Prof. Dr. Boas Pucker

Boas Pucker

Positions

 

  • since 2021: Plant Biotechnology and Bioinformatics, TU Braunschweig
  • 2020-2021: Evolution and Diversity, Department of Plant Sciences, University of Cambridge
  • 2019-2020: Molecular Genetics and Physiology of Plants, Ruhr-University Bochum
  • 2016-2019: Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University

 

Degrees

  • Dr. rer. nat. (Faculty of Biology, Bielefeld University)
  • PhD program Bioinformatics (Bielefeld University)
  • PhD program Biology (Bielefeld University)
  • M.Sc. Genome-based Systems Biology (Bielefeld University)
  • B.Sc. Biology (Bielefeld University)

 

Awards, Funding, and Scholarships

  • DFG Research Fellowship 'Understanding the convergent evolution of a complex metabolic trait, the Betalains, through comparative genomics and co-expression networks' at the Department of Plant Sciences, University of Cambridge
  • Research Fellowship for Plant Genomics and Bioinformatics
  • Fellowship for Digital Innovations in Academic Teaching (Stifterverband)
  • DAAD scholarship
  • Award for excellent Master thesis (Friedrich Wilhelm Helweg foundation)
  • Deutschlandstipendium

Publications

Please see my Google scholar profile for an automatically updated list

2022

  • Movahedi A, Wei H, Pucker B, Sun W, Li W, Yang L, Zhuge Q (2022). Regulation of poplar isoprenoid biosynthesis by methylerythritol phosphate and mevalonic acid pathways interactions. bioRxiv 2020.07.22.216804; doi: 10.1101/2020.07.22.216804.

  • Rajput, R., Tyagi, S., Naik, J. et al. The R2R3-MYB gene family in Cicer arietinum: genome-wide identification and expression analysis leads to functional characterization of proanthocyanidin biosynthesis regulators in the seed coat. Planta 256, 67 (2022). doi:10.1007/s00425-022-03979-z.

  • Mengist MF, Grace MH, Mackey T, Munoz B, Pucker B, Bassil N, Luby C, Ferruzzi M, Lila MA and Iorizzo M (2022) Dissecting the genetic basis of bioactive metabolites and fruit quality traits in blueberries (Vaccinium corymbosum L.). Front. Plant Sci. 13:964656. doi: 10.3389/fpls.2022.964656.

  • Busche M., Pucker B., Weisshaar B., Stracke R. Three R2R3-MYB transcription factors from banana (Musa spp.) activate structural anthocyanin biosynthesis genes as part of an MBW complex. bioRxiv 2022.08.15.503939; doi: doi.org/10.1101/2022.08.15.503939

  • Schilbert H. M., Pucker B., Ries D., Viehöver P., Micic Z., Dreyer F., Beckmann K., Wittkop B., Weisshaar B., Holtgräwe D.. Mapping-by-sequencing reveals genomic regions associated with seed quality parameters in Brassica napus. Genes 2022, 13(7), 1131; https://doi.org/10.3390/genes13071131

  • Ballmann, R.; Hotop, S.; Bertoglio, F.; Steinke, S.; Heine, P.A.; Chaudhry, M.; Jahn, D.; Pucker, B.; Baldanti, F.; Piralla, A.; Schubert, M.; Čičin-Šain, L.; Hust, M.; Dübel, S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-Cov-2 Spike Protein. Viruses 2022, 14, 1326. doi: 10.3390/v14061326.

  • Pucker B (2022). Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 23, 220 (2022). https://doi.org/10.1186/s12864-022-08452-5.

  • Pucker B, Irisarri I, de Vries J and Xu B (2022). Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Quantitative Plant Biology, 3, E5. doi: 10.1017/qpb.2021.18

  • Pucker B & Selmar D (2022). Biochemistry and Molecular Basis of Intracellular Flavonoid Transport in Plants. Plants 2022, 11, 963. doi:  10.3390/plants11070963

  • Pucker B & Iorizzo M (2022). Apiaceae FNS I originated from F3H through tandem gene duplication. bioRxiv 2022.02.16.480750; doi: 10.1101/2022.02.16.480750

  • Sielemann K, Pucker B, Schmidt N, Viehoever P, Weisshaar B, Heitkam T, Holtgraewe D (2021). Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics 23, 113 (2022). doi: 10.1186/s12864-022-08336-8.

  • Pellegrinelli, V., Rodriguez-Cuenca, S., Rouault, C., Schilbert, H., Virtue, S., Moreno-Navarrete, J. M., Bidault, G., Borrego, M. del C. V., Dias, A. R., Pucker, B., et al. (2022). Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance. Nature Metabolism 4, 476-494. full text preprint

2021

  • Pucker B (2021). Automatic identification and annotation of MYB gene family members in plants. bioRxiv 2021.10.16.464636; doi: 10.1101/2021.10.16.464636.
  • Movahedi A, Wei H, Pucker B, Sun W, Li W, Yang L, Zhuge Q (2021). Regulation of poplar isoprenoid biosynthesis by methylerythritol phosphate and mevalonic acid pathways interactions. bioRxiv 2020.07.22.216804; doi: 10.1101/2020.07.22.216804.
  • Schilbert H, Kleinbölting N, Weisshaar B, Pucker B. (2021). Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads. Bielefeld University.
    full text PUB
  • Pucker, B.*, Kleinbölting, N.* and Weisshaar, B. (2021). Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. doi: 10.1186/s12864-021-07877-8
    full text PDF preprint PUB github github
  • Pucker B., Singh H.B., Kumari M., Khan M.I., Brockington S.F. (2021) The report of anthocyanins in the betalain-pigmented genus Hylocereus is not well evidenced and is not a strong basis to refute the mutual exclusion paradigm. BMC Plant Biology 21(1): 297.
    full text PDF PUB data
  • Montero, H., Lee, T., Pucker, B., Ferreras-Garrucho, G., Oldroyd, G., Brockington, S.F., Miyao, A. and Paszkowski, U. A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage. PNAS (2021). doi:10.1073/pnas.2105281118
    full text(peer-reviewed) PDF PUB
  • Naik, J., Rajput, R., Pucker, B., Stracke, R. and Pandey, A. The R2R3-MYB transcription factor MtMYB134 orchestrates flavonol biosynthesis in Medicago truncatula. Plant Mol Biol (2021). doi:10.1007/s11103-021-01135-x
    full text(peer-reviewed) PDF
  • Sielemann, K., Weisshaar, B. and Pucker, B. (2021). Reference-based QUantification Of gene Dispensability (QUOD). Plant Methods 17, 18. doi: 10.1186/s13007-021-00718-5. full text(peer-reviewed) bioRxiv PDF PUB github
  • Xu B., Taylor L., Pucker B., Feng T., Glover B. J. and Brockington S. (2021). 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

2020

  • 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. Plants 2020, 9(11), 1548; doi:10.3390/plants9111548.
    full text(peer-reviewed) preprint PDF 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
  • 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) PUB
  • 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
  • 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. 2020. doi:10.1111/nph.16089
    full text(peer-reviewed) PDF PubMed PUB Apollo

2019

  • 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
  • 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

2018

  • 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

2017 and older

  • 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