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Recent updates

You can have a look at my gitlab and my github account. These days, I’m mostly programming in Kotlin for backend and data processing, TypeScript for frontend and sometimes in Python, especially for data-exploration and cleaning. I’m working with ontologies (BFO, OBO-Foundry), semantic-web/linked-data (mainly with RDF4j but also with Jena). In term of database, I favor PostgreSQL and stay away from schema-less nosql DBs except: when I need K/V caching then I use Redis or when I need advanced text-search where I’m going to use Solr and ElasticSearch.
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Authors: Adriano Rutz ORCID , Maria Sorokina , Jakub Galgonek , Daniel Mietchen , Egon Willighagen , Arnaud Gaudry , James G. Graham ORCID , Ralf Stephan , Roderic Page , Jiří Vondrášek , Christoph Steinbeck ORCID , Guido F. Pauli ORCID , Jean-Luc Wolfender ORCID , Jonathan Bisson ORCID , Pierre-Marie Allard ORCID
Journal: bioRxiv
Subjects:
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges to data access, either within the discipline or to integration and interoperability between related domains. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified.
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categories publications science
Authors: David Ribnicky , Seon Beom Kim , Alexander Poulev , Yang Wang , Anik Boudreau , Ilya Raskin , Jonathan Bisson ORCID , G. Joseph Ray , Shao-Nong Chen ORCID , Allison Richard , Jacqueline M. Stephens , Guido F. Pauli ORCID
Journal: Journal of Natural Products (RoMEO status: White)
Subjects:
Two new diprenylated coumaric acid isomers (1a and 1b) and two known congeners, capillartemisin A (2) and B (3), were isolated from Artemisia scoparia as bioactive markers using bioactivity-guided HPLC fractionation. Their structures were determined by spectroscopic means, including 1D and 2D NMR methods and LC-MS, with their purity assessed by 1D 1H pure shift qNMR spectroscopic analysis. The bioactivity of compounds was evaluated by enhanced accumulation of lipids, as measured using Oil Red O staining, and by increased expression of several adipocyte marker genes, including adiponectin in 3T3-L1 adipocytes relative to untreated negative controls.
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categories publications science
Authors: Seon Beom Kim , Jonathan Bisson ORCID , J. Brent Friesen ORCID , Luca Bucchini , Stefan Gafner , David C. Lankin ORCID , Shao-Nong Chen ORCID , Guido F. Pauli ORCID , James B. McAlpine ORCID
Journal: Journal of Natural Products (RoMEO status: White)
Subjects:
NMR
Curcuma longa (turmeric) has an extensive history of ethnomedical use for common ailments, and “curcumin”-containing dietary supplements (CDS) are a highly visible portion of today’s self-medication market. Owing to raw material cost pressure, CDS products are affected by economically motivated, nefarious adulteration with synthetic curcumin (“syncumin”), possibly leading to unexpected toxicological issues due to “residual” impurities. Using a combination of targeted and untargeted (phyto)chemical analysis, this study investigated the botanical integrity of two commercial “turmeric” CDS with vitamin and other additives that were associated with reported clinical cases of hepatotoxicity.
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categories publications science

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