Citation Network Main Path Identification Based on Associated Attributes of Articles: Case Study from Synthetic Biology
Wei Ling1,2,3, Liu Chunjiang2, Xu Haiyun2, Fang Shu2
1. School of Information and Management, Shanxi University of Finance and Economics, Taiyuan 030006; 2. Chengdu Documentation and Information Center, Chinese Academy of Sciences, Chengdu 610041; 3. University of Chinese Academy of Sciences, Beijing 100049
隗玲, 刘春江, 许海云, 方曙. 基于文献关联属性的引文网络主路径识别——以合成生物学领域为例[J]. 情报学报, 2018, 37(4): 351-361.
Wei Ling, Liu Chunjiang, Xu Haiyun, Fang Shu. Citation Network Main Path Identification Based on Associated Attributes of Articles: Case Study from Synthetic Biology. 情报学报, 2018, 37(4): 351-361.
[1] Hummon N P, Doreian P.Connectivity in a citation network: The development of DNA theory[J]. Social Networks, 1989, 11(1): 39-63. [2] Hummon N P, Doreian P.Computational methods for social network analysis[J]. Social Networks, 1990, 12(4): 273-288. [3] Lu L Y, Liu J S.A survey of intellectual property rights literature from 1971 to 2012: the main path analysis. Management of Engineering & Technology (PICMET)[C]// Proceedings of 2014 Portland International Conference on IEEE, 2014: 1274-1280. [4] Liu J S, Lu L Y Y, Lu W M. Research fronts in data envelopment analysis[J]. Omega, 2016, 58: 33-45. [5] Chuang T C, Liu J S, Lu L Y Y, et al. The main paths of eTourism: trends of managing tourism through Internet[J]. Asia Pacific Journal of Tourism Research, 2017, 22(2): 213-231. [6] Hung S C, Liu J S, Lu L Y Y, et al. Technological change in lithium iron phosphate battery: the key-route main path analysis[J]. Scientometrics, 2014, 100(1): 97-120. [7] Yuan F, Miyazaki K.Understanding the dynamic nature of technological change using trajectory identification based on patent citation network in the Electric Vehicles industry[C]// Proceedings of 2014 Portland International Conference on Management of Engineering and Technology. IEEE, 2014: 2780-2790. [8] Verspagen B.Mapping technological trajectories as patent citation networks: A study on the history of fuel cell research[J]. Advances in Complex Systems, 2007, 10(1): 93-115. [9] Liu J S, Lu L Y.An integrated approach for main path analysis: The development of the Hirsch index as an example[J]. Journal of the American Society for Information Science and Technology, 2012, 63(3): 528-542. [10] Bekkers R, Martinelli A.Knowledge positions in high-tech markets: Trajectories, standards, strategies and true innovators[J]. Technological Forecasting and Social Change, 2012, 79(7): 1192-1216. [11] 隗玲, 方曙. 引文网络主路径研究进展评述及展望[J]. 情报理论与实践, 2016, 39(9): 128-133. [12] 祝清松. 语义增强的引文分析方法与应用实验研究[D]. 北京: 中国科学院文献情报中心, 2014. [13] 陈亮, 杨冠灿, 张静, 等. 面向技术演化分析的多主路径方法研究[J]. 图书情报工作, 2015, 59(10): 124-130, 115. [14] Batagelj V. Efficient algorithms for citation network analysis [EB/OL]. [2017-04-20]. http://www.researchgate.net/publication/ 1956732. [15] Sun Y Z, Han J W, Yan X F, et al.PathSim: Meta path-based top-k similarity search in heterogeneous information networks[J]. Proceedings of the VLDB Endowment, 2011, 4(11): 992-1003. [16] Wouter D N, Andrey M, Vladimir B.蜘蛛: 社会网络分析技术[M]. 林枫, 译. 北京: 世界图书出版公司, 2014. [17] Hobom B.Surgery of gene: At the doorstep of synthetic biology[J]. Medizin Klinik, 1980, 75: 14-21. [18] Hendrickson C L, Devine K G, Benner S A.Probing minor groove recognition contacts by DNA polymerases and reverse transcriptases using 3-deaza-2°-deoxyadenosine[J]. Nucleic Acids Research, 2004, 32(7): 2241-2250. [19] Benner S A.Understanding nucleic acids using synthetic chemistry[J]. Cheminform, 2004, 36(2): 784-797. [20] Sismour A M, Lutz S, Park J H, et al.PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency Virus-1[J]. Nucleic Acids Research, 2004, 32(2): 728-735. [21] Ball P.Synthetic biology: starting from scratch[J]. Nature, 2004, 431: 624-626. [22] Benner S A, Sismour A M.Synthetic biology[J]. Nature Reviews Genetics, 2005, 6: 533-543. [23] Sismour A M, Benner S A.The use of thymidine analogs to improve the replication of an extra DNA base pair: a synthetic biological system[J]. Nucleic Acids Research, 2005, 33(17): 5640-5646. [24] Sismour A M, Benner S A.Synthetic biology[J]. Expert Opinion on Boilogical Therapy, 2005, 5(11): 1409-1414. [25] Chin J W.Programming and engineering biological networks[J]. Current Opinion in Structural Biology, 2006, 16(4): 551-556. [26] Drubin A, Way J C, Silver P A.Designing biological systems[J]. Genes & Development, 2007, 21(3): 242-254. [27] Filipovska A, Rackham O.Building a parallel metabolism within the cell[J]. ACS Chemical Biology, 2008, 3(1): 51-63. [28] Purnick P E, Weiss R.The second wave of synthetic biology: from modules to systems[J]. Nature Reviews Molecular Cell Biology, 2009, 10(6): 410. [29] Carr P A, Church G M.Genome engineering[J]. Nature Biotechnology, 2009, 27(12): 1151-1162. [30] Lu T K, Collins J J.Engineering synthetic bacteriophage to combat antibiotic-resistant bacteria[C]// Proceedings of 2009 IEEE 35th Annual Northeast Bioengineering Conference. IEEE, 2009, 104: 1-2. [31] Callura J M, Collins J J.Tracking, tuning, and terminating microbial physiology using synthetic riboregulators[J]. Proceedings of the National Academy of Sciences, 2010, 107(36): 898-903. [32] Khalil A S, Collins J J.Synthetic biology: applications come of age[J]. Nature Reviews Genetics, 2010, 11: 367-379. [33] Nissim L, Bar-Ziv R H. A tunable dual-promoter integrator for targeting of cancer cells[J]. Molecular Systems Biology, 2010, 6: 444. [34] Ajo-Franklin C M, Drubin D A, Eskin J A, et al. Rational design of memory in eukaryotic cells[J]. Genes & Development, 2007, 21(18): 2271-2276. [35] Anderson J C, Voigt C A, Arkin A P.Environmental signal integration by a modular and gate[J]. Molecular Systems Biology, 2007, 3(1): 133. [36] Czar M J, Cai Y, Peccoud J.Writing DNA with GenoCAD™[J]. Nucleic Acids Research, 2009, 37(Web Server issue): W40-W47. [37] Serrano L. Synthetic biology: promises and challenges[J]. Molecular Systems Boilogy, 2007, 3: Article No. 158. [38] Peccoud J, Blauvelt M F, Cai Y, et al.Targeted development of registries of biological parts[J]. PLoS ONE, 2008, 3(7): e2671. [39] Burbelo P D, Ching K H, Han B L, et al.Synthetic biology for translational research[J]. American Journal of Translational Research, 2010, 2(4): 381. [40] Weber W, Fussenegger M.Synthetic gene networks in mammalian cells[J]. Current Opinion in Biotechnology, 2010, 21(5): 690-696. [41] Rodríguez-Martínez J A, Peterson-Kaufman K J, Ansari A Z. Small-molecule regulators that mimic transcription factors[J]. Biochimica et Biophysica Acta, 2010, 1799(10-12): 768-774. [42] Ghim C M, Lee S K, Takayama S, et al.The art of reporter proteins in science: past, present and future applications[J]. BMB Reports, 2010, 43(7): 451. [43] Zhou X C, Cai S Y, Hong A L, et al.Microfluidic picoarray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences[J]. Nucleic Acids Research, 2004, 32(18): 5409-5417. [44] Tian J D, Gong H, Sheng N J, et al.Accurate multiplex gene synthesis from programmable DNA microchips[J]. Nature, 2005, 432(7020): 1050-1054. [45] McDaniel R, Weiss R. Advances in synthetic biology: on the path from prototypes to applications[J]. Current Opinion in Biotechnology, 2005, 16(4): 476-483. [46] Sprinzak D, Elowitz M B.Reconstruction of genetic circuits[J]. Nature, 2005, 438: 443-448. [47] Isaacs F J, Dwyer D J, Collins J J.RNA synthetic biology[J]. Nature Biotechnology, 2006, 24(5): 545-554. [48] Savage D F, Way J, Silver P A.Defossiling fuel: how synthetic biology can transform biofuel production[J]. ACS Chemical Biology, 2008, 3(1): 13-16. [49] Beisel C L, Bayer T S, Hoff K G, et al.Model-guided design of ligand-regulated RNAi for programmable control of gene expression[J]. Molecular Systems Biology, 2008, 4(1): 224. [50] Lucks J B, Qi L, Whitaker W R, et al.Toward scalable parts families for predictable design of biological circuits[J]. Current Opinion in Microbiology, 2008, 11: 567-573. [51] Gulati S, Rouilly V, Niu X, el al. Opportunities for microfluidic technologies in synthetic biology[J]. Journal of the Royal Society Interface, 2009, 6(Suppl 4): S493-S506. [52] Basu S, Mehreja R, Thiberge S, et al.Spatiotemporal control of gene expression with pulse-generating networks.[J] Proceedings of the National Academy of Sciences of the United States of America, 2004, 101: 6355-6360. [53] Ferber D.Synthetic biology: Microbes made to order[J]. Science, 2004, 303(5655): 158-161. [54] Win M N, Smolke C D.A modular and extensible RNA-based gene-regulatory platform for engineering cellular function[J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(36): 14283-14288. [55] Lee S K, Chou H, Ham T S, et al.Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels[J]. Current Opinion in Biotechnology, 2008, 19(6): 556. [56] Ellis T, Wang X, Collins J J.Diversity-based, model-guided construction of synthetic gene networks with predicted functions[J]. Nature Biotechnology, 2009, 27(5): 465. [57] Mukherji S, Oudenaarden A V.Synthetic biology: understanding biological design from synthetic circuits[J]. Nature Reviews Genetics, 2009, 10: 859-871. [58] Tanouchi Y, Pai A, You L.Decoding biological principles using gene circuits[J]. Molecular Biosystems, 2009, 5(7): 695-703. [59] Kramer B P, Fussenegger M.Hysteresis in a synthetic mammalian gene network[J]. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102(27): 9517-9522. [60] Kramer B P, Fischer M, Fussenegger M.Semi-synthetic mammalian gene regulatory networks[J]. Metabolic Engineering, 2005, 7(4): 241. [61] Weber W, Kramer B P, Fussenegger M.A genetic time-delay circuitry in mammalian cells[J]. Biotechnology & Bioengineering, 2007, 98(4): 894-902. [62] Weber W, Stelling J, Rimann M, et al.A synthetic time-delay circuit in mammalian cells and mice[J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(8): 2643-2648. [63] Greber D, Fussenegger M.Mammalian synthetic biology: engineering of sophisticated gene networks[J]. Journal of Biotechnology, 2007, 130(4): 329-345. [64] Weber W, Daoud-El B M, Fussenegger M. Synthetic ecosystems based on airborne inter- and intrakingdom communication[J]. Proceedings of the National Academy of Sciences of the United States of America, 2007, 104(25): 10435-10440. [65] Andrianantoandro E, Basu S, Karig D K, et al.Synthetic biology: new engineering rules for an emerging discipline[J]. Molecular Systems Biology, 2006, 2: Article No. 2006.0028. [66] Anderson J C, Clarke E J, Arkin A P, et al.Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria[J]. Journal of Molecular Biology, 2006, 355(4): 619-627. [67] Silva-Rocha R, De L V.Noise and robustness in prokaryotic regulatory networks[J]. Annual Review of Microbiology, 2010, 64(1): 257-275. [68] de las Heras A, Carreño C A, Martínez-García E, et al. Engineering input/output nodes in prokaryotic regulatory circuits[J]. FEMS Microbiology Reviews, 2010, 34(5): 842-865. [69] Agapakis C M, Silver P A.Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks[J]. Molecular Biosystems, 2009, 5(7): 704-713. [70] Fernández-Tresguerres M E, de la Espina S M D, Gasset-Rosa F, et al. A DNA-promoted amyloid proteinopathy in Escherichia coli[J]. Molecular Microbiology, 2010, 77(6): 1456-1469. [71] Giraldo R.Amyloid assemblies: protein legos at a crossroads in bottom-up synthetic biology[J]. Chembiochem, 2010, 11(17): 2347-2357. [72] Lorenzo V D, Danchin A.Synthetic biology: discovering new worlds and new words[J]. EMBO Reports, 2008, 9: 822-827. [73] de Lorenzo V. Synthetic biology: something old, something new…[J]. BioEssays, 2010, 32: 267-270. [74] Danchin A.Bacteria as computers making computers[J]. FEMS Microbiology Reviews, 2009, 33(1): 3-26. [75] Danchin A.Myopic selection of novel information drives evolution[J]. Current Opinion in Biotechnology, 2009, 20(4): 504-508.
