK3CAH1047R in HER2/ER-positive breast cancer.]]**--- Breast Cancer Res Treat. 2016 Dec;160(3):457-474.
~1) Cheng, Feixiong, **Junfei Zhao**, Michaela Fooksa, and Zhongming Zhao . ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27026610 A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes.]]**--- J Am Med Inform Assoc. 2016 Jul;23(4):681-91.
~1) Pora Kim, Feixiong Cheng, **Junfei Zhao** (co-first author), and Zhongming Zhao. ---**[[http://nar.oxfordjournals.org/content/early/2015/10/29/nar.gkv1128.abstract ccmGDB: a database for cancer cell metabolism genes.]]**--- Nucleic acids research 44.D1 (2016): D959-D968.
~1) **Zhao J**, Cheng F, Wang Y, Arteaga CL, Zhao Z. ---**[[http://www.mcponline.org/content/15/2/642.long Systematic prioritization of druggable mutations in ~5,000 genomes across 16 cancer types using a structural genomics-based approach.]]**--- Molecular & Cellular Proteomics (2015): mcp-M115.
~1) Cheng F, **Zhao J**, Zhao Z. ---**[[http://bib.oxfordjournals.org/content/early/2015/08/24/bib.bbv068.full.pdf+html Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes.]]**--- Brief Bioinform (2015) doi: 10.1093/bib/bbv068.
~1) Feixiong Cheng, Chuang Liu, Chen-Ching Lin, **Junfei Zhao**, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao. ---**[[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004497 A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types.]]**--- PLOS Computational Biology (2015). DOI: 10.1371/journal.pcbi.1004497.
~1) Zhao M, Kim P, Mitra R, **Zhao J**, Zhao Z. ---**[[http://nar.oxfordjournals.org/content/44/D1/D1023.long TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes.]]**--- Nucleic acids research (2015): gkv1268.
~1) **Junfei Zhao**,Xiang-Sun Zhang, Shihua Zhang.---**[[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944117/ Predicting cooperative drug effects by the quantitative cellular profiling of response to individual drugs.]] **---CPT Pharmacometrics Syst. Pharmacol (2014) 3, e1; doi:10.1038/psp.2013.79.
~1) James C Costello et al. (**Junfei Zhao** is listed as one co-author).---**[[http://www.nature.com/nbt/journal/v32/n12/pdf/nbt.2877.pdf The challenge of drug sensitivity prediction: an assessment of methods through collaborative competition.]] **---Nature Biotechnology (2014), doi: 10.1038/nbt.2877..
~1) Mukesh Bansal et al. (**Junfei Zhao** is listed as one co-author).---**[[http://www.nature.com/nbt/journal/v32/n12/pdf/nbt.3052.pdf A community computational challenge to predict the activity of pairs of compounds.]] **---Nature biotechnology 32.12 (2014): 1213-1222.
~1) **Junfei Zhao**, Shihua Zhang, Ling-Yun Wu, and Xiang-Sun Zhang.---**[[http://bioinformatics.oxfordjournals.org/content/early/2012/09/14/bioinformatics.bts564.abstract?keytype=ref&ijkey=jTZqXD6CglnPsUI Efficient methods for identifying mutated driver pathways in cancer.]] **---//Bioinformatics//, doi: 10.1093/bioinformatics/bts564, 2012.
~1) Shihua Zhang, **Junfei Zhao**, Xiang-Sun Zhang.---**[[http://pre.aps.org/abstract/PRE/v85/i5/e056110 Common community structure in time-varying networks.]] **---//Physical Review E//, 85, 056110, 2012.
~1) Chen Chen, **Junfei Zhao**, Qiang Huang, Rui-Sheng Wang, Xiang-Sun Zhang.---**[[http://www.biomedcentral.com/1752-0509/6/S1/S7 Inferring domain-domain interactions from protein-protein interactions in the complex network conformation]].**---BMC Systems Biology (2012), 6(Suppl 1):S7.
~1) **Junfei Zhao**, Jiguang Wang, Xiang-Sun Zhang.---**[[http://www.aporc.org/LNOR/14/ISORA2011F15.pdf A SVC-based Method to Detect Multi-scalar Noisy Communities in Complex Networks.]] **---ISORA 2011, pp. 133-143.
~1) Junhua Zhang, Shihua Zhang, Yong Wang, **Junfei Zhao**, Xiang-Sun Zhang. ---**[[http://ieeexplore.ieee.org/xpl/abstractAuthors.jsp?tp=&arnumber=6314154&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D6314154 Identifying Mutated Core Modules in Glioblastoma by Integrative Network Analysis.]]**--- 2012 IEEE International Conference on Systems Biology (ISB), pp. 304-309.
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=== {{color c="blue" text="Links"}} ===
~- [[http://www.nature.com Nature]]
~- [[http://www.plos.org PLoS]]
~- [[http://www.sciencemag.org Science]]
~- [[http://www.pnas.org PNAS]]
~- [[http://www.ctex.org CTEX]]
""<a href="http://www.clustrmaps.com/map/zhangroup.aporc.org/JunfeiZhao" title="Visitor Map for zhangroup.aporc.org/JunfeiZhao"><img src="//www.clustrmaps.com/map_v2.png?u=kkpr&d=u9PujgO0Xl9556aBY5EWr1QA5ICOxWQcuiZDaaud7iM" /></a>""
