Education Background
Molecular Biology and Virology Ph.D. - Cornell University
Cell Biology AB - University of California, Berkeley
Courses Taught
- BY419/519 Immunology
- BY476/BY576 - Current Topics in Biology and Medicine
- BY488/BY588 - Stem Cells and Regenerative Medicine
Research Interests
我们的研究方向是发育基因组学和再生医学的新领域，重点是控制脊柱发育的分子机制，并强调早期胚胎发生和胚胎干细胞对特定分化途径的承诺, but from a novel Systems Biology point of view. We use both mouse and zebrafish as model animals. 特别是，我们正在努力了解基因调控网络(grn)控制脊柱和椎间盘(IVD)的正常胚胎发育。. 我们正在研究转录调节因子在限制多能胚胎干细胞进入特定谱系中的作用，这些谱系反过来又包括功能性的产前和产后椎体元素，目的是将这些知识应用于使用患者特异性诱导多能干细胞(iPS)和成体间充质干细胞的再生医学.
腰痛(LBP)的发病率非常高，是全世界社会和财政关注的一个原因. In the USA alone, LBP的经济影响表明，它是45岁以下人群限制生活方式的头号原因, 2nd highest complaint seen by physician’s, 第三大手术原因和第五大住院需求. The economic impact of LBP is striking, 超过了冠状动脉疾病的费用和中风的总费用, respiratory infection, rheumatoid disease and diabetes combined. 美国每年的直接医疗费用超过300亿美元. Most often, LBP is due to degenerative changes in the disc, spinal disc herniation, trauma and fractures. 外科医生有许多方法来修复受损的椎间盘. The most common strategies provide pain relief, but fail to prevent further disc degeneration, or completely restore disc function. Thus these surgical procedures are less than ideal, 因为它们不能防止受损的脊柱进一步退变.
Our current focus is on the Pax, Sox, Bapx和Runx grn在细胞向形成胎儿骨骼的软骨/成骨细胞谱系的承诺中的作用. 我们的目标是为胚胎骨骼发育建立一个统一的GRN，因为它与脊柱有关，并利用这一知识指导iPS细胞走向具有临床意义的命运，并为逆转创伤和年龄相关的脊柱退变提供资源. In particular the IVD. 我们的方法是多学科、协作和技术驱动的. 我们已经非常成功地开发了新的实验策略，将现代分子遗传学和转基因方法与最新的生物信息学和基因组学技术(如比较基因组学)结合在小鼠和斑马鱼身上, microarray, Ditag-Seq, ChIP-Seq, RNA-Seq and others. By applying these approaches in developing embryos, 我们展示了如何产生相关的生物学数据来解释器官发生中的多效效应，并最终将这些方法与多个相互关联的基因同时结合起来, 我们已经展示了如何详细的网络图可以阐明发展中的脊柱, 重申在复杂过程中建立基因调控网络的重要性.
近几十年来，发育生物学家已经成功地确定了一些控制脊柱发育的分子水平机制, such as the genes governing cell fate decisions, 但在其他同样重要的领域，如图案设计方面，进展相对较少, morphogenesis, size control and regeneration. There is a major reason for this failure. 这些问题不能用一个基因的还原论逻辑来回答, one mutant, one phenotype, one function. 理解这些现象将需要更多的系统生物学方法，使用基因组方法来观察多个基因及其在原生体内环境中的综合活性.
Patents
- U.S. Patent. 6030794. 基因工程小鼠和细胞系含有编码维甲酸受体和类维甲酸X受体蛋白基因的改变. Issue Date: 2000-02-29
- U.S. Patent. 6031149. 基因工程小鼠含有维甲酸受体蛋白编码基因的改变. Issue Date: 2000-02-29
- U.S. Patent. 6486381. 基因工程小鼠含有维甲酸受体蛋白编码基因的改变. Issue Date: 2002-11-2
- U.S. Patent. 20090233986A1. Methods and compositions for using the Sax2 gene. Issue Date: 2009-09-17
- U.S. Patent. 20110165570A1. Method Of Effecting De-Differentiation Of A Cell. Issue Date: 2011-07-07
Publications
- Complete List of Published Work at NCBI: http://www.ncbi.nlm.nih.gov/sites/myncbi/thomas.lufkin.1/bibliography/public/
- Murphy K, Lufkin T, Kraus P. 椎间盘的发育和退变——跨物种的见解. Vet Sci. 2023 Aug 24;10(9). doi: 10.3390/vetsci10090540. Review. PubMed PMID: 37756062; PubMed Central PMCID: PMC10534844.
- Hadynski JC, Diggins J, Goad Z, Joy M, Dunckel S, Kraus P, Lufkin T, writ M. 金属-有机框架作为检测SARS-CoV-2基因组基因序列的荧光和比色双信号读出生物传感器平台. ACS Appl Mater Interfaces. 2023 Aug 16;15(32):38163-38170. doi: 10.1021/acsami.3c03518. Epub 2023 Aug 3. PubMed PMID: 37535905.
- Samanta A, Lufkin T, Kraus P. 椎间盘退变——当前的治疗选择和挑战. Front Public Health. 2023;11:1156749. doi: 10.3389/fpubh.2023.1156749. eCollection 2023. Review. PubMed PMID: 37483952; PubMed Central PMCID: PMC10359191.
- Basatvat S, Bach FC, Barcellona MN, Binch AL, Buckley CT, Bueno B, Chahine NO, Chee A, Creemers LB, Dudli S, Fearing B, Ferguson SJ, Gansau J, Gantenbein B, Gawri R, Glaeser JD, Grad S, Guerrero J, Haglund L, Hernandez PA, Hoyland JA, Huang C, Iatridis JC, Illien-Junger S, Jing L, Kraus P, Laagland LT, Lang G, Leung V, Li Z, Lufkin T, van Maanen JC, McDonnell EE, Panebianco CJ, Presciutti SM, Rao S, Richardson SM, Romereim S, Schmitz TC, Schol J, Setton L, Sheyn D, Snuggs JW, Sun Y, Tan X, Tryfonidou MA, Vo N, Wang D, Williams B, Williams R, Yoon ST, Le Maitre CL. 髓核细胞提取和培养方法的统一和标准化. JOR Spine. 2023 Mar;6(1):e1238. doi: 10.1002/jsp2.1238. eCollection 2023 Mar. PubMed PMID: 36994456; PubMed Central PMCID: PMC10041384.
- Lufkin L, Samanta A, Baker D, Lufkin S, Schulze J, Ellis B, Rose J, Lufkin T, Kraus P. Glis1和草酰乙酸在髓核间质细胞体细胞重编程和存活中的作用. Front Mol Biosci. 2022;9:1009402. doi: 10.3389/fmolb.2022.1009402. eCollection 2022. PubMed PMID: 36406265; PubMed Central PMCID: PMC9671658.
- 余文伟，关丽，谭世忠，Shrestha S, Or YZ, Lufkin T，林文伟，林立伟. 敲除四肽重复结构域9A可诱导雌性小鼠社交焦虑并损害攻击行为. Iran J Basic Med Sci. 2022 Jun;25(6):698-703. doi: 10.22038/IJBMS.2022.63044.13932. PubMed PMID: 35949301; PubMed Central PMCID: PMC9320210.
- Kraus P, Samanta A, Lufkin S, Lufkin T. 干细胞在椎间盘再生中的应用——多说少做?. Biocell. 2021 Dec 15;46(6):893-898. DOI:10.32604/biocell.2022.018432. PubMed PMID: 34966192
- Li K, Varden L, Henderson A, Lufkin T, Kraus P. 用单细胞分辨率同时检测牛IVD细胞和组织中的多种mrna和蛋白. Biotechnol Lett. 2021 Jan;43(1):13-24. DOI: 10.1007/s10529-020-02997-9. Epub 2020 Sep 9. PubMed PMID: 32902710
- Varden LJ, Kraus P, Michalek AJ, Lufkin T, Sur S. 用于椎间盘修复和再生的肽基生物材料. In: Guler MO, editor. Peptide-based Biomaterials [Internet] London: Royal Society of Chemistry; 2021. Chapter 13; p.429–458. DOI:10.1039/9781839161148-00429.
- 关玲，余文伟，Shrestha S, Or YZ, Lufkin T，陈永元，林伟林，林立伟. TTC9A缺乏诱导雌二醇介导的雌性小鼠海马和杏仁核神经可塑性相关基因表达的变化. Brain Res Bull. 2020 Apr;157:162-168. DOI: 10.1016/j.brainresbull.2020.02.004. Epub 2020 Feb 10. PubMed PMID: 32057953.
- Li, K., D. Kapper, B. Youngs, V. Kocsis, S. Mondal, P. Kraus, and T. Lufkin，在单细胞水平鉴定成熟椎间盘的潜在生物标志物. J Anat, 2019. 234(1): p. 16-32. DOI: 10.1111/joa.12904
- Li, K., D. Kapper, S. Mondal, T. Lufkin, and P. Kraus, 生物标志物的定量单细胞转录评估支持牛IVD细胞异质性. Veterinary Sciences, 2019. 6(2): p. 1-19. DOI: 10.3390/vetsci6020042
- Kraus, P., K. Li, D. Sipes, L. Varden, R. Yerden, A. Henderson, S. Sur, and T. Lufkin, 复杂异质组织的单细胞表型, in Handbook of Single Cell Technologies, T.S. Santra and F.-G. Tseng, Editors. 2019, Springer Singapore: Singapore. p. 1-17. DOI: 10.1007/978-981-10-4857-9_16-1. ISBN 978-981-10-4857-9
- Sivakamasundari, V., P. Kraus, and T. Lufkin, Pax1和Pax9在哺乳动物细胞中的调控功能, 哺乳动物细胞中基因表达与调控的研究——转录迈向新疗法的建立, A. Sebata, Editor 2018, InTech: Rijeka. p. Ch. 9, 181-207. DOI: 10.5772/intechopen.71920. ISBN 978-953-51-3868-6
- Kraus, P., R. Yerden, D. Sipes, S. Sur, and T. Lufkin, 单细胞分辨率细胞培养的定量和定性RNA表达谱分析. Cytotechnology, 2018. 70(1): p. 185-192. DOI: 10.1007/s10616-017-0132-1
- Kraus, P., V. Sivakamasundari, V. Olsen, V. Villeneuve, A. Hinds, and T. Lufkin, Klhl14反义RNA是椎间盘发育过程中关键成骨转录因子的靶标. Spine (Phila Pa 1976), 2018. DOI: 10.1097/BRS.0000000000002827
- Sivakamasundari, V., P. Kraus, W. Sun, X. Hu, S.L. Lim, S. Prabhakar, and T. Lufkin, 胚胎椎间盘发育中Pax1和Pax9的发育转录组学分析. Biol Open, 2017. 6(2): p. 187-199. DOI: 10.1242/bio.023218
- Nusspaumer, G., S. Jaiswal, A. Barbero, R. Reinhardt, D. Ishay Ronen, A. Haumer, T. Lufkin, I. Martin, and R. Zeller, 小鼠肢体和长骨发育过程中间充质间质细胞群的鉴定与分析. Stem Cell Reports, 2017. 9(4): p. 1124-1138. DOI: 10.1016/j.stemcr.2017.08.007
- Nichane, M., A. Javed, V. Sivakamasundari, M. Ganesan, L.T. Ang, P. Kraus, T. Lufkin, K.M. Loh, and B. 多能Sox9(+)小鼠肺祖细胞的分离和三维扩增. Nat Methods, 2017. 14(12): p. 1205-1212. DOI: 10.1038/nmeth.4498
- Nichane, M., A. Javed, V. Sivakamasundari, M. Ganesan, L.T. Ang, P. Kraus, T. Lufkin, K.M. Loh, and B. Lim, 多能Sox9+小鼠胚胎肺祖细胞的三维培养:分离, Expansion and Cryopreservation. Protocol Exchange, 2017. DOI: 10.1038/protex.2017.106
- Lee, W.J., S. Chatterjee, S.P. Yap, S.L. Lim, X. Xing, P. Kraus, W. Sun, X. Hu, V. Sivakamasundari, H.Y. Chan, P.R. Kolatkar, S. Prabhakar, and T. Lufkin, 综合发育基因组学和系统生物学方法鉴定小鼠胚胎中Sox三联体介导的基因调控网络. Biomed Res Int, 2017. 2017: p. 8932583. DOI: 10.1155/2017/8932583
- Kraus, P., R. Yerden, V. Kocsis, and T. Lufkin, 非酶源性牛椎间盘细胞系的RNA原位杂交鉴定提示祖细胞潜能. Acta Histochemistry, 2017. 119(2): p. 150-160. DOI: 10.1016/j.acthis.2016.12.004
- Kraus, P. and T. Lufkin, 基于干细胞再生医学方法治疗人椎间盘退变的意义. Front Cell Dev Biol, 2017. 5: p. 17. DOI: 10.3389/fcell.2017.00017
- Lim, L.W., S. Shrestha, Y.Z. Or, S.Z. Tan, H.H. Chung, Y. Sun, C.L. Lim, S. Khairuddin, T. Lufkin, and V.C. 四肽重复结构域9A调节雌性小鼠的焦虑样行为. Sci Rep, 2016. 6: p. 37568. DOI: 10.1038/srep37568
- Kumar, V., N.A. Rayan, M. Muratani, S. Lim, B. Elanggovan, X. Lixia, T. Lu, H. Makhija, J. Poschmann, T. Lufkin, H.H. Ng, and S. Prabhakar, 综合基准分析显示H2BK20乙酰化是细胞状态特异性增强子和启动子的独特标志. Genome Research, 2016. 26(5): p. 612-23. DOI: 10.1101/gr.201038.115
- Kraus, P. and T. Lufkin，从椎间盘分离的牛纤维环细胞系. Genomics Data, 2016. 10: p. 83-89. DOI: 10.1016/j.gdata.2016.09.012
- Chatterjee, S., P. Kraus, V. Sivakamasundari, S.P. Yap, V. Kumar, S. Prabhakar, and T. Lufkin，小鼠Bapx1和Sox9蛋白在体内和体外的基因组宽结合(ChIP-Seq). Genomics Data, 2016. 10: p. 51-59. DOI: 10.1016/j.gdata.2016.09.002
- Shrestha, S., Y. Sun, T. Lufkin, P. Kraus, Y. Or, Y.A. Garcia, N. Guy, P. Ramos, M.B. Cox, F. Tay, and V.C. 四肽重复结构域9A负调控雌激素受体α活性. International Journal of Biological Sciences, 2015. 11(4): p. 434-47. DOI: 10.7150/ijbs.9311
- Kraus, P., C.L. Winata, and T. 转基因斑马鱼的转录启动子和增强子研究. Methods Mol Biol, 2015. 1227: p. 245-58. DOI: 10.1007/978-1-4939-1652-8_12
- Kraus, P., V. Kocsis, C. Williams, B. Youngs, and T. Lufkin, 平板原位杂交(PISH)是一种既省时又经济的RNA表达方法，可在单细胞分辨率下研究培养小鼠细胞群体的表型异质性. Biotechnology Letters, 2015. 37(8): p. 1573-1577. DOI: 10.1007/s10529-015-1833-1
- Chatterjee, S., V. Sivakamasundari, P. Kraus, S.P. Yap, V. Kumar, S. Prabhakar, and T. Lufkin, 野生型和无胚小鼠胚胎中表达FACS分选细胞的基因表达谱. Genomics Data, 2015. 5: p. 103-105. DOI: 10.1016/j.gdata.2015.05.031
- Yeo, J.C., J. Jiang, Z.Y. Tan, G.R. Yim, J.H. Ng, J. Goke, P. Kraus, H. Liang, K.A. Gonzales, H.C. Chong, C.P. Tan, Y.S. Lim, N.S. Tan, T. Lufkin, and H.H. Klf2是维持基态多能性的重要因子. Cell Stem Cell, 2014. 14(6): p. 864-872. DOI: 10.1016/j.stem.2014.04.015
- Kraus, P., S. V, H.B. Yu, X. Xing, S.L. Lim, T. Adler, J.A. Pimentel, L. Becker, A. Bohla, L. Garrett, W. Hans, S.M. Holter, E. Janas, K. Moreth, C. Prehn, O. Puk, B. Rathkolb, J. Rozman, J. Adamski, R. Bekeredjian, D.H. Busch, J. Graw, M. Klingenspor, T. Klopstock, F. Neff, M. Ollert, T. Stoeger, A.O. Yildrim, O. Eickelberg, E. Wolf, W. Wurst, H. Fuchs, V. Gailus-Durner, M.H. de Angelis, T. Lufkin, and L.W. 转录因子Zscan10的多效功能. PLoS ONE, 2014. 9(8): p. e104568. DOI: 10.1371/journal.pone.0104568
- Kraus, P., V. Sivakamasundari, X. Xing, and T. 生成用于谱系追踪和基因敲除研究的小鼠系. Methods Mol Biol, 2014. 1194: p. 37-62. DOI: 10.1007/978-1-4939-1215-5_3
- Chatterjee, S., V. Sivakamasundari, S.P. Yap, P. Kraus, V. Kumar, X. Xing, S.L. Lim, J. Sng, S. Prabhakar, and T. Lufkin, 多种组织的体内全基因组分析鉴定基因调控网络, 哺乳动物脊柱中Bapx1的新功能和下游调控基因及其与Sox9的共调控. BMC Genomics, 2014. 15(1): p. 1072. DOI: 10.1186/1471-2164-15-1072
- Sng, J. and T. 第17章:干细胞治疗的进展，在多能干细胞，N. Lenka, Editor 2013, InTech: Rijeka. p. 375-396. DOI: 10.5772/55061. ISBN 978-953-51-1192-4
- Sivakamasundari, V. and T. Lufkin, 阻止退变:IVD干细胞和干细胞再生治疗退行性椎间盘疾病. Advances in Stem Cells, 2013. Article ID 724547: p. 1-22. DOI: 10.5171/2013.724547
- Sivakamasundari, V., P. Kraus, S. Jie, and T. Lufkin, Pax1(EGFP):用于分子和命运定位研究的新的野生型和突变型EGFP小鼠系. Genesis: J of Genetics and Development, 2013. 51(6): p. 420-9. DOI: 10.1002/dvg.22379
- Ng, J.H., V. Kumar, M. Muratani, P. Kraus, J.C. Yeo, L.P. Yaw, K. Xue, T. Lufkin, S. Prabhakar, and H.H. 生殖细胞的体内表观基因组分析揭示了生殖细胞的分子特征. Developmental Cell, 2013. 24(3): p. 324-33. DOI: 10.1016/j.devcel.2012.12.011
- Kumar, V., M. Muratani, N.A. Rayan, P. Kraus, T. Lufkin, H.H. Ng, and S. Prabhakar，深度测序数据映射的统一优化信号处理. Nature Biotechnology, 2013. 31(7): p. 615-22. DOI: 10.1038/nbt.2596
- Kraus, P., V. Sivakamasundari, S.L. Lim, X. Xing, L. Lipovich, and T. Lufkin, Making sense of Dlx1 antisense RNA. Developmental Biology, 2013. 376: p. 224–235. DOI: 10.1016/j.ydbio.2013.01.035
- Chatterjee, S., P. Kraus, V. Sivakamasundari, X. Xing, S.P. Yap, S. Jie, and T. Lufkin, 使用增强绿色荧光蛋白对Sox9功能丧失细胞进行谱系追踪的条件小鼠系. Biotechnology Letters, 2013. 35(12): p. 1991-6. DOI: 10.1007/s10529-013-1303-6
- Sng, J. and T. 《esball国际app》. Genetics Research International, 2012. 2012 Article ID 748698: p. 1-9 Epub 2012 Dec 4. DOI: 10.1155/2012/748698
- Sng, J. and T. 新兴干细胞疗法:治疗、安全性和生物学. Stem Cells International, 2012. 2012: p. 521343. DOI: 10.1155/2012/521343
- Sivakamasundari, V. and T. 弥合差距:理解胚胎椎间盘发育. Cell & Developmental Biology, 2012. 1(2): p. 1-7. DOI: 10.4172/cdb.1000103
- Sivakamasundari, V., H.Y. Chan, S.P. Yap, X. Xing, P. Kraus, and T. Lufkin，用于谱系追踪和条件敲除研究的新Bapx1(Cre-EGFP)小鼠系. Genesis: J of Genetics and Development, 2012. 50(4): p. 375-83. DOI: 10.1002/dvg.20802
- Lee, W.J., P. Kraus, and T. Lufkin, 用血凝素内源性标记小鼠转录因子Sox5进行功能研究. Transgenic Research, 2012. 21(2): p. 293-301. DOI: 10.1007/s11248-011-9531-9
- Lee, M.Y. and T. Lufkin, “三步MACS”的发展:一种在缺乏已知细胞表面标记的情况下从复杂动物组织中分离稀有细胞群的新策略. J Biomolecular Techniques, 2012. 23(2): p. 69-77. DOI: 10.7171/jbt.12-2302-003
- Kraus, P., X. Xing, S.L. Lim, M.E. Fun, V. Sivakamasundari, S.P. Yap, H. Lee, R.K. Karuturi, and T. Lufkin, 胚胎Illumina芯片表达谱分析小鼠品系特异性基因表达差异. BMC Research Notes 2012. 5: p. 232. DOI: 10.1186/1756-0500-5-232
- Chatterjee, S., V. Sivakamasundari, W.J. Lee, H.Y. Chan, and T. 《esball国际app》. Trends in Developmental Biology, 2012. 6: p. 45-52. DOI: 00000
- Chatterjee, S. and T. 调控基因组学:来自斑马鱼的见解. Current Topics in Genetics, 2012. 5: p. 1-10. DOI: 00000