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Dr Boas Pucker

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Biography:

Boas studied Biochemistry at the Heinrich-Heine University Düsseldorf and Biology at Bielefeld University. His bachelor thesis is about the flavonoid biosynthesis in sugar beet. From 2014 to 2019, Boas participated in the synthetic biology competition iGEM in various roles. While completing the Master of Science program Genome-based Systems Biology, he shifted from molecular biology to bioinformatics and genomics. His doctoral thesis is about comparative analysis of different Arabidopsis thaliana genomes. Boas also investigated non-canonical splice sites in the genome sequences of numerous plant species. Parts of this research were performed during a visit in the Brockington group. In 2019, Boas received his doctoral degree from the Faculty of Biology at Bielefeld University. He was a member of the Computational Methods for the Analysis of the Diversity and Dynamics of Genomes (DiDy) graduate school and completed PhD programs in Biology and Bioinformatics.
Boas conducted many ONT long read sequencing and plant genome assembly projects at the Genetics and Genomics of Plants group (Center for Biotechnology, Bielefeld University) and at the Department of Molecular Genetics and Physiology of Plants (Ruhr-University Bochum). Since 2020, he is working as a postdoctoral fellow on the evolution of the betalain biosynthesis supported by a DFG fellowship.

Research Interests

Boas is interested in the evolution of specialised metabolism in plants with a particular focus on the betalain and flavonoid biosynthesis in Caryophyllales. He combines molecular biology and bioinformatics approaches including ONT long read sequencing, genome and transcriptome assembly, comparative genomics, gene expression analysis, and mapping-by-sequencing to address evolutionary questions. Boas is particularly interested how biosynthetic gene clusters are associated with the production of betalains.

Other Professional Activities

A comprehensive list of teaching activities, other professional activities, and previous research can be found here. Guest editor for the special issue Harnessing the Power of Genome and Transcriptome Assemblies at Plants.

Key Publications

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., 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

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

Other Publications

Pucker B., Schwandner A., Becker S., Hausmann L., Viehöver P., Töpfer R., Weisshaar B., Holtgräwe D. (2020). RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile. bioRxiv 2020.10.18.344176; doi: https://doi.org/10.1101/2020.10.18.344176.
full text PDF PUB

Xu B., Taylor L., Pucker B., Feng T., Glover B. J. and Brockington S. (2020). The land plant-specific MIXTA-MYB lineage is implicated in the early evolution of the plant cuticle and the colonization of land. New Phytologist. doi: 10.1111/nph.16997.
full text(peer-reviewed) PUB

Pucker B. and Brockington S. (2020). Pitaya transcriptome assemblies and investigation of transcript abundances. Bielefeld University. doi: 10.4119/unibi/2946374.
PUB github

Pucker B., Pandey A., Weisshaar B. and Stracke R. (2020). The R2R3-MYB gene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns. PLOS ONE 15(10): e0239275. doi:10.1371/journal.pone.0239275
full text(peer-reviewed) preprint PDF PUB github

Sielemann, K.*, Hafner, A.* and Pucker B. (2020). The Reuse of Public Datasets in the Life Sciences: Potential Risks and Rewards. PeerJ 8:e9954. doi: 10.7717/peerj.9954
full text(peer-reviewed) PDF preprint PUB *shared first authorship

Pucker, B., Reiher, F. and Schilbert, H. M. Automatic identification of players in the flavonoid biosynthesis with application on the biomedicinal plant Croton tiglium. Plants 2020, 9, 1103. doi:10.3390/plants9091103.
full text(peer-reviewed) PDF bioRxiv PUB github

Pellegrinelli V., Rodriguez-Cuenca S., Rouault C., Schilbert H., Virtue S., Moreno-Navarrete J. M., Bidault G., del Carmen Vazquez Borrego M., Dias A. R., Pucker B., Dale M., Campbell M., Carobbio S., Aron-Wisnewsky J., Mora S., Masiero M., Emmanouilidou A., Mukhopadhyay S., Dougan G., den Hoed M., Loos R., Fernandez-Real J. M., Chiarugi D., Clement K. and Vidal-Puig T. Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance. doi:10.21203/rs.3.rs-57182.
full text PDF

Frey, K., Weisshaar, B. and Pucker, B. (2020). Reference-based QUantification Of gene Dispensability (QUOD). bioRxiv. doi:10.1101/2020.04.28.065714.
full text PDF PUB github

Choi, J., Lee, T., Cho, J., Servante, E., Pucker, B., Summers, W., et al. The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. Nature Communications 11, 2114 (2020). doi:10.1038/s41467-020-16021-1.
full text(peer-reviewed) Apollo (free full text)

Schilbert H. M., Rempel A. and Pucker, B. (2020). Comparison of read mapping and variant calling tools for the analysis of plant NGS data. Plants. doi:10.3390/plants9040439.
full text(peer-reviewed) bioRxiv PDF PUB data

Siadjeu C.*, Pucker B.*, Viehoever P., Albach D. and Weisshaar B. (2020). High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing. Genes. doi:10.3390/genes11030274.
full text(peer-reviewed) bioRxiv PDF PUB github DNA extraction protocol data (PUB)
*shared first authorship

Frey K. & Pucker, B. (2020). Animal, fungi, and plant genome sequences harbour different non-canonical splice sites. Cells. doi:10.3390/cells9020458.
full text(peer-reviewed) PDF bioRxiv PUB github data (fungi) data (animals)

Holtgräwe, D., Rosleff Sörensen, T., Hausmann, L., Pucker, B., Viehöver, P., Töpfer, R., Weisshaar, B. (2020). 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. Front. Plant Sci. doi:10.3389/fpls.2020.00156.
full text(peer-reviewed) PDF bioRxiv PUB data set 1 data set 2 data set 3

Busche M*, Pucker B*, Viehöver P, Weisshaar B, Stracke R. (2020). Genome Sequencing of Musa acuminata Dwarf Cavendish Reveals a Duplication of a Large Segment of Chromosome 2. G3: Genes|Genomes|Genetics. doi:10.1534/g3.119.400847.
full text(peer-reviewed) PDF PUB bioRxiv github genome assemblies sequence variants
*shared first authorship

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

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., 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

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