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Li Cai, PhD

Selected Publications

1.   Li Y, Hao H, Tzatzalos E, Lin RK, Doh S, Liu LF, Lyu YL, Cai L. Topoisomerase IIbeta is required for proper retinal development and survival of postmitotic cells. Biology open. 2014;3(2):172-84. doi: 10.1242/bio.20146767. PubMed PMID: 24463367.

2.   Hao H, Li Y, Tzatzalos E, Gilbert J, Zala D, Bhaumik M, Cai L. Identification of a transient Sox5 expressing progenitor population in the neonatal ventral forebrain by a novel cis-regulatory element. Developmental biology. 2014; doi: 10.1016/j.ydbio.2014.06.010.

3.   Kim J, Islam MM, Tzatzalos E, Hao H, Li Y, Tawil HY, Doh ST, Cai L. Computational and Experimental Approach for the Identification of Mesencephalon-Specific Cis-Element of Dbx1 Gene. JSM Biotechnol Bioeng. 2013;1(3):1017. Epub Oct. 3, 2013.

4.   Islam MM, Li Y, Luo H, Xiang M, Cai L. Meis1 regulates Foxn4 expression during retinal progenitor cell differentiation. Biology open. 2013;2(11):1125-36. doi: 10.1242/bio.20132279. PubMed PMID: 24244849; PubMed Central PMCID: PMC3828759.

5.   Tzatzalos E, Smith SM, Doh ST, Hao H, Li Y, Wu A, Grumet M, Cai L. A cis-element in the Notch1 locus is involved in the regulation of gene expression in interneuron progenitors. Developmental biology. 2012;372(2):217-28. doi: 10.1016/j.ydbio.2012.09.015. PubMed PMID: 23022658; PubMed Central PMCID: PMC3518388.

6.   Smith SM, Cai L. Cell specific CD44 expression in breast cancer requires the interaction of AP-1 and NFkappaB with a novel cis-element. PLoS One. 2012;7(11):e50867. doi: 10.1371/journal.pone.0050867. PubMed PMID: 23226410; PubMed Central PMCID: PMC3511339.

7.   Luo H, Jin K, Xie Z, Qiu F, Li S, Zou M, Cai L, Hozumi K, Shima DT, Xiang M. Forkhead box N4 (Foxn4) activates Dll4-Notch signaling to suppress photoreceptor cell fates of early retinal progenitors. PNAS. 2012;109(9):E553-62. Epub 2012/02/11. doi: 10.1073/pnas.1115767109. PubMed PMID: 22323600; PubMed Central PMCID: PMC3295323.

8.   Islam MM, Doh ST, Cai L. In ovo electroporation in embryonic chick retina. J Vis Exp. 2012(60). Epub 2012/02/15. doi: 10.3791/3792. PubMed PMID: 22330044.

9.   Cai L, Lyu YL. Analysis of Retinal Development and Diseases Using RNA-Seq. Cell Dev Biol. 2012;1(5). doi: 10.4172/2168-9296.1000e113. PubMed PMID: 23667856; PubMed Central PMCID: PMC3648879.

10. Wu TY, Khor TO, Saw CL, Loh SC, Chen AI, Lim SS, Park JH, Cai L, Kong AN. Anti-inflammatory/Anti-oxidative stress activities and differential regulation of Nrf2-mediated genes by non-polar fractions of tea Chrysanthemum zawadskii and licorice Glycyrrhiza uralensis. AAPS J. 2011;13(1):1-13. Epub 2010/10/23. doi: 10.1208/s12248-010-9239-4. PubMed PMID: 20967519; PubMed Central PMCID: PMC3032091.

11. So JY, Lee HJ, Smolarek AK, Paul S, Wang CX, Maehr H, Uskokovic M, Zheng X, Conney AH, Cai L, Liu F, Suh N. A novel Gemini vitamin D analog represses the expression of a stem cell marker CD44 in breast cancer. Mol Pharmacol. 2011;79(3):360-7. Epub 2010/12/01. doi: 10.1124/mol.110.068403. PubMed PMID: 21115634; PubMed Central PMCID: PMC3061370.

12. Li Y, Huang H, Cai L. Prediction of Transcriptional Regulatory Networks for Retinal Development. In: Lopes HS, Cruz LM, editors. Computational Biology and Applied Bioinformatics. Rijeka, Croatia: InTech; 2011.

13. Nair S, Barve A, Khor TO, Shen GX, Lin W, Chan JY, Cai L, Kong AN. Regulation of Nrf2- and AP-1-mediated gene expression by epigallocatechin-3-gallate and sulforaphane in prostate of Nrf2-knockout or C57BL/6J mice and PC-3 AP-1 human prostate cancer cells. Acta Pharmacol Sin. 2010;31(9):1223-40. Epub 2010/08/24. doi: 10.1038/aps.2010.147. PubMed PMID: 20729872.

14. Liu J, Sandoval J, Doh ST, Cai L, Lopez-Rodas G, Casaccia P. Epigenetic modifiers are necessary but not sufficient for reprogramming non-myelinating cells into myelin gene-expressing cells. PLoS One. 2010;5(9):e13023. Epub 2010/10/05. doi: 10.1371/journal.pone.0013023. PubMed PMID: 20885955; PubMed Central PMCID: PMC2946387.

15. Duffield DS, Cai L, Kim S. Simultaneous determination of multiple mRNA levels utilizing MALDI-TOF mass spectrometry and biotinylated dideoxynucleotides. RNA. 2010;16(6):1285-91. Epub 2010/04/23. doi: 10.1261/rna.1859810. PubMed PMID: 20410241; PubMed Central PMCID: PMC2874180.

16. Doh ST, Hao H, Loh SC, Patel T, Tawil HY, Chen DK, Pashkova A, Shen A, Wang H, Cai L. Analysis of retinal cell development in chick embryo by immunohistochemistry and in ovo electroporation techniques. BMC Dev Biol. 2010;10:8. Epub 2010/01/22. doi: 10.1186/1471-213x-10-8. PubMed PMID: 20089190; PubMed Central PMCID: PMC2822752.

17. Nair S, Doh ST, Chan JY, Kong AN, Cai L. Regulatory potential for concerted modulation of Nrf2- and Nfkb1-mediated gene expression in inflammation and carcinogenesis. Br J Cancer. 2008;99(12):2070-82. Epub 2008/12/04. doi: 10.1038/sj.bjc.6604703. PubMed PMID: 19050705; PubMed Central PMCID: PMC2607222.

18. Huang H, Cai L, Wong WH. Clustering analysis of SAGE transcription profiles using a Poisson approach. Methods Mol Biol. 2008;387:185-98. Epub 2008/02/22. PubMed PMID: 18287632.

19. Kim K, Zhang S, Jiang K, Cai L, Lee IB, Feldman LJ, Huang H. Measuring similarities between gene expression profiles through new data transformations. BMC Bioinformatics. 2007;8:29. Epub 2007/01/30. doi: 10.1186/1471-2105-8-29. PubMed PMID: 17257435; PubMed Central PMCID: PMC1804284.

20. Hars ES, Qi H, Ryazanov AG, Jin S, Cai L, Hu C, Liu LF. Autophagy regulates ageing in C. elegans. Autophagy. 2007;3(2):93-5. Epub 2007/01/06. PubMed PMID: 17204841.

21. Doh ST, Zhang Y, Temple MH, Cai L. Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. BMC Bioinformatics. 2007;8:94. Epub 2007/03/17. doi: 10.1186/1471-2105-8-94. PubMed PMID: 17362514; PubMed Central PMCID: PMC1838437.

22. Blackshaw S, St Croix B, Polyak K, Kim JB, Cai L. Serial analysis of gene expression (SAGE): experimental method and data analysis. Curr Protoc Hum Genet. 2007;Chapter 11:Unit 11 7. Epub 2008/04/23. doi: 10.1002/0471142905.hg1107s53. PubMed PMID: 18428405.

23. Blackshaw S, Croix BS, Polyak K, Kim JB, Cai L. Serial analysis of gene expression (SAGE): experimental method and data analysis. Curr Protoc Mol Biol. 2007;Chapter 25:Unit 25B 6. Epub 2008/02/12. doi: 10.1002/0471142727.mb25b06s80. PubMed PMID: 18265400.

24. Lyu YL, Lin CP, Azarova AM, Cai L, Wang JC, Liu LF. Role of topoisomerase IIbeta in the expression of developmentally regulated genes. Mol Cell Biol. 2006;26(21):7929-41. Epub 2006/08/23. doi: 10.1128/mcb.00617-06. PubMed PMID: 16923961; PubMed Central PMCID: PMC1636731.

25. Lepourcelet M, Tou L, Cai L, Sawada J, Lazar AJ, Glickman JN, Williamson JA, Everett AD, Redston M, Fox EA, Nakatani Y, Shivdasani RA. Insights into developmental mechanisms and cancers in the mammalian intestine derived from serial analysis of gene expression and study of the hepatoma-derived growth factor (HDGF). Development. 2005;132(2):415-27. Epub 2004/12/18. doi: 10.1242/dev.01579. PubMed PMID: 15604097.

26. Hu M, Yao J, Cai L, Bachman KE, van den Brule F, Velculescu V, Polyak K. Distinct epigenetic changes in the stromal cells of breast cancers. Nat Genet. 2005;37(8):899-905. Epub 2005/07/12. doi: 10.1038/ng1596. PubMed PMID: 16007089.

27. Cai L, Huang H, Blackshaw S, Liu JS, Cepko C, Wong WH. Clustering analysis of SAGE data using a Poisson approach. Genome Biol. 2004;5(7):R51. Epub 2004/07/09. doi: 10.1186/gb-2004-5-7-r51. PubMed PMID: 15239836; PubMed Central PMCID: PMC463327.

28. Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo WP, Weber G, Lee K, Fraioli RE, Cho SH, Yung R, Asch E, Ohno-Machado L, Wong WH, Cepko CL. Genomic analysis of mouse retinal development. PLoS Biol. 2004;2(9):E247. Epub 2004/07/01. doi: 10.1371/journal.pbio.0020247. PubMed PMID: 15226823; PubMed Central PMCID: PMC439783.

29. Allinen M, Beroukhim R, Cai L, Brennan C, Lahti-Domenici J, Huang H, Porter D, Hu M, Chin L, Richardson A, Schnitt S, Sellers WR, Polyak K. Molecular characterization of the tumor microenvironment in breast cancer. Cancer Cell. 2004;6(1):17-32. Epub 2004/07/21. doi: 10.1016/j.ccr.2004.06.010. PubMed PMID: 15261139.

30. Goh KL, Cai L, Cepko CL, Gertler FB. Ena/VASP proteins regulate cortical neuronal positioning. Curr Biol. 2002;12(7):565-9. Epub 2002/04/09. PubMed PMID: 11937025.

31. Cai L, Hayes NL, Takahashi T, Caviness VS, Jr., Nowakowski RS. Size distribution of retrovirally marked lineages matches prediction from population measurements of cell cycle behavior. J Neurosci Res. 2002;69(6):731-44. Epub 2002/09/03. doi: 10.1002/jnr.10398. PubMed PMID: 12205666.

32. Lu QR, Cai L, Rowitch D, Cepko CL, Stiles CD. Ectopic expression of Olig1 promotes oligodendrocyte formation and reduces neuronal survival in developing mouse cortex. Nat Neurosci. 2001;4(10):973-4. Epub 2001/09/28. doi: 10.1038/nn718. PubMed PMID: 11574831.

33. Lin JC, Cai L, Cepko CL. The external granule layer of the developing chick cerebellum generates granule cells and cells of the isthmus and rostral hindbrain. J Neurosci. 2001;21(1):159-68. Epub 2001/01/11. PubMed PMID: 11150332.

34. Cai L, Morrow EM, Cepko CL. Misexpression of basic helix-loop-helix genes in the murine cerebral cortex affects cell fate choices and neuronal survival. Development. 2000;127(14):3021-30. PubMed PMID: 10862740.

35. Cai L, Hayes NL, Nowakowski RS. Local homogeneity of cell cycle length in developing mouse cortex. J Neurosci. 1997;17(6):2079-87. PubMed PMID: 9045735.

36. Cai L, Hayes NL, Nowakowski RS. Synchrony of clonal cell proliferation and contiguity of clonally related cells: production of mosaicism in the ventricular zone of developing mouse neocortex. J Neurosci. 1997;17(6):2088-100. PubMed PMID: 9045736.