Hoang T, Wang J, Boyd, P, Wang F, Santiago C, Jiang L, Yoo S, Lahne M, Todd LJ, Jia M, Saez C, Keuthan C, Palazzo I, Squires N, Campbell WA, Rajaii F, Parayil T, Trinh V, Kim DW, Wang G, Campbell LJ, Ash J, Fischer AJ, Hyde DR*, Qian J*, Blackshaw S*, Gene regulatory networks controlling vertebrate retinal regeneration., Science, 2020.

Gao T, Qian J, EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species, Nucleic Acids Res., 2020, 48:D58-D64.

Gao T, Qian J, EAGLE: An algorithm that utilizes a small number of genomic features to predict tissue/cell type-specific enhancer-gene interactions, PLoS Computational Biology, 2019, 15:e1007436.

Hu MW, Kim DW, Liu S, Zack DJ, Blackshaw S, Qian J, PanoView: An iterative clustering method for single-cell RNA sequencing data, PLoS Computational Biology, 2019, 15:e1007040.

Zibetti C, Liu S, Wan J, Qian J, Blackshaw S,Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin, Commun. Biol. 2019, 2:142.

Wang J, Zibetti C, Shang P, Sripathi SR, 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". Nature Communications, 2018, 9:1364.

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

Pan J, Liu S, Zhu H, 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.

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

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.

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.

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.

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.

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.

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, 41, 8503-8514.

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

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, 1844, 244-231.

9. 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

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

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.

Hackler, L.#, Wan, J.#, Swaroop, A., Qian, J.*, Zack, D.J.*, MicroRNA profile of the developing mouse retina, IOVS, 2010, 51, 1823-1831.

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.

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)

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

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.

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.

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.

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.