Publications - Funding - Research Interests - CV - Editor/Reviewer - Teaching - Science Communication
+ My group: Plant Biotechnology and Bioinformatics (Institute of Plant Biology & BRICS, TU Braunschweig, Germany) + email: b.pucker{a}tu-braunschweig.de, bpucker{a}cebitec{dot}uni-bielefeld.de + Google Scholar: Boas Pucker + WebOfScience: Boas Pucker + ORCID: 0000-0002-3321-7471 + Twitter: @boas_pucker + Github: bpucker + LinkedIn: Boas Pucker + Mastodon: Boas Pucker + BlueSky: Boas PuckerCollaborations: I am interested in collaborations involving genomics or bioinformatic analyses and matching the research interests of my group. Please send me an email.
Reviews: Review requests from high quality open access journals are welcome if they match my expertise.
+ 2024 Financial Support for SynBio2024 + 2023 DFG Research Project ['Phylogenomic elucidation of withanolide biosynthesis in Nightshade plants'](https://gepris.dfg.de/gepris/projekt/516566273) + 2023 Financial support for iGEM2023 + 2022 Freiraum2022 Fellowship for ['Data Literacy in Genome Research'](https://www.tu-braunschweig.de/en/ifp/pbb/teaching/dalip) + 2022 Financial support for iGEM2023 + 2019 DFG Research Fellowship for ['Understanding the convergent evolution of a complex metabolic trait, the Betalains, through comparative genomics and co-expression networks'](https://gepris.dfg.de/gepris/projekt/436841671) in Evolution and Diversity, Department of Plant Sciences, University of Cambridge, UK + 2019 Research Fellowship for Plant Genomics and Bioinformatics + 2018 Fellowship for Digital Innovations in Academic Teaching([digital laboratory notebook](https://www.stifterverband.org/digital-lehrfellows/2017/pucker)) + 2018 DAAD scholarship (University of Cambridge, UK) + 2015 Award for excellent master's thesis ([Friedrich Wilhelm Helweg Foundation](https://www.im.nrw/friedrich-wilhelm-helweg-stiftung)) + 2014 [Deutschlandstipendium](https://www.deutschlandstipendium.de/de/english-1700.html)- 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
- De novo transcriptome assembly
- Co-expression analyses
- Differential gene expression analyses
- Evolution of the complex pigmentation in Caryophyllales involving betalain and anthocyanin biosynthesis
- Genome evolution
- Evolution of the R2R3-MYB transcription factor gene family
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
Please find a list of the bioinformatic tools developed by me or my group at our [PBB-tools](https://github.com/bpucker/PBBtools) GitHub respository. There is also a [pbb-tools](https://pbb-tools.de/) web server to run many of our tools online.
- bHLH_annotator identifies all bHLH transcription factors in a given sequence dataset. Read the bHLH_annotator paper or download the tool from GitHub.
- MYB_annotator identifies all R2R3-MYB transcription factors in a given sequence dataset. Read the MYB_annotator paper or download the tool from GitHub.
- KIPEs (Knowledge-based Identification of Pathway Enzymes) identifies all candidates of a metabolic pathway (e.g. flavonoid biosynthesis). Read the KIPEs paper, the KIPEs3 paper 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 MGSE 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 NAVIP preprint or download NAVIP from GitHub.
Scripts underlying my research are generally publicly available on GitHub.
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:
- Applied Python Programming for Life Scientists
Paper, github - Applied Genome Research
Paper, github - Molecular Methods in Genome Research
(funded by 'digi' fellowship and Genetics & Genomics of Plants)
Paper, github - Progress in Synthetic Biology
ekVV
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.
- 2019-2020 Molecular Genetics and Physiology of Plants
- 2018-2019 Genetics and Genomics of Plants, CeBiTec & Faculty of Biology (Bielefeld University)
- 2018 Evolution and Diversity, Department of Plant Sciences, University of Cambridge (UK) funded by DAAD
- 2015-2017 Genome Research, CeBiTec & Faculty of Biology (Bielefeld University)
- 2015 ALACRiS Theranostics GmbH
- 2011-2015 Faculty of Biology (Bielefeld University)
- 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)
- Member of the Editorial Board of BMC Genomics (Plant Genomics section).
- Associate Editor at Frontiers (loop profile)
A detailed list of my reviewer activities is available via [WebOfScience](https://publons.com/researcher/1008011/boas-pucker/) or [ORCID](https://orcid.org/0000-0002-3321-7471). Here is a list of selected journals and communities which I supported with reviews: Nature Catalysis, Nature Communications, The Plant Journal, Genomics, Bioinformatics, GigaScience, Horticultural Research, Journal of Experimental Botany, Molecular Plant, BMC Plant Biology, BMC Genomics, Frontiers in Plant Sciences, Molecular Biology Reports, Scientific Reports, PeerJ, Plant Cell Reports, PLOS ONE, Communications Biology, Journal of Integrative Plant Biology (JIPB), Theoretical and Applied Genetics (TAAG), pyOpenSci, Methods in Ecology and Evolution
A full list of publications is available at my Google scholar profile.
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Pucker B & Brockington S F (2021). The evidence for anthocyanins in the betalain-pigmented genus Hylocereus is weak.
bioRxiv 2021.11.16.468878; doi: https://doi.org/10.1101/2021.11.16.468878.
full text PDF -
Pucker B (2021). Automatic identification and annotation of MYB gene family members in plants.
bioRxiv 2021.10.16.464636; doi: https://doi.org/10.1101/2021.10.16.464636
full text PDF -
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.
bioRxiv 2021.10.08.463637; doi: 10.1101/2021.10.08.463637.
full text PDF -
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.
full text PDF - Chibani K., Pucker B., Dietz K.-J., Cavanagh A. (2021). Genome-wide analysis and transcriptional regulation of the typical and atypical thioredoxins in Arabidopsis thaliana. doi:10.1002/1873-3468.14197.
full text PDF - 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. BMC Genomics. doi: 10.1186/s12864-021-07877-8
full text PDF preprint PUB github github
*shared first authorship - 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 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: 10.1101/2021.03.03.433755
full text PDF PUB github github
*shared first authorship - 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 -
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 -
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 -
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