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cathteam:rentzsch [2010/04/12 17:19]
cathteam
cathteam:rentzsch [2012/08/08 13:50] (current)
cathteam
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 +====== CATH Team ======
 +
 +{{ :cathteam:robs_pic.jpg|Me}}
 +
 +===== Former PhD student =====
 +
 +I did my PhD in the lab between 2007 and 2012, funded by a EU grant (ENFIN). The [[http://www.enfin.org/page.php?page=home|ENFIN Network of Excellence]] aims at close collaboration between experimental and computational groups throughout Europe. I've also worked as a research assistant here.
 +
 +===== PhD Research =====
 +
 +My PhD work focused on protein functional annotation using sequence, sequence profile, and clustering-based methods. This is to enrich functional annotation data for the CATH and Gene3D resources and will form the basis of domain-centric comparative (meta)genomic studies. 
 +
 +In a large-scale sequence comparison study I revisited sequence identity thresholds for safe function transfer between known and uncharacterised protein sequences. The use of CATH domain superfamily-specific thresholds, comparing sequences at the domain level, proved to yield higher transfer rates than comparisons on the whole protein level. Following that I wrote a review on protein function annotation.
 +
 +Finally, I developed a pipeline that enables the subclustering of large Gene3D domain superfamilies (see [[:projects:gemma|GeMMA]]). Due to the high computational demands of this project it was implemented on the UCL high-performance compute cluster [[http://www.ucl.ac.uk/research-computing/information/services/cluster|Legion]] and other, smaller HPC resources.
 +
 +===== Pre-Doc Research =====
 +
 +For my M.Sc. thesis at [[http://www.cubic.uni-koeln.de/|CUBIC]] in Cologne, Germany (now relocated to [[http://bibc.tu-bs.de/bioinf/index.html|TU Braunschweig]], headed by Dietmar Schomburg and home of the [[http://www.brenda-enzymes.info/|BRENDA enzyme database]]) I established a novel protocol for the annotation of prokaryotic genomes and in particular the genome of C. glutamicum. This 'reverse' protocol omits the gene prediction step (the conventional approach being gene prediction followed by similarity searches, i.e. spatial followed by functional annotation): all annotation is done by integrating the results of exhaustive similarity searches against the given genome. 
 +
 +Prior to this I had studied Biology at the [[http://www.uni-muenster.de/en/index.html|Westfalian Wilhelms University]] in Muenster, Germany, including work on site-dependent evolutionary constraints in bHLH transcription factor proteins in the group of Erich Bornberg-Bauer. Believe it or not, I also did some very enjoyable wet lab biochemistry on human Grx2 in Arne Holmgren's lab at the [[http://ki.se/ki/jsp/polopoly.jsp?d=130&l=en|Karolinska Institute]] in Stockholm, Sweden.
 +
 +===== Publications =====
 +
 +{{pubmed>long:19923231}}
 +{{pubmed>long:19251332}}
 +{{pubmed>long:19135455}}
 +
 +===== Other Interests =====
 +
 +I quite enjoy listening to and making music (git, drums, voc). The same goes for the lyrics that often come along with it. Poetry, films and philosophy are good too. And running.
 +
 +Here you can find my attempts with scientific writing, the outcome of an internship at Nature's Munich office:
 +
 +{{pubmed>short:16555376}}
 +{{pubmed>short:16421530}}\\
 +Rentzsch R [[http://www.nature.com/news/2006/060224/full/news060220-18.html|Nature News, doi:10.1038/news060220-18]] (2006 Feb 24)\\
 +Giles J & Rentzsch R [[http://www.nature.com/news/2006/060220/full/news060220-4.html|Nature News, doi:10.1038/news060220-4]] (2006 Feb 20)
 +
 +===== Other CATH Team Members =====
 +
 +~~DIR?cols=page;description&hdrs=Person; Description~~
 +
  
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