Selected Publications


Wang J, Zibetti C, Shang P, Sripathi SR, Zhang P, Cano M, Hoang T, Xia S, Ji H, Merbs S, Zack DJ, Handa JT, Sinha D, Blackshaw S, Qian J. ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration, Nat Communications, 2018, accepted.

Uzoma I, Hu J, Cox E, Xia S, Zhou J, Rho H, Guzzo C, Paul C, Ajala O, Goodwin CR, Jeong J, Moore C, Zhang H, Meluh P, Blackshaw S, Matunis M, Qian J*, Zhu H*. Global Identification of SUMO Substrates Reveals Crosstalk between SUMOylation and Phosphorylation Promotes Cell Migration, Mol Cell Proteomics, 2018, accepted.

Song G, Rho H, Pan J, Ramos P, Yoon K, Medina FA, Lee EM, Eichinger D, Ming G, Muñoz-Jordan JL, Tang H, Pino I, Song H, Qian J, Zhu H, Multiplexed biomarker panels discriminate Zika and Dengue virus infection in humans, Mol Cell Proteomics. 2017, accepted.

Pan J, Liu S, Zhu H, and Qian J, AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases, Nucleic Acids Research, 2017, accepted.

Wang G, Luo X, Wang J, Wan J, Xia S, Zhu H, Qian J, Wang Y. MeDReaders: a database for transcription factors that bind to methylated DNA, Nucleic Acids Res. 2018, accepted.

Wei S, Wang J, Oyinlade O, Ma D, Wang S, Kratz L, Lal B, Xu Q, Liu S, Shah SR, Zhang H, Li Y, Quinones-Hinojosa A, Zhu H, Huang ZY, Cheng L, Qian J, Xia S. Heterozygous IDH1 R132H/WT created by "single base editing" inhibits human astroglial cell growth by downregulating YAP, Oncogene. 2018, accepted.

Newman EA, Kim DW, Wan J, Wang J, Qian J, Blackshaw S. Foxd1 is required for terminal differentiation of anterior hypothalamic neuronal subtypes, Dev Biol. 2018, accepted.


Ghosh S, Shang P, Yazdankhah M, Bhutto I, Hose S, Montezuma SR, Luo T, Chattopadhyay S, Qian J, Lutty GA, Ferrington DA, Samuel Zigler J Jr, Sinha D. Activating the AKT2/NFκB/LCN-2 axis elicits an inflammatory response in age-related macular degeneration, J Pathol., 2017, 241, 583-588.

Hu CJ, Pan JB, Song G, Wen XT, Wu ZY, Chen S, Mo WX, Zhang FC, Qian J, Zhu H, Li YZ. Identification of novel biomarkers for Behcet Disease diagnosis using HuProt array approach, Mol Cell Proteomics 2017, 16, 147-156.

Cox, E., Hwang, W., Jeong, J., Hu, J., Guzzo, C., Uzoma, I., Matunis, M., Qian, J.*, Zhu, H.*, and Blackshaw, S.*, Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex, Mol Cell Proteomics, 2017, 16, 812-823.

Yang Z, Hou Y, Hao T, Rho HS, Wan J, Luan Y, Gao X, Yao J, Pan A, Xie Z, Qian J, Liao W, Zhu H, Zhou, A Human Proteome Array Approach to Identifying Key Host Proteins Targeted by Toxoplasma Kinase ROP18, Mol Cell Proteomics, 2017, 16, 469-484.

Shang P, Valapala M, Grebe R, Hose S, Ghosh S, Bhutto IA, Handa JT, Lutty GA, Lu L, Wan J, Qian J, Sergeev Y, Puertollano R, Zigler JS Jr, Xu GT, Sinha D, The amino acid transporter SLC36A4 regulates the amino acid pool in retinal pigmented epithelial cells and mediates the mechanistic target of rapamycin, complex 1 signaling, Aging Cell, 2017, 16, 349-359.

Wan J, Su Y, Song Q, Tung B, Oyinlade O, Liu S, Ying M, Ming G, Song H, Qian J*, Zhu H*, Xia S*, Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration, eLife, 2017, 6, e20068.

Huang Y, Pan J, Chen D, Zheng J, Qiu F, Li F, Wu Y, Wu W, Huang X, Qian J. Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq. Oncotarget, 2017, 8, 35973-35983.

Liu S, Zibetti C, Wan J, Wang G, Blackshaw S, Qian J., Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility, BMC Bioinformatics, 2017, 18:355.

Yoon K, Song G, Qian X, Pan J, Xu D, Rho H, Kim N, Habela C, Zheng L, Jacob F, Zhang F, Lee EM, Huang W, Ringeling F, Vissers C, Li C, Yuan L, Kang K, Kim S, Yeo J, Cheng Y, Liu S, Wen Z, Qin C, Wu Q, Christian KM, Tang H, Jin P, Xu Z, Qian J, Zhu H, Song H, Ming G, Zika-Virus-Encoded NS2A Disrupts Mammalian Cortical Neurogenesis by Degrading Adherens Junction Proteins, Cell Stem Cell, 2017, accepted.

Han X, Wang J, Wang J, Liu S, Hu J, Zhu H, Qian J., ScaPD: a database for human scaffold proteins, BMC Bioinformatics, 2017, accepted.

Pan J, Song G, Chen D, Li Y, Liu S, Hu S, Rosa C, Eichinger DJ, Pino I, Zhu H, Qian J, and Huang Y. Identification of serological biomarkers for early diagnosis of lung cancer using a protein array-based approach, Mol Cell Proteomics. 2017, accepted.

Zhang P, Zhu M, Zhao Y, Qian J, Dufresne C, Turner R, Semba R, and Solomon S, A proteomic approach to understanding the pathogenesis of idiopathic macular hole formation, Clin Proteom, 2017, accepted.


Gao T, He B, Liu S, Zhu H, Tan K, Qian J, EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types, Bioinformatics, 2016, accepted.

Zhu H, Wang G, Qian J, Transcription factors as readers and effectors of DNA methylation. Nature Reviews Genetics, 2016, accepted.

Masuda T, Wan J, Yerrabelli A, Berlinicke C, Kallman A, Qian J, Zack DJ. Off Target, but Sequence-Specific, shRNA-Associated Trans-Activation of Promoter Reporters in Transient Transfection Assays, PLoS ONE, 2016, 11:e0167867.

Liu Y, Zhang P, Pan J, D'Souza MA, Dufresne CP, Semba RD, Qian J, Edward DP. Anatomical differences of the protein profile in the rabbit sclera during growth, Exp Eye Res., 2016, 154:53-63.

Wang Y, An R, Umanah GK, Nambiar K, Park H, Eacker SM, Kim BW, Harraz MM, Chang C, Chen R, Kam TI, Jeong JS, Xie Z, Neifert S, Qian J, Blackshaw S, Zhu H, Song H, Ming G, Dawson VL, Dawson TM, A Nuclease that Mediates Cell Death induced by DNA Damage and Poly(ADP-ribose) (PAR) polymerase-1, Science, 2016, 354, aad6872.

Zeng Y, Yao B, Shin J, Lin L, Kim N, Song Q, Liu S, Su Y, Guo JU, Huang L, Wan J, Wu H, Qian J, Cheng X, Zhu H, Ming GL, Jin P, Song H. Lin28A binds active promoters and recruits Tet1 to regulate gene expression. Mol Cell. 2016, 61, 153-160.

de Melo J, Zibetti C, Clark BS, Hwang W, Miranda-Angulo AL, Qian J, Blackshaw S, Lhx2 Is an Essential Factor for Retinal Gliogenesis and Notch Signaling, J Neurosci. 2016, 36, 2391-2405.

Wang J, Xia S, Arand B, Zhu H, Machiraju R, Huang K, Ji H, Qian J, Single-cell co-expression analysis reveals distinct functional modules, co-regulation mechanisms and clinical outcomes, PLoS Comput. Biol., 2016, accepted.

Campochiaro PA, Hafiz G, Mir TA, Scott AW, Zimmer-Galler I, Shah SM, Wenick AS, Brady CJ, Han I, He L, Channa R, Poon D, Meyerle C, Aronow MB, Sodhi A, Handa JT, Kherani S, Han Y, Sophie R, Wang G, Qian J, Pro-permeability Factors in Diabetic Macular Edema; the Diabetic Macular Edema Treated with Ozurdex Trial, American Journal of Ophthalmology, 2106, accepted.

White DT, Eroglu A, Wang G, Zhang L, Sengupta S, Rajpurohit S, Walker SL, Qian J, Mumm JS, ARQiv-HTS: A Versatile Whole-organism Screening Platform Enabling in vivo Drug Discovery at High-throughput Rates, Nature Protocols, 2016, accepted.

Pan J, Liu S, Farkas M, Consugar M, Zack DJ, Kozak I, Arevalo JF, Pierce E, Qian J*, Kahtani E*, Serum Molecular Signature for Proliferative Diabetic Retinopathy in Saudi Patients with Type 2 Diabetes, Mol. Vis. 2016, accepted.


Hu J, Neiswinger J, Zhang J, Zhu H, Qian J. Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction. PLoS Compt. Biol., 2015. e1004508.

Maruotti J, Sripathi SR, Bharti K, Fuller J, Wahlin KJ, Ranganathan V, Sluch VM, Berlinicke CA, Davis J, Kim C, Zhao L, Wan J, Qian J, Corneo B, Temple S, Dubey R, Olenyuk BZ, Bhutto I, Lutty GA, Zack DJ. Small-molecule-directed, efficient generation of retinal pigment epithelium from human pluripotent stem cells, Proc Natl Acad Sci U S A, 2015, 112, 10950-10955.

Li R, Liao G, Nirujogi RS, Pinto SM, Shaw PG, Huang TC, Wan J, Qian J, Gowda H, Wu X, Lv DW, Zhang K, Manda SS, Pandey A, Hayward SD. Phosphoproteomic profiling reveals Epstein-Barr virus protein kinase integration of DNA damage response and mitotic signaling. PLoS Pathog. 2015, e1005346.

Wan, J., Oliver, V.F., Wang, G., Zhu, H., Zack, D.J., Merbs, S.L., Qian, J., Characterization of tissue-specific differential DNA methylation suggests distinct modes of positive and negative gene expression regulation, BMC Genomics, 2015, accepted.

Hwang, W., Oliver, V.F., Merbs, S.L., Zhu, H., and Qian, J., Prediction of promoters and enhancers using multiple DNA methylation-associated features, BMC Genomics, 2015, accepted.

Valapala M., Edwards M., Hose S., Hu J., Wawrousek E., Lutty G.A., Zigler JS., Qian, J., and Sinha, D., βA3/A1-crystallin is a critical mediator of STAT3 signaling in optic nerve astrocytes, Scientific Report, 2015, 5, 8755.

Campochiaro, P.A., Mir T.A., Hafiz, G., Scott, A., Sophie, R., Shah, S.M., Ying, H., Lu, L., Chen, C., Campbell, P., Kherani, S., Zimmer-Galler, I., Wenick, A., Han, I., Paulus, Y., Sodhi, A., Handa, J.T., Wang, G., Qian, J., Reduction of Macular Edema and Pro-permeability Factors after Dexamethasone Implant Injection in Retinal Vein Occlusion; the Ozurdex for Retinal Vein Occlusion (ORVO) Study, American Journal of Ophthalmology, 2015, accepted

Woodard, C., Liao, G., Goodwin, C.R., Hu, J., Zhi, X., Reis, T., Newman, R., Rho, H., Qian, J., Zhu, H., and Hayward, S.D., A screen for ERK primed GSK-3 substrates identifies the p53 inhibitor iASPP, Journal of Virology, 2015, accepted.

Kolson, D. R., Wan, J., Wu, J., Dehoff, M., Brandebura, A.N., Qian, J., Mathers, P.H., Spirou, G.A., Temporal Patterns of Gene Expression During Calyx of Held Development, Developmental Neurobiology, 2015, accepted.

Oliver, V., Jaffe, A.E., Song, J., Wang, G., Branham, K.E., Swaroop, A., Campochiaro, B., Zack, D.J., Qian, J.*, Merbs, S.L.*, Differential DNA Methylation Identified in the Blood and Retina of AMD Patients, Epigenetics, 2015, accepted.


Cano, M., Wang, L., Wan, J., Barnett, B.P., Ebrahimi, K., Qian, J., Handa, J.T., Oxidative Stress Induces Mitochondrial Dysfunction and a Protective Unfolded Protein Response in RPE cells, Free Radical Biology & Medicine, 2014, (accepted).

Matthaei, M., Hu, J., Kallay, L., Eberhart, C.G., Cursiefen, C., Qian, J., Lackner, E., Jun, A.S., Endothelial Cell MicroRNA Expression in Human Late-Onset Fuchs Dystrophy, IOVS, 2014, 55, 216-225.

Lee, Y.I., Giovinazzo, D., Kang, H.C., Lee, Y., Jeong, J.S., Doulias, P.T., Xie, Z., Hu, J., Ghasemi, M., Ischiropoulos, H., Qian, J., Zhu, H., Blackshaw, S., Dawson, V.L., Dawson, T.M., Protein microarray characterization of the S-nitrosoproteome, Mol. Cell. Proteomics, 2014, 13, 63-72.

Masuda ,T., Wahlin, K., Wan, J., Hu, J., Maruotti, J., Yang, X., Iacovelli, J., Wolkow, N., Kist, R., Dunaief, J.L,, Qian, J., Zack, D.J., Esumi, N. SOX9 Plays a Key Role in the Regulation of Visual Cycle Gene Expression in the Retinal Pigment Epithelium, J. Biol. Chem. 2014, 289, 12908-12921.

Prusevich, P., Kalin, J.H., Ming, S.A., Basso, M., Givens, J., Li, X., Hu, J., Taylor, M.S., Cieniewicz, A.M., Hsiao, P.Y., Huang, R., Roberson, H., Adejola, N., Avery, L.B., Casero, Jr. R.A., Taverna, S.D., Qian, J., Tackett, A.J., Ratan, R.R., McDonald, O.G., Feinberg, A.P., Philip A. Cole, A Selective Phenelzine Analogue Inhibitor of Histone Demethylase LSD1, ACS Chem. Biol. 2014, 9, 1284-93.

Bedont, J.L., Legates, T.A., Slat, E.A., Byerly, M.S., Wang, H., Hu, J., Rupp, A.C., Qian, J., Wong, G.W., Herzog, E.D., Hattar, S., Blackshaw, S., Lhx1 controls terminal differentiation and circadian function of the suprachiasmatic nucleus, Cell Reports, 2014, 7, 609-622.

Wu, X., Renuse, S., Sahasrabuddhe, N. A, Zahari, M. S., Chaerkady, R., Kim, M. S., Nirujogi, R. S., Mohseni, M., Kumar, P., Raju, R., Zhong, J., Yang, J., Neiswinger, J., Jeong, J. S., Newman, R., Powers, M. A., Somani, B. L., Gabrielson, E., Sukumar, S., Stearns, V., Qian, J., Zhu, H., Vogelstein, B., Park, B. H. and Pandey, A. Activation of diverse signaling pathways by oncogenic PIK3CA mutations. Nature Communications, 2014, 5, 4961.


Hu, J., Rho, H.S., Newman, R.H., Zhang, J., Zhu, H., Qian, J. Phosphonetworks: A database for a high-resolution map of human phosphorylation networks, Bioinformatics, 2013, (accepted).

Hu, S.#, Wan, J.#, Su, Y.#, Song, Q., Zeng, Y., Nguyen, H. N., Shin, J., Cox, E., Rho, H., Woodard, C., Xia, S., Ming, G., Wade, H.*, Song, H.*, Qian, J.*, Zhu, H.*, DNA Methylation Presents Distinct Binding Sites for Human Transcription Factors, eLife, 2013, 2:e00726.

Oliver, VF, Franchina,M., Jaffe,A.E., Branham,K.E., Othman,M., Heckenlively,J.R., Swaroop,A., Campochiaro,B., Vote,B.J., Craig,J.E., Saffery,R., Mackey,D.A., Qian,J., Zack,D.J., Hewitt,A.W.*, Merbs, S.L*,Hypomethylation of the IL17RC Promoter in Peripheral Blood Leukocytes is Not A Hallmark of Age-Related Macular Degeneration, Cell Reports, 2013, (accepted).

Wan, J.#, Oliver, V.F.#, Zhu, H., Zack, D.J., Qian, J.*, Merbs, S.L.*, Integrative Analysis of Tissue-Specific Methylation and Alternative Splicing Identifies Conserved Transcription Factor Binding Motifs, Nucleic Acids Research, 2013, (accepted).

Oliver, V.F., Wan, J., Agarwal, S., Zack, D.J., Qian, J., Merbs, S.L., A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples, Epigenetics Chromatin, 2013, 6:17.

Matthaei, M., Hu, J., Meng, H., Lackner, E-M., Eberhart, C., Qian, J., Hao, H., Jun, A., Endothelial Cell Whole Genome Expression Analysis in a Mouse Model of Early-Onset Fuchs Endothelial Corneal Dystrophy, IOVS, 2013, 54, 1931-1940.

Lee, Y.I., Giovinazzo, D., Kang, H.C., Lee, Y., Jeong, J.S., Doulias, P., Xie, Z., Hu, J., Ghasemi, M., Ischiropoulos, H., Qian, J., Zhu, H., Blackshaw, S., Dawson, V., Dawson, T.M., Protein Microarray Characterization of the S-Nitrosoproteome, Molecular Cellular Proteomics, 2013, accepted.

Sutandy, F.X., Qian, J., Chen, C.S., Zhu, H., Overview of Protein Microarray, Current Protocols in Protein Science, 2013, 27.1

Woodard, C.L., Goodwin, C.R., Wan, J., Xia, S., Newman, R., Hu, J., Zhang, J., Hayward, S.D., Qian, J., Laterra, J., Zhu, H., Profiling the Dynamics of a Human Phosphorylome Reveals New Components in HGF/c-Met SignalingPLoS One, 2013, 8:e72671.

Hu, J#. Hwang, W.#, Rho, H.#, Newman, R.H.#, Neiswinger, J., Zhu, H., Zhang, J., Qian. J., Global analysis of phosphorylation networks in humans, BBA proteins and proteomics, 2013, (in press).

Newman, R.H.#, Hu, J.#, Rho, H.#, Xie, Z.#, Woodard, C., Neiswinger, J., Hwang, W., Shirley, M., Hu, S., Cooper, C., Jeong, J., Wu, G., Lin, J., Gao, X., Ni, Q., Goel, R., Ji, H., Desiderio, S., Dalby, K.N., Birnbaum, M.J., Cole, P.A., Knapp, S., Ryazanov, A., Zack, D.J., Blackshaw, S., Pawson, T., Gingras, A., Pandey, A., Turk, B.E., Zhang, J.*, Zhu, H.*, Qian, J.*, Construction of Human Activity-Based Phosphorylation Networks, Molecular Systems Biology, 2013, 9:655


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, 8:e1002972.

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, 11:5301-5310.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

Qian, J., Hentschke, R., and Knoll, W. “Superstructures of cyclodextrine derivatives on Au(111): A combined random planting - molecular dynamics Approach.”, Langmuir 1997, 13, 7092-7098.