Penny Nymark

Penny Nymark

Research Specialist
Visiting address: Nobels väg 13, 17177 Stockholm
Postal address: C6 Institutet för miljömedicin, C6 Ledningskansliet, 171 77 Stockholm
Part of:

About me

  • I am a researcher at the Institute of Environmental Medicine at Karolinska
    Institutet with a background in genetics, cancer and toxicology. In recent
    years, my main focus has turned towards development of Adverse Outcome
    Pathways (AOPs) and New Approach Methodologies (NAMs), as well as their
    application in risk assessment and in safe and sustainable development of new
    technologies. Coupled to this focus, I also have a broad interest in making
    data Findable, Accessible, Interoperable and Reusable (FAIR). In addition to
    research, I function as coordinator within the Swedish platform for
    Nanosafety, SweNanoSafe [1], where I focus on communication, education and
    sustainability (e.g. Safe and Sustainable by Design, SSbD) aspects within
    nanosafety.

    *Ongoing projects and involvements:*
    Toward risk assessment without animals: Development of Adverse Outcome
    Pathways for lung cancer [2]

    PARC [3]- European Partnership for the Assessment of Risks from Chemicals

    HARMLESS [4] - Advanced high aspect ratio multicomponent materials: towards
    comprehensive intelligent testing and safe by design strategies

    *Selected previous projects and involvements:*
    Gov4Nano [5] - Implementation of Risk Governance: meeting the needs of
    nanotechnology

    eNanoMapper [6] - A Database and Ontology Framework for Nanomaterials Design
    and Safety Assessment

    NANoREG [7] - A common European approach to the regulatory testing of
    nanomaterials

    NANOSOLUTIONS [8] - Biological Foundation for the Safety Classification of
    Engineered Nanomaterials (ENM): Systems Biology Approaches to Understand
    Interactions of ENM with Living Organisms and the Environment

    NanoReg2 [9] - Development and implementation of Grouping and Safe-by-Design
    approaches within regulatory frameworks

    caLIBRAte [10] - Performance testing, calibration and implementation of a
    next generation system-of-systems Risk Governance Framework for nanomaterials

    PATROLS [11] – Physiologically Anchored Tools for Realistic nanOmateriaL
    hazard aSsessment

    NanoSolveIT [12] – Innovative Nanoinformatics models and tools: towards a
    Solid, verified and Integrated Approach to Predictive (eco)Toxicology

    miRNAno [13] - Toxicogenomic studies on engineered carbon nanomaterials
    Application of the Adverse Outcome Pathway concept and bioinformatics for
    mechanistic understanding of COVID-19 [14]

    [1] https://swenanosafe.ki.se/
    [2] https://ki.se/en/imm/toward-risk-assessment-without-animals-development-of-adverse-outcome-pathways-for-lung-cancer
    [3] https://news.ki.se/unique-eu-project-to-develop-next-generation-chemical-risk-assessment
    [4] https://www.harmless-project.eu/
    [5] https://www.gov4nano.eu/
    [6] http://www.enanomapper.net/
    [7] https://cordis.europa.eu/project/id/310584
    [8] https://cordis.europa.eu/project/id/309329
    [9] https://cordis.europa.eu/project/id/646221
    [10] https://cordis.europa.eu/project/id/686239
    [11] https://www.patrols-h2020.eu/
    [12] https://nanosolveit.eu/
    [13] https://cordis.europa.eu/project/id/299525
    [14] https://ki.se/en/imm/application-of-the-adverse-outcome-pathway-concept-and-bioinformatics-for-mechanistic

Research

  • *Selected publications:*

    Wittwehr C, Clerbaux LA, Edwards S, Angrish M, Mortensen H, Carusi A,
    Gromelski M, Lekka E, Virvilis V, Martens M, Bonino da Silva Santos
    LO, *Nymark P. *Why adverse outcome pathways need to be FAIR. [1] ALTEX.
    2023 Aug 1. doi: 10.14573/altex.2307131. Online ahead of print.

    Dumit, V. I., Ammar, A., Bakker, M. I., Bañares, M. A., Bossa, C., Costa,
    A., Cowie, H., Drobne, D., Exner, T. E., Farcal, L., Friedrichs, S., Furxhi,
    I., Grafström, R., Haase, A., Himly, M., Jeliazkova, N., Lynch, I., Maier,
    D., Noorlander, C. W., ... *Nymark, P*. (2023). From principles to reality.
    FAIR implementation in the nanosafety community. [2] /Nano Today/, /51/,
    [101923]. doi: 10.1016/j.nantod.2023.101923

    Grafström R, Haase A, Kohonen P, Jeliazkova N, *Nymark P. *Reply to:
    Prospects and challenges for FAIR toxicogenomics data. [3] Nat Nanotechnol.
    2021 Dec 23. doi: 10.1038/s41565-021-01050-8. Online ahead of print.

    Lynch I, *Nymark P*, Doganis P, Gulumian M, Yoon TH, Martinez DST, Afantitis
    A. Methods, models, mechanisms and metadata: Introducing the Nanotoxicology
    collection at F1000Research. [4] F1000Res. 2021 Nov 24
  • 10:1196. doi:
    10.12688/f1000research.75113.1. eCollection 2021.

    Bossa C, Andreoli C, Bakker M, Barone F, De Angelis I, Jeliazkova N, *Nymark
    P*, Battistelli CL. FAIRification of nanosafety data to improve
    applicability of (Q)SAR approaches: A case study on /in vitro/ Comet assay
    genotoxicity data. [5] Comput Toxicol. 2021 Nov
  • 20:100190. doi:
    10.1016/j.comtox.2021.100190.

    Jeliazkova N, Apostolova MD, Andreoli C, Barone F, Barrick A, Battistelli C,
    Bossa C, Botea-Petcu A, Châtel A, De Angelis I, Dusinska M, El Yamani N,
    Gheorghe D, Giusti A, Gómez-Fernández P, Grafström R, Gromelski M,
    Jacobsen NR, Jeliazkov V, Jensen KA, Kochev N, Kohonen P, Manier N, Mariussen
    E, Mech A, Navas JM, Paskaleva V, Precupas A, Puzyn T, Rasmussen K, Ritchie
    P, Llopis IR, Rundén-Pran E, Sandu R, Shandilya N, Tanasescu S, Haase A,
    *Nymark P.* Towards FAIR nanosafety data. [6]Nat Nanotechnol. 2021 May 20.
    doi: 10.1038/s41565-021-00911-6.

    *Nymark P*, Karlsson HL, Halappanavar S, Vogel U. Adverse Outcome Pathway
    development for assessment of lung carcinogenicity by nanoparticles [7].
    Frontiers in Toxicology, 29 April 2021. doi: 10.3389/ftox.2021.653386

    *Nymark P, * Sachana M, Batista-Leite S, Sund J, Krebs C.E., Sullivan K,
    Edwards S, Viviani L, Willett K, Landesmann B, Wittwehr C. Systematic
    Organization of COVID-19 Data Supported by the Adverse Outcome Pathway
    Framework [8]. Frontiers in Public Health, 19 May 2021, doi:
    10.3389/fpubh.2021.638605

    Halappanavar S, van den Brule S, * Nymark P*, Gaté L, Seidel C, Valentino S,
    Zhernovkov V, Høgh Danielsen P, De Vizcaya A, Wolff H, Stöger T, Boyadziev
    A, Poulsen SS, Sørli JB, Vogel U. Adverse outcome pathways as a tool for the
    design of testing strategies to support the safety assessment of emerging
    advanced materials at the nanoscale. [9] Part Fibre Toxicol. 2020 May
    25
  • 17(1):16. doi: 10.1186/s12989-020-00344-4.

    *Nymark P*, Bakker M, Dekkers S, Franken R, Fransman W, García-Bilbao A,
    Greco D, Gulumian M, Hadrup N, Halappanavar S, Hongisto V, Hougaard KS,
    Jensen KA, Kohonen P, Koivisto AJ, Dal Maso M, Oosterwijk T, Poikkimäki M,
    Rodriguez-Llopis I, Stierum R, Sørli JB, Grafström R. Toward Rigorous
    Materials Production: New Approach Methodologies Have Extensive Potential to
    Improve Current Safety Assessment Practices. [10]Small. 2020
    Feb
  • 16(6):e1904749. doi: 10.1002/smll.201904749. Epub 2020 Jan 8.

    Soeteman-Hernandez LG, Apostolova MD, Bekker C, Dekkers S, Grafström RC,
    Groenewold M, Handzhiyski Y, Herbeck-Engel P, Hoehener K, Karagkiozaki V,
    Kelly S, Kraegeloh A, Logothetidis S, Micheletti C, *Nymark P*, Oomen A,
    Oosterwijk T, Rodríguez-LLopis I, Sabella S, Sanchez Jiménez A, Sips A,
    Suarez-Merino B, Tavernaro I, van Engelen J, Wijnhoven SWP, Noorlander CW.
    Safe innovation approach: Towards an agile system for dealing with
    innovations. [11] Materials Today Communications, Volume 20, 2019, 100548,
    ISSN 2352-4928, doi: 10.1016/j.mtcomm.2019

    Giusti A, Atluri R, Tsekovska R, Gajewicz A, Apostolova MD, Battistelli CL,
    Bleeker EAJ, Bossa C, Bouillard j, Dusinska M, Gómez-Fernández P,
    Grafström R, Gromelski M, Handzhiyski Y, Jacobsen NR, Jantunen P, Jensen KA,
    Mech A, Navas JM, *Nymark P*, Oomen AG, Puzyn T, Rasmussen K, Riebeling C,
    Rodriguez-Llopis I, Sabella S, Riego Sintes J, Suarez-Merino B, Tanasescu S,
    Wallin H, Haase A. Nanomaterial grouping: Existing approaches and future
    recommendations [12]. NanoImpact, Volume 16, 2019, 100182, ISSN 2452-0748,
    doi: 10.1016/j.impact.2019.100182

    *Nymark P*, Kohonen P, Hongisto V, Grafström RC. Toxic and Genomic
    Influences of Inhaled Nanomaterials as a Basis for Predicting Adverse
    Outcome. [13]Ann Am Thorac Soc. 2018 Apr
  • 15(Suppl 2):S91-S97. doi:
    10.1513/AnnalsATS.201706-478MG.

    *Nymark P*, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H,
    Evelo CT, Hongisto V, Kohonen P, Willighagen E, Grafström RC. A Data Fusion
    Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions.
    [14]Toxicol Sci. 2018 Mar 1
  • 162(1):264-275. doi: 10.1093/toxsci/kfx252.

    *Nymark P*, Wijshoff P, Cavill R, van Herwijnen M, Coonen ML, Claessen S,
    Catalán J, Norppa H, Kleinjans JC, Briedé JJ. Extensive temporal
    transcriptome and microRNA analyses identify molecular mechanisms underlying
    mitochondrial dysfunction induced by multi-walled carbon nanotubes in human
    lung cells. [15] Nanotoxicology, 2015. 9(5): p. 624-635. doi:
    10.3109/17435390.2015.1017022

    *Nymark P*, Guled M, Borze I, Faisal A, Lahti L, Salmenkivi K, Kettunen E,
    Anttila S, Knuutila S. Integrative Analysis of microRNA, mRNA and aCGH Data
    Reveals Asbestos-Related Changes in Non-Small Cell Lung Cancer. [16] Genes,
    Chromosom. Cancer, 2011. 50(8):585-97. doi: 10.1002/gcc.20880

    *Nymark P*, Wikman H, Hienonen-Kempas T, Anttila S. Molecular and genetic
    changes in asbestos-related lung cancer [17]. Cancer Lett. 2008. 265(1):1-15.
    Doi: 10.1016/j.canlet.2008.02.043

    [1] https://pubmed.ncbi.nlm.nih.gov/37528748/
    [2] https://doi.org/10.1016/j.nantod.2023.101923
    [3] https://doi.org/10.1038/s41565-021-01050-8
    [4] https://doi.org/10.12688/f1000research.75113.1
    [5] https://doi.org/10.1016/j.comtox.2021.100190
    [6] https://doi.org/10.1038/s41565-021-00911-6
    [7] https://doi.org/10.3389/ftox.2021.653386
    [8] https://doi.org/10.3389/fpubh.2021.638605
    [9] https://pubmed.ncbi.nlm.nih.gov/32450889/
    [10] https://pubmed.ncbi.nlm.nih.gov/31913582/
    [11] https://doi.org/10.1016/j.mtcomm.2019
    [12] https://doi.org/10.1016/j.impact.2019.100182
    [13] https://pubmed.ncbi.nlm.nih.gov/29676641/
    [14] https://pubmed.ncbi.nlm.nih.gov/29149350/
    [15] http://doi.org/10.3109/17435390.2015.1017022
    [16] http://doi.org/10.1002/gcc.20880
    [17] http://doi.org/10.1016/j.canlet.2008.02.043

Teaching

  • *Teaching:*
    I am course leader for the PhD course /Human Cell Culture. Methods and
    Applications/. (code 3127). I also lead course modules in the Master Program
    in Toxicology, including on bioinformatics and omics, as well as a workshop
    on toxicological high-throughput screening assays and data (ToxCast
    workshop). Furthermore, I provide a number of lectures both at KI and other
    universities and external courses in the areas of human cell culture methods,
    alternative (3R) methods, toxicogenomics and systems toxicology,
    bioinformatics, high-throughput screening approaches, data management (FAIR
    principles), Adverse Outcome Pathways (AOPs) and Safe and Sustainable by
    Design (SSbD).

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