Dr. Boas Pucker

Projects for students: Please send me an email if you are interested in a project involving the topics listed below.

Collaborations: I am always interested in collaborations involving genomics or bioinformatic analyses. Please send me an email.

Reviews: Review requests from high quality open access journals are welcome if they match my expertise (see below).

Genome Research


Transcriptomics / RNA-Seq analyses


Evolution


Synthetic Biology (iGEM)

iGEM is the largest competition for synthetic biology. Student teams from all over the world participate and present their project at the annual Giant Jamboree. iGEM Bielefeld-CeBiTec participates in iGEM since 2010. I was involved in 2014 (team member), 2016 (supervision), 2017 (supervision), 2018 (supervision), and 2019 (supervision). In addition, I severed as a Judge at the Giant Jamboree and mentored several other teams including Athens 2019 and Thessaly 2019. After iGEM selected me as 'iGEMer of the month' in September 2019.


Teaching

The ekVV provides an overiew of my courses (German & English) at Bielefeld University. In addition, I am teaching through supervison of iGEM Bielefeld-CeBiTec teams as outlined above. My projects about digitial innovations in higher education were kindly supported by a fellowship from the Stifterverband. Here is a list of my courses with links to slides and data sets:


CV

Positions Education
  • 05/2019: Dr. rer. nat. (very good), Faculty of Biology (Bielefeld University), thesis: De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analyses across plant species
    Dissertation Boas Pucker
  • 2017-2019 Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (DiDy) | GRK1906
  • 2017-2020 PhD Program Bioinformatics (Bielefeld University)
  • 2016-2019 PhD Program Biology (Bielefeld University)
  • 2013-2015 Genome-Based Systems Biology (GBSB)(Bielefeld University)
  • 2010-2013 Biology (Genetics, Cell Biology, Physiology) (Bielefeld University)
  • 2009-2010 Biochemistry (Heinrich Heine University Duesseldorf)
Awards, funding, and scholarships
Peer Review Activity

A comprehensive list of my review activities is available via Publons.

Agriculture, Agronomy, BMC Genomics, Frontiers in Plant Sciences, Molecular Biology Reports, Scientific Reports, Genes, Journal of Limnology and Freshwater Fisheries Research, PeerJ, PLOS ONE, Springer, Plants

Memberships
  • Plantae / American Society of Plant Biologists (ASPB)
  • Deutscher Hochschul Verband (DHV)
  • Deutsche Botanische Gesellschaft (DBG)



Publications

  • Frey K., Pucker, B. (2020). Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. bioRxiv 616565. doi:10.1101/616565.
    full text PDF PUB github data (fungi) data (animals)
  • Busche M*, Pucker B*, Viehöver P, Weisshaar B, Stracke R. Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2. G3: Genes|Genomes|Genetics. 2020.doi:10.1534/g3.119.400847.
    full text(peer-reviewed) PDF PUB bioRxiv github genome assemblies sequence variants
    *shared first authorship
  • Holtgräwe, D., Rosleff Sörensen, T., Hausmann, L., Pucker, B., Viehöver, P., Töpfer, R., Weisshaar, B. (2019). A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia x Vitis cinerea) and its Exploitation for Marker Development and Targeted Mapping. bioRxiv 854687. doi: https://doi.org/10.1101/854687
    full text PDF PUB data set 1 data set 2 data set 3
  • Pucker B & Schilbert H. Genomics and Transcriptomics Advance in Plant Sciences. Molecular Approaches in Plant Biology and Environmental Challenges. Springer. 2019. ISBN 978-981-15-0690-1. doi:10.1007/978-981-15-0690-1
    springer(peer-reviewed book chapter) PUB
  • Pucker B, Rückert C, Stracke R, Viehöver P, Kalinowski J, Weisshaar B. Twenty-Five Years of Propagation in Suspension Cell Culture Results in Substantial Alterations of the Arabidopsis Thaliana Genome. Genes. 2019. doi:10.3390/genes10090671
    full text(peer-reviewed) PDF bioRxiv PubMed PUB github
  • Sheehan, H., Feng, T., Walker-Hale, N., Lopez-Nieves, S., Pucker, B., Guo, R., Yim, W. C., Badgami, R., Timoneda, A., Zhao, L., Tiley, H., Copetti, D., Sanderson, M. J., Cushman, J. C., Moore, M. J., Smith, S. A., Brockington, S. F. Evolution of L-DOPA 4,5-dioxygenase activity allows for recurrent specialisation to betalain pigmentation in Caryophyllales. New Phytologist. 2019. doi:10.1111/nph.16089
    full text(peer-reviewed) PDF PubMed PUB Apollo
  • Timoneda, A., Feng, T., Sheehan, H., Walker-Hale, N., Pucker, B., Lopez-Nieves, S., Guo, R., Brockington, S. (2019). The evolution of betalain biosynthesis in Caryophyllales. New Phytologist. doi:10.1111/nph.15980
    full text(peer-reviewed) PDF PubMed PUB
  • Pucker, B. Schilbert, H.M., Schumacher, S.F. (2019). Integrating Molecular Biology and Bioinformatics Education. Journal of Integrative Bioinformatics. doi:10.1515/jib-2019-0005.
    full text(peer-reviewed) PDF PubMed preprint PUB
    Applied Genome Research (github) Molecular Methods in Genome Research (github)
  • Pucker, B., Feng, T., Brockington, S. (2019). Next generation sequencing to investigate genomic diversity in Caryophyllales. bioRxiv 646133; doi:10.1101/646133.
    full text PDF PUB data github
  • Pucker, B., Holtgraewe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., & Weisshaar, B. (2019). A Chromosome-level Sequence Assembly Reveals the Structure of the Arabidopsis thaliana Nd-1 Genome and its Gene Set. PLOS ONE: e0216233. doi: 10.1371/journal.pone.0216233
    full text(peer-reviewed) PDF PubMed bioRxiv PUB data github
  • Pucker, B. (2019). Mapping-based genome size estimation. bioRxiv. doi:10.1101/607390.
    full text PDF PUB github (MGSE)
  • Baasner, J.-S., Howard, D., Pucker, B. (2019). Influence of neighboring small sequence variants on functional impact prediction. bioRxiv. doi:10.1101/596718.
    full text PDF PUB github (NAVIP) github (other scripts)
  • Pucker, B. (2019). De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analyses across plant species. Dissertation. doi:10.4119/unibi/2935794.
    PDF PUB DOI
  • Pucker, B. and Brockington, S.F. (2018). Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5360-z.
    full text(peer-reviewed) PDF PubMed bioRxiv PUB Apollo data github
  • Schilbert, H.M., Pellegrinelli, V., Rodriguez-Cuenca, S., Vidal-Puig, A. & Pucker, B. (2018). Harnessing natural diversity to identify key amino acid residues in prolidase. bioRxiv 423475; doi:10.1101/423475.
    full text PDF PUB github zenodo
  • Brinkrolf, C., Henke, N. A., Ochel, L., Pucker, B., Kruse, O., and Lutter, P. (2018). Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. Journal of Integrative Bioinformatics 15. doi:10.1515/jib-2018-0018.
    full text(peer-reviewed) PDF PubMed PUB VANESA
  • Whitford, C. M., Dymek, S., Kerkhoff, D., März, C., Schmidt, O., Edich, M., Droste, J., Pucker, B., Rückert, C. and Kalinowski, J. (2018). Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications. Journal of Biological Engineering, 12(1). doi:10.1186/s13036-018-0105-8.
    full text(peer-reviewed) PDF PubMed PUB Apollo iGEM
  • Haak, M., Vinke, S., Keller, W., Droste, J., Rückert, C., Kalinowski, J., & Pucker, B. (2018). High Quality de novo Transcriptome Assembly of Croton tiglium. Frontiers in Molecular Biosciences, 5. doi:https://doi.org/10.3389/fmolb.2018.00062.
    full text(peer-reviewed) PDF PubMed PUB RNA-Seq data assembly
  • Friedrich, A., & Pucker, B. (2018). Peer-review as a teaching method. Working Paper der AG Forschendes Lernen in der dghd, 2, 2018. Carl von Ossietzky Universität Oldenburg.
    full text(peer-reviewed) PDF PUB github
  • Pucker, B., Holtgräwe, D., & Weisshaar, B. (2017). Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. BMC Research Notes, 10, 667. doi:10.1186/s13104-017-2985-y.
    full text(peer-reviewed) PDF PubMed PUB
  • Karsten, L., Bergen, D., Drake, C., Dymek, S., Edich, M., Haak, M., Kerkhoff, D., Kerkhoff, Y., Liebers, M., März, C., Schlüter, L., Schmidt, O., Vinke, S., Whitford, C.M., Pucker, B., Droste, J., Rückert, C., Müller, K.M., Kalinowski, J. (2017). Expanding The Genetic Code. Bielefeld University. doi:10.13140/RG.2.2.20342.91203.
    full text PUB
  • Alkhateeb, R., Rückert, C., Rupp, O., Pucker, B., Hublik, G., Wibberg, D., Niehaus, K., Pühler, A., Vorhölter, F.J. (2017). Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data. Journal of Biotechnology. doi:10.1016/j.jbiotec.2017.05.009.
    full text(peer-reviewed) PubMed PUB
  • Pucker, B., Holtgräwe, D., Rosleff Sörensen, T., Stracke, R., Viehöver, P., and Weisshaar, B. (2016). A de novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PloS-ONE 11:e0164321. doi:10.1371/journal.pone.0164321.
    full text(peer-reviewed) PDF PubMed PUB NCBI BioProject
  • Frommer, B, Hain, C., Kampa, J., Königs, C., Linder, M., Perez Knoche, S., Sahin, M., Schmidt, P., Schöller, M., Kalinowski, J., Müller, K.M., Droste, J., Hoffmann, N., Roeloffs, F., Pucker, B. (2016). Generating Binding Proteins - via in vivo directed evolution in E. coli. doi:10.13140/RG.2.2.23164.95367.
    full text
  • Fust A., Hollmann B., Pucker, B., Wollborn D., Tiemann J., Droste J., Brosda S., Blunk S., Riedl S., Bleckwehl T. (2014). The Transformers. From Carbon Dioxide to Biofuel. doi:10.13140/RG.2.2.30504.98566.
    full text PUB PLOS Report
  • Stracke, R., Holtgräwe, D., Schneider, J., Pucker, B., Sörensen, T.R., and Weisshaar, B. (2014). Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris). BMC Plant Biol. 14: 249. doi:10.1186/s12870-014-0249-8.
    full text(peer-reviewed) PDF PubMed PUB RNA-Seq data