• P Lambrix, A Edberg. Evaluation of ontology merging tools in bioinformatics. Proceedings of the Pacific Symposium on Biocomputing-PSB03, 2003. Available free online

• MJ Rytkonen. Not all maps are equal: GIS and spatial analysis in epidemiology. Int J Circumpolar Health. 2004 Mar;63(1):9-24. Available online.

• Pietrobon R, Shah A, Kuo P, Harker M, McCready M, Butler C, Martins H, Moorman CT, Jacobs DO. Duke Surgery Research Central: an open-source Web application for the improvement of compliance with research regulation. BMC Med Inform Decis Mak. 2006 Jul 27;6:32. PMID: 16872540. Available online

• Saraiya, P.; North, C.; Duca, K. An insight-based methodology for evaluating bioinformatics visualizations. IEEE Transactions on Visualization and Computer Graphics, 11(4):443-456, July-Aug. 2005. Available online

• Pratt, W. Unruh, K., Civan, A. and Skeels, M.M. (2006). Personal health information management. Communications of the ACM 49(1): 51-55. Available online.

• B. de Bruijn, J. Martin. Getting to the (c)ore of knowledge: mining biomedical literature. International Journal of Medical Informatics, Volume 67, Issue 1-3, Pages 7-18. Available online

• David W Kane, Moses M Hohman, Ethan G Cerami, Michael W McCormick, Karl F Kuhlmman and Jeff A Byrd. Agile methods in biomedical software development: a multi-site experience report. BMC Bioinformatics 2006, 7:273 (May 2006). Available online

• Samaan G, Patel M, Olowokure B, Roces MC, Oshitani H; World Health Organization Outbreak Response Team. Rumor surveillance and avian influenza H5N1.Emerg Infect Dis. 2005 Mar;11(3):463-6. PMID: 15757567. Available free online
• Eysenbach G. SARS and population health technology. J Med Internet Res. 2003 Apr-Jun;5(2):e14. PMID: 12857670. Available free online
• Larkin, Marilynn. Blogs: new way to communicate about infectious diseases, The Lancet Infectious Diseases, Volume 5, Issue 12, , December 2005, Page 748. Available online.

• Nicholas R Anderson, Peter Tarczy-Hornoch, Roger E Bumgarner. On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics 2006, 7:260 Available free online

• Allen, James, et al. Chester: Towards a personal medication advisor. Journal of Biomedical Informatics (Corrected Proof, available online 3 March 2006). Available online.

• Edberg SC. Global Infectious Diseases and Epidemiology Network (GIDEON): a world wide Web-based program for diagnosis and informatics in infectious diseases. Clinical Infectious Diseases 2005 Jan 1;40(1):123-126. PMID: 15614701. Available online.
• Berger SA. GIDEON: a comprehensive Web-based resource for geographic medicine. Int'l Journal of Health Geographics 2005 Apr 22;4(1):10. PMID: 15847698. Available online.

• Tsui FC, Espino JU, Dato VM, Gesteland PH, Hutman J, Wagner MM. Technical description of RODS: a real-time public health surveillance system. J. American Medical Informatics Assoc. 2003 Sep-Oct;10(5):399-408. PMID: 12807803. Available free online.
• Espino et al. Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project. MMWR Morb Mortal Wkly Rep. 2004 Sep 24;53 Suppl:32-9. PMID: 15714624. Available free online.
• Gesteland PH, Gardner RM, Tsui FC, Espino JU, Rolfs RT, James BC, Chapman WW, Moore AW, Wagner MM. Automated syndromic surveillance for the 2002 Winter Olympics. J. American Medical Informatics Assoc. 2003 Nov-Dec;10(6):547-54. PMID: 12925547. Available free online.

• Brillman JC, Burr T, Forslund D, Joyce E, Picard R, Umland E. Modeling emergency department visit patterns for infectious disease complaints: results and application to disease surveillance. BMC Medical Informatics and Decision Making 2005 Mar 2;5(1):4. PMID: 15743535. Available free online.

• Beuscart-Zephir MC, Anceaux F, Crinquette V, Renard JM. Integrating users' activity modeling in the design and assessment of hospital electronic patient records: the example of anesthesia. Int J Med Inform. 2001 Dec;64(2-3):157-71. PMID: 11734383. Available online.

• Johnson, C. & Turley J. (2006). The significance of cognitive modeling in building healthcare interfaces. International Journal of Medical Informatics, Volume 75, Issue 2, Pages 163-172. PMID: 16085454. Available online.

• King OD, Foulger RE, Dwight SS, White JV, Roth FP. Predicting gene function from patterns of annotation. Genome Research 2003 May;13(5):896-904. PMID: 12695322. Available free online.

• Malin, Bradley and Latanya Sweeney. How (not) to protect genomic data privacy in a distributed network: using trail re-identification to evaluate and design anonymity protection systems. Journal of Biomedical Informatics 37(3), June 2004, Pp. 179-192. PMID: 15196482. Available online.

• Becker, S. A. 2004. A study of web usability for older adults seeking online health resources. ACM Trans. Comput.-Hum. Interact. 11, 4 (Dec. 2004), 387-406. Available online.

• Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003 19: 1275-1283. PMID: 12835272. Available online.

• Brad Hemminger will discuss preliminary results of an ongoing study of biomedical scientists' information seeking behavior. There is no journal article, but attendees should look at the slides and survey instrument linked above.

• Hastings S, Oster S, Langella S, Kurc TM, Pan T, Catalyurek UV, Saltz JH. A grid-based image archival and analysis system. J Am Med Inform Assoc. 2005 May-Jun;12(3):286-95. PMID: 15684129. Available online.

• Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. In Proceedings of the 2005 American Medical Informatics Association (AMIA) Annual Symposium, 46-50. Available online - use Onyen & password to access.

• Hulse NC, Rocha RA, Del Fiol G, Bradshaw RL, Hanna TP, Roemer LK. KAT: A flexible XML-based knowledge authoring environment. J Am Med Inform Assoc. 2005 Jul-Aug;12(4):418-30. PMID: 15802477. Available online.

• Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 2005; 6 Suppl 1:S17. PMID: 15960829. Available online.

• Leser U. A query language for biological networks. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii33-ii39. PMID: 16204121. Available online

• Dolan ME, Ni L, Camon E, Blake JA. A procedure for assessing GO annotation consistency. Bioinformatics. 2005 Jun 1;21 Suppl 1:i136-i143. PMID: 15961450 Available online

• Rother K, Michalsky E, Leser U. How well are protein structures annotated in secondary databases? Proteins. 2005 Sep 1;60(4):571-6. PMID: 16021624. Available online; see also the Protein Data Bank (PDB) site.

• Wong JW, Cartwright HM. Deterministic projection by growing cell structure networks for visualization of high-dimensionality datasets. J Biomedical Informatics 2005 Aug;38(4):322-30. PMID: 16084474. Available online

• Eppig, J.T., Bult, C.J., Kadin, J.A., Richardson, J.E., Blake, J.A., & the Mouse Genome Database Group. (2005). The Mouse Genome Database (MGD): From genes to mice: A community resource for mouse biology. Nucleic Acids Research 33(1), D471-D47. Available online; see also Jackson Labs' Mouse Genome Informatics site.

• MacMullen, W. John and Denn, Sheila O. (2005). Information problems in molecular biology and bioinformatics. Journal of the American Society for Information Science & Technology 56(5), 447-456. Available online

• Yong-Chuan, T. and Leibel, R.L. (2002) Identifying functional relationships among human genes by systematic analysis of biological literature. Available online

• Rubin DL, Thorn CF, Klein TE, Altman RB. A statistical approach to scanning the biomedical literature for pharmacogenetics knowledge. J Am Med Inform Assoc. 2005 Mar-Apr;12(2):121-9. Available online
• Secondary article (a good framework for exploring the previous paper): Allen D. Roses, Daniel K. Burns, Stephanie Chissoe, Lefkos Middleton and Pamela St. Jean. Disease-specific target selection: a critical first step down the right road. Drug Discovery Today, Volume 10, Issue 3, 1 February 2005, Pages 177-189. Available online

• Marc Weeber, et al. (2003). Generating Hypotheses by Discovering Implicit Associations in the Literature: A Case Report of a Search for New Potential Therapeutic Uses for Thalidomide. Journal of the American Medical Informatics Association 10(3): 252?59. Available online

• Collier N, Takeuchi K. Comparison of character-level and part of speech features for name recognition in biomedical texts. Journal of Biomedical Informatics 2004 Dec;37(6):423-435. PMID: 15542016 Available online

• Baumgartner, C. et al. Supervised machine learning techniques for the classification of metabolic disorders in newborns. Bioinformatics 2004 20: 2985-2996. PMID: 15180934. Available online

• Srinivasan P, Hristovski D. Distilling Conceptual Connections from MeSH Co-Occurrences. MEDINFO 2004; 808-12. Available online (use amia/medinfo as usr/pwd)

• Chen, H., & Sharp, B. M. Content-rich biological network constructed by mining pubmed abstracts. BMC Bioinformatics 5, 147 (October 2004). Available online

• Yeh, A.S., Hirschman, L., & Morgan, A.A. (2003). Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup. Bioinformatics Vol. 19 Suppl. 1, pp. i331-i339. Available online

• Wren JD, et al. (2004). Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics, 20(3):389-398. Available online

• Jenuwine, Elizabeth S. & Floyd, Judith A. Comparison of Medical Subject Headings and text-word searches in MEDLINE to retrieve studies on sleep in healthy individuals. JMLA 2004 July; 92(3): 349-354. Available online

• Gupta, Indrani & Dasgupta, Purnamita. Health-seeking Behavior in Urban Delhi: An Exploratory Study. Journal of Health and Population in Developing Countries, vol 3, no 2. Available online

• Nylenna, Magne; Gjerlow Aasland, Olaf (2000). Primary care physicians and their information-seeking behaviour. Scandinavian Journal of Primary Health Care 18(1), 9-13. Available online

• Case, Donald O.; Johnson, J. David; Andrews, James E.; Allard, Suzanne L.; Kelly, Kimberly M. (2004). From two-step flow to the Internet: The changing array of sources for genetics information seeking. Journal of the American Society for Information Science and Technology, 55(8), 660-669. Available online

• Whitmire, Ethelene (2002). Disciplinary differences and undergraduates' information-seeking behavior. Journal of the American Society for Information Science and Technology 53(8), 631-638. Available online

• Ellis, David; Cox, Deborah; Hall, Katherine. (1993). A comparison of the information seeking patterns of researchers in the physical and social sciences. Journal of Documentation, 49(4), 356-369. Available online, use your Onyen and password to access

• Tenopir, Carol; King, Donald W.; Bush, Amy. (2004). Medical faculty's use of print and electronic journals: changes over time and in comparison with scientists. J Med Libr Assoc. 92(2): 233-241. Available online
• Complete and comment on the 'Information Seeking Behavior of Science Researchers' survey Available online (use Onyen & password to access)

• Bates, Marcia J. (1989). The Design of Browsing and Berrypicking Techniques for the Online Search Interface. Online Review, 13(5): 407-424. Available online

• Wickramasinghe, N., Sharma, S.K. & Reddy, H.P. (2005). Evidence-Based Medicine: A New Approach in the Practice of Medicine. In N. Wickramasinghe, J.N.D. Gupta & S. Sharma (eds.), Creating Knowledge-Based Healthcare Organizations (pp. 125-135), Hershey, PA: Idea Group Publishing. Available online, use your Onyen and password to access

• Owen DJ, Fang ML. (2003). Information-seeking behavior in complementary and alternative medicine (CAM): an online survey of faculty at a health sciences campus. J Med Libr Assoc, 91(3): 311-321. PMCID: 164394 Available online

• Brown, C.M. (1999). Information seeking behavior of scientists in the electronic information age: astronomers, chemists, mathematicians, and physicists [at the University of Oklahoma]. Journal of the American Society for Information Science, 50(10), 929-943. Available online

• Ellis, David (1993). Modeling the information-seeking patterns of academic researchers: A grounded theory approach. Library Quarterly 63(4), 469-486. Available online, use your Onyen and password to access

• MacMullen, W. John and Denn, Sheila O. (to appear). Information problems in molecular biology and bioinformatics. To appear in the forthcoming JASIS&T special issue on bioinformatics. Available online, use your Onyen and password to access

• Buttler, David, et al. (2002). Quering multiple bioinformatics information sources: Can semantic web research help? ACM SIGMOD Record 31(4), 59-64. Available online

• Wilkinson, Mark D. & Links, Matthew (2002). BioMOBY: An open source biological web services proposal. Briefings In Bioinformatics, 3(4),331-341. Available online

• Nikolai Daraselia, et al. (2004). Extracting human protein interactions from MEDLINE using a full-sentence parser. Bioinformatics, 20(5), 604-611; DOI: 10.1093/bioinformatics/btg452 Available online

• Clement J. McDonald, et al. (2003). Open Source software in medical informatics -- why, how and what. International Journal of Medical Informatics, 69(2-3),175-184. Available online

• Stitziel, Tseng, Pervouchine, Goddeau, Kasif, Liang (2003). Structural Location of Disease-associated Single-nucleotide Polymorphisms. JMB 327, 1021-1030

• reading available from presenter

• Nguyen, Huong Q; Virginia Carrieri-Kohlman; Sally H. Rankin; Robert Slaughter; Michael S. Stulbarg. (2004). Internet-based patient education and support interventions: a review of evaluation studies and directions for future research. Computers in Biology and Medicine, 34(2), 92-112. Available online

• Galperin, MY (2004) "The Molecular Biology Database Collection: 2004 Update." Nucelic Acids Research 32 (Database Issue): D3-D22. Available online
• Molecular Biology Database Collection
• NCBI Entrez Global Search Portal
• HealthLinks: University of Washington BioResearcher Toolkit
• Bioinformatics Links Directory

• Li Zhang, Yehoshua Perl, Michael Halper, and James Gellera (in press). Designing metaschemas for the UMLS enriched semantic network. Journal of Biomedical Informatics. Available online

• Tropsha, Alex. (2000). Recent trends in computer-aided drug discovery. Current Opinion in Drug Discovery & Development 3(3):310-313. Available online as an MS-Word document, but requires Onyen + password

• Jakobsen, Ingrid B.; Saleeba, Jennifer A.; Poidinger, Michael; and Littlejohn, Timothy G. (2001). TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases. Bioinformatics 17(6), 535-540. Available online

• Bassett, Jr, Douglas E.; Eisen, Michael B.; & Boguski, Mark S. (1999). Gene expression informatics ?it's all in your mine. Nature Genetics 21, Supplement, 51-55. Available online

• Rocco, Daniel & Critchlow, Terence (2003). Automatic discovery and classification of bioinformatics Web sources. Bioinformatics 19: 1927-1933. Available online

• Harris, Zellig S. (2002). The structure of science information. Journal of Biomedical Informatics, 35, 215-221. Available online

• Banerjee, Sandeepan (2000). A database platform for bioinformatics. In VLDB 2000, Proceedings of 26th International Conference on Very Large Data Bases, 705-710. Available online

• Kwon, Andrew Tae-Jun; Hoos, Holger H.; & Ng, Raymond (2003). Inference of transcriptional regulation relationships with gene expression data. In Proceedings of the 18th ACM Symposium on Applied Computing (SAC 2003). Available online. See also the revised version in Bioinformatics.

• Karp, P.D. (2001). Pathway Databases: A Case Study in Computational Symbolic Theories. Science, 293:2040-2044. Available online

• Alpi, Kristine (2003). Bioinformatics training by librarians and for librarians: Developing the skills needed to support molecular biology and clinical genetics information instruction. Issues in Science and Technology Librarianship. Spring 2003. Available online

• Nenadic, G., Spasic, I., & Ananiadou, S. (2003). Terminology-driven mining of biomedical literature. Bioinformatics 19(8), 938-943. Available online

• Willinsky, John (2003). Scholarly Associations and the Economic Viability of Open Access Publishing. Journal of Digital Information, 4.2. Available online

• Florance, V.; Giuse, N. & Ketchell, D. (2002). Information in context: Integrating information specialists into practice settings. Journal of the Medical Library Association, 90(1), 49-58. Available online

• PubMed Central: An NIH-Operated Site for Electronic Distribution of Life Sciences Research Reports. Available online
  See also: PubMed Central

• Nelson, Stuart J.; Johnston, Douglas, Humphreys, Betsy L. (2001). Relationships in Medical Subject Headings. In Bean, Carol A. & Green, Rebecca (eds). Relationships in the Organization of Knowledge. New York: Kluwer Academic Publishers; 2001. p.171-184. Available online

• Yarfitz, S. and Ketchell, D.S. (2000) A library-based bioinformatics services program. Bulletin of the Medical Library Association, 88(1), 36-48. Available online

• Lagoze, Carl and Van de Sompel, Herbert (2001). "The Open Archives Initiative: Building a low-barrier interoperability framework." Proceedings of the First ACM/IEEE-CS Joint Conference on Digital Libraries. Available online

• Lawrence, Steve, Giles, C. Lee, & Bollacker, Kurt (1999). Digital Libraries and Autonomous Citation Indexing. IEEE Computer, 32(6), 67-71. Available online

• Tomaiuolo, N.G., Packer, J.G. (2000). Preprint servers: Pushing the envelope of electronic scholarly publishing. Searcher 8(9), 53-61. Available online

• Blake, Catherine & Pratt, Wanda (2002). Collaborative information synthesis. In Proceedings of the 65th Annual Meeting of the American Society for Information Science & Technology (ASIS&T), pp. 44-56.
  http://www.ics.uci.edu/~cblake/Papers/BlakeASISTFinal.pdf
• Poster version of the project: http://www.ics.uci.edu/~cblake/Papers/AMIAFinal2.ppt

• Simon Buckingham Shum, Victoria Uren, Gangmin Li, John Domingue, Enrico Motta, Clara Mancini (2002). Designing Representational Coherence into an Infrastructure for Collective Sensemaking. 2nd International Workshop on Infrastructures for Distributed Collective Practices. Available: http://kmi.open.ac.uk/projects/scholonto/docs/SBS_DCP2002.pdf
• Scholarly Ontologies project

• Ginsparg, Paul. Creating a global knowledge network. Available: http://arxiv.org/blurb/pg01unesco.html
• Odlyzko, Andrew. The Economics of Electronic Journals. First Monday, 2(8) (August 1997). Available: http://www.press.umich.edu/jep/04-01/odlyzko.html

• Lindsay, R.K. & Gordon, M.D. (1999). Literature-based discovery by lexical statistics. Journal of the American Society for Information Science, 50(7), 574-587. Available online
• (Optional) Gordon, M.D. & Lindsay, R.K. (1996). Toward discovery support systems: A replication, re-examination, and extension of Swanson's work on literature-based discovery of a connection between Raynaud's and fish oil. Journal of the American Society for Information Science, 47(2), 116-128. Available online

• Perez-Iratxeta, Carolina, Peer Bork & Miguel A. Andrade. (2002) Association of Genes to Genetically Inherited Diseases Using Data Mining. Nature Genetics 31(3), 316-319. Available online
• Mirnics, Karoly, et al. (2001) Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse. Trends in Neurosciences, 24(8), 479-486. Available online

• Stevens, Robert, Carole A. Goble, and Sean Bechhofer (2002). "Ontology-based Knowledge Representation for Bioinformatics." Briefings in Bioinformatics. Available online

• No reading, but take a look at the resources and tools available at the Center for Bioinformatics: http://bioinformatics.unc.edu/

• Robert Stevens, Carole Goble, Patricia Baker, and Andy Brass (2001). A classification of tasks in bioinformatics. Bioinformatics 17:180-188. (Available online from UNC campus)

• Shug, Jonathan et. al. (2002). "Predicting Gene Ontology Functions from ProDom and CDD Protein Domains." Genome Research 12(4),648-655. (Available online from UNC campus)

• Gale, M.D. & Devos, K.M. (1998). Plant Comparative Genetics after 10 Years. Science 282: 656-659. (Available online from UNC campus)

• Swanson, Don R. and Smalheiser, Neil E. (1997). An interactive system for finding complementary literatures: a stimulus to scientific discovery. Artificial Intelligence 91(2), 183-202. (Available online from UNC campus)

• Chapter 14, Phylogenetic Analysis, in Baxevanis & Ouellette's Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 2nd ed. A copy has been placed in the PAM box for this class (INLS 310-109) in the SILS Library. You can also read an earlier edition online (Chapter 9 in that edition), via the UNC Libraries web site. This works only within the UNC domain; if you're outside the domain accessing via the proxy, you must have a NetLibrary account.

• The Gene Ontology Consortium (2001). Creating the Gene Ontology Resource: Design and Implementation. Genome Research 11:1425-1433. (Available online)
• Ringwald, Martin, et al. (2001). The mouse gene expression database (GXD). Nucleic Acids Research 29(1), 98-101. (Available online)
• Blake, Judith A., et al, (2002) The mouse genome database (MGD): the model organism database for the laboratory mouse. Nucleic Acids Research, 30(1):113-115. (Available online)

• Karp, Richard M. (2002). Mathematical Challenges from Genomics and Molecular Biology. Notices of the American Mathematical Society 49(5), 544-553. (Online version available here)

• Claustres, Mireille, et al. (2002). Time for a Unified System of Mutation Description and Reporting: A Review of Locus-Specific Mutation Databases. Genome Research 12: 680-688. (Online version available here)

• Long, Jeffrey G. and Denning, Dorothy E. (1995). Ultra-Structure: A Design Theory for Complex Systems and Processes. Communications of the ACM 38:1:103.

• Brazma, Alvis. On the Importance of Standardisation in Life Sciences. Bioinformatics 2001 17: 113-114. (http://bioinformatics.oupjournals.org/content/vol17/issue2/)
• Ouzounis, Christos. Two or three myths about bioinformatics. Bioinformatics 2000 16: 187-189. (http://bioinformatics.oupjournals.org/content/vol16/issue3/)
  

• Go to http://lists.unc.edu/read/all_forums/subscribe?name=bioinfo-sils and fill out the form.

  OR

• Send an email to listserv@unc.edu with the following line in the body of the message:

  subscribe bioinfo-sils firstname lastname

  substituting your name for "firstname lastname".

unsubscribe bioinfo-sils

Template for session summary

• Program in Bioinformatics and Computational Biology
• UNC Biomedical Engineering / Medical Informatics Program
• UNC Microarray Discussion Group
• CCGS Seminar Series
• Biochemistry / Biophysics seminar series
• Biology Department seminars

• The Center for Bioinformatics at UNC Chapel Hill
• UNC System Bioinformatics Shared Resource
• UNC Chapel Hill Proteomics Core facility
• Carolina Center for Genome Sciences
• Cystic Fibrosis National Bioinformatics Center at UNC Chapel Hill
• Bioinformatics Resources at the UNC Health Sciences Library

• NCSU Genomics and Bioinformatics curriculum
• Duke University Institute for Genome Sciences and Policy
• National Library of Medicine (NLM)
• National Center for Biotechnology Information (NCBI) at the NLM

• Bioinformatics
• Journal of Biomedical Informatics (JBI)
• Journal of the American Medical Informatics Association (JAMIA)
• International Journal of Medical Informatics
• BMC Bioinformatics
• IEEE/ACM transactions on computational biology and bioinformatics
• JMLA/BMLA
• Journal of the American Society for Information Science and Technology (JASIST)
• Nucleic Acids Research annual database issue
• PubMed
• PubMed Central
• Citeseer
• Google Scholar