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Nanoinformatics Bibliography

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Conference Proceedings

Allarakhia M, Walsh S, Wensley A. 2007. Models of cooperation and knowledge management: The case of biomedical technology management. [presentation] PICMET ’07: Portland International Center for Management of Engineering and Technology Vols. 1 – 6 Proceedings – Management of Converging Technologies: 438 – 447. Conference of the Portland-International Center for for Management of Engineering and Technology (PICMET 2007), Portland OR, August 5 – 9, 2007.

Chau M, Chen H, Qin J, Zhou Y, Qin Y, Sung WK, McDonald D. 2002. Comparison of Two Approaches to Building a Vertical Search Tool: A case study in the nanotechnology domain. Proceedings of the 2nd ACM/IEEE-CS joint conference on Digital Libraries [presentation] . International Conference on Digital Libraries, Portland OR, July 14 – 18, 2002. DOI: 10.1145/544220.544246.

Chiesa S, Garcia-Remesal M; de la Calle G, de la Iglesia D, Bankauskaite V, Maojo V. 2008. Building an Index of Nanomedical Resources: An automatic approach based on text mining. Knowledge-Based Intelligent Information and Engineering Systems, Pt 2, Proceedings 5178: 50-57. [presentation] 12th International Conference on Knowledge-Based Intelligent Information and Engineering Systems, Zagreb Croatia, September 3 – 5, 2008.

de la Iglesia D, Chiesa S, Kern J, Maojo V, Martin-Sanchez F, Potamias G, Moustakis V, Mitchell JA. 2009. Nanoinformatics: New challenges for biomedical informatics at the nano level . Medical Informatics in a United and Healthy Europe - Proceedings of MIE 2009 – The XXIInd International Congress of the European Federation for Medical Informatics, Vol 150: 987 – 991. [presentation] The XXIInd International Congress of the European Federation for Medical Informatics, Sarajevo, August 30 – September 2, 2009. DOI: 10.3233/978-1-60750-044-5-987.

Harper S. 2010. Resource Identification: Forming the Future Interoperable, Federated System [unpublished] Prepared for the caBIG Nanotechnology Working Group Face-to-Face Meeting, February 3, 2010.

Hey, Tony. 2010. The Fourth Paradigm. [plenary] 31st Annual IATUL Conference, West Lafayette, IN, June 20 – 24, 2010.

Lyons, KW. 2007. Integration, Interoperability, and Information Management: What are the key issues for nanomanufacturing? Proceedings of SPIE Vol. 6648: 66480D [presentation]. SPIE Optics and Photonics, August 29, 2007. DOI:10.1117/12.735615.

Martin-Sanchez F, Lopez-Alonso V, Hermosilla-Gimeo I, Lopez-Campos G. 2008. A primer in knowledge management for nanoinformatics in medicine. Knowledge-Based Intelligent Information and Engineering Systems, Pt 2, Proceedings 5178: 66-72. [presentation] 12th International conference on Knowledge-Based Intelligent Information and Engineering Systems, Zagreb Croatia, September 3 – 5 2008.

Molnar LK. 2007. Nanobioinformatics: The enabling technology of personalized medicine. Proceedings of the 7th IEEE International symposium on Bioinformatics and Bioengineering, Vols. 1 – 11: 11. [presentation] 7th IEEE International Conference on Bioinformatics and Bioengineering, Boston MA, October 14 – 17, 2007.

Nelson B, Friedman D, Geisz J, Albin D, Benner J, and Wang Q. 2003. To data management and beyond….for photovoltaic applications. Materials Research Society Symposium Proceedings, Vol 804: 295 – 300. [presentation] Combinatorial and Artificial Intelligence Methods in Materials Science II, Boston MA, December 1 – 4, 2003.

Nowak S. 2003. Technical Nanosystems Based on the Biological Solutions. Third IEEE Conference on Nanotechnology Proceedings Vol II: 195 – 198. [presentation] Third IEEE Conference on Nanotechnology, San Francisco CA, August 12 – 14, 2003. DOI: 10.1109/NANO.2003.1231749.

Paik DS. 2007. Toward a Nanobioinformatics Infrastructure for Nanotechnology-based Prostate Cancer Therapeutic Response Tracking. Proceedings of the 7th IEEE International Symposium on Bioinformatics and biogengineering, Vols. 1 and 11: 486. [presentation] 7th IEEE International Conference on Bioinformatics and Bioengineering, Boston MA, October 14 – 17, 2007. Postek MT and Lyons K. 2007. Instrumentation, Metrology, and Standards: Key elements for the future of nanomanufacturing. Proceeding of SPIE Vol. 6648: 664802 [presentation]. SPIE Optics and Photonics, August 29, 2007. DOI: 10.1117/12.730855.

Reznik-Zellen R, Stevens B, Thorn M, Morse J, Smucker MD, Allan J, Mimno D, McCallum A, and Tuominen MT. 2008. InterNano: e-Science for the nanomanufacturing community. [poster] eScience, pp.382-383, 2008 Fourth IEEE International Conference on eScience, Indianapolis IN, December 7 – 12, 2008. DOI: 10.1109/eScience.2008.142.

Ruping K, Sherman BW. 2004. Nanoinformatics: Emerging computational tools in nano-scale research. NSTI NanoTech 2004 Vol 3 Technical Proceedings: 525-528. [presentation]. Nanotechnology Conference and Trade Show (Nanotech 2004), Boston MA, March 7 – 11, 2004.

Stokes TH, Phan J, Quo CF, Nie SM, Wang MD. 2006. Bio-nano-informatics: An integrated information management system for personalized oncology. 2006 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Vols 1 – 15: 6425-6428. [presentation] 28th Annual International Conference of the IEEE-Engineering-in-Medicine-and-Biology-Society, New York NY, August 30 – September 3, 2006. DOI: 10.1109/IEMBS.2006.259752.

Stukowski M, Suh C, Rajan K, Tall PD, Beye AC, Ramirez AG, Soboyejo WO, Benson ML Liaw PK. 2006. Informatics for Combinatorial Experiments: Accelerating data interpretation. Combinatorial Methods and Informatics in Materials Science 894: 301-306. [presentation] Symposium on Combinatorial Methods and Informatics in Materials Science held at 2005 MRS Fall Meeting, Boston MA, November 28 – December 1, 2005.

Thomas DG, Pappu RV, Baker NA. 2009. NPO: Ontology for cancer nanotechnology research. Available from Nature Precedings . DOI: 10.1038/npre.2009.3514.1.

Thomas DG, Pappu RV, Baker NA. 2009. Ontologies for Cancer Nanotechnology Research. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Society: Engineering the Future of Biomedicine, EMBC 2009, 4158-4161. [presentation] 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, Minneapolis MN, September 2 – 6, 2009.

Articles

Aourag H, Saidi F, Broderick S, Rajan K. 2009. Designing Superlattices Ultra Hard Coatings: Datamining Approach. Journal of Computational and Theoretical Nanoscience 6(4): 828-833. DOI: 10.1166/jctn.2009.1114.

Balachandran PV, Broderick SR, and Rajan K. 2011. Identifying the “inorganic gene” for high temperature piezoelectric perovksites through statistical learning. Proceedings of the Royal Society A (in press)

Bowman DM, Ludlow K. 2009. Filling the Information Void: Using public registries as a tool in nanotechnologies regulation. Bioethical Inquiry 6: 25-36. DOI: 10.1007/s11673-009-9134-9.

Chau M, Huang Z, Qin J, Zhou Y, Chen H. 2006. Building a scientific knowledge web portal: The NanoPort Experience. Decision Support Systems 42: 1216-1238. DOI: 10.1016/j.dsss.2006.01.004.

Davidson and Friere. 2008. Provenance and Scientific Workflows: Challenges and Opportunities. Proceedings of the 2008 ACM SIGMOD International Conference on Management of Data. DOI: 10.1145/1376616.1376772.

De la Iglesia D, Maojo V, Chiesa S, Martin-Sanchez F, Kern J, Potamias G, Crespo J, Garcia-Remesal M, Keuchkerian S, Kulikowski C, Mitchell JA. 2011. International efforts in nanoinformatics research applied to nanomedicine. Methods Inf Med. 50(1):84-95.

Ellenbecker M, and Tsai SJ. 2008. Interim Best Practices for Working with Nanoparticles [documentation]. Center for High-rate Nanomanufacturing. (Unpublished) Available from: http://eprints.internano.org/34/

Gil Y, Deelman E, Ellisman M, Fahringer T, Fox G, Gannon D, Goble C, Livny M, Moreau L, Myers J. 2007. Examining the Challenges of Scientific Workflows. Computer 40(12): 24-32 DOI: 10.1109/MC.2007.421.

Gold A. 2007. Cyberinfrastructure, Data, and Libraries Pt. 1. D-Lib Magazine 13 9/10. DOI: 10.1045/september20september-gold-pt1.

Klimeck G, McLennan M, Brophy SP, Adams GB, Lundstrom MS. 2008. nanoHUB.org: Advancing Education and Research in Nanotechnology. Computing in Science and Engineering 10(5): 17-23. DOI: 10.1109/MCSE.2008.120.

Kulinowski, K. M. and Jaffe MP. 2009. "The GoodNanoGuide: A novel approach for developing good practices for handling engineered nanomaterials in an occupational setting." Nanotechnology Law & Business 6(1): 37-44.

Li X, Petersen L, Broderick S, Narasimhan B, and Rajan K. 2011. Identifying Factors Controlling Protein Release from Combinatorial Biomaterial Libraries via Hybrid Data Mining Methods; ACS Combinatorial Sciences 13: 50-58

Maojo V, Martin-Sanchez F, Kulikowski C, Rodriguez-Patron A, Fritts M. 2010. Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine. Pediatric Research 67(5): 481-489. McKinney BA. 2009. Informatics approaches for identifying biologic relationships in time-series data. Wiley Interdisciplinary Reviews—Nanomedicine and Nanobiotechnology 1(1):60-68. DOI: 10.1002/wnan.012.

Miller AL, Hoover MD, Mitchell DM, Stapleton BP. 2007. The Nanoparticle Information Library (NIL): A Prototype for Linking and Sharing Emerging Data. Journal of Occupational and Environmental Hygiene 4(12): D131-D134, 2007.

Ostrowski AD., Martin T, et al. 2009. "Nanotoxicology: characterizing the scientific literature, 2000-2007." Journal of Nanoparticle Research 11(2): 251-257.

Porter AL, Youtie J, Shapira P, Shoeneck DJ. 2008. Refining search terms for nanotechnology. Journal of Nanoparticle Research 10(5): 715 – 728. DOI: 10.1007/s11051-007-9266-y.

Porter, AL, Youtie J. 2009. How interdisciplinary is nanotechnology? Journal of Nanoparticle Research 11: 1023-1041. DOI: 10.1007/s11051-009-9607-0.

Rafols I. 2007. Strategies for Knowledge Acquisition in Bionanotechnology: Why are interdisciplinary practices less widespread than expected? Innovation 20(4): 395-412. DOI: 10.1080/13511610701760770.

Schulte P, Geraci C, Zumwalde R, Hoover M, Castranova V, Kuempel V, Murashov V, Vainio H, and Savolainen K. 2018. Sharpening the focus on occupational safety and health of nanotechnology. Scandinavian Journal of Work, Environment & Health 34(6): 471-478. Available from: http://www.sjweh.fi/show_abstract.php?abstract_id=1292

Whitling, JM, Spreitzer G, Wright DW. 2000. Combinatorial and informatics approach to CdS nanoclusters. Advanced Materials 12(18): 1377-1380. DOI: <1377::AID-ADMA1377>3.0.CO;2-X 10.1002/1521-4095(200009)12:18<1377::AID-ADMA1377>3.0.CO;2-X.

Wilkins-Diehr N, Gannon D, Klimeck G, Oster S, Pamidighantam S. 2008. TeraGrid Science Gateways and Their Impact on Science. Computer 41(11): 32-41. DOI: 10.1109/MC.2008.470.

Books and Book Chapters

Hey T, Tansley S, and Tolle K eds. 2009. The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research. 284 pp. Available from: http://research.microsoft.com/en-us/collaboration/fourthparadigm/

Hofmann DWM and Kuleshova LN (eds). 2010. Data Mining and Inorganic Crystallography in Data Mining in Crystallography ; Series: Structure and Bonding , Vol. 134 pp.59-89; Springer-Verlag.

C. Kamath C, Wade N, Karypis G, Pandey G, Kumar V, Rajan K, Samatova NF, Breimyer P, Kora G, Pan C, and Yoginath S. 2009. Scientific Data Analysis in Scientific Data Management. Shoshani A and Rotem D (eds). Taylor and Francis pp.263-301.

Walsh S and Medley T. 2008. A Framework for Responsible Nanotechnology [chapter 18]. Fisher E, et al. (eds.). The Yearbook of Nanotechnology in Society, Vol. 1. Springer Science+Business Media B.V. 2008. pp. 207-213. DOI: 10.1007/978-1-4020-8416-4_18.

Rajan K. 2008. Combinatorial Materials Sciences: Experimental Strategies for Accelerated Knowledge Discovery; Annual Reviews of Materials Research 38: 299-322. DOI: 10.1146/annurev.matsci.38.060407.130217.

Whitepapers

Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG. 2009. Nanotechnology Informatics White Paper. Prepared for the National Cancer Institute by the caBIG® Integrative Cancer Research Nanotechnology Working Group.

Baker NA, Fritts M, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG. 2009. Ontologies in Cancer Nanotechnology Research. Prepared for the National Cancer Institute by the caBIG Integrative Cancer Research Nanotechnology Working Group.

Baker NA, Freund ET, Gaheen S, Guccione S, Paik DS, Pappu RV, Patri A, Rubin D, Shaw SY, Thomas DG. 2009. The Need for Minimum Information Standards for Development and Advancement of Nanomaterials as Cancer Diagnostics and Therapeutics. Prepared for the National Cancer Institute by the caBIG Integrative Cancer Research Nanotechnology Working Group.

IRGC White Paper on Nanotechnology Risk Governance (2006). Available from: http://www.irgc.org/IMG/pdf/IRGC_white_paper_2_PDF_final_version-2.pdf

Maojo V, Martín-Sánchez F et al. The ACTION-Grid White Paper on Nanoinformatics (2010). Available from: http://www.action-grid.eu/index.php?url=whitepapernano.

Relevant Reports

Atkins D, et. al. 2003. Revolutionizing Science and Engineering through Cyberinfrastructure. Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure. 84 pp. Available from: http://www.nsf.gov/cise/sci/reports/atkins.pdf

Berman F, Berman J, Pancake C, and Wu L. 2006. A Process –Oriented Approach to Engineering Cyberinfrastructure. Report from the Engineering Advisory Committee Subcommittee on Cyberinfrastructure. 21 pp. Available from: http://director.sdsc.edu/pubs/ENG/report/EAC_CI_Report-FINAL.pdf

Committee on Integrated Computational Materials Engineering, National Research Council. 2008. Integrated Computational Materials Engineering: A Transformational Discipline for Improved Competitiveness and National Security. 152 pp. Available from: http://www.nap.edu/catalog.php?record_id=12199

Committee on Science, Engineering, and Public Policy (COSEPUP). 2007. Rising Above the Gathering Storm: Energizing and Employing America for a Brighter Economic Future. National Academies Press, Washington D.C. 592pp. Available from: http://www.nap.edu/catalog.php?record_id=11463#toc

Committee on Science, Engineering, and Public Policy (COSEPUP). 2009. Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age. National Academies Press, Washington D.C. 180 pp. Available from: http://www.nap.edu/catalog.php?record_id=12615

Davis, J. 2006. Cyberinfrastructure in Chemical and Biological Process Systems: Impact and Directions. NSF Cyberinfrastructure Workshop Report. 268 pp. Available from: http://www.oit.ucla.edu/nsfci/NSFCIFullReport.pdf

Deelman E and Gil Y. 2006. Workshop on the Challenges of Scientific Workflows. Report from Workshop on the Challenges of Scientific Workflows: May 1-2, 2006. 22 pp. Available from: https://confluence.pegasus.isi.edu/download/attachments/2031787/NSFWorkflow-Final.pdf?version=1&modificationDate=1254437518000.

DOE Office of Scientific and Technical Information. 2004. The State of Data Management in the DOE Research and Development Complex. Report of the Meeting DOE Data Centers: Preparing for the Future, July 14 – 15, 2004. Available from: http://www.osti.gov/publications/2007/datameetingreport.pdf.

Friedlander A, and Adler P. 2006. To Stand the Test of Time: Long-term Stewardship of Digital Data Sets in Science and Engineering. A report to the National Science Foundation from the ARL Workshop on New Collaborative Relationships: The Role of Academic Libraries in the Digital Data Universe September 26 – 27, 2006. 159 pp. Available from: http://www.arl.org/bm~doc/digdatarpt.pdf

Interagency Working Group on Digital Data. 2009. Harnessing the Power of Digital Data for Science and Society. Report to the committee on Science of the National Science and Technology council. 24pp. Available from : http://www.nitrd.gov/about/harnessing_power_web.pdf

IRGC White Paper on Nanotechnology Risk Governance (2006).

Lyon, L. 2007. Dealing with Data: Roles, Rights, Responsibilities and Relationships. JISC Consultancy Report. 65pp. Available from: http://www.jisc.ac.uk/media/documents/programmes/digitalrepositories/dealing_with_data_report-final.pdf

Lyon L. 2009. Open Science at Web-Scale: Optimizing Participation and Predictive Potential. JISC Consultative Report. 45 pp. Available from: http://www.jisc.ac.uk/publications/reports/2009/opensciencerpt.aspx

National Science Foundation Cyberinfrastructure Council. 2007. Cyberinfrastructure Vision for 21st Century Discovery. 64 pp. Available from: http://www.nsf.gov/pubs/2007/nsf0728/index.jsp

NIOSH [2009]. Approaches to safe nanotechnology: managing the health and safety concerns with engineered nanomaterials. Cincinnati, OH: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, DHHS (NIOSH) Publication No. 2009-125.

NIOSH [2010a]. Progress toward safe nanotechnology in the workplace: A report from the NIOSH Nanotechnology Research Center. Cincinnati, OH: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, DHHS (NIOSH) Publication No. 2010-104.

NIOSH [2010b]. Strategic plan for NIOSH nanotechnology research and guidance: Filling the knowledge gaps. Cincinnati, OH: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, DHHS (NIOSH) Publication No. 2010-105.

Novotny MA, Ceperly D, Jayanthi CS, and Martin RM. 2004. Materials Research Cyberscience Enabled by Cyberinfrastructure. Report from The National Science Foundation (NSF) Computational Materials Science Review: June 17—19, 2004. 42pp. Available from: http://www.nsf.gov/mps/dmr/csci.pdf

OECD Environment Directorate. 2008. Working Party on Manufactured Nanomaterials: List of Manufactured Nanomaterials and List of Endpoints for Phase One of the OECD Testing Programme. Series on the Safety of Manufactured Nanomaterials, Number 6.

Steering Committee on the Role of Scientific and Technical Data and Information in the Public Domain. 2003. The Role of Scientific and Technical Data and Information in the Public Domain: Proceeding of a Symposium. 238 pp. Available from: http://www.nap.edu/catalog.php?record_id=10785

Reade, C, et. al. 2011. Nanomaterials Society Technical Discussion Group (Approx. 1,500 global members) within Linkedin. Available from: http://www.linkedin.com/groups?gid=1875083&mostPopular=&trk=tyah

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