Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

Andrew Williams and Sabina Halappanavar
Beilstein J. Nanotechnol. 2015, 6, 2438–2448. https://doi.org/10.3762/bjnano.6.252

Cite the Following Article

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials
Andrew Williams and Sabina Halappanavar
Beilstein J. Nanotechnol. 2015, 6, 2438–2448. https://doi.org/10.3762/bjnano.6.252

How to Cite

Williams, A.; Halappanavar, S. Beilstein J. Nanotechnol. 2015, 6, 2438–2448. doi:10.3762/bjnano.6.252

Download Citation

Citation data can be downloaded as file using the "Download" button or used for copy/paste from the text window below.
Citation data in RIS format can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Zotero.

Citations to This Article

Up to 20 of the most recent references are displayed here.

Scholarly Works

  • Bahl, A.; Halappanavar, S.; Wohlleben, W.; Nymark, P.; Kohonen, P.; Wallin, H.; Vogel, U.; Haase, A. Bioinformatics and machine learning to support nanomaterial grouping. Nanotoxicology 2024, 18, 373–400. doi:10.1080/17435390.2024.2368005
  • Patrício, A.; Costa, R. S.; Henriques, R. On the challenges of predicting treatment response in Hodgkin's Lymphoma using transcriptomic data. BMC medical genomics 2023, 16, 170. doi:10.1186/s12920-023-01508-9
  • Solorio-Rodriguez, S. A.; Williams, A.; Poulsen, S. S.; Knudsen, K. B.; Jensen, K. A.; Clausen, P. A.; Danielsen, P. H.; Wallin, H.; Vogel, U.; Halappanavar, S. Single-Walled vs. Multi-Walled Carbon Nanotubes: Influence of Physico-Chemical Properties on Toxicogenomics Responses in Mouse Lungs. Nanomaterials (Basel, Switzerland) 2023, 13, 1059. doi:10.3390/nano13061059
  • Jagiello, K.; Ciura, K. In vitro to in vivo extrapolation to support the development of the next generation risk assessment (NGRA) strategy for nanomaterials. Nanoscale 2022, 14, 6735–6742. doi:10.1039/d2nr00664b
  • Nymark, P.; Sachana, M.; Leite, S. B.; Sund, J.; Krebs, C. E.; Sullivan, K.; Edwards, S. W.; Viviani, L.; Willett, C.; Landesmann, B.; Wittwehr, C. Systematic Organization of COVID-19 Data Supported by the Adverse Outcome Pathway Framework. Frontiers in public health 2021, 9, 638605. doi:10.3389/fpubh.2021.638605
  • Halappanavar, S.; Nymark, P.; Krug, H. F.; Clift, M. J. D.; Rothen-Rutishauser, B.; Vogel, U. Non-Animal Strategies for Toxicity Assessment of Nanoscale Materials: Role of Adverse Outcome Pathways in the Selection of Endpoints. Small (Weinheim an der Bergstrasse, Germany) 2021, 17, 2007628. doi:10.1002/smll.202007628
  • Halappanavar, S.; van den Brule, S.; Nymark, P.; Gaté, L.; Seidel, C.; Valentino, S.; Zhernovkov, V.; Danielsen, P. H.; De Vizcaya, A.; Wolff, H.; Stöger, T.; Boyadziev, A.; Poulsen, S. S.; Sørli, J. B.; 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. Particle and fibre toxicology 2020, 17, 16. doi:10.1186/s12989-020-00344-4
  • Rahman, L.; Williams, A.; Gelda, K.; Nikota, J. K.; Wu, D.; Vogel, U.; Halappanavar, S. 21st Century Tools for Nanotoxicology: Transcriptomic Biomarker Panel and Precision‐Cut Lung Slice Organ Mimic System for the Assessment of Nanomaterial‐Induced Lung Fibrosis. Small (Weinheim an der Bergstrasse, Germany) 2020, 16, 2000272. doi:10.1002/smll.202000272
  • Nymark, P.; Bakker, M.; Dekkers, S.; Franken, R.; Fransman, W.; García-Bilbao, A.; Greco, D.; Gulumian, M.; Hadrup, N.; Halappanavar, S.; Hongisto, V.; Hougaard, K. S.; Jensen, K. A.; Kohonen, P.; Koivisto, A. J.; Dal Maso, M.; Oosterwijk, T.; Poikkimäki, M.; Rodriguez-Llopis, I.; Stierum, R.; Sørli, J. B.; Grafström, R. C. Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices. Small (Weinheim an der Bergstrasse, Germany) 2020, 16, 1904749. doi:10.1002/smll.201904749
  • Yauk, C. L.; Cheung, C.; Barton-Maclaren, T. S.; Boucher, S.; Bourdon-Lacombe, J.; Chauhan, V.; Gagne, M.; Gillespie, Z.; Halappanavar, S.; Honeyman, M.; Jones, S. R.; Jones-McLean, E.; Labib, S.; MacAulay, J.; Moore, J.; Paquette, M. A.; Petronella, N.; Semalulu, S.; Slot, A.; Vespa, A.; Woodland, C. L. Toxicogenomic applications in risk assessment at Health Canada. Current Opinion in Toxicology 2019, 18, 34–45. doi:10.1016/j.cotox.2019.02.005
  • Karim, M. B.; Kanaya, S.; Altaf-Ul-Amin. Implementation of BiClusO and its comparison with other biclustering algorithms. Applied Network Science 2019, 4, 1–15. doi:10.1007/s41109-019-0180-x
  • Gusfield, D. 2019.
  • Gusfield, D. Part II. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 233–234. doi:10.1017/9781108377737.015
  • Gusfield, D. Part I. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 1–2. doi:10.1017/9781108377737.002
  • Gusfield, D. Biological Networks, Graphs, and High-Density Subgraphs. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 15–48. doi:10.1017/9781108377737.004
  • Gusfield, D. Introduction. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; xi–xviii. doi:10.1017/9781108377737.001
  • Gusfield, D. Maximum Likelihood Pedigree Reconstruction. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 331–342. doi:10.1017/9781108377737.022
  • Gusfield, D. Character Compatibility with Corrupted Data and Generalized Phylogenetic Models. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 260–272. doi:10.1017/9781108377737.017
  • Gusfield, D. Integer Programming in Molecular Sequence Analysis. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 186–204. doi:10.1017/9781108377737.012
  • Gusfield, D. What's Next?. Integer Linear Programming in Computational and Systems Biology; Cambridge University Press, 2019; pp 382–384. doi:10.1017/9781108377737.025
Other Beilstein-Institut Open Science Activities