2012

Woodard, C., Shamay, M., Liao, G., Zhu, J., Ng, A., Li, R., Newman, R., Rho, H., Hu, J., Wan, J., Qian, J., Zhu, H, and Hayward, S.D. Phosphorylation of the Chromatin Binding Domain of KSHV LANA. PLoS Pathogen, 2012, (In press).

Ren, YR, Chaerkady, R, Hu, S, Wan, J, Qian, J, Zhu, H, Pandey, A, Kern,S.E.Unbiased Discovery of Interactions at a Control Locus Driving Expression of the Cancer-Specific Therapeutic and Diagnostic Target, Mesothelin, J Proteome Res, 2012, (In press).

Hwang, W., Hackler Jr., L., Wu, G., Ji, H., Zack, D.J., Qian, J., Dynamics of Regulatory Networks in the Developing Mouse Retina, PLoS One, 2012, 7: e46521.

Zhu, H., Qian, J. Applications of functional protein microarrays in basic and clinical research, Adv Genet. 2012; 79, 123-55.

Kandpal, R.P., Rajasimha, H.K., Brooks, M.J., Nellissery, J., Wan, J., Qian, J., Kern, T.S., Swaroop, A. Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs, Mol Vis. 2012, 18, 1123-46.

Tarrant, M.K., Rho, H.S., Xie, Z., Jiang, Y.L., Gross, C., Culhane, J.C., Qian, J., Ichikawa, Y., Matsuoka, T., Zachara, N., Etzkorn, F.A., Hart, G.W., Jeong, J., Blackshaw, S., Zhu, H., Cole, P.A., Multi-faceted Regulation of Protein Kinase CK2 by Phosphorylation and O- GlcNAcylation Revealed through Semisynthesis , Nat. Chem. Biol., 2012, 8, 262-269.

Yi, H., Hu, J., Qian, J., and Hackam, A.S., Expression of brain-derived neurotrophic factor is regulated by the Wnt signaling pathway, Neuroreport, 2012, 23, 189-194.

Jeong, J.S., Jiang, L., Albino, E., Marrero, J., Rho, H.S., Hu, J., Hu, S., Vera, C., Bayron-Poueymiroy, D., Rivera-Pacheco, Z.A., Ramos, L., Torres-Castro, C., Qian, J., Bonaventura, J., Boeke, J.D., Yap, W.Y., Pino, I., Eichinger, D.J., Zhu, H., Blackshaw, S. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.Mol. Cell Proteomics, 2012,

Sharmay, M., Liu, J., Li, R., Liao, G., Greenway, M., Zhu, J., Zhi, X., Ambinder, R.F., Qian, J., Zhu, H., Hayward, S.D., A Protein Array Screen for KSHV LANA Interactors Links LANA to TIP60, PP2A activity and Telomere Shortening. Journal of Virology, 2012,

Merbs, S.L., Khan, M.A., Hackler, L Jr, Oliver, V.F., Wan, J., Qian, J., Zack, D.J. Cell-specific DNA methylation patterns of retina-specific genes, PLoS One, 2012

2011

Cheng, C., Yan, K.K., Hwang, W., Qian, J., Bhardwaj, N., Rozowsky, J., Lu, Z.J., Niu, W., Alves, P., Kato, M., Snyder, M., Gerstein, M., Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data., PLoS Comput. Biol., 2011, e1002190.

Li, R., Zhu, J., Xie, Z., Liao, G., Liu, J., Chen, M-R., Hu, S., Woodard, C., Lin, J., Taverna, S., Desai, P., Ambinder, R., Hayward, G.S., Qian, J., Zhu, H., Hayward, S.D., Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication., Cell Host & Microbe, 2011, 10, 390-400.

Zheng, D., Wan, J., Cho, Y.G., Wang, L., Chiou, C-J., Pai, S., Woodard, C., Zhu, J., Liao, G., Martinez-Maza, O., Qian, J., Zhu, H., Hayward, G.S., Ambinder, R.F., Hayward, S.D. Comparison of Humoral Immune Responses to Epstein-Barr Virus and Kaposi’s Sarcoma Associated Herpesvirus Using a Viral 10, 390-400Proteome Microarray. J Infect Dis., 2011, 204, 1683-1691.

Wan, J., Masuda, T., Hackler, L., Torres, K.M., Merbs, S.L., Zack, D.J., Qian, J., Dynamic usage of alternative splicing exons during mouse retina development, Nucleic Acids Research, 2011, 39, 7920-7930.

Hyland, E.M., Molina, H., Poorey, K., Jie, C., Xie, Z., Dai, J., Qian, J., Bekiranov, S.,Auble, D.T., Pandey, A., Boeke, J.D., Evolutionarily "young" lysine residue in histone H3 attenuates transcription output in Saccharomyces cerevisiae, Genes Dev., 2011, 25, 1306-1319.

Xie, Z., Hu, S., Qian, J., Blackshaw, S., Zhu, H., Systematic characterization of protein-DNA interactions., Cell Mol. Life Sci., 2011, 68, 1657-1668.

Hu, S., Xie, Z., Blackshaw, S., Qian, J., Zhu, H., Characterization of Protein-DNA Interactions Using Protein Microarrays, CSH protocols, 2011, pdb.prot5614.

2010

Hu, S., Xie, Z., Qian, J., Blackshaw, S., Zhu, H., "Functional Protein Microarray Technology", Wiley Interdiscip. Rev. Syst. Biol. Med. 2010, (Accepted).

Hu, J., Wan, J., Hackler, L., Zack, D.J., Qian, J., "Computational analysis of tissue-specific gene networks: application to murine retinal functional studies", Bioinformatics, 2010, 26, 2289-2297.

Shimogori, T., Lee, D.A., Miranda-Angulo, A., Yang, Y., Yoshida, A.C., Kataoka, A., Mashiko, H., Jiang, L., Avetisyan, M., Qi, L., Qian, J., and Blackshaw, S., “A genomic atlas of mouse hypothalamic development”. Nature Neuroscience, 2010, 13, 767-775.

Lin, J.#, Xie, Z.#, Zhu, H., Qian, J., "Understanding Protein Phosphorylation on a Systems Level", Briefings in Functional Genomics and Proteomics, 2010, 9, 32-42. (#co-first authors)

Xie, Z., Hu, S., Blackshaw, S., Zhu, H., Qian, J.,"hPDI: a database of experimental human protein-DNA interactions", Bioinformatics, 2010, 26, 287-289.

Hackler, L.#, Wan, J.#, Swaroop, A., Qian, J.*, Zack, D.J.*, "MicroRNA profile of the developing mouse retina", IOVS, 2010, 51, 1823-1831. (#co-first authors, * co-corresponding authors).

Xie, Z., Kulasiri, D., Samarasinghe, S., Qian, J. "An Unbiased Sensitivity Analysis Reveals Important Parameters Controlling Periodicity of Circadian Clock". Biotechnology and bioengineering, 2010, 105, 250-259.

2009

Kung, L., Tao, S-C., Qian, J., Smith, M., Snyder, M., Zhu, H., “Global analysis of the glycoproteome in S. cerevisiae reveals new roles for protein glycosylation”, Mol. Syst. Biol, 2009, 5:308.

Hu, S.#, Xie, Z.#, Onishi, A., Yu, X., Jiang, L., Lin, J., Rho, H., Woodard, C., Wang, H., Jeong, J., Long, S., He, X., Wade, H., Blackshaw, S.*, Qian, J.* Zhu, H.,* ”Profiling the Human Protein-DNA Interactome Reveals ERK2 as a Transcriptional Repressor of Interferon Signalling”, Cell, 2009, 139, 610-622. (# co-first authors, * co-corresponding authors) (Highlighted in Cell, Nature Reviews Genetics, Nature Reviews Molecular Cell Biology, and Faculty 1000).

Wan, J., Lin, J., Zack, D.J., Qian, J., “Relating periodicity of nucleosome organization and gene regulation”, Bioinformatics, 2009, 25, 1782-1788.

Lin, Y., Lu, J., Zhang, J., Walter, W., Dang, W., Wan, J., Tao. S., Qian., J., Zhao., Y., Boeke, J.D., Berger, S. L., and Zhu., H., “Protein Acetylation Microarray Reveals NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis”, Cell, 2009, 136, 1073-1084.

2008

Lu, J., Lin, Y., Qian, J., Tao, S., Zhu, J., Pickart, C., and Zhu, H., “Functional dissection of a HECT domain ubiquitin E3 ligase”, Mol. Cell Proteomics, 2008, 7, 35-45.

Liu, X., Yu, X., Zack, D.J., Zhu, H., and Qian, J., “TiGER: a database for tissue-specific gene expression and regulation”, BMC Bioinformatics, 2008, 9, 271.

Tao, S., Li, Y., Zhou, J., Qian, J., Schnaar, R.L., Zhang, Y., Goldstein, I.J., Zhu, H., and Schneck, J.P., “Lectin microarrays identify cell-specific and functionally significant cell surface glycan markers”, Glycobiology, 2008, 18, 761-769.

Yu, X., Lin, J., Zack, D.J., Mendell, J.T., and Qian, J., “Analysis of regulatory network topology reveals functionally distinct classes of microRNAs”, Nucleic Acids Research, 2008, 36, 6494-6503.

2007

Meir, T., Dror, R., Yu, X., Qian, J., Simon, I., Pe’er, J. and Chowers, I., “Molecular Characteristics of Liver Metastases from Uveal Melanoma”, Investigative Ophthalmology & Vision Science, 2007, 48, 4890-4896.

Yu, H., Nguyen, K., Royce, T., Qian, J., Nelson, K., Snyder, M., and Gerstein, M., “Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool.”, Nucleic Acids Research, 2007, 35, e8.

Yang, Z., Quigley, H.A., Pease, M.E., Yang, Y., Qian, J., Valenta, D., and Zack, D.J., “Changes in Gene Expression in Experimental Glaucoma and Optic Nerve Transection: The Equilibrium between Protective and Detrimental Mechanisms”, Investigative Ophthalmology & Vision Science, 2007, 48,5539-5548.

Yu, X., Lin, J., Zack, D.J., and Qian, J., “Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors”, BMC Bioinformatics, 2007, 8: 437.

2006

Yu, X., Lin, J., Zack, D. and Qian, J. “Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues”, Nucleic Acids Research, 2006, 34, 4925-4936.

Qian, J., Lin, J. and Zack, D., “Characterization of binding sites of eukaryotic transcription factors”, Genomics, Proteomics & Bioinformatics 2006, 4, 67-79.

Yu, X., Lin, J., Masuda, T., Esumi, N., Zack, D.J., and Qian, J., “Genome-wide prediction and characterization of interactions between transcription factors in S. cerevisiae”, Nucleic Acids Research, 2006, 34, 917-927.

2005

Qian, J. Esumi, N., Chen, Y., Wang, Q., Chowers, I., Zack, D., “Identification of regulatory targets of tissue-specific transcription factors: application to retina-specific gene regulation”, Nucleic Acids Research, 2005, 33, 3479-3491.

Xia, S., Yang, J., Su, Y., Qian, J., Ma, E., Haddad, G.G. “Identification of new targets of Drosophila pre-mRNA adenosine deaminase.” Physiol. Genomics. 2005, 20, 195-202.

2004

Farkas, R., Qian, J., Goldberg, J., Quigley, H., Zack, D. “Gene Expression Profiling of Purified Rat Retinal Ganglion Cells”, Investigative Ophthalmology & Vision Science, 2004, 45, 2503-2513

Hackam A.S., Qian J., Liu D., Gunatilaka T., Farkas R.H., Chowers I., Kageyama M., Parmigiani G., Zack D.J. “Comparative gene expression analysis of murine retina and brain”, Mol. Vis., 2004, 10, 637-649.

Hackam, A.S., Strom, R., Liu, D., Qian, J., Gunatilaka, T., Farkas, R., Chowers, I., Kageyama, M., Leveillard, T., Sahel, J., Campochiaro, P., Parmigiani, P., Zack. D., “Identification of Gene Expression Changes Associated with the Progression of Retina Degeneration in the rd1 Mouse”, Investigative Ophthalmology & Vision Science, 2004, 45, 2929-2942.

2003

Qian. J., Kluger, Y., Yu. H., Gerstein, M., “Identification and correction of spurious spatial correlation in microarray data“, Biotechniques, 2003, 35, 42-46.

Yu, H., Luscombe, N.M., Qian, J., Gerstein. M., “Genomic analysis of gene expression relationships in transcriptional regulatory networks”, Trends in Genetics, 2003, 19, 422-427.

Qian, J., Lin, J., Luscombe, N.M., Yu. H., Gerstein, M. “Predictions of regulatory networks: genome wide identification of transcription factor targets from gene expression data“, Bioinformatics, 2003, 19, 1917-1926.

Kluger, Y., Yu, H., Qian, J., Gerstein, M., “Relationship between gene co-expression and probe localization on microarray slides”, BMC Genomics, 2003, 4, 49.

Chowers, I., Gunatilaka, T.L., Farkas, R.H., Qian, J., Hackam, A.S., Duh, E., Kageyama, M., Wang, C., Vora, A., Campochiaro, P.A., Zack, D, “Identification of novel genes preferentially expressed in the retina using a custom human retina cDNA microarray”, Investigative Ophthalmology & Vision Science, 2003, 44, 3732-3741.

2002

Luscombe, N.M, Qian, J., Zhang, Z., Johnson, T., Gerstein, M., "The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties", Genome Biology, 2002, 3, research0040.1-0040.7

Horak, C.E., Luscombe, N.M, Qian, J., Piccirrillo, S., Gerstein, M., Snyder, M., “Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae”,, Genes & Development, 2002, 16, 3017-3033.

Lin, J., Qian, J., Greebaum, D., Bertone, P., Das, R., Echols, N., Senes, A., Stenger, B., Gerstein, M., "GeneCensus: Global Genome Comparisons in terms of Metabolic Pathway Activity and Protein Family Sharing", Nucleic Acids Research, 2002, 30, 4574-4582.

Jansen, R., Lan, N., Qian, J., Gerstein, M., "Integration of genomic datasets to predict protein complexes in yeast", Journal of Structural and Functional Genomics, 2002, 2, 71-81.

2001

Qian, J., Stenger, B., Wilson, C.A., Lin, J., Jansen, R., Teichmann, S.A., Park, J., Krebs, W., Alexandrov, V., Echols, N., and Gerstein, M. “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, 1750-1764.

Qian, J., Luscombe, N.M., Gerstein, M. “Protein fold and family occurrence in genomes: Power-law behaviour and evolutionary model”, J. Mol. Biol. 2001, 313, 673-681.

Qian, J., Dolled-Filhart, M., Lin, J., Gerstein, M. “Beyond synexpression relationships: Local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions”, J. Mol. Biol. 2001, 314, 1053-1066.

Earlier

Eckstein, E., Qian, J., Hentschke, R., Thurn-Albrecht, T., Steffen, W., Fischer, E. W. “X-ray scattering study and molecular simulation of glass forming liquids: Propylene carbonate and Salol.”, J. Chem. Phys. 2000, 113, 4751-4762.

Qian, J., and Heuer, A. “Exchange rates of dynamic heterogeneities in a glass-forming liquid.”, Euro. Phys. J. B., 2000, 18, 501-505.

Qian, J., Stoeckelmann, E., and Hentschke, R. “Polarization effects in water clusters: A genetic algorithm approach.”, J. Mol. Model. 1999, 5, 281-286.

Qian, J., Hentschke, R., and Heuer, A. “Dynamic heterogeneities of translational and rotational motion of a molecular glass former from computer simulations.”, J. Chem. Phys. 1999, 110, 4514-4522.

Qian, J., Hentschke, R., and Heuer, A. “On the origin of dynamic heterogeneities in glass-forming liquids.”, J. Chem. Phys. 1999, 111, 10177-10182.