Publications

2021

  1. Chiaro, J, Kasanen, HHE, Whalley, T, Capasso, C, Grönholm, M, Feola, S et al.. Viral Molecular Mimicry Influences the Antitumor Immune Response in Murine and Human Melanoma. Cancer Immunol Res. 2021; :. doi: 10.1158/2326-6066.CIR-20-0814. PubMed PMID:34103348 .
  2. Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J et al.. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun. 2021;12 (1):3297. doi: 10.1038/s41467-021-23143-7. PubMed PMID:34078885 PubMed Central PMC8172540.
  3. Scala, G, Federico, A, Greco, D. CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events. BMC Bioinformatics. 2021;22 (1):278. doi: 10.1186/s12859-021-04191-8. PubMed PMID:34039269 PubMed Central PMC8157658.
  4. Kinaret, PAS, Ndika, J, Ilves, M, Wolff, H, Vales, G, Norppa, H et al.. Toxicogenomic Profiling of 28 Nanomaterials in Mouse Airways. Adv Sci (Weinh). 2021;8 (10):2004588. doi: 10.1002/advs.202004588. PubMed PMID:34026454 PubMed Central PMC8132046.
  5. Procaccini, C, Garavelli, S, Carbone, F, Di Silvestre, D, La Rocca, C, Greco, D et al.. Signals of pseudo-starvation unveil the amino acid transporter SLC7A11 as key determinant in the control of Treg cell proliferative potential. Immunity. 2021;54 (7):1543-1560.e6. doi: 10.1016/j.immuni.2021.04.014. PubMed PMID:34004141 .
  6. Yohannes, DA, Kaukinen, K, Kurppa, K, Saavalainen, P, Greco, D. Clustering based approach for population level identification of condition-associated T-cell receptor β-chain CDR3 sequences. BMC Bioinformatics. 2021;22 (1):159. doi: 10.1186/s12859-021-04087-7. PubMed PMID:33765908 PubMed Central PMC7993519.
  7. Pavel, A, Del Giudice, G, Federico, A, Di Lieto, A, Kinaret, PAS, Serra, A et al.. Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. Brief Bioinform. 2021;22 (2):1430-1441. doi: 10.1093/bib/bbaa417. PubMed PMID:33569598 PubMed Central PMC7929418.
  8. Mouchlis, VD, Afantitis, A, Serra, A, Fratello, M, Papadiamantis, AG, Aidinis, V et al.. Advances in de Novo Drug Design: From Conventional to Machine Learning Methods. Int J Mol Sci. 2021;22 (4):. doi: 10.3390/ijms22041676. PubMed PMID:33562347 PubMed Central PMC7915729.
  9. Saarimäki, LA, Federico, A, Lynch, I, Papadiamantis, AG, Tsoumanis, A, Melagraki, G et al.. Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials. Sci Data. 2021;8 (1):49. doi: 10.1038/s41597-021-00808-y. PubMed PMID:33558569 PubMed Central PMC7870661.
  10. Acevedo, N, Scala, G, Merid, SK, Frumento, P, Bruhn, S, Andersson, A et al.. DNA Methylation Levels in Mononuclear Leukocytes from the Mother and Her Child Are Associated with IgE Sensitization to Allergens in Early Life. Int J Mol Sci. 2021;22 (2):. doi: 10.3390/ijms22020801. PubMed PMID:33466918 PubMed Central PMC7830007.
  11. Lynch, I, Afantitis, A, Greco, D, Dusinska, M, Banares, MA, Melagraki, G et al.. Editorial for the Special Issue From Nanoinformatics to Nanomaterials Risk Assessment and Governance. Nanomaterials (Basel). 2021;11 (1):. doi: 10.3390/nano11010121. PubMed PMID:33430326 PubMed Central PMC7825746.
  12. Rocha, V, Fraga, S, Moreira, C, Carmeli, C, Lenoir, A, Steptoe, A et al.. Life-course socioeconomic disadvantage and lung function: a multicohort study of 70 496 individuals. Eur Respir J. 2021;57 (3):. doi: 10.1183/13993003.01600-2020. PubMed PMID:33214206 .
  13. Ottman, N, Barrientos-Somarribas, M, Fyhrquist, N, Alexander, H, Wisgrill, L, Olah, P et al.. Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites. Allergy. 2021;76 (4):1173-1187. doi: 10.1111/all.14606. PubMed PMID:33001460 PubMed Central PMC8246754.

Search PubMed

2020

  1. Yohannes, DA, de Kauwe, A, Kaukinen, K, Kurppa, K, Mäki, M, Anderson, RP et al.. Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease. Front Immunol. 2020;11 :594243. doi: 10.3389/fimmu.2020.594243. PubMed PMID:33362776 PubMed Central PMC7759501.
  2. Lynch, I, Afantitis, A, Exner, T, Himly, M, Lobaskin, V, Doganis, P et al.. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?. Nanomaterials (Basel). 2020;10 (12):. doi: 10.3390/nano10122493. PubMed PMID:33322568 PubMed Central PMC7764592.
  3. Fortino, V, Wisgrill, L, Werner, P, Suomela, S, Linder, N, Jalonen, E et al.. Machine-learning-driven biomarker discovery for the discrimination between allergic and irritant contact dermatitis. Proc Natl Acad Sci U S A. 2020;117 (52):33474-33485. doi: 10.1073/pnas.2009192117. PubMed PMID:33318199 PubMed Central PMC7776829.
  4. Gallud, A, Delaval, M, Kinaret, P, Marwah, VS, Fortino, V, Ytterberg, J et al.. Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect. Adv Sci (Weinh). 2020;7 (22):2002221. doi: 10.1002/advs.202002221. PubMed PMID:33240770 PubMed Central PMC7675037.
  5. Acevedo, N, Benfeitas, R, Katayama, S, Bruhn, S, Andersson, A, Wikberg, G et al.. Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients. Sci Rep. 2020;10 (1):18020. doi: 10.1038/s41598-020-74798-z. PubMed PMID:33093567 PubMed Central PMC7582180.
  6. Federico, A, Hautanen, V, Christian, N, Kremer, A, Serra, A, Greco, D et al.. Manually curated and harmonised transcriptomics datasets of psoriasis and atopic dermatitis patients. Sci Data. 2020;7 (1):343. doi: 10.1038/s41597-020-00696-8. PubMed PMID:33051456 PubMed Central PMC7555498.
  7. Ottman, N, Barrientos-Somarribas, M, Fyhrquist, N, Alexander, H, Wisgrill, L, Olah, P et al.. Microbial and transcriptional differences elucidate atopic dermatitis heterogeneity across skin sites. Allergy. 2021;76 (4):1173-1187. doi: 10.1111/all.14606. PubMed PMID:33001460 PubMed Central PMC8246754.
  8. Ruokolainen, L, Fyhrquist, N, Laatikainen, T, Auvinen, P, Fortino, V, Scala, G et al.. Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence. Clin Exp Allergy. 2020;50 (10):1148-1158. doi: 10.1111/cea.13728. PubMed PMID:32865840 PubMed Central PMC7589450.
  9. Kinaret, PAS, Del Giudice, G, Greco, D. Covid-19 acute responses and possible long term consequences: What nanotoxicology can teach us. Nano Today. 2020;35 :100945. doi: 10.1016/j.nantod.2020.100945. PubMed PMID:32834832 PubMed Central PMC7416770.
  10. Serra, A, Fratello, M, Del Giudice, G, Saarimäki, LA, Paci, M, Federico, A et al.. TinderMIX: Time-dose integrated modelling of toxicogenomics data. Gigascience. 2020;9 (5):. doi: 10.1093/gigascience/giaa055. PubMed PMID:32449777 PubMed Central PMC7247400.
  11. Federico, A, Serra, A, Ha, MK, Kohonen, P, Choi, JS, Liampa, I et al.. Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. Nanomaterials (Basel). 2020;10 (5):. doi: 10.3390/nano10050903. PubMed PMID:32397130 PubMed Central PMC7279140.
  12. Ndika, J, Ilves, M, Kooter, IM, Gröllers-Mulderij, M, Duistermaat, E, Tromp, PC et al.. Mechanistic Similarities between 3D Human Bronchial Epithelium and Mice Lung, Exposed to Copper Oxide Nanoparticles, Support Non-Animal Methods for Hazard Assessment. Small. 2020;16 (36):e2000527. doi: 10.1002/smll.202000527. PubMed PMID:32351023 .
  13. Kinaret, PAS, Serra, A, Federico, A, Kohonen, P, Nymark, P, Liampa, I et al.. Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. Nanomaterials (Basel). 2020;10 (4):. doi: 10.3390/nano10040750. PubMed PMID:32326418 PubMed Central PMC7221878.
  14. Serra, A, Fratello, M, Cattelani, L, Liampa, I, Melagraki, G, Kohonen, P et al.. Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment. Nanomaterials (Basel). 2020;10 (4):. doi: 10.3390/nano10040708. PubMed PMID:32276469 PubMed Central PMC7221955.
  15. Kinaret, PAS, Scala, G, Federico, A, Sund, J, Greco, D. Carbon Nanomaterials Promote M1/M2 Macrophage Activation. Small. 2020;16 (21):e1907609. doi: 10.1002/smll.201907609. PubMed PMID:32250056 .
  16. Afantitis, A, Melagraki, G, Isigonis, P, Tsoumanis, A, Varsou, DD, Valsami-Jones, E et al.. NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. Comput Struct Biotechnol J. 2020;18 :583-602. doi: 10.1016/j.csbj.2020.02.023. PubMed PMID:32226594 PubMed Central PMC7090366.
  17. Gupta, G, Gliga, A, Hedberg, J, Serra, A, Greco, D, Odnevall Wallinder, I et al.. Cobalt nanoparticles trigger ferroptosis-like cell death (oxytosis) in neuronal cells: Potential implications for neurodegenerative disease. FASEB J. 2020;34 (4):5262-5281. doi: 10.1096/fj.201902191RR. PubMed PMID:32060981 .
  18. Scala, G, Federico, A, Palumbo, D, Cocozza, S, Greco, D. DNA sequence context as a marker of CpG methylation instability in normal and cancer tissues. Sci Rep. 2020;10 (1):1721. doi: 10.1038/s41598-020-58331-w. PubMed PMID:32015379 PubMed Central PMC6997448.
  19. Serra, A, Saarimäki, LA, Fratello, M, Marwah, VS, Greco, D. BMDx: a graphical Shiny application to perform Benchmark Dose analysis for transcriptomics data. Bioinformatics. 2020;36 (9):2932-2933. doi: 10.1093/bioinformatics/btaa030. PubMed PMID:31950985 .
  20. Nymark, P, Bakker, M, Dekkers, S, Franken, R, Fransman, W, García-Bilbao, A et al.. Toward Rigorous Materials Production: New Approach Methodologies Have Extensive Potential to Improve Current Safety Assessment Practices. Small. 2020;16 (6):e1904749. doi: 10.1002/smll.201904749. PubMed PMID:31913582 .
  21. Laine, JE, Baltar, VT, Stringhini, S, Gandini, M, Chadeau-Hyam, M, Kivimaki, M et al.. Reducing socio-economic inequalities in all-cause mortality: a counterfactual mediation approach. Int J Epidemiol. 2020;49 (2):497-510. doi: 10.1093/ije/dyz248. PubMed PMID:31855265 PubMed Central PMC7266549.
  22. Kere, M, Gruzieva, O, Ullemar, V, Söderhäll, C, Greco, D, Kull, I et al.. Effects of inhaled corticosteroids on DNA methylation in peripheral blood cells in children with asthma. Allergy. 2020;75 (3):688-691. doi: 10.1111/all.14043. PubMed PMID:31498880 .
  23. Serra, A, Önlü, S, Festa, P, Fortino, V, Greco, D. MaNGA: a novel multi-niche multi-objective genetic algorithm for QSAR modelling. Bioinformatics. 2020;36 (1):145-153. doi: 10.1093/bioinformatics/btz521. PubMed PMID:31233136 .

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