The Comprehensive Systems Biology Project (CSB)
csbdb CSB.DB (CSB.DB@MPIMP)
- A Comprehensive Systems-Biology Database -		 mpimp
Hosted at Max Planck Institute of Molecular Plant Physiology
Databases: Associated DB | Transcriptome DB | Metabolome DB | Co-Response DB | BestFit
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NOTIFICATION: Permanent migration of all CSB.DB services and functionalities on 1.1.2016.
Herewith we inform you that all CSB.DB databases have been migrated at the beginning of 2016. This includes all gene correlation and expression databases, the GMD@CSB.DB module and all associated databases
The BestFit software, a tool for non-aqueous fractionation data analysis, will also be available by the Experimental Systems Biology Research Group headed by Dr. Patrick Giavalisco.
We thank all users, contributors, and collaborators of CSB.DB at the Max Planck Institute for their long-standing support.
Yours sincerely, the CSB.DB Curator and the CSB.DB Developmental Core Team
CSB.DB Scientific Publications
CSB.DB
For our comprehensive systems biology approach we integrate knowledge, ideas and concepts from diverse research areas and activities. This page represents the sources of the basis for these ideas, concepts etc..

To get information of your choice use the links listed below.
CSB Associated Paper

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*Lisso,J., *Steinhauser,D., Altmann,T., Kopka,J. & Müssig,C. (2005).
Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Res., 33, 2685-2696. [PubMed]
Schauer,N., Steinhauser,D., Strelkov,S., Schomburg,D., Allison,G., Moritz,T., Lundgren,K., Roessner-Tunali,U., Forbes,M.G., Willmitzer,L., Fernie,A.R. & Kopka,J. (2005).
GC–MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett., 579, 1332-1337. [PubMed]
Kopka,J., Schauer,N., Krueger,S., Birkemeyer,C., Usadel,B., Bergmüller,E., Doermann,P., Weckwerth,W., Gibon,Y., Stitt,M., Willmitzer,L., Fernie,A.R. & Steinhauser,D. (2005).
GMD@CSB.DB: The Golm Metabolome Database. Bioinformatics, 21, 1635-1638. [PubMed]
Usadel,B., Kuschinsky,A.M., Steinhauser,D. and Pauly,M. (2005).
Transcriptional co-response analysis as a tool to identify new components of the wall biosynthetic machinery. Plant Biosystems, 139, 69-73. [Taylor & Francis Online Journals ]
Steinhauser,D., Junker,B.H., Luedemann,A., Selbig,J. & Kopka,J. (2004a).
Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics, 20, 1928-1939. [PubMed]
*Steinhauser,D., *Usadel,B., Luedemann,A., Thimm,O. & Kopka,J. (2004b).
CSB.DB: a comprehensive systems-biology database. Bioinformatics, 20, 3647-3651. [PubMed]
CSB.DB: Used Books
Book Navigation Bar
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z |
E

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Efron,B. & Tibshirani,R. (1993).
An Introduction to the Bootstrap. Chapman and Hall, New York, London.
M

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Mirkin,B. (1996).
Mathematical Classification and Clustering. (Book Series: Nonconvex Optimisation and Its Application: Volume 11). Kluwer Academic Publishers.
S

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Sokal,R.R. & Rohlf,F.J. (1995).
Biometry: The principles and practice of statistics in biological research. 3rd ed.. W.H. Freeman and Company New York.
CSB.DB: Used Paper
Paper Navigation Bar
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z |
A

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Allen,T. E., Herrgård,M.J., Liu,M., Qiu,Y., Glasner,J.D., Blattner,F.R. & Palsson,B.Ø. (2003).
Genome-scale analysis of the uses of the Escherichia coli genome: a model-driven analysis of heterogeneous datasets. J. Bacteriol., 185, 6392-6399. [PubMed]
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. & Lipman,D.J. (1990).
Basic local alignments search tool. J. Mol. Biol., 215, 403-410. [PubMed]
B

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Berlyn,M.K. (1998).
Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol Mol Biol Rev., 62, 814-928. [PubMed]
Bernstein,A.J., Khodursky,A.B., Lin.,P.-H., Lin-Chao,S. & Cohen,S.N. (2002).
Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarray. Proc. Natl. Acad. Sci. USA, 99, 9697-9702. [PubMed]
Bonett,D.G. & Wright,T.A. (2000).
Sample size requirements for estimating Pearson, Kendall and Spearman crrelations Psychometrika., 65, 23-28.
C

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Christie,K.R., Weng,S., Balakrishnan,R., Costanzo,M.C., Dolinski,K., Dwight,S.S., Engel,S.R., Feierbach,B., Fisk,D.G, Hirschman,J.E, Hong,E.L., Issel-Tarver,L., Nash,R., Sethuraman,A., Starr,B., Theesfeld,C.L., Andrada,R., Binkley,G., Dong,Q., Lane,C., Schroeder,M., Botstein,D. and Cherry,J.M. (2004).
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms Nucleic Acid Res., 32, D311-D314. [PubMed]
Colebatch,G., Desbrosses,G., Ott,T., Krussel,L., Montanari,O., Kloska,S., Kopka,J. & Udvardi,MK. (2004).
Global changes in transcription orchestrate metabolic differentiation during symbiotic nitrogen fixation in Lotus japonicus. (in preparation)
Craigon, D.J., James, N., Okyere, J. Higgins, J., Jotham, J. & May, S. (2004).
NASCArrays: a repository for microarray data generated by NASC`s transcriptomics service. Nucleic Acid Res., 32, D575-D577. [PubMed]
Courcelle,J., Khodursky,A., Peter,B., Brown,P.O. & Hanawalt,P.C. (2001).
Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli . Genetics, 158, 41-64. [PubMed]
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Glasner,J.D., Liss,P., Plunkett III,G., Darling,A., Prasad,T., Rusch,M., Byrnes,A., Gilson,M., Biehl,B., Blattner,F.R. & Perna,N.T. (2003).
ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acid Res., 31, 147-151. [PubMed]
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Khodursky,A.B., Peter,B.J., Cozzarelli,N.R., Botstein,D., Brown,P.O. & Yanofsky,C. (2000).
DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli. Proc. Natl. Acad. Sci. USA, 97, 12170-12175. [PubMed]
P

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Peterson,J.D., Umayam,L.A., Dickinson,T., Hickey,E.K. and White,O. (2001).
The Comprehensive Microbial Resource. Nucleic Acid Res., 29, 123-125. [PubMed]
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Rudd,K.E. (2000).
EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acid Res., 28, 60-64. [PubMed]
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Shannon,C.E. (1948).
A mathematical theory of communication. The Bell System Technical Journal., 27, 379-423. ibid, 623-656
Sherlock,G., Hernandez-Boussard,T., Kasarskis,A., Binkley,G., Matese,J.C., Dwight,S.S., Kaloper,M., Wenig,S., Jin,H., Ball.,C.A., Eisen,M.B., Spellman,P.T., Brown,P.O., Botstein,D. & Cherry,J.M. (2001).
The Stanford Microarray Database. Nucleic Acid Res., 29, 152-155. [PubMed]
Steuer,R., Kurths,J., Daub,C.O., Weise,J. & Selbig,J.(2002).
The mutual information: Detecting and evaluating dependencies between variables Bioinformatics, 18, S231-S240. [PubMed]
T

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Thimm,O., Bläsing,O., Gibon,Y., Nagel,A., Meyer,S. Krüger,P., Selbig,J., Müller,L.A., Rhee,S.Y. & Stitt,M. (2004).
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J., 37, 914-939. [PubMed]
W

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Wagner,C., Sefkow,M. & Kopka,J. (2003).
Construction and application of a mass spectral and retention time index database generated from plant GC/EI-TOF-MS metabolite profiles. Phytochemistry 62(6) 887-900. [PubMed]
Wu,L.F., Hughes,T.R., Davierwala,A.P., Robinson,M.D., Stoughton,R. & Altschuler,S.J. (2003).
Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet. , 31 , 255-265. [PubMed]

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