User:Torsten Waldminghaus

Me after being productive

Hi, my name is Torsten Waldminghaus, and I'm PI of the Waldminghaus Lab. I was let to OpenWetWare by google years back, searching for certain protocols. I benefit a lot from people sharing their protocols on the internet and thought it might be a good idea to also let the world participate on my wisdom and experince. If you still want to you can email me through OpenWetWare. Below I'll describe a bit more about myself and the stuff I'm interested in.

CV

• since 2011: Professor for Synthetic Microbiology at SYNMIKRO - Center for Synthetic Microbiology of the Philipps-Universität Marburg (Germany) and PI of the Waldminghaus Lab

• 2007-2011: Postdoc at the Department of Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo (Norway) in the lab of Kirsten Skarstad

• 2004-2007: PhD at the Ruhr-University Bochum (Germany) PhD-thesis: ‘RNA-thermometers in bacteria’ in the lab of Franz Narberhaus

• 2002-2004: Studies in bioinformatics at the University of applied science Berlin (Germany) Master-thesis: ‘In silico analysis and selection of RNA secondary structures’ at the Max Planck Institute for Infection Biology under supervision of Volker Patzel

• 1999-2002: Studies in biology at the Ernst-Moritz-Arndt-University Greifswald (Germany) Diploma-thesis: ‘Investigations on the expression of clpX in Bacillus subtilis’ at the Division for Microbial Physiology and Molecular Biology in the lab of Michael Hecker

• 1996-1999: Basic studies in biology at the University of Potsdam (Germany)

• 1996: Theological studies and volunteer at the International Torchbearer Bibleschool in Holsby Brunn (Sweden)

Grants and Awards

• 2008-2010: Two year postdoc grant of the German Research Council (DFG)
• 2008: Ruth Massenberg Prize of Ruhr-University Bochum (Germany) for outstanding PhD thesis
• 2008: Travel grant of FEMS
• 2006: Travel grant of Ruth und Gert Massenberg Stiftung

Research interests

In general I like bacteria and complex systems.

A bit more detailed I enjoy working on:

• Regulation of replication in bacteria
• Synthetic chromosomes
• Searching funny patterns on chromosomes or in proteins [1]

Publications

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5. Waldminghaus T and Skarstad K. ChIP on Chip: surprising results are often artifacts. BMC Genomics. 2010 Jul 5;11:414. DOI:10.1186/1471-2164-11-414 |
9. Waldminghaus T, Gaubig LC, and Narberhaus F. Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers. Mol Genet Genomics. 2007 Nov;278(5):555-64. DOI:10.1007/s00438-007-0272-7 |

Links to follow

• http://reuter.mit.edu/dfgwiki wiki about german stipendiats abroad (in german)
• http://anabench.bcm.umontreal.ca/anabench/ nice starting point for computational biology stuff
• http://collections.plos.org/ploscompbiol/tensimplerules.php 10 rule collection for stuff important for scientist

Personal Links

• My Notebook
• Flow cytometry notes

• My strain list
• My qPCR-primer list
• My primer list
• My double strand oligo list
• primer concentrations
• blogger profile
• CiteULike library
• Protein gel and Western

OWW

• How to present research well
• Reviews
• OpenWetWare:Ideas
• /sandbox
• Affinity purification of antibodies
• ChIP-Chip E. coli
• Baby cell column
• Sodium azide
• Chromosomal DNA isolation from E. coli
• Temperature mixing formula
• Methylation analysis with qPCR
• Hardcore PubMeding (advanced PubMed searching)
• OriC/ter ratio determination
• Cell cycle analysis
• Berkmen lab
• Mazel lab

Lost and found protocols:

• Overlap Extension PCR
• Methylcellulose
• Bone Marrow Macrophages
• GHV-68 Plaque Assay
• Neutral red