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st Century. 1998, http://www2.whitehouse.gov/WH/EOP/OSTP/NSTC/html/bioinformaticsreport.html . Experts in bioinformatics and related fields identify problems and challenges. Required reading for policy makers and those interested in the field.
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MitBASE: A comprehensive and integrated mitochondrial DNA database
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Attimonelli M., Altamura N., Benne R., Boyen C., Brennicke A., Carone A., Cooper J.M., D'Elia D., de Montalvo A., de Pinto B.et al. MitBASE: a comprehensive and integrated mitochondrial DNA database. Nucleic Acids Res. 27:1999;128-133.
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The University of Minnesota Biocatalysis/Biodegradation Database: Specialized metabolism for functional genomics
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Ellis L.B.M., Hershberger C.D., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics. Nucleic Acids Res. 27:1999;373-376.
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The University of Minnesota Biocatalysis/Biodegradation Database: Microorganisms, genomics, and prediction
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Ellis L.B.M., Hershberger C.D., Wackett L.P. The University of Minnesota Biocatalysis/Biodegradation Database: microorganisms, genomics, and prediction. Nucleic Acids Res. 28:2000;377-379.
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Ellis L.B.M., Speedie S., McLeish R. Representing metabolic pathways: an object-oriented approach. Bioinformatics. 14:1998;803-806.
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Public biological databases, freely available to all on the web, have shaky financial foundations. This paper is a wake-up call to all who value these essential resources
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Ellis L.B., Kalumbi D. Financing a future for public biological data. Bioinformatics. 9:1999;717-722. Public biological databases, freely available to all on the web, have shaky financial foundations. This paper is a wake-up call to all who value these essential resources.
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Ellis, L.B.1
Kalumbi, D.2
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A predictive thermodynamic model for the bioreduction of acetophenone to phenethyl alcohol using resting cells of Saccharomyces cerevisiae
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Zhao Y., DeLancey G.B. A predictive thermodynamic model for the bioreduction of acetophenone to phenethyl alcohol using resting cells of Saccharomyces cerevisiae. Biotechnol Bioeng. 64:1999;442-451.
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Klapa M.I., Park S.M., Sinskey A.J., Stephanopoulos G. Metabolite and isotopomer balancing in the analysis of metabolic cycles: I. Theory. Biotechnol Bioeng. 62:1999;375-391.
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Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications
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Park S.M., Klapa M.I., Sinskey A.J., Stephanopoulos G. Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. Biotechnol Bioeng. 62:1999;392-401.
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Park, S.M.1
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0002166989
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The prediction of microbial biodegradation and biocatalysis
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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.et al. The prediction of microbial biodegradation and biocatalysis. Am Soc Microbiol News. 65:1999;87-93.
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Spormann, A.6
Walsh, C.T.7
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Knowledge-based systems for toxicity and metabolism prediction
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P.W. Erhardt. Oxford: Blackwell Science Ltd
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Greene N. Knowledge-based systems for toxicity and metabolism prediction. Erhardt P.W. Drug Metabolism. 1999;289-296 Blackwell Science Ltd, Oxford.
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Drug Metabolism
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Greene, N.1
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15
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0033527918
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Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures
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A model based on data derived from single substrate experiments could accurately predict biodegradation kinetics of binary and teriary PAH mixtures
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Guha S., Peters C.A., Jaffe P.R. Multisubstrate biodegradation kinetics of naphthalene, phenanthrene, and pyrene mixtures. Biotechnol Bioeng. 65:1999;491-499. A model based on data derived from single substrate experiments could accurately predict biodegradation kinetics of binary and teriary PAH mixtures.
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Guha, S.1
Peters, C.A.2
Jaffe, P.R.3
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0033527415
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Independent prediction of naphthalene transport and biodegradation in soil with a mathematical model
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Ahn I-S., Ghiorse W.C., Lion L.W. Independent prediction of naphthalene transport and biodegradation in soil with a mathematical model. Biotechnol Bioeng. 65:1999;65-75.
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Ahn, I.-S.1
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Lion, L.W.3
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0033524367
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Kinetics and modeling of autotrophic thiocyanate biodegradation
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Hung C-H., Pavlostathis S.G. Kinetics and modeling of autotrophic thiocyanate biodegradation. Biotechnol Bioeng. 62:1999;1-11.
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Hung, C.-H.1
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0033586962
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Kinetic model of biosurfactant-enhanced hexadecame biodegradation by Pseudomonas aeruginosa
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Sekelsky A.M., Shreve G.S. Kinetic model of biosurfactant-enhanced hexadecame biodegradation by Pseudomonas aeruginosa. Biotechnol Bioeng. 63:1999;401-409.
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Sekelsky, A.M.1
Shreve, G.S.2
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0033179739
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Kinetic modelling of biological phosphorus removal with a pure culture of Acinetobacter sp. under aerobic, anaerobic and transient operating conditions
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Zafiri C., Kornaros M., Lyberator G. Kinetic modelling of biological phosphorus removal with a pure culture of Acinetobacter sp. under aerobic, anaerobic and transient operating conditions. Water Res. 33:1999;2769-2788.
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Lyberator, G.3
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0033586942
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Biomass accumulation and clogging in biotrickling filters for waste gas treatment: Evaluation of a dynamic model using dichloromethane as a model pollutant
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Okkerse W.J., Ottengraf S.P., Osinga-Kuipers B., Okkerse M. Biomass accumulation and clogging in biotrickling filters for waste gas treatment: evaluation of a dynamic model using dichloromethane as a model pollutant. Biotechnol Bioeng. 63:1999;418-430.
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Okkerse, W.J.1
Ottengraf, S.P.2
Osinga-Kuipers, B.3
Okkerse, M.4
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21
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0033526033
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An analysis of a trickle-bed bioreactor: Carbon disulfide removal
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Lobo R., Revah S., Viveros-Garcia T. An analysis of a trickle-bed bioreactor: carbon disulfide removal. Biotechnol Bioeng. 63:1999;98-109.
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Lobo, R.1
Revah, S.2
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Modelling heavy metal mobilisation in solid waste deposits - A predictive tool for environmental risk assessment
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Petersen J., Petrie J.G. Modelling heavy metal mobilisation in solid waste deposits - a predictive tool for environmental risk assessment. Water Sci Technol. 39:1999;193-196.
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Water Sci Technol
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Petersen, J.1
Petrie, J.G.2
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23
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0033585420
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Understanding the influence of temperature change and cosolvent addition on conversion rate of enzymatic suspension reactions based on regime analysis
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Enzyme suspension reactions are an important tool for biotransformations. They are modeled to accurately predict overall process time to develop heuristic rules to optimize such reactions
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Wolff A., Zhu L., Wong Y.W., Straathof A.J.J., Jongejan J.A., Heijnen J.J. Understanding the influence of temperature change and cosolvent addition on conversion rate of enzymatic suspension reactions based on regime analysis. Biotechnol Bioeng. 62:1999;125-134. Enzyme suspension reactions are an important tool for biotransformations. They are modeled to accurately predict overall process time to develop heuristic rules to optimize such reactions.
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Biotechnol Bioeng
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Wolff, A.1
Zhu, L.2
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Straathof, A.J.J.4
Jongejan, J.A.5
Heijnen, J.J.6
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24
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0032749401
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A kinetic model incorporating energy spilling for substrate removal in substrate-sufficient batch culture of activated sludge
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Liu Y., Chen G.H., Rols J.L. A kinetic model incorporating energy spilling for substrate removal in substrate-sufficient batch culture of activated sludge. Appl Microbiol Biotechnol. 52:1999;647-651.
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Appl Microbiol Biotechnol
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Liu, Y.1
Chen, G.H.2
Rols, J.L.3
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0033302935
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Modeling the impact of oxygen reaeration on natural attenuation
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Holder A.W., Bedient P.B., Hughes J.B. Modeling the impact of oxygen reaeration on natural attenuation. Bioremediation J. 3:1999;137-149.
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Bioremediation J
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Holder, A.W.1
Bedient, P.B.2
Hughes, J.B.3
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0032990166
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Mathematical models of metabolic pathways
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Varner J., Ramkrishna D. Mathematical models of metabolic pathways. Curr Opin Biotechnol. 10:1999;146-150.
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Curr Opin Biotechnol
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Varner, J.1
Ramkrishna, D.2
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27
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0033103838
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Evaluation and application of models for the prediction of ready biodegradability in the MITI-I test
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The first reported comparison of several different models of biodegradability using the same dataset permits these authors to better evaluate the strengths and weakensses of each method and the field as a whole
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Rorije E., Loonen H., Mullen M., Klopman G., Peijnenburg W.J.G.M. Evaluation and application of models for the prediction of ready biodegradability in the MITI-I test. Chemosphere. 38:1999;1409-1417. The first reported comparison of several different models of biodegradability using the same dataset permits these authors to better evaluate the strengths and weakensses of each method and the field as a whole.
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Chemosphere
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, pp. 1409-1417
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Rorije, E.1
Loonen, H.2
Mullen, M.3
Klopman, G.4
Peijnenburg, W.J.G.M.5
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Stochastic analysis of biodegradation fronts in one-dimensional heterogeneous porous media
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Xin J., Zhang D. Stochastic analysis of biodegradation fronts in one-dimensional heterogeneous porous media. Adv Water Resources. 22:1998;103-116.
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Adv Water Resources
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Risk assessment using stochastic modeling of pollutant transport in landfill clay liners
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Lo I.M-C., Law W.K-W., Shen H.M. Risk assessment using stochastic modeling of pollutant transport in landfill clay liners. Water Sci Technol. 39:1999;337-341.
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Water Sci Technol
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Lo, I.M.-C.1
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Shen, H.M.3
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0033586357
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Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic
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This paper describes kinetic models suitable for pathway modeling with incomplete enzyme mechanisms
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Lee B., Yen J., Yang L., Liao J.C. Incorporating qualitative knowledge in enzyme kinetic models using fuzzy logic. Biotechnol Bioeng. 62:1999;722-729. This paper describes kinetic models suitable for pathway modeling with incomplete enzyme mechanisms.
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Biotechnol Bioeng
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Lee, B.1
Yen, J.2
Yang, L.3
Liao, J.C.4
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0032804397
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Modeling of phenol degradation system using artificial neural networks
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Although neural networks were classed with (usually less accurate) stochastic models in this review, they might be preferred to deterministic models in some cases. These authors show that a neural network model outperforms a deterministic multiple regression model for this application
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Balan S.M., Annadurai G., Sheeja R.Y., Srinivasamoorthy V.R., Murugesan T. Modeling of phenol degradation system using artificial neural networks. Bioprocess Eng. 21:1999;129-134. Although neural networks were classed with (usually less accurate) stochastic models in this review, they might be preferred to deterministic models in some cases. These authors show that a neural network model outperforms a deterministic multiple regression model for this application.
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Bioprocess Eng
, vol.21
, pp. 129-134
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Balan, S.M.1
Annadurai, G.2
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Srinivasamoorthy, V.R.4
Murugesan, T.5
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Coping with ever larger problems, models, and databases
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Good overview of the challenges facing developers of environmental models
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Beck M.B. Coping with ever larger problems, models, and databases. Water Sci Technol. 39:1999;1-11. Good overview of the challenges facing developers of environmental models.
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Water Sci Technol
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Beck, M.B.1
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NCBI Databases on World Wide Web URL
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NCBI Databases on World Wide Web URL: http://www.ncbi.nlm.nih.gov:80/Database/index.html.
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