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UM-BBD/EAWAG-BBD Publications and Reviews

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  • Ellis LB, Wackett LP. (2012) "Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation" Microbial Informatics and Experimentation 2: 1 (4 January 2012). Abstract | Full Text.

  • Gao J, Ellis LB, Wackett LP. (2011) "The University of Minnesota Pathway Prediction System: multi-level prediction and visualization." Nucleic Acids Research 39 Suppl 2: W406-11. Abstract | Full Text.

  • Helbling DE, Hollender J, Kohler HP, Singer H, Fenner K. (2010) "High-throughput identification of microbial transformation products of organic micropollutants." Environ Sci Technol. 44: 6621-7. Abstract

  • Wicker J, Fenner K, Ellis L, Wackett L, Kramer S (2010) "Predicting Biodegradation Products and Pathways: A Hybrid Knowledge-Based and Machine Learning Based Approach" Bioinformatics 26: 814-21. Abstract | Full Text.

  • Gao, J., Ellis, L.B.M., and Wackett, L.P. (2010) "The University of Minnesota Biocatalysis/Biodegradation Database: improving public access" Nucleic Acids Research 38: D488-D491. Abstract | Full Text.

  • Kern S, Fenner K, Singer HP, Schwarzenbach RP, Hollender J. (2009) "Identification of transformation products of organic contaminants in natural waters by computer-aided prediction and high-resolution mass spectrometry." Environ Sci Technol. 43:7039-46. Abstract

  • Fenner, K., Gao, J., Kramer, S., Ellis, L.B.M., Wackett, L.P. (2008) "Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction." Bioinformatics, 24: 2079 - 2085. Abstract | Full Text

  • Ellis, L.B.M., Gao, J., Fenner, K., and Wackett, LP. (2008) "The University of Minnesota pathway prediction system: predicting metabolic logic." Nucleic Acids Research 36: W427-W432. Abstract | Full Text.

  • Ellis, L.B.M., Roe, D., and Wackett, L.P. (2006) "The University of Minnesota Biocatalysis/Biodegradation Database: The First Decade" Nucleic Acids Research 34: D517-D521. Abstract | Full Text.

  • Hou, B.K., Ellis, L.B.M., and Wackett, L.P. (2004) "Encoding Microbial Metabolic Logic: Predicting Biodegradation" Journal of Industrial Microbiology and Biotechnology, 31: 261-272. SpringerLink.

  • Wackett, L.P., Dodge, A.G., and Ellis, L.B.M. (2004) "Microbial Genomics and the Periodic Table" (minireview) Applied and Environmental Microbiology, 70: 647-65. Full Text.

  • Hou, B.K., Wackett, L.P., and Ellis, L.B.M. (2003) "Predicting Microbial Catabolism: A Functional Group Approach" Journal of Chemical Information and Computer Sciences, 43: 1051-1057. Abstract | Full Text.

  • Ellis, L.B.M., Hou, B.K., Kang, W., and Wackett, L.P. (2003) "The University of Minnesota Biocatalysis/Biodegradation Database: Post-Genomic Datamining" Nucleic Acids Research 31: 262-265. Abstract | Full Text.

  • Ellis, L.B.M. and Attwood, T.K. (2001) "Molecular biology databases: today and tomorrow" Drug Discovery Today 6: 509-513.

  • Wackett, L.P. and Hershberger, C.D. (2001) Biocatalysis and Biodegradation: Microbial Transformation of Organic Compounds. ASM Press, Wash. DC. xxiii+228p. ISBN 1-55581-179-5 ASM Press

  • Ellis, L.B.M., Hershberger, C.D., Bryan, E.M., and Wackett, L.P. (2001) "The University of Minnesota Biocatalysis/Biodegradation Database: Emphasizing Enzymes" Nucleic Acids Research 29: 340-343. Abstract. Full Text (PDF).

  • Ellis, Lynda B.M. (2000) "Environmental Biotechnology Informatics" Current Opinion in Biotechnology, 11: 232-235. Abstract.

  • Ellis, L.B.M., Hershberger, C.D., and Wackett, L.P. (2000) "The University of Minnesota Biocatalysis/Biodegradation Database: Microorganisms, genomics, and prediction" Nucleic Acids Research 28: 377-379. Abstract. Full Text (PDF).

  • Wackett, L.P. and Ellis, L.B.M. (1999) "Microbial Biocatalysis Databases" in Flickinger, M. and Drew, S. (eds) Encyclopedia of Bioprocess Technology: Fermentation, Biocatalysis & Bioseparation, New York: Wiley, pp. 260-267. ISBN 0-471-13822-3.

  • Wackett, L.P. and Ellis, L.B.M. (1999) "Predicting Biodegradation" Environmental Microbiology 1: 119-24. Abstract.

  • Ellis, L.B.M., Hershberger, C.D., and Wackett, L.P. (1999) "The University of Minnesota Biocatalysis/Biodegradation Database: Specialized metabolism for functional genomics" Nucleic Acids Research 27: 373-376. Abstract. Full Text (PDF).

  • Wackett, L.P., Ellis, L.B.M., Speedie, S., Hershberger, C.D., Knackmuss, H-J, Spormann, A., Walsh, C.T., Forney, L.J., Punch, W.F., Kazic, T., Kanehisa, M., Berndt, D.J. (1999) "The Prediction of Microbial Biodegradation and Biocatalysis" American Society for Microbiology News, 65: 87-93.

  • Ellis, L.B.M., Speedie, S.M., and McLeish, R. (1998) "Representing metabolic pathway information: An object-oriented approach" Bioinformatics 14: 803-806. Abstract.

  • Wackett, L.P. (1997) "Biocatalysis, biodegradation and informatics" Journal of Industrial Microbiology & Biotechnology 19: 350-354. Abstract.

  • Ellis, L.B.M. and Wackett, L.P. (1997) "Microbial biocatalysis and biodegradation informatics" Nature Biotechnology 15: 1406.

  • Ellis, L.B.M., Young, E.C. and Wackett, L.P. (1996) "Teaching Biodegradation on the World Wide Web" Proceedings of the Second Australian Web Symposium (AUSWEB'96), July 7-9, 1996, Gold Coast, Queensland, Australia.

  • Ellis, L.B.M. and Wackett, L.P. (1996) "Biocatalysis/Biodegradation Database: New Weaving on the Web" Invited Software Demonstration, The Fourth International Conference on Computational Biology: Intelligent Systems for Molecular Biology '96, June 12 to 15, 1996, Washington University, St. Louis, Missouri USA.

  • Wackett, L.P. & Ellis, L.B.M. (1996) "The University of Minnesota Biocatalysis/Biodegradation Database: A novel microbiological method on the World Wide Web." J. Microbiol. Meth., 25: 91-93.

  • Ellis, L.B.M. & Wackett, L.P. (1995)"A Microbial Biocatalysis Database" Soc. Ind. Microb. News 45(4): 167-173.

Reviews

The main - if not the only - public resource for quantitative studies on microbial biotransformations is the University of Minnesota Biocatalysis/Biodegradation Database (UMBBD, http://umbbd.msi.umn.edu). The system - permanently maintained and updated by Lynda Ellis and Larry Wackett - represents a colossal effort to collect primary data from literature on such processes. At the time of writing this article, UMBBD lists 177 pathways, 1220 reactions, 1133 compounds, 786 enzymes, and 462 micro-organisms of environmental interests. The resource is endowed with a number of user-friendly features for different applications. Most important, the data are accessible in formats that can be subject to computational analyses of all sorts from remote locations.
Victor deLorenzo (2008) Current Opinion in Biotechnology 19: 579-589.
DATABASE: Eating Pollution
To us, the molecule cyclohexane is a noxious solvent for making products such as rubber and wood stains. But to the bacterium Brachymonas petroleovorans, it's dinner. A strain of the bug can break down cyclohexane and use it as a source of carbon. Researchers hoping to harness microbial metabolism for environmental clean up should visit the Biocatalysis/Biodegradation Database at the University of Minnesota. The site displays the biochemical pathways that allow various kinds of bacteria to disassemble a long list of pollutants, from the carcinogen carbon tetrachloride to the pesticide parathion.
Leslie, Mitch "Netwatch" Science (2005) 309: 1795.

Multimedia Educational Resources for Learning and Online Teaching (MERLOT) (2002) reviewed the UM-BBD and awarded it high scores:
Content Quality: 5/5
Potential Effectiveness as a Teaching Tool: 4/5
Ease of Use for Students and Faculty: 5/5

Burgard A.P.; Maranas C.D. "Review of the University of Minnesota Biocatalysis/Biodegradation Database" Metabolic Engineering (2002) 4(2): 111-113.

Wittig, Ulrike; De Beuckelaer, Ann. "Analysis and comparison of metabolic pathway databases." Briefings in Bioinformatics May 2001, 2: 126-142.

Professor Dr. Uwe T. Bornscheuer "The University of Minnesota Biocatalysis/Biodegradation Database" Angew. Chem. (2001) 113: 3817; Angew. Chem. Int. Ed. Engl. (2001) 40: 3703.

"Another biochemically-oriented site that is loaded with information is the "University of Minnesota Biocatalysis/ Biodegradation Database" available at: http://umbbd.msi.umn.edu/index.html. This site covers microbial biocatalytic reactions and biodegradation pathways and metapathways primarily for xenobiotic chemical compounds. Try this site out and you will see why I have picked it and why it has received awards. As chemical companies shift to using biocatalysis more and more for expanding their available synthetic methods (see "Biocatalysis Boom," Chemical & Engineering News, March 19, 2001, p.12) because of cost or because the molecule can't be made any other way, this site is invaluable and a must for inclusion as an electronic database available over corporate intranets. The environmental division of a company should also find this site useful."
Johner, Paul E. (2001), The Pointer, 67(1), Spring 2001.

"Need to know how microbes break down chemical compounds not commonly found in nature? This award-winning site provides a wealth of information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic organic compounds. The database recently added its 100th pathway, after starting with just four in 1995.

The database currently covers approximately 650 reactions, 600 compounds, 50 organic functional groups, 400 enzymes, and 250 microorganisms. Most known microbial catabolic reaction types are included. You can search the database in a variety of ways (including by name, formula, CAS registry number, and EC number), and links are provided to other chemical and biological databases. The site also contains an extensive list of almost 100 Internet resources.

At the site, you can learn to use the database by taking the "guided tour", join the e-mail user list, or even enroll in a graduate-level Internet course titled "Biocatalysis and Biodegradation".

The co-directors of the site (Lynda Ellis (ACS '85) and Larry Wackett (ACS '99)) and their Scientific Advisory Board pay special attention to documenting the credibility of the database information. Future additions to the database will include additional mirror sites, fold prediction for its sequenced enzymes, closer ties to genome and microbial strain databases, and the prediction of biodegradation pathways for compounds not contained in the database."
Wedin, R. (2000) "Review: The University of Minnesota Biocatalysis/Biodegradation Database" Chemistry, Fall 2000, American Chemical Society, p. 6.

"Microbes that devour or otherwise help break down exotic chemicals are cleaning up the environment, spawning new technologies, and deepening our understanding of microbial life. While biodegradation and biocatalysis are young fields, much of what is known can be found in the University of Minnesota Biocatalysis/Biodegradation Database.

The site provides detailed explanations of 99 "pathways"--chains of reactions that break down various chemicals --as well as data on hundreds of individual reactions, compounds, enzymes, and microorganisms. The site focuses on the reactions that begin to break down compounds not commonly found in nature, for example, those involving naphthalene, the stuff of mothballs. For information on the more common metabolic pathways that complete the breakdown, the site links to databases such as the Kyoto Encyclopedia of Genes and Genomes. All data display their pedigrees, and a guided tour helps first-time visitors find their way around.

The site lacks only for style. Hyperlinked graphics accompany most pages of data; however, by default, reactions and pathways are rendered in old-fashioned diagrams made with text and keyboard symbols. "We made a conscious design decision to use text as much as possible," says computational biologist and site co-director Lynda Ellis, "and to have the graphics a click away for those whose computers are fast enough to use them."
Cho, A. (2000) "Munching on Strange Chemicals" Netwatch, Science, 288(5471): 1543.

"The University of Minnesota Biocatalysis Biodegradation Database (UM-BBD) provides a slightly different take on pathways. It incorporates 'information on microbial enzyme-catalyzed reactions that are important for biotechnology.' Instead of focusing on an organism, the starting point of this database is a chemical, like glyphosate or chlorobenzene. This extensive and well-organized resource contains both graphic and text-based maps of reactions and pathways. Both contain links to more-detailed information about the bacteria, enzymes, and compounds involved. The UM-BBD Search Page is a good place to locate a pathway containing a specific compound or enzyme. A search on a specific microorganism name will pull up pathways in which it is involved, as well as links to Hunting Microbial Information for Bacteria from the World Data Centre for Microorganisms. About the UM-BBD and the Guided Tour of the UM-BBD provide more detailed information about using this resource."
Fluet, Amy (1999) "Pathways to Enlightenment" HMS Beagle, Reviews In Situ, Issue 55.

"The University of Minnesota Biocatalysis/Biodegradation Database, maintained by Lynda Ellis, is a very handy website providing extensive information on microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds. This retrieval system allows one to establish links between compounds, pathways, reactions, enzymes or microorganisms by entering a single query of these categories."
Boulay, Jean-Louis (1999) "Web Alert: Biochemical Technology" Current Opinion in Biotechnology 10: 113.

"Understanding biocatalytic reaction pathways is important for both pollution control and applications in biotechnology. The University of Minnesota Biocatalysis/Biodegradation Database aids learning about these reactions and provides extensive links to Web resources on microbial enzyme-catalyzed chemistry. Each chemical pathway is described in text and is accompanied by a graphical represention of the reaction. There is also a graduate level course on biocatalysis offered over the Internet by the site's creators L. Ellis and L. Wackett."
Voss, D. (1997) "Webwatch" Science 277(5322): 53.

Schmidt, M. (1996) "Review: The University of Minnesota Biocatalysis/Biodegradation Database" Amer. Soc. Microbiol. News 62: 102.

"Information on the details of known metabolic pathways can be found on the World Wide Web Biodegradation site recently set up by Lynda Ellis and Lawrence Wackett, which will be an important new tool in metabolic pathway design. This facility should enable researchers not only to engineer enzymes involved inxenobiotic degradation, but perhaps also to divert catabolic pathways for the synthesis of industrially desirable compounds."
Minshull, J. (1995) "Cleaning up our own backyard: developing new catabolic pathways to degrade pollutants" Chemistry & Biology 2: 775-780.

"Another database in the first stages of preparation is the University of Minnesota Biocatalysis/Biodegradation Database. The UM-BBD is the creation of pathology professor Lynda B.M. Ellis at the Minneapolis campus and biochemistry professor Lawrence P. Wackett in St Paul. The eventual aim of this collection is to help genetic engineers find out what metabolic pathways are in what microorganisms so that they can insert several at once into such bacteria as Escherichia coli. The genes in the engineered bacertia would be expressed simultaneously to carry out a sequence of biotransformations on one substrate. For now, the UM-BBD has only 120 reactions cataloged and users cannot yet search but only 'browse.' But use of the database on the World Wide Web is free."
Stinson, S.C. (1995) "Chiral Drugs" Chem. & Engin. News October 9 44-74.

Kreiger, J. (1995) "New database offers biocatalysis information" C&EN September 11 36-37.