Publications - Funding - Research Interests - CV

Dr. Boas Pucker

Dr. Boas Pucker

Projects for students: Please send me an email if you are interested in a project related to my research interests.

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.

Current project (DFG fellowship)

Investigation of the betalain pathway evolution with Dr. Samuel Brockington at the Department of Plant Sciences (University of Cambridge, UK): Boas Pucker (Plant Sciences)

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. Plants 2020, 9(11), 1548; doi:10.3390/plants9111548.
    full text(peer-reviewed) preprint 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
  • 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
  • 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
  • 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
  • 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


Awards, funding, and scholarships

Research Interests

Genome Research

  • high molecular weigth DNA extraction and long read sequencing (Oxford Nanopore Technologies, ONT)
  • de novo genome assembly and annotation
  • comparative genomics and pangenomics
  • read mapping, variant calling (SNVs, InDels, SVs), and variant annotation
  • genome size and transposable elements

Transcriptomics / RNA-Seq

  • De novo transcriptome assembly
  • Non-canonical splice sites
  • Differential gene expression analyses
  • Flowering time control and berry ripening in Vitis vinifera

Evolution

  • Evolution of the betalain and flavonoid biosynthesis
  • Genome evolution
  • Evolution of the R2R3-MYB transcription factor gene family (Beta vulgaris and Musa acuminata)

Studied Plant Species

Arabidopsis thaliana, Arabidopsis halleri, Beta vulgaris, Beta coroliflora, Beta lomatogona, Brassica napus, Cicer arietinum, Croton tiglium, Dioscorea dumetorum, Kewa caespitosa, Macarthuria australis, Medicago truncatula, Musa acuminata, Pharnaceum exiguum, Simmondsia chinensis, Vitis vinifera

various other plant species especially members of the Caryophyllales


Developed Bioinformatic Tools

  • KIPEs (Knowledge-based Identification of Pathway Enzymes) identifieds all candidates of a metabolic pathway (e.g. flavonoid biosynthesis) or all members of a gene family (e.g. R2R3 MYBs). Read the publication or download KIPEs from github.
  • MGSE (Mapping-based Genome Size Estimator) utilizes the mapping of short reads to a long read genome assembly to estimate the genome size. Read the preprint or download MGSE from github.
  • NAVIP (Neighborhood-Aware Variant Impact Predictor) predicts the functional impact of sequence variants by considering all variants in a coding sequences simultaneously. Read the preprint or download NAVIP from github.
  • Most of my scripts are publicly available at github: bpucker.

Teaching

Courses

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:

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.



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)

Editor Activity

Currently, I am a guest editor for a special issue about Harnessing the Power of Genome and Transcriptome Assemblies in Plants. This Special Issue is open to all research articles providing new insights into the biology of plants based on genome or transcriptome assemblies.


Reviewer Activities

A comprehensive list of my reviewer activities is available via Publons. Here is a list of journals which I supported with reviews:

Agriculture, Agronomy, Biology, BMC Genomics, Frontiers in Plant Sciences, Microorganisms, Molecular Biology Reports, Scientific Reports, Genes, Journal of Limnology and Freshwater Fisheries Research, PeerJ, Plant Cell Reports, PLOS ONE, Springer Nature, Plants, Communications Biology, International Journal of Molecular Sciences Journal of Integrative Plant Biology (JIPB)

Memberships

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