TAP family clustering from PlantTAPDB Wordle

research

We are interested in the evolution of plants sensu lato - i.e., the photosynthetic eukaryotes.
A main focus is the moss, Physcomitrella patens.
Methods encompass molecular and cellular biology, phylogeny, phylogenomics and comparative genomics.
In terms of systems biology we are interested in gene regulatory networks.
We are studying the evolution of plant interactions with fungi and bacteria to mutually exchange nutrients.

Bryophyta in the Tree of Life & worldwide distribution of Funariaceae

Most cited paper - Most recent important paper

Our lab's research ranks 23rd in German plant science (source: Laborjournal)

list of publications
(Orcid id orcid_icon)
hosted locally (including PDFs)
@ Google Scholar google_scholar_icon (sorted by # of citations)
@ PubMed NCBI_icon (sorted chronologically)
@ Researchgate Researchgate_icon

General tools and resources

P. patens resources and links

GTP and ATP2 - Green Targeting Predictor and Ambiguous mt/pt Targeting Predictor 2
Fuss J., Liegmann O., Krause K., Rensing S.A. (2013) New Phytol 200:1022

Gene model v3.3 annotation spreadsheet
Ecotype Reute pseudogenome sequence

ATP - ambiguous mt/pt protein targeting predictor
Mitschke J., Fuss J., Blum T., Höglund A., Reski R., Kohlbacher O., Rensing S.A. (2009) Prediction of dual protein targeting to plant organelles. New Phytol 183:224

The P. patens genome browser
& other resources @ cosmoss.org

cosmoss.org logo
KeyS - software for paralog clustering and Ks distribution plots (please contact Stefan Rensing)
Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R (2007) An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol 7:130

The P. patens genome @ JGI / NCBI
& more resources @ Physcobase / plant-biotech.net


PlanTAPDB - plant transcription associated proteins
Richardt S, Lang D, Reski R, Frank W and Rensing SA (2007) PlanTAPDB: A phylogeny-based resource of plant transcription associated proteins. Plant Physiol 143:1452-1466

Phylogenetic trees of several gene families
Rensing SA, Lang D, Zimmer AD et al. (2008) The genome of the moss Physcomitrella patens reveals evolutionary insights into the conquest of land by plants. Science 319:64-69
  SSR markers and P. patens ecotypes
von Stackelberg M, Rensing SA and Reski R (2006) Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biology 6:9
  SVM-based splice site prediction for P. patens
Rensing SA, Fritzowsky D, Lang D and Reski R (2005) Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens. BMC Genomics 6:43
  P. patens UTR repeats
Rensing SA, Lang D and Reski R (2003) In silico prediction of UTR repeats using clustered EST data. In: Proceedings of the German Conference on Bioinformatics 2003, Mewes H-W, Heun V, Frishman D, Kramer S (eds.), pp 117-122, Belleville Verlag Michael Farin, Munich, Germany
 

 

We are grateful for funding by

BMWI logo  DFG logo  BMBF  FRISYS  bioss

Uni Freiburg MWK BW DAAD

Seed Adapt Seed Adapt MWK BW