1993 …2020

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2020

Integration of IgA and IgG autoantigens improves performance of biomarker panels for early diagnosis of lung cancer

Pan, J., Yu, L., Wu, Q., Lin, X., Liu, S., Hu, S., Rosa, C., Eichinger, D., Pino, I., Zhu, H., Qian, J. & Huang, Y., Jan 1 2020, In : Molecular and Cellular Proteomics. 19, 3, p. 490-500 11 p.

Research output: Contribution to journalArticle

2019

Development and application of a high-content virion display human GPCR array

Syu, G. D., Wang, S. C., Ma, G., Liu, S., Pearce, D., Prakash, A., Henson, B., Weng, L. C., Ghosh, D., Ramos, P., Eichinger, D., Pino, I., Dong, X., Xiao, J., Wang, S., Tao, N., Kim, K. S., Desai, P. & Zhu, H., Dec 1 2019, In : Nature communications. 10, 1, 1997.

Research output: Contribution to journalArticle

Open Access

Discovery and validation of a serologic autoantibody panel for early diagnosis of esophageal squamous cell carcinoma

Pan, J., Zheng, Q. Z., Li, Y., Yu, L. L., Wu, Q. W., Zheng, J. Y., Pan, X. J., Xie, B. S., Wu, Y. A., Qian, J., Zhu, H. & Huang, Y., Sep 1 2019, In : Cancer Epidemiology Biomarkers and Prevention. 28, 9, p. 1454-1460 7 p.

Research output: Contribution to journalArticle

Discovery of a Potent GLUT Inhibitor from a Library of Rapafucins by Using 3D Microarrays

Guo, Z., Cheng, Z., Wang, J., Liu, W., Peng, H., Wang, Y., Rao, A. V. S., Li, R. J., Ying, X., Korangath, P., Liberti, M. V., Li, Y., Xie, Y., Hong, S. Y., Schiene-Fischer, C., Fischer, G., Locasale, J. W., Sukumar, S., Zhu, H. & Liu, J. O., Nov 25 2019, In : Angewandte Chemie - International Edition. 58, 48, p. 17158-17162 5 p.

Research output: Contribution to journalArticle

Insight into novel RNA-binding activities via large-scale analysis of lncRNA-bound proteome and IDH1-bound transcriptome

Liu, L., Li, T., Song, G., He, Q., Yin, Y., Lu, J. Y., Bi, X., Wang, K., Luo, S., Chen, Y. S., Yang, Y., Sun, B. F., Yang, Y. G., Wu, J., Zhu, H. & Shen, X., Jan 1 2019, In : Nucleic acids research. 47, 5, p. 2244-2262 19 p.

Research output: Contribution to journalArticle

Open Access

Proteome-wide tyrosine phosphorylation analysis reveals dysregulated signaling pathways in ovarian tumors

Song, G., Chen, L., Zhang, B., Song, Q., Yu, Y., Moore, C., Wang, T-L., Shih, I. M., Zhang, H., Chan, D. W-Y., Zhang, Z. & Zhu, H., Mar 1 2019, In : Molecular and Cellular Proteomics. 18, 3, p. 448-460 13 p.

Research output: Contribution to journalArticle

Structural Features of Transcription Factors Associating with Nucleosome Binding

Fernandez Garcia, M., Moore, C. D., Schulz, K. N., Alberto, O., Donague, G., Harrison, M. M., Zhu, H. & Zaret, K. S., Sep 5 2019, In : Molecular cell. 75, 5, p. 921-932.e6

Research output: Contribution to journalArticle

2018

AAgMarker 1.0: A resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases

Pan, J., Liu, S., Zhu, H. & Qian, J., Jan 1 2018, In : Nucleic Acids Research. 46, D1, p. D886-D893

Research output: Contribution to journalArticle

Analysis of KLF4 regulated genes in cancer cells reveals a role of DNA methylation in promoter- enhancer interactions

Oyinlade, O., Wei, S., Kammers, K., Liu, S., Wang, S., Ma, D., Huang, Z. Y., Qian, J., Zhu, H., Wan, J. & Xia, S., Jan 1 2018, (Accepted/In press) In : Epigenetics.

Research output: Contribution to journalArticle

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

Venkataraman, A., Yang, K., Irizarry, J., Mackiewicz, M., Mita, P., Kuang, Z., Xue, L., Ghosh, D., Liu, S., Ramos, P., Hu, S., Kain, D. B., Keegan, S., Saul, R., Colantonio, S., Zhang, H., Pauli-Behn, F., Song, G., Albino, E., Asencio, L. & 35 others, Ramos, L., Lugo, L., Morell, G., Rivera, J., Ruiz, K., Almodovar, R., Nazario, L., Murphy, K., Vargas, I., Rivera-Pacheco, Z. A., Rosa, C., Vargas, M., McDade, J., Clark, B., Yoo, S. Y., Khambadkone, S. G., De Melo, J., Stevanovic, M., Jiang, L., Li, Y., Yap, W. Y., Jones, B., Tandon, A., Campbell, E., Montelione, G. T., Anderson, S., Myers, R. M., Boeke, J. D., Fenyö, D., Whiteley, G., Bader, J. S., Pino, I., Eichinger, D. J., Zhu, H. & Blackshaw, S., Apr 27 2018, In : Nature Methods. 15, 5, p. 330-338 9 p.

Research output: Contribution to journalArticle

Emetine inhibits Zika and Ebola virus infections through two molecular mechanisms: Inhibiting viral replication and decreasing viral entry

Yang, S., Xu, M., Lee, E. M., Gorshkov, K., Shiryaev, S. A., He, S., Sun, W., Cheng, Y. S., Hu, X., Tharappel, A. M., Lu, B., Pinto, A., Farhy, C., Huang, C. T., Zhang, Z., Zhu, W., Wu, Y., Zhou, Y., Song, G., Zhu, H. & 15 others, Shamim, K., Martínez-Romero, C., García-Sastre, A., Preston, R. A., Jayaweera, D. T., Huang, R., Huang, W., Xia, M., Simeonov, A., Ming, G., Qiu, X., Terskikh, A. V., Tang, H., Song, H. & Zheng, W., Dec 1 2018, In : Cell Discovery. 4, 1, 31.

Research output: Contribution to journalArticle

Global identification of Small Ubiquitin-related Modifier (SUMO) substrates reveals crosstalk between SUMOylation and phosphorylation promotes cell migration

Uzoma, I., Hu, J., Cox, E., Xia, S., Zhou, J., Rho, H. S., Guzzo, C., Paul, C., Ajala, O., Goodwin, C. R., Jeong, J., Moore, C., Zhang, H., Meluh, P., Blackshaw, S., Matunis, M. J., Qian, J. & Zhu, H., May 1 2018, In : Molecular and Cellular Proteomics. 17, 5, p. 871-888 18 p.

Research output: Contribution to journalArticle

Heterozygous IDH1R132H/WT created by “single base editing” inhibits human astroglial cell growth by downregulating YAP

Wei, S., Wang, J., Oyinlade, O., Ma, D., Wang, S., Kratz, L., Lal, B., Xu, Q., Liu, S., Shah, S. R., Zhang, H., Li, Y., Quiñones-Hinojosa, A., Zhu, H., Huang, Z. Y., Cheng, L., Qian, J. & Xia, S., May 30 2018, (Accepted/In press) In : Oncogene. p. 1-15 15 p.

Research output: Contribution to journalArticle

High-Throughput Chip Assay for Investigating Escherichia coli Interaction with the Blood-Brain Barrier Using Microbial and Human Proteome Microarrays (Dual-Microarray Technology)

Feng, Y., Chen, C. S., Ho, J., Pearce, D., Hu, S., Wang, B., Desai, P., Kim, K. S. & Zhu, H., Sep 18 2018, In : Analytical Chemistry. 90, 18, p. 10958-10966 9 p.

Research output: Contribution to journalArticle

Measuring Ligand Binding Kinetics to Membrane Proteins Using Virion Nano-oscillators

Ma, G., Syu, G. D., Shan, X., Henson, B., Wang, S., Desai, P., Zhu, H. & Tao, N., Sep 12 2018, In : Journal of the American Chemical Society. 140, 36, p. 11495-11501 7 p.

Research output: Contribution to journalArticle

MeDReaders: A database for transcription factors that bind to methylated DNA

Wang, G., Luo, X., Wang, J., Wan, J., Xia, S., Zhu, H., Qian, J. & Wang, Y., Jan 1 2018, In : Nucleic Acids Research. 46, D1, p. D146-D151

Research output: Contribution to journalArticle

Multiplexed Biomarker Panels Discriminate Zika and Dengue Virus Infection in Humans

Song, G., Rho, H. S., Pan, J., Ramos, P., Yoon, K. J., Medina, F. A., Lee, E. M., Eichinger, D., Ming, G. L., Muñoz-Jordan, J. L., Tang, H., Pino, I., Song, H., Qian, J. & Zhu, H., Feb 1 2018, In : Molecular and Cellular Proteomics. 17, 2, p. 349-356 8 p.

Research output: Contribution to journalArticle

Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons

McClymont, S. A., Hook, P. W., Soto, A. I., Reed, X., Law, W. D., Kerans, S. J., Waite, E. L., Briceno, N. J., Thole, J. F., Heckman, M. G., Diehl, N. N., Wszolek, Z. K., Moore, C. D., Zhu, H., Akiyama, J. A., Dickel, D. E., Visel, A., Pennacchio, L. A., Ross, O. A., Beer, M. & 1 others, McCallion, A. S., Dec 6 2018, In : American Journal of Human Genetics. 103, 6, p. 874-892 19 p.

Research output: Contribution to journalArticle

Targeting UDP-α-d-glucose 6-dehydrogenase inhibits glioblastoma growth and migration

Oyinlade, O., Wei, S., Lal, B., Laterra, J. J., Zhu, H., Goodwin, C. R., Wang, S., Ma, D., Wan, J. & Xia, S., Feb 26 2018, (Accepted/In press) In : Oncogene. p. 1-15 15 p.

Research output: Contribution to journalArticle

2017

A human proteome array approach to identifying key host proteins targeted by toxoplasma kinase ROP18

Yang, Z., Hou, Y., Hao, T., Rho, H. S., Wan, J., Luan, Y., Gao, X., Yao, J., Pan, A., Xie, Z., Qian, J., Liao, W., Zhu, H. & Zhou, X., Mar 1 2017, In : Molecular and Cellular Proteomics. 16, 3, p. 469-484 16 p.

Research output: Contribution to journalArticle

Evaluation of autoantibody signatures in meningioma patients using human proteome arrays

Gupta, S., Mukherjee, S., Syed, P., Pandala, N. G., Choudhary, S., Singh, V. A., Singh, N., Zhu, H., Epari, S., Noronha, S. B., Moiyadi, A. & Srivastava, S., 2017, In : Oncotarget. 8, 35, p. 58443-58456 14 p.

Research output: Contribution to journalArticle

Global analysis of SUMO-binding proteins identifies SUMOylation as a key regulator of the INO80 chromatin remodeling complex

Cox, E., Hwang, W., Uzoma, I., Hu, J., Guzzo, C. M., Jeong, J., Matunis, M. J., Qian, J., Zhu, H. & Blackshaw, S., May 1 2017, In : Molecular and Cellular Proteomics. 16, 5, p. 812-823 12 p.

Research output: Contribution to journalArticle

Identification of novel biomarkers for behcet disease diagnosis using human proteome microarray approach

Hu, C. J., Pan, J. B., Song, G., Wen, X. T., Wu, Z. Y., Chen, S., Mo, W. X., Zhang, F. C., Qian, J., Zhu, H. & Li, Y. Z., Feb 1 2017, In : Molecular and Cellular Proteomics. 16, 2, p. 147-156 10 p.

Research output: Contribution to journalArticle

Identification of serological biomarkers for early diagnosis of lung cancer using a protein array-based approach

Pan, J., Song, G., Chen, D., Li, Y., Liu, S., Hu, S., Rosa, C., Eichinger, D., Pino, I., Zhu, H., Qian, J. & Huang, Y., Dec 1 2017, In : Molecular and Cellular Proteomics. 16, 12, p. 2069-2078 10 p.

Research output: Contribution to journalArticle

Methylated cis-regulatory elements mediate KLF4-dependent gene transactivation and cell migration

Wan, J., Su, Y., Song, Q., Tung, B., Oyinlade, O., Liu, S., Ying, M., Ming, G. L., Song, H., Qian, J., Zhu, H. & Xia, S., May 29 2017, In : eLife. 6, e20068.

Research output: Contribution to journalArticle

ScaPD: A database for human scaffold proteins

Han, X., Wang, J., Wang, J., Liu, S., Hu, J., Zhu, H. & Qian, J., Oct 3 2017, In : BMC Bioinformatics. 18, 386.

Research output: Contribution to journalArticle

Zika-Virus-Encoded NS2A Disrupts Mammalian Cortical Neurogenesis by Degrading Adherens Junction Proteins

Yoon, K. J., Song, G., Qian, X., Pan, J., Xu, D., Rho, H. S., Kim, N. S., Habela, C., Zheng, L., Jacob, F., Zhang, F., Lee, E. M., Huang, W. K., Ringeling, F. R., Vissers, C., Li, C., Yuan, L., Kang, K., Kim, S., Yeo, J. & 13 others, Cheng, Y., Liu, S., Wen, Z., Qin, C. F., Wu, Q., Christian, K. M., Tang, H., Jin, P., Xu, Z., Qian, J., Zhu, H., Song, H. & Ming, G. L., Sep 7 2017, In : Cell Stem Cell. 21, 3, p. 349-358.e6

Research output: Contribution to journalArticle

2016

A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1

Wang, Y., An, R., Umanah, G., Park, H., Nambiar, K., Eacker, S., Kim, B., Bao, L., Harraz, M., Chang, C., Chen, R., Wang, J. E., Kam, T-I., Jeong, J. S., Xie, Z., Neifert, S., Qian, J., Andrabi, S. A., Blackshaw, S., Zhu, H. & 4 others, Song, H., Ming, G. L., Dawson, V. & Dawson, T. M., Oct 7 2016, In : Science. 354, 6308, aad6872.

Research output: Contribution to journalArticle

Applications in high-content functional protein microarrays

Moore, C. D., Ajala, O. Z. & Zhu, H., Feb 1 2016, In : Current Opinion in Chemical Biology. 30, p. 21-27 7 p.

Research output: Contribution to journalArticle

Characterization of lipid-protein interactions using nonquenched fluorescent liposomal nanovesicles and yeast proteome microarrays

Lu, K. Y., Chen, C. S., Neiswinger, J. & Zhu, H., Oct 1 2016, In : Cold Spring Harbor Protocols. 2016, 10, p. 887-891 5 p.

Research output: Contribution to journalArticle

Characterization of protein-protein interactions using protein microarrays

Paul, C., Rho, H., Neiswinger, J. & Zhu, H., Oct 1 2016, In : Cold Spring Harbor Protocols. 2016, 10, p. 877-880 4 p.

Research output: Contribution to journalArticle

Characterization of RNA-Binding proteins using protein microarrays

Song, G., Neiswinger, J. & Zhu, H., Oct 1 2016, In : Cold Spring Harbor Protocols. 2016, 10, p. 881-886 6 p.

Research output: Contribution to journalArticle

EnhancerAtlas: A resource for enhancer annotation and analysis in 105 human cell/tissue types

Gao, T., He, B., Liu, S., Zhu, H., Tan, K. & Qian, J., 2016, In : Bioinformatics. 32, 23, p. 3543-3551 9 p.

Research output: Contribution to journalArticle

Functional characterization of schizophrenia-associated variation in CACNA1C

Eckart, N., Song, Q., Yang, R., Wang, R., Zhu, H., McCallion, A. S. & Avramopoulos, D., Jun 1 2016, In : PLoS One. 11, 6, e0157086.

Research output: Contribution to journalArticle

Identification of serum biomarkers for gastric cancer diagnosis using a human proteome microarray

Yang, L., Wang, J., Li, J., Zhang, H., Guo, S., Yan, M., Zhu, Z., Lan, B., Ding, Y., Xu, M., Li, W., Gu, X., Qi, C., Zhu, H., Shao, Z., Liu, B. & Tao, S. C., Feb 1 2016, In : Molecular and Cellular Proteomics. 15, 2, p. 614-623 10 p.

Research output: Contribution to journalArticle

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

the CPTAC Investigators, Jul 28 2016, In : Cell. 166, 3, p. 755-765 11 p.

Research output: Contribution to journalArticle

Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression

Zeng, Y., Yao, B., Shin, J., Lin, L., Kim, N., Song, Q., Liu, S., Su, Y., Guo, J. U., Huang, L., Wan, J., Wu, H., Qian, J., Cheng, X., Zhu, H., Ming, G. L., Jin, P. & Song, H., Jan 7 2016, In : Molecular Cell. 61, 1, p. 153-160 8 p.

Research output: Contribution to journalArticle

Microarray-based phospho-proteomic profiling of complex biological systems

Goodwin, C. R., Woodard, C. L., Zhou, X., Pan, J., Olivi, A., Xia, S., Bettegowda, C., Sciubba, D., Pevsner, J. A., Zhu, H. & Laterra, J. J., Apr 1 2016, In : Translational Oncology. 9, 2, p. 124-129 6 p.

Research output: Contribution to journalArticle

Posttranslational modification assays on functional protein microarrays

Neiswinger, J., Uzoma, I., Cox, E., Rho, H., Jeong, J. S. & Zhu, H., Oct 1 2016, In : Cold Spring Harbor Protocols. 2016, 10, p. 892-899 8 p.

Research output: Contribution to journalArticle

Protein microarrays: Flexible tools for scientific innovation

Neiswinger, J., Uzoma, I., Cox, E., Rho, H., Song, G., Paul, C., Jeong, J. S., Lu, K. Y., Chen, C. S. & Zhu, H., Oct 1 2016, In : Cold Spring Harbor Protocols. 2016, 10, p. 837-839 3 p.

Research output: Contribution to journalArticle

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

Wang, J., Xia, S., Arand, B., Zhu, H., Machiraju, R., Huang, K., Ji, H. K. & Qian, J., Apr 1 2016, In : PLoS Computational Biology. 12, 4, e1004892.

Research output: Contribution to journalArticle

The DPYSL2 gene connects mTOR and schizophrenia

Pham, X., Song, G., Lao, S., Goff, L., Zhu, H., Valle, D. & Avramopoulos, D., Nov 1 2016, In : Translational Psychiatry. 6, 11, e933.

Research output: Contribution to journalArticle

Transcription factors as readers and effectors of DNA methylation

Zhu, H., Wang, G. & Qian, J., Sep 1 2016, In : Nature Reviews Genetics. 17, 9, p. 551-565 15 p.

Research output: Contribution to journalArticle

2015

A screen for extracellular signal-regulated kinase-primed glycogen synthase kinase 3 substrates identifies the p53 inhibitor iASPP

Woodard, C., Liao, G., Goodwin, C. R., Hu, J., Xie, Z., dos Reis, T. F., Newman, R., Rho, H., Qian, J., Zhu, H. & Hayward, S. D., 2015, In : Journal of Virology. 89, 18, p. 9232-9241 10 p.

Research output: Contribution to journalArticle

Autoantibody profiling of glioma serum samples to identify biomarkers using human proteome arrays

Syed, P., Gupta, S., Choudhary, S., Pandala, N. G., Atak, A., Richharia, A., Kp, M., Zhu, H., Epari, S., Noronha, S. B., Moiyadi, A. & Srivastava, S., Sep 15 2015, In : Scientific Reports. 5, 13895.

Research output: Contribution to journalArticle

Autoantibody profiling on human proteome microarray for biomarker discovery in cerebrospinal fluid and sera of neuropsychiatric lupus

Hu, C., Huang, W., Chen, H., Song, G., Li, P., Shan, Q., Zhang, X., Zhang, F., Zhu, H., Wu, L. & Li, Y., May 1 2015, In : PLoS One. 10, 5, e0126643.

Research output: Contribution to journalArticle

Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach

Liu, S., Zhang, H., Dai, J., Hu, S., Pino, I., Eichinger, D. J., Lyu, H. & Zhu, H., Jan 1 2015, In : mAbs. 7, 1, p. 110-119 10 p.

Research output: Contribution to journalArticle

Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray

Cox, E., Uzoma, I., Guzzo, C., Jeong, J. S., Matunis, M., Blackshaw, S. & Zhu, H., 2015, In : Methods in molecular biology (Clifton, N.J.). 1295, p. 455-463 9 p.

Research output: Contribution to journalArticle