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B6 Bioinformatik metabolischer und regulatorischer Netzwerke

(Zeng)

Publikationen/ Publications

2007

Pel,H.J., de Winde,J.H., Archer,D.B., Dyer,P.S., Hofmann,G., Schaap,P.J., Turner,G., de Vries,R.P., Albang,R., Albermann,K., Andersen,M.R., Bendtsen,J.D., Benen,J.A., van den,B.M., Breestraat,S., Caddick,M.X., Contreras,R., Cornell,M., Coutinho,P.M., Danchin,E.G., Debets,A.J., Dekker,P., van Dijck,P.W., van Dijk,A., Dijkhuizen,L., Driessen,A.J., d'Enfert,C., Geysens,S., Goosen,C., Groot,G.S., de Groot,P.W., Guillemette,T., Henrissat,B., Herweijer,M., van den Hombergh,J.P., van den Hondel,C.A., van der Heijden,R.T., van der Kaaij,R.M., Klis,F.M., Kools,H.J., Kubicek,C.P., van Kuyk,P.A., Lauber,J., Lu,X., van der Maarel,M.J., Meulenberg,R., Menke,H., Mortimer,M.A., Nielsen,J., Oliver,S.G., Olsthoorn,M., Pal,K., van Peij,N.N., Ram,A.F., Rinas,U., Roubos,J.A., Sagt,C.M., Schmoll,M., Sun,J., Ussery,D., Varga,J., Vervecken,W., van de Vondervoort,P.J., Wedler,H., Wosten,H.A., Zeng,A.P., van Ooyen,A.J., Visser,J., Stam,H. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger. CBS 513.88. Nat.Biotechnol. 25,221-231 (in Kooperation mit B4).

2006

Sun, J., Wang, W., Hundertmark, C., Zeng, A.-P., Jahn D, Deckwer, W.D. (2006). A protein database constructed from low-coverage genomic sequence of Bacillus megaterium and its use for accelerated proteomic analysis. J Biotechnol. 2006 Jul 25,124(3):486-95

W.-D. Deckwer, D. Jahn, D. Hempel, A.-P. Zeng . System Biology Approach to Bioprocess Development. Life Science Eng. 6: 455-469

W.-D. Deckwer, D. Jahn, A.-P. Zeng, D. Hempel. Systembiologische Ansätze zur Prozessentwicklung. Chem. Ing. Tech. 78, 193-207

Zeng, A.-P. (2006). Editorial. Process Biochemistry (Special Issue: From Biochemical Engineering to Systems Biology - In honour of Dr. Wolf-Dieter Deckwer). 2006. 41(10):2101-2102

Wang, W., Sun, J., Hollmann R, Zeng, A.-P., Deckwer, W.D. (2006). Proteomic characterization of transient expression and secretion of a stress-related metalloprotease in high cell density culture of Bacillus megaterium. J Biotechnol. 2006. 126(3):313-324

Zheng, P., Sun, J., van den Heuvel, J., Zeng, A.-P. (2006). Discovery and investigation of a new, second triose phosphate isomerase in Klebsiella pneumoniae. J Biotechnol. 125(4):462-473

He, F., Zeng, A.-P. (2006). In search of functional association from time-series microarray data based on the change trend and level of gene expression. BMC Bioinformatics. 2006 Feb 15,7:69.

Zheng, P., Wereath K, Sun, J., van den Heuvel, J. and Zeng, A.-P. (2006). Overexpression of genes of the dha regulon and its effects on cell growth, glycerol fermentation to 1,3-propanediol and plasmid stability in Klebsiella pneumoniae. Process Biochemistry. 41(10):2160-2169

Zhou, F., Bi, J-, Zeng, A.-P. and Yuan, J. . A macrokinetic and regulator model for myeloma cell culture based on metabolic balance of pathways. Process Biochemistry. 41(10):2207-2217

2005

Sun, J., Gunzer, F., Westendorf, A.M., Buer, J., Scharfe, M., Jarek, M., Gossling, F., Blocker, H., Zeng, A.-P. (2005). Genomic peculiarity of coding sequences and metabolic potential of probiotic Escherichia coli strain Nissle 1917 inferred from raw genome data. J Biotechnol. 2005 May 4,117(2):147-61

Kim, E.J., Wang, W., Deckwer, W.D., Zeng, A.-P. (2005). Expression of the quorum-sensing regulatory protein LasR is strongly affected by iron and oxygen concentrations in cultures of Pseudomonas aeruginosa irrespective of cell density. Microbiology. 2005 Apr,151(Pt 4):1127-38

Jan Buer, Astrid M. Westendorf, An-Ping Zeng, Wiebke Hansen, Michael Probst-Kepper. Mechanisms of central and peripheral T cell tolerance: An update. Transfus Med Hemother. 32: (DOI:10.1159/000089128)

2004

H. Ma, B. Kumar, U. Ditges, Gunzer F, J. Buerand, A.-P. Zeng (2004). An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Res. 32: 6643-6649

H. Ma, J. Buer and A.-P. Zeng (2004). Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatcs, 5:199

J. Sun, R. Daniel, I. Wagner-Döbler and A.-P. Zeng (2004). Is autoinducer-2 a universal signal for interspecies communication? A comparative and phylogenetic genomic analysis of the synthesis and signal transduction pathways. BMC Evolutionary Biology, 4:36

J. Sun and A.-P. Zeng (2004). Identics - Identification of coding sequences and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequences. BMC Bioinformatics, 5:112

H. Ma, X.-M. Zhao, Y-J. Yuan and A.-P. Zeng (2004). Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics. 20: 1870-1876.

H. Ma and A.-P. Zeng (2004). Phylogenetic comparasion of metabolic capacities of organisms at genome level. Molecular Phylogenetics and Evolution. 31, 204-213.

 

Buchveröffentlichungen/ Released Books

Zeng, A.- P., Sun, J., Wang, W., Ma, H. W., Deckwer, W. D. (2005). Chapter 2. Application of Genomic and Proteomic Data for Bioprocess Analysis and Optimization. Yang, S. T. (ed.) Bioprocessing for value-added products from renewable resources. Elservier Inc, USA, 25-48

Ma, H., Zeng, A.-P. (2005). Reconstruction of metabolic network from genome information and its structural and functional analysis. Eils, R. and Kriete, A.(Eds.) Computational Systems Biology, Elsevier Inc., USA, 169-189

A.-P. Zeng and J. Bi (2005). Cell Culture Kinetics and Modeling. S.S. Ozturk and W.-S. Hu (eds.) Cell Culture Technology for Pharmaceutical and Cellular Therapies. Taylor & Francis Group, Atlanta . pp: 299-347

B. Kumar, H. Ma and A.-P. Zeng (2005). An integrated cellular network of Escherichia coli and its structural analysis. Proceedings of Foundation of Systems Biology in Engineering. University of California , Santa Babara , USA , August 7-10. pp 107-110

Vorträge und Poster/ Conference Presentations

2007

Sun, J. (2007). Towards understanding the secrets of Aspergillus niger as a versatile cellular factory. Invited talk. Tsinghua Univeristy (2007)

2006

Sun, J. (2006). Glycerol metabolism and 1,3-propanediol production - a genomic approach. Invited talk. Tianjin University

Zeng, A.-P. (2006). Industrial biotechnology in the era of systems biology. Invited talk. Tianjin University

Sun, J. (2006). Towards understanding the secrets of Aspergillus niger as a versatile cellular factory. Invited talk. Tianjin University

Zeng, A.-P. (2006). Dynamics and control of biological systems: challenge and opportunity of systems biology and engineering. Invited talk. Tianjin University

Sun, J. (2006). Towards understanding the secrets of Aspergillus niger as a versatile cellular factory. Invited talk. Shandong Univeristy

Zeng, A.-P. (2006). Industrial biotechnology in the era of systems biology. Invited talk. Shandong University

Sun, J. (2006). Comparative genomics for white biotechnology. Invited talk. Hamburg

Zeng, A.-P. Dynamics and Control of Biological Systems: Challenge and Opportunity of Systems Biology. Shanghai Jiatong University. 28.12.06.

A.-P. Zeng. Impact of genomic information and cellular network analysis on bioprocess development. European Biopharm Scale-up Congress. Invited speaker. 12th –14th September 2006. Geneva.

A.-P. Zeng. Microbial production of 1,3-propanediol: the European approach. Annual meeting of the society of industrial microbiology. Invited speaker. 29th July 2006. Baltimore/USA.

A.-P. Zeng. Reconstruction and analysis of genome-scale metabolic and regulatory networks. Universität Hamburg. Invited speaker. Bioinformatics Seminar. 22 June 2006.

A.-P. Zeng. Integrated Molecular Network for System Analysis of Cellular Processes. TU München. Invited speaker. Bioinformatik Kolloquium. 21 June 2006.

A.-P. Zeng. Integrated Molecular Network for System Analysis of Cellular Processes. TU München. Invited speaker. Bioinformatik Kolloquium. 21 June 2006.

A.-P. Zeng. Integrated Molecular Network for System Analysis of Cellular Processes. International Workshop on Molecular Systems Biology. Invited speaker. University of Bielefeld. 05 June 2006.

A.-P. Zeng. Reconstruction and analysis of genome-scale metabolic and regulatory networks. Invited talk. Bioinformatics Seminar. Humboldt Universität Berlin. 24.05.06.

A.-P. Zeng. Integrated analysis of genome-wide metabolic and regulatory networks and functional genomic data. Seminar. Universität des Saarlandes. 11 May 2006.

A.-P. Zeng. Integrated analysis of genome-wide metabolic and regulatory networks and functional genomic data. University of Bielefeld. Invited Seminar Talk. 12 Jan. 2006.

A.-P. Zeng. Reconstruction and analysis of genome-scale metabolic and regulatory networks. Invited Talk. VAAM 2006: Annual Conference of the Association for General and Applied Microbiology, Jena (20.03.2006).

Sun, J., Wang, W., Münch R, Jahn D, W.-D. Deckwer , A.-P. Zeng (2006). A protein database constructed from low-coverage genomic sequence of Bacillus megaterium and its use for accelerated proteomic analysis. VAAM 2006: Annual Conference of the Association for General and Applied Microbiology, Jena

A.-P. Zeng. Reconstruction and analysis of genome-wide metabolic and regulatory networks. University Bielefeld, 12.01.06

2005

A.-P. Zeng. Animal cell culture: from physiology to dynamics and systems biology. Protein Design Labs, Inc. Fremont, CA, USA. 11.08.2005

A.-P. Zeng. Animal cell culture: from physiology to dynamics and systems biology. Bayer HealthCare LLC, Berkeley, USA. 10 August 2005

A.-P. Zeng. Structure and function of large-scale biological networks. University of Cambridge, Engineering Department, UK. 04.October 2005

A.-P. Zeng. Reconstruction and analysis of genome-wide metabolic and regulatory networks. IPK Gartersleben, 02 November 2005

A.-P. Zeng. Integrative analysis of biological data and networks. DSM, Basel, Switzerland . 19.11.05

A.-P. Zeng. Modularity, regulation and kinetic analysis of metabolic network to identify key metabolites and pathways. Workshop "Experimentelle und theoretische Metabolomforschung", University Köln. 14.10.05

A.-P. Zeng. Systems Biotechnology: from microbial to animal cells. Tianjin University, China. 16.12.05

Kumar, B., Ma, H.-W., Zeng, A.- P. (2005). An integrated interaction network of Escherichia coli. Proceedings FOSBE 2005 (Foundations of systems Biology in Engineering), Santa Barbara, 107-110

Sun, J., Jahn, D., Deckwer, W. D., Zeng, A.- P. (2005). Genomic uniqueness and metabolic network of Bacillus megaterium inferred from low coverage genome sequence and by comparative genomics. 2nd European Conference on Prokaryotic Genomes (PROKAGEN 2005), Göttingen

Sun, J., Hempel, D. C., Jahn, D., Lu, X., Rinas, U., Zeng, A.- P. (2005). Identification of protein coding sequences for the reconstruction of metabolic network and proteomic analysis of Aspergillus niger from low coverage genome sequence. German Conference in Bioinformatics (GCB’05), Hamburg

A.-P. Zeng, H. Ma and J. Sun (2005). Rekonstruktion metabolischer und regulatorischer Netzwerke aus Genomdaten und ihre Nutzung zur Analyse von Bioprozessen. Proc. GVC/DECHEMA-Vortrags- und Diskussionstagung „Systembiotechnologie für industrielle Prozesse“, Braunschweig

Zeng, A.-P. (2005). Structure and function of large-scale biological networks. Department of Engineering, University of Cambridge, UK

Zeng, A.-P. (2005). Animal cell culture: from physiology to dynamics and systems biology. Protein Design Lab, California, USA

Zeng, A.-P. (2005). Animal cell culture and systems biotechnology. Bayer Biological Products, California, USA

Zeng, A.-P. (2005). Systembiotechnologische Ansätze zur Prozessentwicklung. TU Hamburg-Harburg

Zeng, A.-P. (2005). Reconstruction and analysis of genome scale biological Networks. Hans-Knöll-Institute (HKI), Jena

Zeng, A.-P. (2005). From Genome to Bioprocess: Systems Biotechnology. Institute of Process Engineering, Chinese Academy of Science, Beijing

Zeng, A.-P. (2005). Systems Biology and Biochemical Biotechnology. Beijing University of Chemical Technology, Beijing

Zeng, A.-P. (2005). From Genome to Bioprocess: Systems Biotechnology. Department of Cehmical and Biochemical Engineering, Zhejiang University, Hanzhou, China

Zeng, A.-P. (2005). Integrated analysis of metabolic pathways and regulatory network. Jena Workshop "Integrative Bioinformatics"

2004

Zeng, A.-P., Wang, W., Sun, J., Deckwer, W.-D. (2004). Systems biology approach for the analysis and optimization of an industrial bioprocess. 227th ACS National Meeting. Anaheim, CA

Zeng, A.-P. (2004). Reconstruction and structural analysis of metabolic and regulatory networks. International Workshop on "Complexity and Modeling of Biological Networks", GBF, Braunschweig, Germany

Zeng, A.-P., Ma, H. (2004). Structural analysis of genome-level metabolic and regulatory networks. Workshop "Modelling of Metabolic and Genetic Networks", Heidelberg, Germany

Zeng, A.-P. (2004). Perspectives of a Genomic Biochemical Engineering. Research Retreat Meeting, Bioprocessing Technology Institute, Singapore

Zeng, A.-P. (2004). From genome to new bioprocess by a systems biology approach. Seminar, Bioprocessing Technology Institute, Singapore

Zeng, A.-P., Ma, H. (2004). Hierarchical organization principle and analysis of metabolic and regulatory networks. Dagstuhl-Seminar: Integrative Bioinformatics, Dagstuhl, Germany

Sun, J., Zeng, A.-P. (2004). IdentiCS - A program to identify coding sequences from unannotated low-coverage genome sequences. GCB'04: German Conference on Bioinformatics, Bielefeld

Sun, J., Zeng, A.-P. (2004). IdentiCS - A program for reconstruction of metabolic network from unfinished genomic sequences. ICSB2004: 5th international conference on systems biology, Heidelberg

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