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Jiang Qian

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F X Reymond Sutandy; Chien-Sheng Chen; Jiang Qian; Heng Zhu
Overview of protein microarrays.
Robert H Newman; QIANG NI; Akhilesh Pandey; Tony Pawson; Hee-Sool Rho; Alexey G Ryazanov; Matthew Shirley; Benjamin E Turk; Crystal Woodard; George Wu; SHULI XIA; Zhi Xie; Donald J Zack; Jin Zhang; Heng Zhu; Jun Seop Jeong; Morris J Birnbaum; Seth Blackshaw; Hillary M Clark; Philip A Cole; Christopher Cooper; Kevin N Dalby; Stephen Desiderio; Xinxin Gao; Anne-Claude Gingras; Renu Goel; Jianfei Hu; Shaohui Hu; Woochang Hwang; Hongkai Ji; Stefan Knapp; Jimmy Lin; John Neiswinger; Jiang Qian
Construction of human activity-based phosphorylation networks.
Mario Matthaei; Huan Meng; Jiang Qian; Eva-Maria Lackner; Charles G Eberhart; Haiping Hao; Jianfei Hu; Albert S Jun
Endothelial cell whole genome expression analysis in a mouse model of early-onset Fuchs' endothelial corneal dystrophy.

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All Publications

2013: F X Reymond Sutandy; Chien-Sheng Chen; Jiang Qian; Heng Zhu
Overview of protein microarrays.
Current protocols in protein science / editorial board, John E. Coligan ... [et al.] 2013;Chapter 27():Unit 27.1.
2013: Robert H Newman; QIANG NI; Akhilesh Pandey; Tony Pawson; Hee-Sool Rho; Alexey G Ryazanov; Matthew Shirley; Benjamin E Turk; Crystal Woodard; George Wu; SHULI XIA; Zhi Xie; Donald J Zack; Jin Zhang; Heng Zhu; Jun Seop Jeong; Morris J Birnbaum; Seth Blackshaw; Hillary M Clark; Philip A Cole; Christopher Cooper; Kevin N Dalby; Stephen Desiderio; Xinxin Gao; Anne-Claude Gingras; Renu Goel; Jianfei Hu; Shaohui Hu; Woochang Hwang; Hongkai Ji; Stefan Knapp; Jimmy Lin; John Neiswinger; Jiang Qian
Construction of human activity-based phosphorylation networks.
Molecular systems biology 2013;9():655.
2013: Mario Matthaei; Huan Meng; Jiang Qian; Eva-Maria Lackner; Charles G Eberhart; Haiping Hao; Jianfei Hu; Albert S Jun
Endothelial cell whole genome expression analysis in a mouse model of early-onset Fuchs' endothelial corneal dystrophy.
Investigative ophthalmology & visual science 2013;54(3):1931-40.
2012: Heng Zhu; Eric Cox; Jiang Qian
Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics.
Proteomics. Clinical applications 2012;6(11-12):548-62.
2012: Yunzhao R Ren; Jun Wan; Heng Zhu; Raghothama Chaerkady; Shaohui Hu; Akhilesh Pandey; Jiang Qian; Scott E Kern
Unbiased discovery of interactions at a control locus driving expression of the cancer-specific therapeutic and diagnostic target, mesothelin.
Journal of proteome research 2012;11(11):5301-10.
2012: Jun Seop Jeong; Lizhi Jiang; Josean Marrero; Ignacio Pino; Jiang Qian; Leonardo Ramos; Hee-Sool Rho; Zully Ann Rivera-Pacheco; Cecil Torres-Castro; Carlos Vera; Wendy Y Yap; Heng Zhu; Jef Boeke; Joseph Bonaventura; Daniel J Eichinger; Jianfei Hu; Shaohui Hu; Edisa Albino; Diane Bayron-Poueymiroy; Seth Blackshaw
Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.
Molecular & cellular proteomics : MCP 2012;11(6):O111.016253.
2012: MEIR SHAMAY; Li Shen; Zhi Xie; Heng Zhu; Jian Zhu; Shaohui Hu; Renfeng Li; Gangling Liao; Jianyong Liu; Jiang Qian; Richard F Ambinder; Melanie Greenway; S Diane Hayward
A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening.
Journal of virology 2012;86(9):5179-91.
2012: Mary Katherine Tarrant; Zhi Xie; Gai Yan; Natasha E Zachara; Heng Zhu; Seth Blackshaw; Jeffrey C Culhane; Felicia A Etzkorn; Christopher Gross; Gerald W Hart; Yoshitaka Ichikawa; Jun Seop Jeong; Yu Lin Jiang; Tatsuji Matsuoka; Jiang Qian; Hee-Sool Rho; Philip A Cole
Regulation of CK2 by phosphorylation and O-GlcNAcylation revealed by semisynthesis.
Nature chemical biology 2012;8(3):262-9.
2012: Hyun Yi; Jianfei Hu; Jiang Qian; Abigail S Hackam
Expression of brain-derived neurotrophic factor is regulated by the Wnt signaling pathway.
Neuroreport 2012;23(3):189-94.
2012: Crystal Woodard; Heng Zhu; Jian Zhu; Jianfei Hu; Renfeng Li; Gangling Liao; Rob Newman; Ai Na Ng; Jiang Qian; Hee-Sool Rho; MEIR SHAMAY; Jun Wan; S Diane Hayward
Phosphorylation of the chromatin binding domain of KSHV LANA.
PLoS pathogens 2012;8(10):e1002972.
2012: Woochang Hwang; Hongkai Ji; George Wu; Donald J Zack; Laszlo Hackler; Jiang Qian
Dynamics of regulatory networks in the developing mouse retina.
PloS one 2012;7(10):e46521.
2012: Heng Zhu; Jiang Qian
Applications of functional protein microarrays in basic and clinical research.
Advances in genetics 2012;79():123-55.
2012: Raj P Kandpal; Timothy S Kern; Jacob Nellissery; Jiang Qian; Harsha K Rajasimha; Matthew J Brooks; Jun Wan; Anand Swaroop
Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs.
Molecular vision 2012;18():1123-46.
2012: Shannath L Merbs; Verity F Oliver; Jiang Qian; Jun Wan; Laszlo Hackler; Miriam A Khan; Donald J Zack
Cell-specific DNA methylation patterns of retina-specific genes.
PloS one 2012;7(3):e32602.
2011: Dasheng Zheng; Heng Zhu; Jian Zhu; Richard F Ambinder; Chuang-Jiun Chiou; Yong Gu Cho; Gary S Hayward; Gangling Liao; Otoniel Martinez-Maza; Shweta Pai; Jiang Qian; Jun Wan; Leyao Wang; Crystal Woodard; S Diane Hayward
Comparison of humoral immune responses to Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus using a viral proteome microarray.
The Journal of infectious diseases 2011;204(11):1683-91.
2011: Chao Cheng; Pedro Alves; Nitin Bhardwaj; Woochang Hwang; Masaomi Kato; Zhi John Lu; Wei Niu; Jiang Qian; Joel S Rozowsky; Michael Snyder; Koon-Kiu Yan; Mark Gerstein
Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.
PLoS computational biology 2011;7(11):e1002190.
2011: Natalie Wolkow; Ting-Di Wu; Jean-Luc Guerquin-Kern; Jiang Qian; Ying Song; Joshua L Dunaief
Aceruloplasminemia: retinal histopathologic manifestations and iron-mediated melanosome degradation.
Archives of ophthalmology 2011;129(11):1466-74.
2011: Renfeng Li; Gangling Liao; Jimmy Lin; Jianyong Liu; Jiang Qian; SEAN TAVERNA; Crystal Woodard; Zhi Xie; Heng Zhu; Jian Zhu; Richard F Ambinder; Mei-Ru Chen; Prashant Desai; Gary S Hayward; Shaohui Hu; S Diane Hayward
Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication.
Cell host & microbe 2011;10(4):390-400.
2011: Jun Wan; Donald J Zack; Kieron M Torres; Laszlo Hackler; Tomohiro Masuda; Shannath L Merbs; Jiang Qian
Dynamic usage of alternative splicing exons during mouse retina development.
Nucleic acids research 2011;39(18):7920-30.
2011: Edel M Hyland; Chunfa Jie; Henrik Molina; Akhilesh Pandey; Kunal Poorey; Jiang Qian; Zhi Xie; David T Auble; Stefan Bekiranov; Junbiao Dai; Jef Boeke
An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.
Genes & development 2011;25(12):1306-19.
2011: Shaohui Hu; Zhi Xie; Seth Blackshaw; Jiang Qian; Heng Zhu
Characterization of protein-DNA interactions using protein microarrays.
Cold Spring Harbor protocols 2011;2011(5):pdb.prot5614.
2011: Zhi Xie; Shaohui Hu; Jiang Qian; Seth Blackshaw; Heng Zhu
Systematic characterization of protein-DNA interactions.
Cellular and molecular life sciences : CMLS 2011;68(10):1657-68.
2011: Shaohui Hu; Zhi Xie; Jiang Qian; Seth Blackshaw; Heng Zhu
Functional protein microarray technology.
Wiley interdisciplinary reviews. Systems biology and medicine 2011;3(3):255-68.
2010: Jianfei Hu; Jun Wan; Laszlo Hackler; Donald J Zack; Jiang Qian
Computational analysis of tissue-specific gene networks: application to murine retinal functional studies.
Bioinformatics (Oxford, England) 2010;26(18):2289-97.
2010: Hui Ren; Gezhi Xu; Jiang Qian; Min Zhou; John Gonzales; Yingqin Ni
Müller cells upregulate the expression of SAP97 in light-injured rat retina.
Neuroreport 2010;21(12):832-6.
2010: Tomomi Shimogori; Daniel A Lee; Ana Miranda-Angulo; Yanqin Yang; Hong Wang; Lizhi Jiang; Aya C Yoshida; Ayane Kataoka; Hiromi Mashiko; Marina Avetisyan; Lixin Qi; Jiang Qian; Seth Blackshaw
A genomic atlas of mouse hypothalamic development.
Nature neuroscience 2010;13(6):767-75.
2010: Laszlo Hackler; Jun Wan; Anand Swaroop; Jiang Qian; Donald J Zack
MicroRNA profile of the developing mouse retina.
Investigative ophthalmology & visual science 2010;51(4):1823-31.
2010: Zhi Xie; Don Kulasiri; Sandhya Samarasinghe; Jiang Qian
An unbiased sensitivity analysis reveals important parameters controlling periodicity of circadian clock.
Biotechnology and bioengineering 2010;105(2):250-9.
2010: Zhi Xie; Shaohui Hu; Seth Blackshaw; Heng Zhu; Jiang Qian
hPDI: a database of experimental human protein-DNA interactions.
Bioinformatics (Oxford, England) 2010;26(2):287-9.
2010: Jimmy Lin; Zhi Xie; Heng Zhu; Jiang Qian
Understanding protein phosphorylation on a systems level.
Briefings in functional genomics 2010;9(1):32-42.
2009: Shaohui Hu; Zhi Xie; Akishi Onishi; Xueping Yu; Lizhi Jiang; Jimmy Lin; Hee-Sool Rho; Crystal Woodard; Hong Wang; Jun Seop Jeong; Shunyou Long; Xiaofei He; HERSCHEL WADE; Seth Blackshaw; Jiang Qian; Heng Zhu
Profiling the human protein-DNA interactome reveals ERK2 as a transcriptional repressor of interferon signaling.
Cell 2009;139(3):610-22.
2009: Jun Wan; Jimmy Lin; Donald J Zack; Jiang Qian
Relating periodicity of nucleosome organization and gene regulation.
Bioinformatics (Oxford, England) 2009;25(14):1782-8.
2009: Yu-Yi Lin; Jin-ying Lu; Junmei Zhang; Wendy Walter; Weiwei Dang; Jun Wan; Sheng-Ce Tao; Jiang Qian; Yingming Zhao; Jef Boeke; Shelley L Berger; Heng Zhu
Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis.
Cell 2009;136(6):1073-84.
2009: Li A Kung; Sheng-Ce Tao; Jiang Qian; Michael G Smith; Michael Snyder; Heng Zhu
Global analysis of the glycoproteome in Saccharomyces cerevisiae reveals new roles for protein glycosylation in eukaryotes.
Molecular systems biology 2009;5():308.
2008: Xueping Yu; Jimmy Lin; Donald J Zack; Joshua T Mendell; Jiang Qian
Analysis of regulatory network topology reveals functionally distinct classes of microRNAs.
Nucleic acids research 2008;36(20):6494-503.
2008: Sheng-Ce Tao; Yu Li; Jiangbing Zhou; Jiang Qian; Ronald Schnaar; Ying Zhang; Irwin J Goldstein; Heng Zhu; Jonathan P Schneck
Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers.
Glycobiology 2008;18(10):761-9.
2008: Xiong Liu; Xueping Yu; Donald J Zack; Heng Zhu; Jiang Qian
TiGER: a database for tissue-specific gene expression and regulation.
BMC bioinformatics 2008;9():271.
2008: Jin-Ying Lu; Yu-Yi Lin; Jiang Qian; Sheng-Ce Tao; Jian Zhu; Cecile M Pickart; Heng Zhu
Functional dissection of a HECT ubiquitin E3 ligase.
Molecular & cellular proteomics : MCP 2008;7(1):35-45.
2007: Zhiyong Yang; Harry A Quigley; Mary Ellen Pease; Yanqin Yang; Jiang Qian; Danielle Valenta; Donald J Zack
Changes in gene expression in experimental glaucoma and optic nerve transection: the equilibrium between protective and detrimental mechanisms.
Investigative ophthalmology & visual science 2007;48(12):5539-48.
2007: Tal Meir; Rinat Dror; Xueping Yu; Jiang Qian; Itamar Simon; Jacob Pe'er; Itay Chowers
Molecular characteristics of liver metastases from uveal melanoma.
Investigative ophthalmology & visual science 2007;48(11):4890-6.
2007: Jimmy Lin; Jiang Qian
Systems biology approach to integrative comparative genomics.
Expert review of proteomics 2007;4(1):107-19.
2007: Xueping Yu; Jimmy Lin; Donald J Zack; Jiang Qian
Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.
BMC bioinformatics 2007;8():437.
2007: Haiyuan Yu; Katherine Nguyen; Thomas E Royce; Jiang Qian; Kenneth Nelson; Michael Snyder; Mark Gerstein
Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.
Nucleic acids research 2007;35(2):e8.
2006: Jiang Qian; Jimmy Lin; Donald J Zack
Characterization of binding sites of eukaryotic transcription factors.
Genomics, proteomics & bioinformatics 2006;4(2):67-79.
2006: Jimmy Lin; Donald J Zack; Jiang Qian
Transcriptional regulatory network prediction.
Biotechnology & genetic engineering reviews 2006;22():45-62.
2006: Xueping Yu; Jimmy Lin; Donald J Zack; Jiang Qian
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues.
Nucleic acids research 2006;34(17):4925-36.
2006: Xueping Yu; Jimmy Lin; Tomohiro Masuda; Noriko Esumi; Donald J Zack; Jiang Qian
Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.
Nucleic acids research 2006;34(3):917-27.
2005: SHULI XIA; Jinghua Yang; Yingjun Su; Jiang Qian; Enbo Ma; Gabriel G Haddad
Identification of new targets of Drosophila pre-mRNA adenosine deaminase.
Physiological genomics 2005;20(2):195-202.
2005: Jiang Qian; Noriko Esumi; Yangjian Chen; Qingliang Wang; Itay Chowers; Donald J Zack
Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation.
Nucleic acids research 2005;33(11):3479-91.
2004: Abigail S Hackam; Richelle Strom; Dongmei Liu; Jiang Qian; Chenwei Wang; Deborah C Otteson; Tushara L Gunatilaka; Ronald H Farkas; Itay Chowers; Masaaki Kageyama; Thierry Leveillard; José-Alain Sahel; Peter A Campochiaro; Giovanni Parmigiani; Donald J Zack
Identification of gene expression changes associated with the progression of retinal degeneration in the rd1 mouse.
Investigative ophthalmology & visual science 2004;45(9):2929-42.
2004: Abigail S Hackam; Jiang Qian; Dongmei Liu; Tushara L Gunatilaka; Ronald H Farkas; Itay Chowers; Masaaki Kageyama; Giovanni Parmigiani; Donald J Zack
Comparative gene expression analysis of murine retina and brain.
Molecular vision 2004;10():637-49.
2004: Ronald H Farkas; Jiang Qian; Jeffrey L. Goldberg; Harry A Quigley; Donald J Zack
Gene expression profiling of purified rat retinal ganglion cells.
Investigative ophthalmology & visual science 2004;45(8):2503-13.
2003: Yuval Kluger; Haiyuan Yu; Jiang Qian; Mark Gerstein
Relationship between gene co-expression and probe localization on microarray slides.
BMC genomics 2003;4(1):49.
2003: Jiang Qian; Jimmy Lin; Nicholas M Luscombe; Haiyuan Yu; Mark Gerstein
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinformatics (Oxford, England) 2003;19(15):1917-26.
2003: Itay Chowers; Tushara L Gunatilaka; Ronald H Farkas; Jiang Qian; Abigail S Hackam; Elia J Duh; Masaaki Kageyama; Chenwei Wang; Amit Vora; Peter A Campochiaro; Donald J Zack
Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray.
Investigative ophthalmology & visual science 2003;44(9):3732-41.
2003: Haiyuan Yu; Nicholas M Luscombe; Jiang Qian; Mark Gerstein
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
Trends in genetics : TIG 2003;19(8):422-7.
2003: Jiang Qian; Yuval Kluger; Haiyuan Yu; Mark Gerstein
Identification and correction of spurious spatial correlations in microarray data.
BioTechniques 2003;35(1):42-4, 46, 48.
2002: Christine E Horak; Nicholas M Luscombe; Jiang Qian; Paul Bertone; Stacy Piccirrillo; Mark Gerstein; Michael Snyder
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes & development 2002;16(23):3017-33.
2002: Jimmy Lin; Jiang Qian; Dov Greenbaum; Paul Bertone; R Das; Nathaniel Echols; Alessandro Senes; B Stenger; Mark Gerstein
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing.
Nucleic acids research 2002;30(20):4574-82.
2002: Nicholas M Luscombe; Jiang Qian; Zhaolei Zhang; Ted Johnson; Mark Gerstein
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Genome biology 2002;3(8):RESEARCH0040.
2002: Ronald Jansen; Ning Lan; Jiang Qian; Mark Gerstein
Integration of genomic datasets to predict protein complexes in yeast.
Journal of structural and functional genomics 2002;2(2):71-81.
2001: Jiang Qian; Marisa Dolled-Filhart; J Lin; H Yu; Mark Gerstein
Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
Journal of molecular biology 2001;314(5):1053-66.
2001: Jiang Qian; Nicholas M Luscombe; Mark Gerstein
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
Journal of molecular biology 2001;313(4):673-81.
2001: Dov Greenbaum; Nicholas M Luscombe; Ronald Jansen; Jiang Qian; Mark Gerstein
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
Genome research 2001;11(9):1463-8.
2001: Jiang Qian; B Stenger; C A Wilson; Jimmy Lin; Ronald Jansen; Sarah A Teichmann; J Park; WG Krebs; Haiyuan Yu; Vadim Alexandrov; Nathaniel Echols; Mark Gerstein
PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.
Nucleic acids research 2001;29(8):1750-64.