User:Ford Xingyuan Ma

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Ford Xingyuan Ma (an artistic interpretation)
Ford Xingyuan Ma (an artistic interpretation)
  • Name: Dr. Xingyuan Ma(马兴元)

  • Professor of molecular Biology and Biopharmaceuticals

No.130 Meilong Road, School of Biotechnology, East China University of Science & Technology, Shanghai 200237, P.R.China

马兴元  男,博士,华东理工大学生物工程学院 教授,上海市“浦江学者”入选者,生物化学与分子生物学博士生/硕士研究生导师、
生物工程与技术博士生导师、药学专业研究生导师和生物工程硕士导师。生物反应器国家重点实验室学 固定研究人员;
基因与蛋白质药物(G&P-Lb:www.gene-protein-drug.com)研究室主任。
  • Dept. of Biochemistry, School of Bioengineering

State Key Laboratory of Bioreactor Engineering (SKLBE) East China University of Science and Technology(ECUST)

简要履历:2003年6月毕业于中国人民解放军军需大学(现吉林大学)获博士学位,师从殷震院士、朱平研究员。硕士与博士期间在军需大学研究所 (军事医学科学院 第11所) 全军基因工程重点实验室从事分子生物学与基因工程药物的研究。2003年博士毕业后在华东理工大学生物工程博士后流动站从事博士后研究工作,2010.12—2011.12新加坡国立大学 国家公派(A类)访问学者。现为国家“千人计划“学者研究助理、生工学院纳米生物工程实验室、生物医药纳米技术中心成员。

研究领域: 细胞分子生物学与生物技术药物、生物制品

主要研究方向: 1)抗癌蛋白新药(疫苗/抗体)及其转载传递系统;2)微生物与蛋白质(酶)工程及合成生物学研究。


学术兼职:

Drug Discoveries & Therapeutics编委; Chinese Journal of Biology编委,《中华现代临床医学杂志》常务编委; 《中国医药导报杂志》编委; 国内、外多个杂志的特约Reviewer;中国生化与分子生物学会工业生化与分子生物学分会第9届常务理事、副秘书长;中国药学会 生化与生物技术药物专业委员会 第23届委员会 委员; 美国The Society for Biological Engineering (SBE)、中国/上海生物工程学会会员。

Contents

Education

2012.09---Professor, molecular Biology and Biopharmaceuticals, Dept. of Biochemistry, School of Bioengineering,State Key Laboratory of Bioreactor Engineering (SKLBE),East China University of Science and Technology(ECUST)

2010.12/2011.12: Visiting Scholar. Molecular Biology and Genetic engineering, National University of Singapore (NUS).

2008.9/2010.11: Teacher & Researcher. Molecular Biology and Genetic engineering, Dept. of Biotechnology, ECUST, Associate Professor

2005.10/2008.8: Researcher & Teacher. Molecular Biology and Genetic engineering, College of Biotechnology, ECUST, Associate Professor

2003.9/2005.9: Post-Doc. Molecular Biology and Genetic engineering, Institute of Biochemistry, ECUST

1999.9/2003.6: Ph. D Microbial Molecular Biology, Quartermaster University of PLA

1999.7/2003.9: Teacher Study and teaching on animal medicine and science in AUS

1996.9/1999.7: M. Sc Animal Medicine, Agricultural University of Shenyang(AUS)

1995.7/1996.9: Pre-M. Sc work. Working on Husbandry Bureau of Xing County, Shan’xi

1991.9/1995.7: B. Sc Animal Medicine, Agricultural University of Shan’xi


Research interests

1. Recombinant proteins (Drugs/Vaccine/Antibody) from genetic engineering based on molecular biology and their transduction and evaluation system. Study field involves the upstream to downstream of pharmaceutical biotechnology.

2. Recombinant enzymes and their modification and expression used for bio-production, bioenergy, biomaterials and so on. Research program focuses on experimental and theoretical aspects of applied genetics and metabolic engineering to natural strains, and genetic/protein engineering of key enzymes under help of bioinformatics.

Publications

==2013==

1. Nanjing Lin, Wenyun Zheng, Linfeng Li, Ping Wang, Xingyuan Ma*, A novel system enhancing the endosomal escapes of peptides promotes Bak BH3 peptide inducing apoptosis in lung cancer A549 cells. Targeted Oncology. 2013. DOI: 10.1007/s11523-013-0282-9, IF[2011]=3.614

2. 石磊,唐莉莉,马兴元*, 王天文,马飞,王平. 利用类弹性蛋白可逆相变和内含肽自切割功能高效制备TmSm抗肿瘤蛋白.中国生物工程杂志. 2013,33(10):89-95

3. 马兴元. 非小细胞肺癌治疗性疫苗及相关生物标志物研发进展. 生物产业技术. 2013,5(9)22-29


==2012==

1.Tianwen Wang, Xingyuan Ma*, Hu Zhu, Aitao LI, Guocheng Du, Jian Chen. Available methods for assembling expression cassettes for synthetic biology. Applied Microbiology and Biotechnology. Appl Microbiol Biotechnol (2012) 93:1853–1863

2.Rijun Gui, Xueqin An∗, Hongjuan Su, Weiguo Shen, Linyong Zhu, Xingyuan Ma, Zhiyun Chen, Xiaoyong Wang..Rhodamine 6G conjugated-quantum dots used for highly sensitive and selective ratiometric fluorescence sensor of glutathione. Talanta, 94 (2012) 295-300

3.Yuxin Xu, Wenyun Zheng, Tianwen Wang, Ping Wang, Ling Zhu, Xingyuan Ma*. Genetic protein TmSm(T34A) enhances sensitivity of chemotherapy to breast cell lines as a synergistic drug to doxorubicin. Biomedicine & Pharmacotherapy, 2012, 66(5):368–372

4.Hailong Chen, Xingyuan Ma*, Zhi Li, Qiaoyun Shi, Wenyun Zheng, Yang Liu, Ping Wang. Functionalization of single-walled carbon nanotubes enables efficient intracellular delivery of siRNA targeting MDM2 to inhibit breast cancer cells growth. Biomedicine & Pharmacotherapy, 2012, 66(5):334–338

5.Wang T, Ma X*, Du G, Chen J. Overview of Regulatory Strategies and Molecular Elements in Metabolic Engineering of Bacteria. Mol Biotechnol. 2012, 52: 300–308

6.Dan Qiu, Xueqin An∗, Zhiyun Chen, Xingyuan Ma. Microstructure study of liposomes decorated by hydrophobic magnetic nanoparticles. Chemistry and Physics of Lipids 165 (2012) 563-570

7.Wang T, Li A, Ma X*, DU G, Chen J. A simple and universal method to express protein in unfused form. Protein Pept Lett. 2012 19(9):930-933

8.朱玲,石磊,唐莉莉,许玉馨,张翼,马兴元*。TATm-Survivin(T34A)冻干注射剂的制备及体外抗肿瘤效果。中国新药杂志,2012.21(17):15-19

==2011==

1.Wenyun Zheng, Yanyan Kang, Linfeng Li, Yuxin Xu, Xingyuan Ma*, Levels of effectiveness of gene therapies targeting survivin and its splice variants in human breast cancer cells. Drug Discoveries & Therapeutics. 2011; 5(6):293-298

2.康燕燕, 唐莉莉,石磊,陈海龙,马兴元*。重组蛋白TATm-Survivin(T34/117A)对乳腺癌细胞周期变化与凋亡的影响。中国癌症杂志,2011, 22(2):91-98

3.张翼,李林凤,马兴元*。细胞培养环境中4 种常见基础性因子对乳腺癌细胞生长的影响. 中国科技论文2011.11在线发表 (http://www.paper.edu.cn).

==2010==

1.Xingyuan Ma, Bi Yao, Wenyun Zheng, Linfeng Li*. Comparative study on characterization of recombinant B subunit of E. coli heat-labile enterotoxin (rLTB) prepared from E. coli and P. patoris. J. Microbiol. Biotechnol. 2010, 20(3):550-557

2.马兴元。细胞分裂与凋亡的重要调节者Survivin:一个抗癌新药靶。生命的化学,2010,30(3):338-344

3.刘琨,陈海龙,马兴元*,康燕燕,许玉馨。酵母Bir1p同源物Survivin对毕赤酵母的分子重组与生长影响。生物技术通报,2010,220(11):230-233

==2009==

1.Haiyi Zhang, Yu Zheng, QinghaiLiu, Xinyi Tao, Wenyun Zheng, Xingyuan Ma*, Dongzhi Wei*. Development of a fed-batch process for the production of anticancerdrug TATm-survivin(T34A) in Escherichia coli. Biochemical Engineering Journal. 2009, 43(2):163–168

2.Li Zhao, Yu Zheng, Xingyuan Ma* and Dongzhi Wei*. Effects of over-expression of glycerol dehydrogenase and 1, 3-propanediol oxidoreductase on bioconversion of glycerol into 1, 3-propandediol by Klebsiella pneumoniae under micro-aerobic conditions. Bioprocess and Biosystems Engineering, 2009, 32(3): 313-320

3.Li Zhao, Xingyuan Ma, Yu Zheng, Jianguo Zhang, Guodong Wei, Dongzhi Wei. Over-expression of glycerol dehydrogenase and 1, 3-propanediol oxidoreductase in Klebsiella pneumoniae and their effects on conversion of glycerol into 1, 3-propanediol in resting cell system. Journal of Chemical Technology & Biotechnology. 2009, 84(4): 626-632

4.姚碧,刘琨,陈海龙, 马兴元*。组成新发典型甲型H1N1流感病毒八个基因片段的变异分析与疫病流行原因初探。 中国兽医科学,2009,39(8):679-684

5.刘琨,陈海龙,姚碧, 马兴元*。 新发甲型H1N1流感病毒HA分子的变异分析。 现代生物医学进展,2009,9(20):3801-3806

==2008==

1.Yu Zheng, Li Zhao, Xingyuan Ma, Dongzhi Wei*. Production of 1, 3-propanediol from glucose by co-expressing glycerol-3-phosphate dehydrogenase and glycerol-3-phosphatase in Klebsiella pneumoniae. Journal of Bioscience and Bioengineering, 2008, 105 (5): 508–512.

2.Xingyuan Ma, Meiyun Liu, Yushu Ma, Yi Gong *, Dongzhi Wei*, Shengli Yang. Disulfide bond Cys30-Cys299 and the fragment “96RIMQAPLT106”of the lid region of lip2 are critical for its biocatalytic activity. Journal of Biotechnology. 2008, S290-334 (V1-Y-046)

3.Xingyuan Ma*, Wenyun Zheng,Haiyi Zhang,Xinyi Tao,Qinghai Liu,Dongzhi Wei*. Large scale preparation and characterization of a genetically engineering protein and biological activity of suppressing proliferation and rapid pro-apoptosis to carcinoma cells. Journal of Biotechnology. 2008, S75-S98 (13-P-022)

4.Yu Zheng, Li Zhao, Haiyi Zhang,Liujin Wei, Xingyuan Ma, Dongzhi Wei*.one-step production of 2,3-butanediol from starch by secretory over-expression of amylase in Klebsiella pneumoniae. Journal of Chemical Technology & Biotechnology. 2008, 83: 1409-1412

==2007==

1.Qinghai Liu, Jinping Lin, Meiyun Liu, Xinyi Tao, Dongzhi Wei, Xingyuan Ma and Shengli Yang Large scale preparation of recombinant human parathyroid hormone 1–84 from Escherichia coli. Protein Expression and Purification, 2007, 54: 212-219

==2006==

1.Xingyuan Ma, Wenyun Zheng, Dongzhi Wei, Yushu Ma, Tianwen Wang, Jinzhi Wang, Qinghai Liu and Shengli Yang. Construction, Expression, and Purification of HIV-TAT-survivin (T34A) mutant: a Pro-apoptosis protein in E.coli. Protein Expression and Purification, 2006, 47:36-44.

2.Xingyuan Ma, Jianhua Tan, Dongzhi Wei, Pin Zhu, Manji Sun. High-level secretion and purifiation of recombinant acetylcholinesterase from human brain in P. pastoris and identification by chromogenic reaction. Applied Microbiology and Biotechnology. 2006, 72: 316-322.

3.Ma Xingyuan, Zheng Wenyun, Wei Dongzhi, Ma Yushu, Wang Tianwen, Wang Jinzhia, Liu Qinghai, Yang Shengli, High-level Expression, Purification and Pro-apoptosis Activity of HIV-TAT-Survivin (T34A) Mutant to Cancer Cells in Vitro, Journal of Biotechnology, 2006, 123:367-378.

4.Xingyuan Ma, Wenyun Zheng, Tianwen Wang, Dongzhi Wei, Yushu Ma. Optimization and high-level expression of a functional GST-tagged rHLT-B in E. coli and GM1 binding ability of purified rHLT-B. Journal of Microbiology, 2006, 44(6): 293-300.

5.Xingyuan Ma, Zheng Wenyun, Tianwen Wang. Leukocyte function-associated antigen-1 structure, function and application prospects. Protein and Peptide Letters, 2006, 13: 397-400.

6.Tianwen Wang, Hu Zhu, Xingyuan Ma, Yushu Ma and Dongzhi Wei. Mutant library construction in directed molecular evolution: casting a net wider. Mol Biotechnol. 2006, 34(1): 55-68.

7.Tianwen Wang, Hu Zhu, Xingyuan Ma, Yushu Ma and Dongzhi Wei. Structure-based stabilization of an enzyme: the case of penicillin acylase from Alcaligenes faecalis. Protein Peptide Letters, 2006, 13 (2):177-183.

8.Tianwen Wang, Hu Zhu, Xingyuan Ma, Zhuoya Fei, Yushu Ma and Dongzhi Wei. Enhancing enzymatic activity of penicillin G acylase by coexpressing pcm gene. Applied Microbiology and Biotechnology, 2006, 72(5): 953-958.

Research Projects or Scientific Foundation

Sept.2013-Aug.2015 Applicant Anti-Survivin nanobody prepared with engineered yeast and its activity in antitumor and on stem cells, funded by Municipal Supports for Pujiang Scholors of Shanghai City (Accession number:F200-2R-13110)

Oct.2009-Dec.2013 Applicant The Fundamental Research Funds for the Central Universities from Education Ministry of China (Accession number: WK0913002)

Jan.2009-Dec.2010 Applicant “A Study on Novel Drug” on the National Science Research Project "Significant New Drugs Created" of Eleventh Five-year Plan (Accession number: 2009ZX09103-693)

Jan.2009-Dec.2010 Participant A Study on Key Technology of Novel Drug Manufacture” on the National Science Research Project "Significant New Drugs Created" of Eleventh Five-year Plan (Accession number: 2009ZX09103-001)

Jan.2009-Dec.2011 Applicant “A study aiming to solve key and basic problems of an anticancer protein drug” By supported by the National Nature Science Foundation of China (Accession number: 30873190)

Jan.2009-Dec.2011 Second Applicant “A study on Functions and Molecular mechanism of an Chinese traditional anticancer drug” By supported by the National Nature Science Foundation of China (Accession number: 30870253)

Jan.2008-Dec.2009 Applicant “Molecular mechanism of TAT-Survivin mutant to breast cancer”, supported by the foundation for young teacher from Education Ministry of China (Accession number: 20070251011).

Jul.2005-Dec.2007 Applicant “State first-class creative engineered anticancer drug TAT-Survivin mutant: pilot scale and pre-clinic research”, supported by the Key Project of Science and Technology Committee of Shanghai City (Accession number: 054319928).

Dec.2004-Aug.2005 Main Participant “Developing the platform technology for large-scale preparation of protein drugs from microbe”, supported by the Chinese National “863” High Tech Project Foundation grant (Accession number: 2004AA2Z3801).

Jul. 2005-Dec. 2006 Applicant “Construction of environment-friendly expression system based on the PFLD1 promoter from Pichia pastoris”, supported by the Nature Science Foundation of Shanghai. (Accession number: 05ZR14033).

Nov.2005-Oct.2007 Applicant “Studies on pharmacodynamics and pharmacology of a novel anticancer drug for breast cancer by skin administration” was supported by Initiation Foundation for Introduced Talent of East China University of Science and Technology. (Accession number: YF0142120).

Jul. 2000-Jun. 2003 Applicant “Studies on cDNA Cloning of Human Brain AChE and High Expression in Pichia Pastoris” was “15th” Key Research Projects of Medicine and Hygiene of PLA (Accession number: 01-Z-023).

Dec.1999-Aug.2002 Main Participant “Studies on a bio-missile LHRH-PE40 of novel anticancer recombinant protein drug”, supported by Jilin Yatai Co., Ltd. and the Chinese National “863” High Tech Project Foundation grant.

Jul.2000 - Dec.2002 Applicant “The establishment of detect technology for the enterotoxin gene of ST and LT from E. coli by multiplied PCR” was supported by “Science Fund For Youth” of Agricultural University of Shenyang (Accession number: 2000-17-A).

Jul.1997 - Dec.1999 Applicant “Studies on PCR Site-directed Mutagenesis in the Cloned LT Gene and Construction of Recombinant Expression Plasmid” was supported by Quartermaster University of PLA.

主要科研项目:

1.主持完成全军医药卫生“十五”规划重点科研基金项目“人脑乙酰胆碱酯酶cDNA克隆及其高效表达、纯化与酶活性鉴定的研究”(项目编号:01-Z-023)。

2.作为主要成员曾参与研究了国家“863”基金和吉林亚泰集团资助“国家一类创新基因工程药物——抗癌生物导弹(商品名:比欧米赛)”,现已获得SFDA的临床许可,已正式进入二期临床试验。

3.作为骨干成员参与国家“863”生物技术制药重大专项“微生物表达蛋白药物规模化制备平台技术”(项目编号:2004AA2Z3801),主要负责重组蛋白药物的工程菌构建、表达与纯化工作。

4.上海市自然科学基金项目: “基于毕赤酵母PFLD1启动子的“绿色”基因表达体系的研究”(项目编号:05ZR14033)(2006.1-2007.9) 负责人。

5.上海市生物医药科技攻关重点项目: “基因工程抗癌新药TAT-Survivin突变体的中试研究与高危HPV检测试剂盒研究" (项目编号:054319928) (2006.1-2007.12)负责人。

6. 华东理工大学引进人才启动基金: “外涂基因工程新药TAT-Survivin突变体对小鼠实体瘤的抑制作用及其促凋亡机理研究” (2005.10-2007.9) 负责人。

7. 教育部博士点科研专项基金项目: “TAT-Survivin突变体对乳腺癌促凋亡分子机理” (2008.1-2010.12)(项目编号:20070251011) 负责人。

8.国家自然科学基金项目:“一种抗肿瘤创新药物的关键基础问题研究”(2009.1-2011.12) (项目编号:30873190) 负责人。 9.国家“十一五”计划“重大新药创制”项目:“重组蛋白TATm-Survivin(T34A)质量体系和临床前药效学与安全性研究”(2009.1-2010.12) (项目编号:2009ZX09103-693) 负责人。

10.国家自然科学基金项目:“水翁花逆转肝癌多药耐药的有效成分及分子机制” (2009.1-2011.12)(项目编号:30870253) 参与(第2)。

11.国家教育部交叉学科与重大项目培育基金项目:“抗肿瘤靶向纳米载药系统研究” (2009.9-2012.12)(项目编号:WK0913002) 项目分负责人。

12.国家“十一五”计划“重大新药创制”(技术平台)“生物技术药物发酵放大与分离技术平台” (项目编号:2009ZX09306-008)(2009.1-2010.12) 参与(10)。

13. 国家“十一五”计划“重大新药创制”上海市配套项目(项目编号:2009ZX09103-693) 负责人

14.生物反应器工程国家重点实验室国际合作开放课题:“Enhancing and stabilizing the bioactivity of biomacromolecules by nanotechnology for effective drug delivery and efficient biotransformation” 国内合作者

15.生物反应器工程国家重点实验室课题: ““月球车”式LT(R192G)肽活性结构组装及其用于旅行及灾后流行性腹泻皮粘膜疫苗的研发”。(2013.01.01-2015.12.31)负责人

16.上海“浦江学者”计划资助项目:“存活素纳米抗体(Survivin-Nb)工程化酵母制备与抗肺癌及其干细胞活性研究” (项目编号:13PJD012)(2013.09.01-2015.8.31)负责人

发明专利:

1.发明名称:大肠杆菌热敏毒素B亚单位的真核表达方法 中国专利授权号:ZL 2005 1 0027957.6 排名第二

2.发明名称:一种用于原核分泌、融合表达大肠杆菌热敏毒素B亚单位的载体 中国专利授权号:ZL 2005 1 0028084.0 排名第二

3.发明名称:含有HIV转导结构域的生存素突变体及制备方法和应用 中国专利授权号:ZL 2005 1 0026847.8 排名第二

4.专利名称: 一种肿瘤化疗药物的蛋白增敏剂, 中国专利授权号: ZL201010608978.8 排名第一


5.发明名称:非甲醇诱导型毕赤酵母蛋白表达系统及其用途 中国专利公开号: CN101104859 排名第一

6.发明名称:抗肿瘤药物TAT(m)-Survivin(T34A)的纯化复性方法 中国专利公开号:CN101139388 排名第二

7. 发明名称:生产二羟基丙酮的基因工程菌,其构建方法及其用途 中国专利公开号:CN 101092604 排名第二

8. 发明名称:重组人甲状旁腺激素1-84的制备方法 中国专利公开号:CN1861790 排名第五

8. 发明名称:一种静息细胞转化甘油生产1,3-丙二醇的方法 中国专利公开号:CN 101157939 排名第二

9. 发明名称:生产抗癌药物TAT(m)-Survivin(T34A)的工程菌的发酵放大工艺 中国专利公开号: CN101157949 排名第二

10.专利名称: 一种抗肿瘤蛋白质药物的质量稳定工艺,专利申请号: 201010616473.6; 专利公开号:CN102366628A 排名第一

11.专利名称: 单壁碳纳米管转载抗肿瘤药物技术及其应用,专利申请号: 20111003490.7专利公开号:CN102370988A 排名第一

12.发明名称:纳米材料固载蛋白酶分子的方法及应用, 专利申请号:201110024154.0; 专利公开号:CN102373192A 排名第一

13.专利名称: 一种survivin及其突变体转基因酵母系统及其应用,201110008959.6; 专利公开号: CN102367422A 排名第一

14.发明名称:一种内含肽介导的类弹性蛋白纯化重组蛋白的方法, 专利申请号:201110236772.1; 专利公开号:CN102373234A 排名第一

15. 发明名称:一种疫苗粘膜免疫佐剂分子的制备方法, 中国专利公开号:CN 102382853A. 排名第一

16. 发明名称:一种增强多肽药物从细胞内体逃离的蛋白载药系统及其应用, 中国专利申请号:201310178357.4 排名第一

17. 发明名称:一种高效、快速的DNA-蛋白质交联方法, 中国专利公开号:CN103361321A 排名第二


近年部分奖励:

1. 第13届国际生物技术大会(大连)(2008年)青年科学家提名奖。

2. 上海市生物工程学会 青年科学家学术年会 刘新垣院士征文一等奖。

3.2006-2007年度 华东理工大学先进工作者。

4.2009年指导大学生创新实践《8株产油酵母的分离鉴定与产油性能研究》获得华东理工大学第九届USRP优秀论文奖。

本科教学:

1.《疫苗抗体工程》(32学时,2学分)课程;(生物技术专业学生) (春季开设);

2.《生物物理学》(32学时,2学分)课程;(生物科学专业学生) (秋季开设)。


教材/著作编写:

1. 主编,《蛋白质与酶工程》,化学工业出版社, ISBN:出版时间: 2010.13(预计)

2. 编译审校,《生物技术和遗传工程词汇》(The FAO Biotechnology Glossary)(2010)联合国粮农组织(FAO)ISBN:1020-0541, 出版时间: 2010年5月

3. 主编,《疫苗工程》(国家十一五规划重点教材),华东理工大学出版社, ISBN:9787562825845 出版时间: 2009.8

4. 主译, 《生物催化剂与酶工程》 科学出版社,ISBN:9787030221957 出版时间: 2008.9

5. 主编,《国家法定猪病诊断与防制》,中国轻工业出版社, ISBN: 9787501958047出版时间: 2007.6

6. 副主编,《国家法定禽病诊断与防制》,中国轻工业出版社,ISBN:7501942722出版时间: 2005.4

7. 副主编,《奶牛养殖顾问》辽宁科技出版社,出版时间: 2004

8. 审校 《面向21世纪课程教材—兽医传染病学》中国农业大学出版社, 出版时间: 2002

联系方式:

联系电话: 021-64250135;

E-mail:maxy@ecust.edu.cn; mxy2008bj@aliyun.com.cn

通讯地址:生物工程学院 生物反应器国家重点实验室 283# 邮编 200237;

         上海市梅陇路130号 华东理工大学 实验十八楼1413室

Useful links

  • Links to some labs

Protein engineering

  1. David Baker's lab: http://depts.washington.edu/bakerpg/drupal/

Metabolic engineering and synthetic biology

  1. http://keaslinglab.lbl.gov/
  • Online tools
  1. Multiple alignment: http://www.ebi.ac.uk/Tools/msa/clustalw2/
  1. 在线基因表达密码子优化: http://www.jcat.de/
  • Information resources

"References texts and information resources."

Videos

  • ScienceHack: Search engine for science videos with a review system for videos.

Please add new resources useful to the community here. Keep this page organized by following the format and organization already here.

  • See also Vectors for information and links related to cloning vectors.
  • See also Searching the literature for information and links on searching the biological literature.
  • See also Synthetic Biology for information and links on Synthetic Biology.

Videos

  • ScienceHack: Search engine for science videos with a review system for videos.

Information resources

References texts and information resources.

Bacterial physiology

  • Escherichia coli statistics by Institute for Biomolecular Design
    • Several tables describing statistical data on E. coli compiled from several sources.
  • EcoSal by ASM Press
    • An incomplete web version of the publication Escherichia coli and Salmonella: Cellular and Molecular Biology. [Subscription required]
  • EcoGene
    • Database of all E. coli genes and sequences
  • Ecocyc
    • Comprehensive biochemical pathway and gene function site for E. coli

Lab techniques

  • Polony Protocols by Church and Mitra Lab
    • Polonies are colonies of PCR amplicons derived from a single molecule of nucleic acid.
  • Protocol-online by Dr. Long-Cheng Li
    • A database of research protocols in a variety of life science fields. It has a popular discussion forum.

Protein

RNA

  • Appendix by Ambion, Inc.
    • Website with many useful nucleic acid parameters.

Research

Online tools

Tools available to use online.

General

  • Colibri by Institut Pasteur
    • E. coli genome site; get sequences, see the position of your gene in the chromosome, see the function of your gene, and other fun stuff. You can also search for protein sequences/motifs within the E. coli genome.
  • NCBI
    • Various tools and databases for molecular biology.
  • The public instance of the JBEI Registry
    • A DNA part, plasmid, microbial strain, and Arabidopsis Seed online repository with physical sample tracking capabilities
    • A site where you can explore the various features of the JBEI Registry software, and even get some work done!
    • Try out the integrated online tools, including DNA sequence editing and annotation (Vector Editor) and auto-aligning sequencing trace files against a template.
    • Follow a link to the underlying open-source software source code.
  • PaR-PaR Laboratory Automation Platform
    • PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour.
  • Biopolymer calculator by Schepartz lab
    • Calculate extinction coefficients, Tm's, and base composition for your DNA or RNA; calculate amino acid composition and extinction coefficient for your protein
    • Currently under construction, with promises that it will be back online soon.
  • Science Gateway
    • Collection of science-related links, including links to journals, catalogs, and tools. See their about page.
  • BioNumbers
    • The database of useful biological numbers.

DNA

  • Clipboard by Austin Che
    • Web tool for getting complement, reverse complement, translation and restriction enzyme analysis of a DNA sequence
  • Gene Design by Boeke lab
    • Collection of online tools for codon optimization and shuffling, restriction site editing, and so on.
  • NEB Cutter by New England Biolabs, Inc.
    • Tool for finding restriction sites, et cetera.
  • Primer3
    • Tool that lets you pick & evaluate primers from a DNA sequence
  • UNAFold
    • Replacement for mFold for predicting nucleic acid folding. Downloadable and some applications are available online also.
  • SIDD
    • Stress induced DNA duplex destabilization. Finds destabilized sites in superhelical DNA.
  • j5, DeviceEditor, and VectorEditor online tools
    • j5: DNA assembly design automation for (combinatorial) flanking homology (e.g., SLIC/Gibson/CPEC/SLiCE/yeast) and type IIs-mediated (e.g., Golden Gate/FX cloning) assembly methods
    • DeviceEditor: a visual DNA design canvas that serves as front-end for j5
    • VectorEditor: a visual DNA editing and annotation tool
    • The j5 and DeviceEditor software has been exclusively licensed to TeselaGen Biotechnologies for commercial use and distribution.

RNA

  • mFold by Michael Zuker.
    • This is the main page with links to sites for predicting RNA and DNA folds, calculating Tm's and free energies.
    • (This has been replaced with the DINAMelt server running UNAfold)
  • Vienna RNA software package: RNA secondary structure prediction and design
  • Sfold: Statistical Folding and Rational Design of Nucleic Acids. Predicts accessible RNA sites

Protein

  • AGADIR by Serrano lab
    • An algorithm to predict the helical content of peptides.
  • AVID by Keating lab
    • An integrative framework for discovering functional relationships among proteins.
  • Cn3D by NCBI
    • A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. It doesn't read PDB files but can be more straightforward to use than DeepView.
  • ExPASy Proteomics server by the Swiss Institute of Bioinformatics
    • Collection of links to many pages to calculate parameters of your favorite proteins
    1. Compute pI/Mw
      • A tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot and/or TrEMBL entries or for user entered sequences.
    2. ProtParam
      • A tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence.
    3. Translate
      • Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
  • GETAREA 1.1 by Sealy Center for Structural Biology
    • Solvent accessible surface areas, atomic solvation energies, and their gradients for macromolecules
  • PAIRCOIL2 by Keating and Berger labs
    • Tool to predict the parallel coiled coil fold from sequence using pairwise residue probabilities.
  • ProteinProspector by UCSF Mass Spectrometry Facility
    • Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.

Statistical tests

Calculators

Office applications

  • gOffice by Silveroffice, Inc.
    • Suite of office applications offered over the web

Writing

  • Writely by Upstartle, LLC.
    • A beta word processor run over the web
  • WriteBoard by 37signals
    • Permits writing of shareable, web-based text documents

Spreadsheets

  • NumSum by TrimPath
    • Permits sharable, web-based spreadsheets
  • iRows by Itai Raz and Yoah Bar-David
    • Permits web-based spreadsheets

Software resources

Software available to download.

General

  • Vector NTI by Informax, Inc.
    • Free-to-academics tool for sequence analysis and data management.

DNA

  • PerlPrimer: Open source PCR primer design. Written in Perl/Tk.
  • Artemis by the Sanger Center
    • A free DNA sequence viewer and annotation tool (Java based).
  • GeneDesigner by DNA2.0
    • Combine genetic building blocks by drag-and-drop, codon optimize, restriction site editing, sequence oligo design etc. See BMC Bioinformatics 2006 Jun 6;7(1):285 for more detail.
    • Free to download and works on Mac or PC. User agreement is somewhat restrictive, i.e. you cannot sell genes designed using the tool without permission.

RNA

  • XRNA: Java tools for creating RNA secondary structure diagrams

Protein

  • Dang by Richardsons' lab
    • A command-line tool that generates a table of several useful geometric measurements for each residue or base from a PDB file.
  • DeepView by GlaxoSmithKline & Swiss Institute of Bioinformatics
    • Awesome program for viewing and studying protein structure.
  • Modeller by Sali lab
    • Program for homology or comparative modeling of protein three-dimensional structures by satisfaction of spatial restraints.
  • PyMOL
    • Molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. The latest version does not run on OSX 10.3. (from Kathleen).
  • VMD by Theoretical and Computational Biophysics Group at UIUC
    • Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. Generates pretty high resolution pictures of protein structures.

Geospatial modelling

Links to some labs

Protein engineering

1.David Baker's lab: http://depts.washington.edu/bakerpg/drupal/ 2.Michael Levitt: http://csb.stanford.edu/levitt/ 3.Protein science: http://fold.doe-mbi.ucla.edu/overview 4.Protein design lab: http://www.cmps.lu.se/biostruct/people/ingemar_andre/ Metabolic engineering and synthetic biology

1.http://keaslinglab.lbl.gov/ SMT

1.Xie,XS. http://bernstein.harvard.edu/pages/AboutProfXie.html DNA chemistry

1.http://dna.caltech.edu/DNAresearch_perspective.html 2.https://www2.physics.ox.ac.uk/research/self-assembled-structures-and-devices 3.http://cadnano.org/windows-installation Enzymes

1.http://en.wikipedia.org/wiki/Malic_enzyme 2.http://en.wikipedia.org/wiki/Malate_dehydrogenase 3.http://seemanlab4.chem.nyu.edu/ Online tools 1.Multiple alignment: http://www.ebi.ac.uk/Tools/msa/clustalw2/ 2.Tools:http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1923.html 3.Signal: http://www.cbs.dtu.dk/services/SignalP/ 4.Solubility: http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam#

hottopics : De novo protein design

http://www.jbc.org/content/272/4/2031.full this article discussed some key points that should be taken into account in de novo protein design. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1459523/

Gene Network Modeling

  • Ingeneue by George von Dassow, Eli Meir, Edwin Munro, and Garret Odell at the Center for Cell Dynamics
    • An open-source java program for modeling gene regulatory networks. Users can rapidly build networks by specifying their topology, initial conditions, connectivity, and known parameters. Ingeneue can then search/explore paramter space for desired behavior, simulate the effects of noise and mutation, and generate statistics/time graphs of the system.

Toolbars

[2]

  1. 1.表达蛋白溶解性预测:http://mips.helmholtz-muenchen.de/prosoII/prosoII.seam#
  • Important Journals
  1. Cell: http://www.cell.com
  2. NPG: http://www.nature.com
  3. Science: http://www.sciencemag.org
  4. PNAS: http://www.pnas.org
  5. JBC: http://www.jbc.org
  6. ASM Journals: http://journlas.asm.org
  7. Biology-direct: http://www.biology-direct.com

Other Researcher ID: http://www.researcherid.com/rid/H-3477-2011

Personal tools