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Publications - Research Interests - Funding - CV - Editor/Reviewer - Teaching - Science Communication

Prof. Dr. Boas Pucker

foto

Collaboration: I am interested in collaborations involving genomics or bioinformatic analyses and matching the research interests of my group. Please send me an email.

Research Interests

Specialized Metabolism: flavonoid biosynthesis

Plants produce a plethora of specialized metabolites to cope with numerous environmental challenges. Examples are terpenoids, flavonoids, and betalains. We are particularly interested in flavonoids which are responsible for the pigmentation of many blue or red flowers. Flavonoids can be separated into several subgroups including flavonols, anthocyanins, proanthocyanidins, and flavones. There are multiple reasons why working on the flavonoid biosynthesis is promising.

  1. The core of the flavonoid biosynthesis is a well understood model system for the regulation of biosynthesis pathways in plants. Decades of work revealed insights into the different enzymes, but also into the transcriptional regulation of the involved genes. Even Nobel Prizes have been won in association with the flavonoid biosynthesis.

  2. Flavonoids have enormous potential in biotechnological applications as natural colorants and due to their high nutritional value. While the general biosynthesis pathway is well conserved across distantly related plant species, their are species-specific differences in the modification of flavonoids. Detailed knowledge about the flavonoid biosynthesis in (orphan) crop species can pave the way to a healthy nutrition. Genome editing or breeding methods can be used to improve crops with respect to their nutritional value.

  3. Visible phenotypes resulting from the knock-out or increased activation of flavonoid biosynthesis genes can be helpful in the identification of promising mutants. Visible phenotypes were one reason why the flavonoid biosynthesis was established as a model system. However, coloration is not only important for basic research. Plants with altered expression of certain flavonoid biosynthesis genes show often fascinating colorations and are favored in horticultural plant species.

  4. Our work investigates the Caryophyllales which represent an outstanding system to study the flavonoid biosynthesis. This order of plants is characterized by a complex pigment evolution. Briefly, specific families in the Caryophyllales show a replacement of anthocyanins (a group of flavonoids) by betalains. Betalains do not occur in plants outside the Caryophyllales and it appears that anthocyanins and betalains are mutually exclusive. The Caryophyllales are a unique opportunity to investigate the interplay of different branches of the flavonoid biosynthesis. The comparison between anthocyanin-pigmented species and species without anthocyanins reveals new insights into the biosynthesis and regulation.

Generally, we are interested in the discovery of promising biosynthesis pathways for biotechnological applications. This is not restricted to the flavonoid biosynthesis, but instead using this model system to develop new genome mining approaches. Different methods for the identification biosynthetic pathways are combined including screens and comparisons of plant genome sequences.

Selected publications:

Plant Genomics: Long Read Sequencing

Plant genome sequences contain the blue print for all proteins (enzymes). Sequencing and investigating genomes is an effective approach to reveal the biochemical potential of plants. Especially the correlation of genomic data (DNA) with transcriptomic (RNA) and metabolomic (chemical compounds) data sets allows the identification of biosynthesis pathways. Rapid developments of long read sequencing technologies allow the cost-effective analysis of large plant genomes. Sequencers distributed by Oxford Nanopore Technologies (ONT) are portable and can even be operated in the field. This so called nanopore sequencing approach analysis individual DNA strands. We use this technology to resolve the genome sequences of of important plant species. This is also a great opportunity for students to contribute to a genome sequencing project. Have look about our review article about the future of long read sequencing in plant genomics. These genome sequencing projects have been conducted in my group or are ongoing:

  • Ceratophyllum submersum (soft hornwort) is an aquatic plant that is very common in (eutrophic) ponds in Germany. We analyzed the plastome (subgenome of the chloroplast) of this species to determine its relationship to other plant species (Meckoni et al., 2023).
  • Digitalis purpurea (floxglove) is known as a medicinal plant, but also appears frequently as horticultural plant in gardens due to its colorfull and large flowers. We are interested in the flavonoid biosynthesis of this plant species with a particular focus on anthocyanins which are responsible for the redish pigmentation and also the name of the species. Read about the details in our Preprint on bioRxiv (Wolff, Friedhoff, Horz et al., 2024).
  • Urtica dioica (stinging nettle) was the medicinal plant of the year in 2022. It is well known for a high flavonoid content and often used to produce tea.
  • Aquilegia vulgaris (common columbine) is a horticultural plant that can be seen in many gardens showing a variety of flower colors. We are interested to understand the molecular basis of different flower colors.
  • Victoria cruziana (giant water lily) is the biggest attraction in the Botanical Garden in Braunschweig. The plant is famous for huge floating leaves that can carry the weight of a small child. It produces beautiful flowers that open at night. We are interested to understand the flavonoid biosynthesis in this aquatic plant species.
  • Rubus armeniacus (blackberry) is a fruit producing plant species that is common throughout Germany. It is well known for the black and sweet fruits that it produces. We are interested to study the formation of anthocyanins, a subgroup of the flavonoids, in blackberry.

Applied Bioinformatics

Specific biological questions require the development of dedicated tools. My group writes such tools mostly in Python and R. The developed tools are freely available on GitHub (PBB-tools) and on our web server (pbb-tools). The following tools are examples of active developments:

  • KIPEs (A): Knowledge-based Identification of Pathway Enzymes allows the automatic annotation of the proteins involved in the core steps of the flavonoid biosynthesis. This supports the identification of molecular mechanisms underlying color differences between cultivars of the same species. In addition, rapid annotation of flavonoid biosynthesis genes in novel/uncharacterized species becomes convenient. Read the KIPEs paper, the KIPEs3 paper or download KIPEs from GitHub.
  • MGSE (B): Mapping-based Genome Size Estimation is a novel approach to infer the true genome size of a species based on sequence reads. This approach harnesses the equal representation of all regions (even repeats) in the read set. The average number of sequence reads (coverage) is estimated based on single copy regions in a reference genome sequence. Dividing the combined coverage of all positions in an assembly by this sequencing depth results in the genome size estimation. Read the MGSE preprint or download MGSE from GitHub.
  • NAVIP (C): Neighborhood-Aware Variant Impact Predictor enables the prediction of functional consequences arising from sequence variants between a sequenced sample and a reference. In contrast to many established tools, NAVIP considers all variants in one gene at the same time when predicting the potential effect of sequence variants. Read the NAVIP preprint or download NAVIP from GitHub.
  • MYB_annotator (D): This tool enables the automatic identification and annotation of MYBs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences. Read the MYB_annotator paper or download the tool from GitHub.
  • bHLH_annotator (E): This tool enables the automatic identification and annotation of bHLHs in a novel transcriptome/genome sequence assembly of a plant species. The identified candidates are functionally annotated based on orthology to previously characterized sequences. Read the bHLH_annotator paper or download the tool from GitHub.

Studied Plant Species: Arabidopsis thaliana, Arabidopsis halleri, Beta vulgaris, Beta coroliflora, Beta lomatogona, Brassica napus, Cicer arietinum, Croton tiglium, Digitalis purpurea, Dioscorea dumetorum, Kewa caespitosa, Macarthuria australis, Medicago truncatula, Musa acuminata, Pharnaceum exiguum, Simmondsia chinensis, Urtica dioica, Vitis vinifera various other plant species especially members of the Caryophyllales.

Awards, funding, and scholarships

Teaching

Teaching activities at TU Braunschweig

Please see my website about courses at TU Braunschweig for latest updates: BP teaching at TUBS.

Teaching activities at Bielefeld University

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 synthetic biology projects at the annual Giant Jamboree. I participated in the teams iGEM Bielefeld-CeBiTec and iGEM TU Braunschweig in multiple years:

  • 2014 (team member)
  • 2016 (supervision)
  • 2017 (supervision)
  • 2018 (supervision)
  • 2019 (supervision); mentoring: Athens and Thessaly; After iGEM selected me as 'iGEMer of the month' in September 2019
  • 2020 (judge)
  • 2021 (judge); mentoring RUBochum
  • 2022 (PI)
  • 2023 (PI)

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/Reviewer Activity

  • Member of the Editorial Board of BMC Genomics (Plant Genomics section).
  • Associate Editor at Frontiers (loop profile)
  • Reviewer Activities: A detailed list of my reviewer activities is available via WebOfScience or ORCID. 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

Memberships

  • 06/2023-present   Verband Biologie, Biowiss. und Biomed in Deutschland e.V (VBIO)
  • 05/2023-present   DSI Scientific Network
  • 01/2023-present   German Association for Synthetic Biology (GASB)
  • 07/2020-present   European Society of Evolutionary Biology (ESEB)
  • 02/2020-present   Plantae / American Society of Plant Biologists (ASPB)
  • 12/2019-present   German Society for Plant Sciences (DBG)
  • 2019-present   bts e.V. (biotechnology students' initiative)
  • Freunde des Braunschweiger Botanischen Gartens e.V.
  • Braunschweiger Hochschulbund e.V. (BHB)
  • Deutscher Hochschul Verband (DHV)

Science Communication

  • FlavonoidFriday: Novel findings about the flavonoid biosynthesis are shared via social media on a weekly basis. Details about these posts are available in the corresponding GitHub repository.
  • MybMonday: Interesting facts about the R2R3-MYB transcription factor family is shared via social media on a weekly basis. Details about these posts are available in the corresponding GitHub repository.

Publications

A full list of publications is available at my Google scholar profile.

  • Wolff K., Friedhoff R., Horz J. M.*, Pucker B. (2024). Genome sequence of the medicinal and ornamental plant Digitalis purpurea reveals the molecular basis of flower color variation. bioRxiv 2024.02.14.580303; doi: 10.1101/2024.02.14.580303.
  • Pucker, B. (2024). Functional Annotation – How to Tackle the Bottleneck in Plant Genomics. Preprints. doi: 10.20944/preprints202402.0645.v1.
  • Baasner J.-S., Rempel A. Howard D., Pucker B. (2024). NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction. bioRxiv 596718; doi: 10.1101/596718.
  • Frommann J.-F., Pucker B., Sielmann L. M., Muller C., Weisshaar B., Stracke R., Schweiger R. (2024). Metabolic fingerprinting reveals roles of Arabidopsis thaliana BGLU1, BGLU3 and BGLU4 in glycosylation of various flavonoids. bioRxiv 2024.01.30.577901; doi: 10.1101/2024.01.30.577901.
  • Choudhary N. & Pucker B. (2024). Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR. bioRxiv 2023.11.05.565693; doi: 10.1101/2023.11.05.565693.
  • Hafner, A.; DeLeo, V.; Deng, C.; Elsik, C.G.; Fleming, D.; Harrison, P.W.; Kalbfleisch, T.S.; Petry, B.; Pucker, B.; Quezada-Rodríguez, E.H.; Tuggle, C.K.; Koltes, J. Data Reuse in Agricultural Genomics Research: Present Challenges and Future Solutions. Preprints 2024, 2024010780. 10.20944/preprints202401.0780.v1.
  • Pucker, B., Walker-Hale, N., Dzurlic, J., Yim, W.C., Cushman, J.C., Crum, A., Yang, Y. and Brockington, S.F. (2024), Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme. New Phytol., 241: 471-489. doi: 10.1111/nph.19341.

2023

  • Schmidt N., Sielemann K., Breitenbach S., Fuchs J., Pucker B., Weisshaar B., Holtgräwe D., Heitkam T. (2023). Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. Plant J. doi: 10.1111/tpj.16599.
  • Thoben C. and Pucker B. (2023). Automatic annotation of the bHLH gene family in plants. BMC Genomics 24, 780 (2023). doi: 10.1186/s12864-023-09877-2.
  • Wolff, K.; Friedhoff, R.; Schwarzer, F.; Pucker, B. (2023). Data Literacy in Genome Research. Journal of Integrative Bioinformatics, 2023, pp. 20230033. doi: 10.1515/jib-2023-0033.
  • Sielemann, K., Pucker, B., Orsini, E. et al. Genomic characterization of a nematode tolerance locus in sugar beet. BMC Genomics 24, 748 (2023). doi: 10.1186/s12864-023-09823-2.
  • Rempel A., Choudhary N. and Pucker B. (2023). KIPEs3: Automatic annotation of biosynthesis pathways. PLOS ONE 18(11): e0294342. doi: 10.1371/journal.pone.0294342.
  • Naik J., Tyagi S., Rajput R., Kumar P., Pucker B., Bisht N. C., Misra P., Stracke R., Pandey A. Flavonols have opposite effects on the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana, Journal of Experimental Botany, 2023;, erad391, doi: 10.1093/jxb/erad391.
  • Natarajan, S., Pucker, B. & Srivastava, S. Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409. Sci Rep 13, 14614 (2023). doi: 10.1038/s41598-023-41738-6.
  • Movahedi A, Pucker B and Kadkhodaei S (2023) Editorial: Genomics and gene editing of orphan plants. Front. Plant Sci. 14:1277625. doi: 10.3389/fpls.2023.1277625.
  • Meckoni, S.N., Nass, B. & Pucker, B. (2023). Phylogenetic placement of Ceratophyllum submersum based on a complete plastome sequence derived from nanopore long read sequencing data. BMC Res Notes 16, 187. doi: 10.1186/s13104-023-06459-z.
  • Siadjeu, C. & Pucker, B. (2023). Medicinal plant genomics. BMC Genomics 24, 429 (2023). doi: 10.1186/s12864-023-09542-8.
  • Feng, T., Pucker, B., Kuang, T., Song B., Yang Y., Lin N., Zhang H., Moore M.J., Brockington S.F., Wang Q., Deng T., Wang H. and Sun H. (2023). The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation. Commun Biol 6, 706 (2023). doi: 10.1038/s42003-023-05044-1.
  • Sielemann K., Schmidt N., Guzik J., Kalina N., Pucker B., Viehöver P., Breitenbach S., Weisshaar B., Heitkam T., Holtgräwe D. (2023). Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet. bioRxiv 2023.06.28.546919; doi: 10.1101/2023.06.28.546919.
  • Bartas M., Volna A., Cerven J. and Pucker B. (2023). Identification of annotation artifacts concerning the CHALCONE SYNTHASE (CHS). BMC Res Notes 16, 109 (2023). doi: 10.1186/s13104-023-06386-z.
  • 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. BMC Res Notes 16, 103 (2023). doi: 10.1186/s13104-023-06375-2.
  • Marin M. F. & Pucker B. (2023). Genetic factors explaining anthocyanin pigmentation differences. bioRxiv 2023.06.05.543820; doi: 10.1101/2023.06.05.543820.
  • Albert N. W., Iorizzo M., Mengist M.F., Montanari S., Zalapa J., Maule A., Edger P. P., Yocca A. E., Platts A. E., Pucker B., Espley R. V. (2023). Vaccinium as a comparative system for understanding of complex flavonoid accumulation profiles and regulation in fruit. Plant Physiology. doi: 10.1093/plphys/kiad250.
  • Göttl V.L., Pucker B., Wendisch V.F., Henke N.A. (2023). Screening of structurally distinct lycopene β-cyclases for production of the cyclic C40 carotenoids β-carotene and astaxanthin by Corynebacterium glutamicum. Journal of Agricultural and Food Chemistry. doi: 10.1021/acs.jafc.3c01492.
  • Pucker B & Iorizzo M (2023). Apiaceae FNS I originated from F3H through tandem gene duplication. PLOS ONE 18(1): e0280155. doi: 10.1371/journal.pone.0280155.

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. Front. Plant Sci. 13:968780. doi: 10.3389/fpls.2022.968780.
  • Rajput, R., Tyagi, S., Naik, J. Pucker, B., Stracke, R., Pandey, A. 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.
  • 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; doi: 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). doi: 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.
  • 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.
  • Pucker B & Brockington S F (2022). The evidence for anthocyanins in the betalain-pigmented genus Hylocereus is weak. BMC Genomics 23, 739. doi: 10.1186/s12864-022-08947-1.

2014-2021

  • 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

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bioinformatics genomics synthetic-biology teaching open-science igem transcriptomics biotechnology specialized-metabolism betalains flavonoids pigment-biosynthesis genome-reserach plant-sciences

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