Publications

Van Drunen R, Dai Y, Wei H, Fekry B, Noori S, Shivshankar S, Bravo R, Zhao Z, Yoo SH, Justice N, Wu JQ, Tong Q, Eckel-Mahan K. Cell-specific regulation of the circadian clock by BMAL1 in the paraventricular nucleus: Implications for regulation of systemic biological rhythms. Cell Rep. 2024 Jun 26;43(7):114380. doi: 10.1016/j.celrep.2024.114380. PMID: 38935503.

Cuevas-Diaz Duran R*, Wei H*, Wu J. Data normalization for addressing the challenges in the analysis of single-cell transcriptomic datasets. BMC Genomics. 2024 May 6;25(1):444. doi: 10.1186/s12864-024-10364-5. PMID: 38711017

Wei H, Wu JQ. Glial progenitor heterogeneity and plasticity in the adult spinal cord. Neural Regen Res. 2024 Dec 1;19(12):2567-2568. doi: 10.4103/NRR.NRR-D-23-01988. Epub 2024 Apr 1. PMID: 38808984

Wei H*, Withrow J*, Rakshit J, Amin FU, Nahm J, Mowry FE, Mao Z, Bhattacharjee MB, Zhu JJ, Yang Y, Wu JQ. The identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease. Aging Dis. 2024 Mar 4. doi: 10.14336/AD.2024.0205-1. PMID: 38502590.

Santhanam A, Shihabeddin E, Wei H, Wu J, O'Brien J. Molecular basis of retinal remodeling in a zebrafish model of retinitis pigmentosa. Cell Mol Life Sci. 2023;80(12):362. Doi:10.1007/s00018-023-05021-1. PMID: 37979052.

Omrani, M., Beyrampour-Basmenj, H., Jahanban-Esfahlan, R., Talebi, M., Raeisi, M., Serej, Z. A., Akbar-Gharalari, N., Khodakarimi, S., Wu, J., & Ebrahimi-Kalan, A. Global trend in exosome isolation and application: an update concept in management of diseases. 2023. Molecular and cellular biochemistry. DOI: 10.1007/s11010-023-04756-6. PMID: 37166542.

Wei, H*., Wu, X*., Withrow, J*., Cuevas-Diaz Duran, R., Singh, S., Chaboub, L. S., Rakshit, J., Mejia, J., Rolfe, A., Herrera, J. J., Horner, P. J., & Wu, J. Q. Glial progenitor heterogeneity and key regulators revealed by single-cell RNA sequencing provide insight to regeneration in spinal cord injury. 2023. Cell reports, 42(5), 112486. DOI: 10.1016/j.celrep.2023.112486. PMID: 37149868

Kobayashi, M., Wei, H., Yamanashi, T., Azevedo Portilho, N., Cornelius, S., Valiente, N., Nishida, C., Cheng, H., Latorre, A., Zheng, W. J., Kang, J., Seita, J., Shih, D. J., Wu, J. Q., and Yoshimoto, M. HSC-independent definitive hematopoiesis persists into adult life. 2023. Cell reports, 42(3), 112239. DOI: 10.1016/j.celrep.2023.112239. PMID: 36906851

Cuevas-Diaz Duran R., González-Orozco JC., Velasco I and Wu, J. Q., Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. 2022. Front. Cell Dev. doi: 10.3389/fcell.2022.884748. PMID: 36353512

Cuevas-Diaz Duran R., Li Y., Garza Carbajal A., You Y., Dessauer CW*., Wu, J. Q*., Walters ET*. Major differences in transcriptional alterations in dorsal root ganglia between spinal cord injury and peripheral neuropathic pain models. J Neurotrauma. 2022 Sep 30. doi: 10.1089/neu.2022.0238. PMID: 36178348.

Wu, X., Wei, H., Wu, J. Q. Coding and long non-coding gene expression changes in the CNS traumatic injuries. Cell Mol Life Sci. 2022 Feb 7;79(2):123. doi: 10.1007/s00018-021-04092-2. PMID: 35129669.

Emily, F. Mendez., Wei, H., Hu, R., Stertz, L., Fries, GR., Wu, X., Najera, KE., Monterey, MD., Lincoln, CM., Kim, JW., Moriel, K., Meyer, TD., Selvaraj, S., Teixeira, AL., MD, Zhao, Z., Xu, J., Wu, J. Q., Walss-Bass, C. Angiogenic Gene Networks are Dysregulated in Opioid Use Disorder: Evidence from Multi-Omics and Imaging of Postmortem Human Brain. Mol Psychiatry. 2021 Aug 12. doi:10.1038/s41380-021-01259-y. PMID: 34385598.

Monterey, MD., Wei, H., Wu, X., Wu, J. Q. The Many Faces of Astrocytes in Alzheimer’s Disease. Front Neurol. 2021 Aug 31;12:619626. doi: 10.3389/fneur.2021.619626. PMID: 34531807.

Yuan, Z., Fan, X., Zhu, JJ., Fu, TM., Wu, J. Q., Xu H., Zhang, N., An, Z., Zheng, W. Presence of complete murine viral genome sequences in patient-derived xenografts. Nat Commun. 2021 Apr 1;12(1):2031. doi: 10.1038/s41467-021-22200-5. PMID: 33795676.

Kondiles, B*., Wei, H*., Chaboub, LS., Horner, PJ., Wu, J. Q*., Perlmutter, SI*. Transcriptome of rat subcortical white matter and spinal cord after spinal injury and cortical stimulation. Sci Data. 2021 Jul 15;8(1):175. https://doi.org/10.1038/s41597-021-00953-4. PMID: 34267212.

Wei, H*., Dong, X*., You, Y., Hai, B., Cuevas-Diaz Duran, RC., Wu, X., Kharas, N., Wu, J. Q. OLIG2 regulates lncRNAs and its own expression during oligodendrocyte lineage formation. BMC Biol. 2021 Jun 25;19(1):132. https://doi.org/10.1186/s12915-021-01057-6. PMID: 34172044.

Wei, H*., Wu, X*., You, Y*., Cuevas-Diaz Duran, R., Zheng, Y., Narayanan, L.K., Hai, B., Li X., Tallapragada, N., Prajapati, T.J, Kim, D.H., Deneen, B., Cao, Q., Wu, J. Q. Systematic analysis of purified astrocytes after SCI unveils Zeb2os function during astrogliosis. Cell Reports. 2021 Feb 2;34(5):108721. doi: 10.1016/j.celrep.2021.108721. PMID: 33535036.

Escartin, C*., Galea, E*., Lakatos, A., O'Callaghan, JP., Petzold, GC., ..., Wu, J. Q., ...., Zheng, B., Zimmer, ER., Zorec, R., Sofroniew, MV., Verkhratsky, A. Reactive astrocyte nomenclature, definitions, and future directions. Nature Neuroscience. 2021. doi: 10.1038/s41593-020-00783-4. PMID: 33589835.

Narayanan, L.K.*, Wu, X.*, Wei, H. and Wu, J. Q. Evolving Roles of Long Noncoding RNAs. The Chemical Biology of Long Noncoding RNAs. 2020 (Chapter 10). Springer Publishing. Netherlands.

Bhoi, J.D., Zhang, Z., Janz, R., You, Y., Wei, H., Wu, J. Q, Ribelayga, C.P. The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock. J Comp Neurol. 2020 Aug 12. doi:10.1002/cne.25004. PMID:32783205

Jin, N., Zhang, Z., Keung, J., Youn, S.B., Ishibashi, M., Tian, L-M., Marshak, D. W., Solessio, E., Umino, Y., Fahrenfort, I., Kiyama, T., Mao, C-A., You, Y., Wei, H., Wu, J. Q., Postma, F., Paul, D. L., Massey, S. C., Ribelayga, C. P. Molecular and functional architecture of the mouse photoreceptor network. Science Advances. 2020 Jul; (6) : 28, eaba7232. doi: 10.1126/sciadv.aba7232. PMID: 32832605

Kobayashi, M., Tarnawsky, S.P., Wei, H., Mishra, A., Azevedo Portilho, N., Wenzel, P., Davis, B., Wu, J., Hadland, B. and Yoshimoto, M. Hemogenic Endothelial Cells Can Transition to Hematopoietic Stem Cells through a B-1 Lymphocyte-Biased State during Maturation in the Mouse Embryo. Stem cell reports. 2019 Jun 10. pii: S2213-6711(19)30193-6. doi: 10.1016/j.stemcr.2019.05.025. PMID:31231025

He, L., Zhou, J., Chen, M., Lin, C., Kim, S. G., Zhou, Y., Xiang, L., Xie, M., Bai, H., Yao, H., Shi, C., Coelho, P. G., Bromage, T. G., Hu, B., Tovar, N., Witek, L., Wu, J., Chen, K., Gu, W., Jinxuan Zheng, J., Christopher L. Ricupero, C.L., Sheu, T., Zhong, J., Wen, J., Niu, Y., Cheng, B., Gong, Q., Owens, D. M., Stanislauskas, M., Pei, J., Chotkowski, G., Wang, S., Yang, G., Shelanski, M., Zegarelli, D.J., Zheng, Y., Shi, X., Finkel, M., Zhang, W., Li, J., Cheng, J., Tarnow, D.P., Zhou, X., Wang, Z., Jiang, X., Romanov, A., Wang, S., Ye, L., Ling, J., Mao, J. J. Parenchymal and Stromal Tissue Regeneration of Tooth Organ by Pivotal Signals Reinstated in Decellularized Matrix. Nature Materials. 2019 Jun;18(6):627-637. doi: 10.1038/s41563-019-0368-6. PMID:31114073

Cuevas-Diaz Duran R, Wang CY, Zheng H, Deneen B, Wu JQ. Brain Region-Specific Gene Signatures Revealed by Distinct Astrocyte Subpopulations Unveil Links to Glioma and Neurodegenerative Diseases. eNeuro. 2019 Apr 2;6(2). doi: 10.1523/ENEURO.0288-18.2019. PMID:30957015.

Cuevas-Diaz Duran, R*, Wei, H*., Kim, D.H., and Wu, J.Q. Long non-coding RNAs: important regulators in the development, function, and disorders of the central nervous system. Neuropathology and Applied Neurobiology. 2019 Jan 13, doi: 10.1111/nan.12541. PMID: 30636336.

You, Y*., Cuevas-Diaz Duran, R.*, Jiang L., Dong X., Zong S., Snyder M., Wu J. Q., An integrated global regulatory network of hematopoietic precursor cell self-renewal and differentiation, Integr Biol (Camb), 2018 Jul 16;10(7):390-405, doi:10.1039/c8ib00059j. PMID: 29892750.(cover story)

Zhou Y., Chen M., Ricupero CL., He L., Wu J., Chen K., Friedman RA., Guarnieri P., Wang Z., Zhou X., Mao JJ. Profiling of Stem/Progenitor Cell Regulatory Genes of the Synovial Joint by Genome-Wide RNA-Seq Analysis. Biomed Res Int. 2018 Jun 26;2018:9327487, doi: 10.1155/2018/9327487. PMID: 30046613.

Dong, X., Cuevas-Diaz Duran, R., You, Y., Wu, J. Q. Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis. J Vis Exp. 2018 Apr 16;(134), doi:10.3791/57547. PMID: 29708547.

Cuevas-Diaz Duran R*., Wei H*., Wu JQ. Single-cell RNA-sequencing of the brain. Clin Transl Med. 2017 Dec;6(1):20, doi:10.1186/s40169-017-0150-9. PMID: 28597408.

Jiang, N., Xiang, L., He, L., Yang, G., Zheng, J., Wang, C., Zhang, Y., Wang, S., Zhou, Y., Sheu, T., Wu, J., Chen, K., Coelho, P.G., Tovar, N.M., Kim, S.H., Chen, M., Zhou, Y-H., and Mao, J. Exosomes Mediate Epithelium−Mesenchyme Crosstalk in Organ Development. ACS Nano. 2017 Jul 27, doi: 10.1021/acsnano.7b01087. PMID: 28727410.

Liu, Y., Zheng, Y., Li, S., Xue, H., Schmitt, K., Hergenroeder, G.W., Wu, JQ., Zhang, Y., Kim, D.H., and Cao, Q. Human Neural Progenitors Derived from Integration-Free iPSCs for SCI therapy.Stem Cell Res. 2017 Mar;19:55-64, doi: 10.1016/j.scr.2017.01.004. PMID: 28073086.

Cuevas-Diaz Duran, R., Yan, H., Zheng, Y., Huang, X., Grill, R., Kim, DH., Cao, Q., and Wu, JQ. The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury, Sci Rep. 2017 Jan 20;7:41008. doi: 10.1038/srep41008. PMID: 28106101.

Dong, X., You, Y., and Wu, J.Q. Building an RNA-sequencing transcriptome of the nervous system. Neuroscientist. 2016 Dec;22(6):579-592. doi: 0.1177/1073858415610541. PMID: 26463470.

Cuevas-Diaz Duran, R., Menon, S., and Wu, J. The Analyses of Global Gene Expression and Transcription Factor Regulation. In Transcriptomics and Gene Regulation. 2016(pp. 1-35). Springer Netherlands.

Dong, X., Muppani, N. R., and Wu, J. Long Noncoding RNAs: Critical Regulators for Cell Lineage Commitment in the Central Nervous System. In Transcriptomics and Gene Regulation. 2016(pp. 73-97). Springer Netherlands.

Wu, J. Q. (ed.). Transcriptomics and Gene Regulation. 2016, Springer Netherlands.

Dong, X., Chen, K., Cuevas-Diaz Duran, R., You, Y., Sloan, S. A., Zhang, Y., Cao, Q., Barres, B. A., and Wu, J. Q. Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination, PLoS Genet. 2015 Dec 18;11(12):e1005669. doi: 10.1371/journal.pgen.1005669. PMID: 26683846

Yan, Q., Weyn-Vanhentenryck, S. M., Wu, J., Sloan, S., Zhang, Y., Chen, K., Wu, J. Q., Barres, B., Zhang, C. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc Natl Acad Sci U S A. 2015 Mar 17;112(11):3445-50. doi: 10.1073/pnas.1502849112. PMID: 25737549.

Chen, K., Dai X., and Wu, J.Q. Alternative splicing: An important mechanism in stem cell biology. World J Stem Cells. 2015 Jan 26;7(1):1-10. doi: 10.4252/wjsc.v7.i1.1. PMID: 25621101.

Chen, K., Dong, X., and Wu, J.Q. The Application of single-cell sequencing in dynamic transcriptomes. Single Cell Sequencing. X. Wang (ed.), Single Cell Sequencing and Systems Immunology, Translational Bioinformatics 5. 2015. 41-63. Springer Publisher Dordrecht.

Zong, S., Deng, S., Chen, K., and Wu, J.Q. Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis. J Vis Exp. 2014 Nov 11;(93):e52104. doi: 10.3791/52104. PMID: 25407807

Zhang, Y., Chen, K., Sloan, S., Bennett, M., Scholze, A., O'Keeffe, S., Phatnani, H., Guarnieri, P., Caneda, C., Ruderisch, N., Deng, S., Liddelow, S., Zhang, C., Daneman, R., Maniatis, T., Barres, B., Wu, J.Q. An RNA-Seq transcriptome and splicing database of neurons, glia and vascular cells of the cerebral cortex. J Neurosci. 2014 Sep 3;34(36):11929-47. doi: 10.1523/JNEUROSCI. PMID: 25186741

Chen, K., Deng, S., Lu, H., Zheng, Y., Yang, G., Kim, D., Cao, Q., and Wu, J.Q. RNA-Seq characterization of spinal cord injury transcriptome in acute/subacute phases: a resource for understanding the pathology at the systems level. PLoS One. 2013 Aug 9;8(8):e72567. doi: 10.1371/journal.pone.0072567. PMID: 23951329.

Wu, J. Q., Seay, M., Schulz, V., Hariharan, M., Tuck, D., Lian, J., Du, J., Shi, M., Ye, Z. J., Gerstein, M., Snyder, M., and Weissman, S. Tcf7 is a key regulator of the self-renewal and differentiation switch in a multipotential hematopoietic cell line. PLoS Genet. 2012;8(3):e1002565. doi: 10.1371/journal.pgen.1002565. PMID: 22412390

Wu, J. Q. Characterize mammalian transcriptome complexity. 2011,Deutschland, Germany: LAP LAMBERT Academic Publishing.

Wu, J. Q., Habegger, L., Noisa, P., Szekely, A., Qiu, C., Hutchison, S., Raha, D., Lin, H., Egholm, M., Weissman, S., Cui, W., Gerstein, M., and Snyder, M. Dynamic Transcriptomes during Neural Differentiation of Human Embryonic Stem Cells Revealed by Integrating Short, Long, and Paired-end Sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5254-9. doi: 10.1073/pnas.0914114107. PMID: 20194744.

The MGC Project Team. The Completion of the Mammalian Gene Collection. Genome Res. 2009 Dec;19(12):2324-33. doi: 10.1101/gr.095976.109. PMID: 19767417.

Wu, J. Q. and Snyder, M. RNA polymerase II promoter proximal stalling: Loading at the start line prepares genes for a sprint. Genome Biol. 2008;9(5):220. doi: 10.1186/gb-2008-9-5-220. PMID: 18466645.

Wu, J. Q., Du, J., Rozowsky, J. Zhang , Z., Weissman, S., Gerstein, M., Snyder, M. Systematic analysis of transcribed loci in selected ENCODE regions using RACE sequencing. Genome Biol. 2008 Jan 3;9(1):R3. doi: 10.1186/gb-2008-9-1-r3. PMID: 18173853.

The ENCODE Project Consortium. The ENCODE pilot project: identification and analysis of functional elements in 1% of the human genome. Nature. 2007 Jun 14;447(7146). doi:799-816.10.1038/nature05874. PMID: 17571346.

Wu, J. Q.*, Trinklein, N.D.* , Karaöz, U.*, Halees, A.*, Aldred, S.F., Collins, P.J., Zheng, D., Zhang , Z., Gerstein, M., Snyder, M., Myers, R.M., and Weng, Z. P. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 Jun;17(6):720-31. PMID: 17567992.

Rozowsky, J. , Newburger, D. , Sayward, F. , Wu J. Q. , Jordan, G., Korbel, J., Nagalakshmi, U., Yang, J., Zheng, D., Guigo, R., Gingeras, T., Weissman, S., Miller, P., Snyder M. and Gerstein M. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. 2007 Jun;17(6):732-45. doi: 10.1101/gr.5696007. PMID: 17567993.

Wu, J. Q. *, Tenney, A.*, Langton L, Klueh P, Quatrano R, Brent M. R. A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices. Genome Res. 2007 Feb;17(2):212-8. doi:10.1101/gr.5661407. PMID: 17210930.

Rozowsky, J., Wu, J.Q., Lian, Z., Nagalakshmi, U., Korbel, J.O., Kapranov, P., Zheng, D., Dyke, S., Newburger, P., Miller, P., Gingeras, T.R., Weissman, S., Gerstein, M., and Snyder, M. Novel transcribed regions in the human genome. Cold Spring Harb Symp Quant Biol. 2006 71:111-6. doi: 10.1101/sqb.2006.71.054. PMID: 17381286.

Wu, J. Q., Garcia, A. M., Hulyk, S., Sneed, A., Kowis, A., Yuan, Y., Steffen, D., McPherson, J. D., Gunaratne, P. H., and Gibbs, R. A. Large scale RT-PCR recovery of full-length cDNA clones. Biotechniques. 2004 Apr;36(4):690-6, 698-700.doi:10.2144/04364DD03. PMID: 15088387.

Wu, J. Q., Shteynberg, D., Arumugam, M., Gibbs, R. A., and Brent, M. R.. Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing. Genome Res. 2004 Apr;14(4):665-71. doi:10.1101/gr.1959604. PMID: 15060008.

Wu, J. Q. *, Dewey, C.*, Cawley, S., Alexandersson, M., Gibbs, R. A. and Pachter, L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res. 2004 Apr;14(4):661-4. doi:10.1101/gr.1939804. PMID: 15060007.

The MGC Project Team. The Status, Quality and Expansion of the NIH Full-length cDNA Project: The Mammalian Gene Collection (MGC).Genome Res. 2004 Oct;14(10B):2121-7. doi:10.1101/gr.2596504. PMID: 15489334.

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521. doi:10.1038/nature02426. PMID: 15057822.

International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature. 2004 Oct 21;431(7011):931-45. doi:10.1038/nature03001.PMID: 15496913.

Zhang, Z., Burch, P. E., Cooney, A. J., Lanz R. B., Pereira, F. A., Wu, J. Q., Gibbs, R. A., Weinstock, G., and Wheeler, D. A. Genomic Analysis of the Nuclear Receptor Family: New Insights into Structure, Regulation, and Evolution from the Rat Genome. Genome Res. 2004 Apr;14(4):580-90. doi:10.1101/gr.2160004. PMID: 15059999.

Gunaratne, P. H., Wu, J. Q., Garcia, A. M., Hulyk, S., Worley, K., Margolin, J. F., and Gibbs, R. A. Concatenation cDNA sequencing for transcriptome analysis. C R Biol. 2003 Oct-Nov;326(10-11):971-7. PMID: 14744103.

Tzafrir, I., McElver, J. A., Liu, C. M., Yang, L. J., Wu, J. Q.,Martinez, A., Patton, D. A., Meinke, D. W. Diversity of TITAN Functions in Arabidopsis Seed Development. Plant Physiol. 2002 Jan;128(1):38-51. PMID: 11788751.