Selected Publications in Bioinformatics

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. P. Cossio, D. Rohr, F. Baruffa, M. Rampp, V. Lindenstruth, G. Hummer. to appear in Computer Physics Communications (2016) (arXiv:1609.06634)

Dnmt2-dependent methylomes lack defined DNA methylation patterns. G. Raddatz, P. M. Guzzardo, N. Olova, M. R. Fantappié, M. Rampp, M. Schaefer, W. Reik, G. J. Hannon, F. Lyko PNAS (2013). doi:10.1073/pnas.1306723110
Genome of the Haloarchaeon Natronomonas moolapensis, a Neutrophilic Member of a Previously Haloalkaliphilic Genus. Dyall-Smith M.L., Pfeiffer F., Oberwinkler T., Klee K., Rampp M., Palm P., Gross K., Schuster S.C., Oesterhelt D. Genome Announc. (2013). doi: 10.1128/genomeA.00095-13
Chloride & organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus. Saum S., Pfeiffer F., Palm P., Rampp M., Schuster S., Müller V., Oesterhelt D., Environmental Microbiology (2012). doi: 10.1111/j.1462-2920.2012.02770.x
The complete genome sequence of Thermoproteus tenax: A physiologically versatile member of the Crenarchaeota. Siebers B., Raddatz G., Zaparty M., Tjaden B., Albers S.V., Bell S.D., Blombach F., Kletzin A., Kyrpides N., Lanz C., Plagens A., Rampp M., Rosinus A., von Jan M., Makarova K., Klenk H.P., Schuster S.C., Hensel R. PLoS ONE 6(10): e24222 (2011). doi:10.1371/journal.pone.0024222.
Haloquadratum walsbyi: Limited Diversity in a Global Pond. Dyall-Smith, M.L., F. Pfeiffer, K. Klee, P. Palm, K. Gross, S.C. Schuster, M. Rampp, D. Oesterhelt PLoS ONE 6(6): e20968 (2011) doi:10.1371/journal.pone.0020968
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581^T. Schwibbert, K., A. Marin Sanguino, I. Bagyan, G. Heidrich, G. Lentzen, H. Seitz, M. Rampp, S.C. Schuster, H.-P. Klenk, F. Pfeiffer, D. Oesterhelt, H.J. Kunte. Environmental Biology (2010)

Pfeiffer, F., A. Broicher, Th. Gillich, K. Klee, J. Mejia, M. Rampp, D. Oesterhelt
Genome information management and integrated data analysis with HaloLex. Archives of Microbiology 190(3), 281-299 (2008)
Rampp, M., T. Soddemann, H. Lederer:
The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Research 34 (Web Server issue), W15-W19 (2006).
Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.:
The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics, 7 169 (2006)
Poinar,H., C. Schwarz, J. Qi, B. Shapiro, R. MacPhee, B. Buigues, A. Tikhonov, D. Huson, L. Tomosho, A. Auch, M. Rampp, W. Miller and S. Schuster:
Metagenomics to paleogenomics: Large scale sequencing of Mammoth DNA. Science 311, 5759, 392-394 (2006).
Rampp,M., T. Soddemann:
A Work Flow Engine for Microbial Genome Research. In "Forschung und wissenschaftliches Rechnen 2004", K.Kremer, V.Macho (eds.), GWDG Report 68, 23-46 (2005).
Baar,C., M. Eppinger, G. Raddatz, J. Simon, C. Lanz, O. Klimmek, R. Nandakumar, R. Gross, A. Rosinus, H. Keller, P. Jagtap, B. Linke, F. Meyer, H. Lederer and S. Schuster:
Complete genome sequence and analysis of Wolinella succinogenes. PNAS 100, 20, 11690-11695 (2003).
Falb,M., Pfeiffer,F., Palm,P., Rodewald,K., Hickmann,V.,Tittor,J. and Oesterhelt,D.: Living with two extremes: Conclusions from the genome sequence of Natronomonas pharaonis. Genome Res. (2005) 15(10):1336-43
Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D.: The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics, 7 169 (2006)
Pfeiffer F, Schuster SC, Broicher A, Falb M, Palm P, Rodewald K, Ruepp A, Soppa J, Tittor J, Oesterhelt D.: Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1. Genomics. 2008 Jun;91(6):548-52
Eppinger, M., Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC: Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLOS Genetics, 2(7), e120 (2006)
Saenz, H.L., P. Engel, M.C. Stoeckli, C. Lanz, G. Raddatz, M. Vayssier-Taussat, R. Birtles, S.C. Schuster, C. Dehio: Genomic analysis of Bartonella identifies type IV secretion systems as host adaptability factors, Nature Genetics, 39(12):1469-76 (2007)
Zimmerer, H.: Evaluation of sequence comparison methods for metagenomics. Diplomarbeit, Eberhard Karls Universität Tübingen, (2007)
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A.: GenDB--an open source Genome annotation system for prokaryote genomes. Nucleic Acids Res. 2003 Apr 15;31(8):2187-95