I533 SUPPLEMENTAL READINGS

Updated:14 February 2006

Major Journals and Other Publications

Books

Willett, Peter. Three-dimensional chemical structure handling. Taunton, Somerset, England: Research Studies Press; New York: Wiley, c1991. QD461 .W598 1991 Chemistry Library

Chemical structure systems: computational techniques for representation, searching, and processing of structural information / editors, Janet E. Ash, Wendy A. Warr, Peter Willett. New York: Ellis Horwood, 1991. QD471 .C522 1991 Chemistry Library

Cancer bioinformatics: from therapy design to treatment / edited by Sylvia Nagl. Chichester, England; Hoboken, NJ: John Wiley & Sons, c2005.

Week 1a GARY WIGGINS: Introduction to Chemistry and Life Sciences Databases

Chemistry

Sild, Sulev; Maran, Uko; Lomaka, Andre; Karelson, Mati. "Open Computing Grid for Molecular Science and Engineering." Journal of Chemical Information and Modeling 2006; ASAP Web Release Date: 06-Jan-2006. DOI: 10.1021/ci050354f

Chen, Jonathan; Swamidass, S. Joshua; Dou, Yimeng; Bruand, Jocelyne; Baldi, Pierre. "ChemDB: a public database of small molecules and related chemoinformatics resources." Bioinformatics 2005, 21(22), 4133-4139.

Wiggins, Gary. “Overview of databases/data sources.” in Gasteiger, Johann, ed. Handbook of Chemoinformatics: From Data to Knowledge in 4 Volumes. Wiley-VCH: 2003, v. 2, pp. 496-506. http://www.indiana.edu/~cheminfo/C571/wiggins_chapter_2003.pdf

Ridley, Damon. "Introduction to structure searching with SciFinder Scholar." Journal of Chemical Education 2001, 78(4), 559-560.

Cooke, Helen; Ridley, Damon D. "The challenges with substance databases and structure search engines." Aust. J. Chem. 2004, 57, 387-392. [650]

European Council Directive on the Legal Protection of databases (Directive 96/9/EC) http://europa.eu.int/ISPO/infosoc/legreg/docs/969ec.html

Database legal protection in the US http://www.bitlaw.com/copyright/database.html

Week 1b Life Sciences

MacMullen, W.J.; Denn, S.O. "Information problems in molecular biology and bioinformatics." Journal of the American Society for Information Science and Technology 2005 (March), 56(5), 447-456.

Stoeckert, C.J. "Functional genomics databases on the web." Cellular Microbiology 2005 (August), 7(8), 1053-1059.

NLM Gateway your entrance to the knowledge resources of the National Library of Medicine

Nucleic Acids Research Database issue (First issue of each calendar year)
http://nar.oupjournals.org/content/vol34/suppl_1/

Introduction to Molecular Biology Information Resources (See the Prerequisite readings for the NLM course.)
http://www.ncbi.nlm.nih.gov/Class/MLACourse/

Pearson, Helen. "Biology's name game." Nature June 7, 2001, 411(6838), 631-632. [644] (doi: 10.1038/35079694)

Austin, Robert. "Biosequence Searching in the Patent Literature."
http://www.stn-international.com/training_center/bioseq/piug2.pdf

The presentation compares patent coverage of STN sequence databases - REGISTRY, DGENE and PCTGEN - to public domain resources, and also STN Databases with each other, e.g. DGENE vs REGISTRY, in some detail. It also offers general advice on how to conduct a multi-database search.

Week 2a GARY WIGGINS:The NLM Roadmap Program and PubChem

NLM's Roadmap Program

Huerta, Michael F.; Farber, Gregory K.; Wilder, Elizabeth L. et al. "NIH Roadmap Interdisciplinary Research Initiatives." PLoS Computational Biololgy 1 (6): e59 Nov 2005.

Zerhouni, E.A. "US biomedical research - Basic, translational, and clinical sciences." JAMA-J AM MED ASSOC 294 (11): 1352-1358 SEP 21 2005.

Zerhouni, Elias. "The NIH Roadmap." Science 3 October 2003, 302, 63-64, 72.

Austin, Christopher P.; Brady, Linda S.; Insel, Thomas R.; Collins, Francis S. "NIH Molecular Libraries Initiative." Science 12 November 2004, 306, 1138-1139.

Week 2b

PubChem

Bradley, David. "Public molecules: small, but perfectly formed." Nature Reviews Drug Discovery December 1, 2004, 3, 988 doi: 10.1038/nrd1596

Gilardoni, Francois; Curcin, Vasa; Karunanayake, Kanishka; Norgaard, Jonas; Guo, Yike. "Integrated informatics in life and materials sciences: an oxymoron?" QSAR & Combinatorial Science 2005, 24(1), 120-130.

Week 3a

DAVID WILD: Cheminformatics Tools, Services, and Workflows-I

Hajduk, P.J.; Huth, J.R.; Tse, C. "Predicting protein druggability." Drug Discovery Today 2005 (December), 10(23-24), 1675-1682.

Weber, L. "Current status of virtual combinatorial library design." QSAR & Combinatorial Science 2005 (September), 24(7), 809-823.

Chin, D. N.; Chuaqui, C. E.; Singh, J. "Integration of virtual screening into the drug discovery process." Mini-Reviews in Medicinal Chemistry 2004, 4(10), 1053-1065.

Bajorath, Juergen. "Integration of virtual and high-throughput screening." Nature Reviews Drug Discovery 2002, 1(11), 882-894.

Ilyin, Sergey E.; Bernal, Alejandro; Horowitz, Daniel; Derian, Claudia K.; Xin, Hong. "Functional informatics: convergence and integration of automation and bioinformatics." Pharmacogenomics 2004, 5(6), 721-730.

Rishton, Gilbert M. "Nonleadlikeness and leadlikeness in biochemical screening." Drug Discovery Today 2003, 8(2), 86-96. [441]

Dill, James D." Tautomers: involvement in searching and registration." ChemBioNews.com 2003, 13(3), 38-39. [602]

Nature's Horizon Symposium "Charting chemical space: finding new tools to explore biology," May 20-22, 2004. (See the Background, Key Questions, and Symposium Highlights sections.) http://www.nature.com/horizon/chemicalspace/index.html

Week 3b

DAVID WILD: Cheminformatics Tools, Services, and Workflows-II

Week 4a

MELANIE WU: Database modeling and design

Gaede, Volker; Guenther, Oliver. "Multidimensional access methods." ACM Computing Surveys June 1998, 30(2), 170-231.

Week 4b

MELANIE WU: General Data Mining Techniques

Fast Algorithms for Mining Association Rules

Week 5a

MELANIE WU: Data Warehousing

Data Cube: A Relational Aggregation Operator Generalizing Group-By, Cross-Tab, and Sub-Totals

Week 5b

LUIS ROCHA: Text mining techniques for PubMed

Cohen, A.M.; Hersh, W.R. "A survey of current work in biomedical text mining." Briefings in Bioinformatics 2005 (March), 6(1), 57-71.

Maguitman, A. G., Rechtsteiner, A., Verspoor, K., Strauss, C.E., Rocha, L.M. Large-Scale Testing Of Bibliome Informatics Using Pfam Protein Families. Pacific Symposium on Biocomputing 2006, 11:76-87.

Week 6a

MALIKA MAHOUI: XML documents, schema, and CML (Chemical Markup Language)

Semantic Grid 101 at GGF16
http://www.semanticgrid.org/GGF/ggf16/SG101.html

Holliday, Gemma L.; Murray-Rust, Peter; Rzepa, Henry S. "Chemical Markup, XML, and the World Wide Web. 6. CMLReact, an XML Vocabulary for Chemical Reactions." Journal of Chemical Information and Modeling 2006, 46(1), 145 - 157. DOI: 10.1021/ci0502698

Wang, X.S.; Gorlitsky, R.; Almeida, J.S. "From XML to RDF: how semantic web technologies will change the design of 'omic' standards." Nature Biotechnology 23 (9): 1099-1103 SEP 2005.

Berman, J.J.; Bhatia, K. "Biomedical data integration: using XML to link clinical and research data sets." Expert Review of Molecular Diagnostics 2005 (May), 5(3), 329-336.

Week 6b

MELANIE WU: Querying XML Data

XPath Tutorial http://www.w3schools.com/xpath

XQuery Tutorial http://www.w3schools.com/xquery/default.asp

Week 7a

KENT HOLADAY: Chemical ontologies

Feldman, H.J.; Dumontier, M.; Ling, S. et al. "CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules." FEBS LETT 579 (21): 4685-4691 AUG 29 2005

Gardner, S.P. "Ontologies and semantic data integration." Drug Discovery Today 2005 (July 15), 10(14), 1001-1007.

Week 7b

GARY GRUMBLING: Life sciences ontologies

Week 8a

MARLON PIERCE: Introduction to Grids

Week 8b

MARLON PIERCE: Building Clients to Grids

Week 9a

MARLON PIERCE: Basic Web Services

Week 9b

Kevin Gilbert: Computational chemistry approaches

Week 10

SPRING BREAK

Week 11a

BETH PLALE: eScience and Data Grids

Schubert, Ulrich S. "Materials informatics: from data to knowledge towards integrated escience approaches." QSAR & Combinatorial Science 2005, 24(1), 5.

Week 11b

RANDY ARNOLD: Data needs in proteomics

Sheeley, D.M.; Breen, J.J.; Old, S.E. "Building integrated approaches for the proteomics of complex, dynamic systems: NIH programs in technology and infrastructure development." Journal of Proteome Research 4 (4): 1114-1122 JUL-AUG 2005.

Creighton, Chad; Hanash, Samir M. "Informatics tools for functional pathway analysis using genomics and proteomics," In: Srivastava, Sudhir, ed. Informatics in Proteomics. CRC Press LLC, Boca Raton, Fla, 2005, 193-203.

Ahrens, Christian; Jespersen, Hans; Schandorff, Soeren. "Bioinformatics for proteomics." Methods of Biochemical Analysis 2005, 45 (Industrial Proteomics), 249-272.

Raman, R.; Raguram, S.; Venkataraman, G.; Paulson, J.C.; Sasisekharan, R. Glycomics: an integrated systems approach to structure-function relationships of glycans." Nature Methods 2005 (November), 2(11), 817-824.

PT J Bienkowska, J. "Computational characterization of proteins." Expert Review of Proteomics 2005 (February), 2(1), 129-138.

Week 12a

HORST HEMMERLE: Chemogenomics and Pharmacogenomics

Roter, A.H. "Large-scale integrated databases supporting drug discovery," Current Opinion in Drug Discovery & Development 2005 (May), 8(3), 309-315.

Lange, B.M.; Ghassemian, M. "Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps." Phytochemistry 2005 (February), 66(4), 413-451.

Belkowski, S.M.; Polkovitch, D.; D'Andrea, M.R. "Synergistic approaches to clinical oncology biomarker discovery." Current Topics in Medicinal Chemistry 2005, 5(11), 1047-1051.

Ohlstein, Eliot H.; Johnson, Anthony G.; Elliott,John D.; Romanic, Anne M. New strategies in drug discovery," Methods in Molecular Biology 2005, 316, 1-11.

"The contribution of molecular informatics to chemogenomics. Knowledge-based discovery of biological targets and chemical lead compounds." Jacoby, Edgar; Schuffenhauer, Ansgar; Acklin, Pierre. Methods and Principles in Medicinal Chemistry 2004, 22 (Chemogenomics in Drug Discovery), 139-166.

Yan, Qing. "Biomedical informatics methods in pharmacogenomics." Methods in Molecular Medicine 2005, 108 (Hypertension), 459-486.

Vyas, H.; Summers, R. "An information-driven approach to pharmacogenomics." Pharmacogenomics 2005 (July), 6(5), 473-480.

Burren, Oliver S.; Healy, Barry C.; Lam, Alex C.; Schuilenburg, Helen; Dolman, Geoffrey E.; Everett, Vincent H.; Laneri, Davide; Nutland, Sarah; Rance, Helen E.; Payne, Felicity; Smyth, Deborah; Lowe, Chris; Barratt, Bryan J.; Twells, Rebecca C. J.; Rainbow, Daniel B.; Wicker, Linda S.; Todd, John A.; Walker, Neil M.; Smink, Luc J. "Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics." Human Genomics 2004, 1(2), 98-109.

Altman, Russ B.; Klein, Teri E. "Challenges for biomedical informatics and pharmacogenomics." Annual Review of Pharmacology and Toxicology 2002, 42, 113-133.

Week 12b

SANTIAGO SCHNELL: Systems Biology

Cary, M.P.; Bader, G.D.; Sander, C. "Pathway information for systems biology." FEBS Letters 2005 (March 21), 579(8), Special Issue SI, 1815-1820.

Vidal, M. "Interactome modeling." FEBS Letters FEBS Letters 2005 (March 21), 579(8), Special Issue SI, 1834-1838.

Aloy, P.; Russell, R.B. "Structure-based systems biology: a zoom lens for the cell." FEBS Letters 2005 (March 21), 579(8), Special Issue SI, 1854-1858.

Souchelnytskyi, S. "Bridging proteomics and systems biology: What are the roads to be traveled?" Proteomics 2005 (November), 5(16), 4123-4137.

Plattner, Gian-Reto. "'SystemsX'-project for a new biological science in Switzerland." Chimia 2004, 58(11), 783-787.

Westerhoff, Hans V.; Palsson, Bernhard O. "The evolution of molecular biology into systems biology." Nature Biotechnology 2004 (October), 22(10), 1249-1252. [685] (This issue focuses on the potential applications of systems biology to biotechnology.)

Week 13a

GEOFFREY FOX: Integration of Chemical Text Tools with Connotea and CiteULike

Return to the I533 Home Page