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Center for Computational and Theoretical Biology

Computational Evolutionary Biology


Research

The capability to evolve is a hallmark of all biological systems. Reconstructing evolutionary history and unraveling underlying mechanisms is the main interest of my group. Currently, we are focusing on three different levels, namely proteins, transcriptomes and genomes. The common denominator of our projects is the use of computational and statistical methods to analyze large-scale data with the aim to understand how biological systems change over time.


Current Projects


Publications

2020[ to top ]
  • Dreyer, I., Sussmilch, F. C., Fukushima, K., Riadi, G., Becker, D., Schultz, J., & Hedrich, R. {{H}ow to {G}row a {T}ree: {P}lant {V}oltage-{D}ependent {C}ation {C}hannels in the {S}potlight of {E}volution}. Trends Plant Sci.
  • Palfalvi, G., Hackl, T., Terhoeven, N., Shibata, T. F., Nishiyama, T., Ankenbrand, M., Becker, D., Förster, F., Freund, M., Iosip, A., Kreuzer, I., Saul, F., Kamida, C., Fukushima, K., Shigenobu, S., Tamada, Y., Adamec, L., Hoshi, Y., Ueda, K., Winkelmann, T., Fuchs, J., Schubert, I., Schwacke, R., Al-Rasheid, K., Schultz, J., Hasebe, M., & Hedrich, R. {{G}enomes of the {V}enus {F}lytrap and {C}lose {R}elatives {U}nveil the {R}oots of {P}lant {C}arnivory}. Curr Biol, 30(12), 2312-2320.
  • Keller, A., Hohlfeld, S., Kolter, A., Schultz, J., Gemeinholzer, B., & Ankenbrand, M. J. BCdatabaser: on-the-fly reference database creation for DNA (meta-)barcoding. Bioinformatics, in press.
2019[ to top ]
  • Sickel, W., Van de Weyer, A. L., Bemm, F., Schultz, J., & Keller, A. {{V}enus flytrap microbiotas withstand harsh conditions during prey digestion}. FEMS Microbiol. Ecol., 95(3), Article 3.
  • Sussmilch, F. C., Schultz, J., Hedrich, R., & Roelfsema, M. R. G. {{A}cquiring {C}ontrol: {T}he {E}volution of {S}tomatal {S}ignalling {P}athways}. Trends Plant Sci., 24(4), 342-351.
2018[ to top ]
  • Ankenbrand, M. J., Pfaff, S., Terhoeven, N., Qureischi, M., Gündel, M., Wei{\ss}, C. L., Hackl, T., & Förster, F. {chloroExtractor}: extraction and assembly of the chloroplast genome from whole genome shotgun data. The Journal of Open Source Software, 3(21), 464. https://doi.org/10.21105/joss.00464
  • Terhoeven, N., Schultz, J., & Hackl, T. reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. Journal of Open Source Software, 3(22), 527. https://doi.org/https://doi.org/10.21105/joss.00527
  • Terhoeven, N., Schultz, J., & Hackl, T. reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome. The Journal of Open Source Software, 3(22), 527. https://doi.org/10.21105/joss.00527
2017[ to top ]
  • Ankenbrand, M. J., Terhoeven, N., Hohlfeld, S., Förster, F., & Keller, A. biojs-io-biom, a {BioJS} component for handling data in Biological Observation Matrix ({BIOM}) format. F1000Research, 5, 2348. https://doi.org/10.12688/f1000research.9618.2
2016[ to top ]
  • Brinkmann, K., Winterhoff, M., Onel, S. F., Schultz, J., Faix, J., & Bogdan, S. {{W}{H}{A}{M}{Y} is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in {D}rosophila}. J. Cell. Sci., 129(3), 604-620.
  • Bemm, F., Becker, D., Larisch, C., Kreuzer, I., Escalante-Perez, M., Schulze, W. X., Ankenbrand, M., Van de Weyer, A. L., Krol, E., Al-Rasheid, K. A., Mithofer, A., Weber, A. P., Schultz, J., & Hedrich, R. {{V}enus flytrap carnivorous lifestyle builds on herbivore defense strategies}. Genome Res., 26(6), 812-825.
  • Bemm, F., Weiss, C. L., Schultz, J., & Forster, F. {{G}enome of a tardigrade: {H}orizontal gene transfer or bacterial contamination?}. Proc. Natl. Acad. Sci. U.S.A.
  • Ja?lan, D., Mueller, T. D., Becker, D., Schultz, J., Cuin, T. A., Marten, I., Dreyer, I., Schonknecht, G., & Hedrich, R. {{G}ating of the two-pore cation channel {A}t{T}{P}{C}1 in the plant vacuole is based on a single voltage-sensing domain}. Plant Biol (Stuttg), 18(5), 750-760.
  • Schwarz, R. F., Tamuri, A. U., Kultys, M., King, J., Godwin, J., Florescu, A. M., Schultz, J., & Goldman, N. {{A}{L}{V}{I}{S}: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments}. Nucleic Acids Res., 44(8), e77.
  • Ankenbrand, M. J., Weber, L., Becker, D., Förster, F., & Bemm, F. TBro: visualization and management of de novo transcriptomes. Database, 2016. https://doi.org/https://dx.doi.org/10.1093/database/baw146
2015[ to top ]
  • Ankenbrand, M. J., Keller, A., Wolf, M., Schultz, J., & Forster, F. {{I}{T}{S}2 {D}atabase {V}: {T}wice as {M}uch}. Mol. Biol. Evol., 32(11), 3030-3032.