logo   Proteome Center Rostock
Schillingallee 69, 18055 Rostock
Phone +49-381-494 4930, Fax +49-381-494 4932

 

Bioinformatics at the Proteome Center Rostock and the Institute of Immunology

The Bioinformatics group established at the Proteome Center Rostock together with the Transcriptomics and Proteomics groups at the center as a sub-project 12 of the BMBF (Federal Ministry for Research and Education) Leitprojekt "Proteom-Analyse des Menschen".

We perform analyses of expression data for collaborators within the University and external partners of the Leitprojekt. Local data and links to external databases are stored in the inhouse developed Laboratory Information Management System (LIMS), that we consider to be the first to provide a combined view on transcriptomics and proteomics expression data. A particular focus of our research is the comprehension of Quantitative Trait Loci (QTL) for the analysis of expression data.


Address

University of Rostock
Institute of Immunology
Proteome Center Rostock
Schillingallee 69
D-18055 Rostock
Germany

Tel: +49 381 494 4930
Fax: +49 381 494 4932		         University of Rostock
Medical Faculty
Institute of Immunology
Schillingallee 70
D-18055 Rostock
Germany

Tel: +49 381 494 5885
Fax: +49 381 494 5882

Resources

ExpressionView Logo   ExpressionView [Mouse] [Rat] [Human]
Integrated display for QTL and gene expression data on EnsEMBL

Pilota Logo   ProteoBase
Lab Information Management System (LIMS) integrating proteomics and transcriptomics projects

QTL and SNP resources Logo   QTL and SNP resources
Tools for comparative genomics, SNP selection, and map conversions

GOery Logo   GOery
Summary of descriptions for genes on the basis of GeneOntology

MS Peak List Logo   MS Peak List Comparison
Compare two lists from MS or MS^n experiments for common peaks or distinguished peaks in either set

mw&pi    mwpi2ensembl
Determine EnsEMBL peptides of a particular pI and molecular weight

MASCOT Logo   msms2mascot
Helps specifying MASCOT searches

wow   WOW
Find repeats, inverted repeats, palindromes and complementary regions in DNA

7+g   Glassify
Prediction of the coupling of G protein-coupled receptors (GPCRs) to their G proteins.

     Zinc Finger Resources
Classification of Krueppel-type (KRAB) zinc finger proteins

     Kruppel type Zinc Finger Gene Database
developed by Guohui Ding SCBIT

     SysZNF - Kruppel type Zinc Finger Gene Database
developed by Guohui Ding SCBIT

     PEPSIMU62 - Peptide simulation based on the BLOSUM 62 Matrix
developed by Guohui Ding SCBIT

     SCBIT Bioinformatic Tools  Utilities2007   Utilities2009
developed by Guohui Ding SCBIT

     InforSense Discovery Portal - KDE - NOT PUBLIC
encouraged by SCBIT

ProteinMap   ProteinMap - based on public website of HUMAN PROTEIN ATLAS
developed by Anne Kunze, Michael Kreutzer

EUROME Logo   EU project EUROME
Web site automatically generated from contents of the ProteoBase with public data

MASCOT   Local MASCOT Application of the Matrix Science MASCOT server NOT PUBLIC
This site features Mascot , a powerful search engine that uses mass spectrometry data to identify proteins from primary sequence databases. To assist you, the help text for Mascot forms a substantial knowledge base concerning protein identification by MS.

Modiro   Local Modiro Application server NOT PUBLIC


EnsEMBL Logo   Local mirror of EnsEMBL
The EnsEMBL project of the Sanger Center and the European Bioinformatics Institute represents a portal for the automated annotation of completely sequenced eukaryotic genomes. The version 16 installed at the PZR is from mid 2003. Although chimp and chicken are not available in this version, man, rat and mouse are well covered and as such our needs is mostly served.
 
    Scan and Find Proteomics MS Results
based stored MALDI MS data.
    Protein Sequence search and Pattern matching search
based on SwissProtNos or SwissProtIDs.
    SwissProt to AffyID lookup
based on Ensembl entries.
    Claudia Voigt - Umrechnung molarer massen
a small tool.

Resources ( extern )

A I D   The AutoImmune Disease Database  - Institute for Medical Informatics and Biometry - University of Rostock [Ver. 1.1]
Autoimmune diseases result from a dysfunction of the immune system in which the body attacks its own organs, tissues and cells. ...

People

Publications work done in Rostock since 8/2001

Steffen Möller, Dirk Koczan, Pablo Serrano-Fernández, Uwe K. Zettl, Hans-Jürgen Thiesen, Saleh M. Ibrahim "Selecting SNPs for association studies based on population frequencies: Generation of a novel interactive tool and its application to multiple sclerosis" In Silico Biol. 4, 0035 (2004). [Full text]

Möller S, Serrano-Fernandez P, Thiesen H-J, Zettl UK, Koczan D, Ibrahim SM (2004) Selecting single nucleotide polymorphisms by genetic linkage analyses and their distribution in populations. (submitted).

Möller S, Serrano-Fernández P, Watson M, Koczan D, Kotsikoris V, Kunz M, Blüggel M, Pahnke J, Illges H, Mikkat S, Thiesen H-J, Glocker MO, Zettl UK, Ibrahim SM (2004) Predicting soluble variants of membrane proteins. (submitted).

Serrano-Fernández P, Ibrahim SM, Thiesen H-J, Zettl UK, Gödde R, Epplen JT, Möller S (2004) Intergenomic Consensuses of Multifactorial Inheritance Loci: the Case of Multiple Sclerosis. (submitted)

Voigt C, Ibrahim SM, Möller S, Serrano-Fernández P (2004) Non-linear conversion between physical and chromosomal distances. Bioinformatics (in press).[Abstract]

Fischer G, Ibrahim SM, Brockmann GA, Pahnke J, Bartocci E, Thiesen HJ, Serrano-Fernández P, Möller S (2003) Expressionview: Visualization of Quantitative Trait Loci and Gene Expression Data in EnsEMBL. Genome Biology 4(2):R77.1-6.[Full text]
(This article reached place 30 under the most viewed publications in 2003 after the BioMed Central index, one month after publication date)

Kunz M, Möller S, Koczan D, Lorenz P, Wenger RH, Glocker MO, Thiesen H-J, Gross G, Ibrahim SM (2003) Mechanisms of hypoxic gene regulation of angiogenesis factor Cyr61 in melanoma cells. J. Biol. Chem. 2003 Aug 25 Abstract

S. Möller, P. Serrano-Fernández, S.M. Ibrahim, R. Gödde, M. Kreutzer, G. Fischer, G. Drews, J.T. Epplen, M.O. Glocker, H.J. Thiesen (2003) Pairwise gene homology vs. syntenic regions for the intergenomics of quantitative trait loci . XII. International Congress on Genes, Gene Families and Isozymes (Berlin, Germany: 2003).[Full text]

Möller S, Toldo L (2003) EnsEMBL, Linux Magazin, pp. 66-68, July 2003
also appeared in the August 2003 UK edition.

Möller S, Weber I, Kreutzer M, Schroeder M (2002) Integration of Heterogenous Data Sources for Proteomics and Transcriptomics. In: Proceedings of NETTAB 2002

Rousseau-Merck M-F, Koczan D, Legrand I, Möller S, Autran S, Thiesen H-J (2002) The KOX zinc finger genes: Genome wide mapping of 386 ZNF PAC clones with zinc finger gene clusters predominantly in 23 chromosomal loci are confirmed by human sequences annotated in EnsEMBL Cytogenetic and Genome Research 98(2-3):147-153 Abstract

Bioinformatics in Rostock


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