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Toxicology and Pharmacology

Publications

2024

  1. Morikka, J, Federico, A, Möbus, L, Inkala, S, Pavel, A, Sani, S et al.. Toxicogenomic assessment of in vitro macrophages exposed to profibrotic challenge reveals a sustained transcriptomic immune signature. Comput Struct Biotechnol J. 2024;25 :194-204. doi: 10.1016/j.csbj.2024.10.010. PubMed PMID:39430886 PubMed Central PMC11490883.
  2. Palviainen, M, Puutio, J, Østergaard, RH, Eble, JA, Maaninka, K, Butt, U et al.. Beyond basic characterization and omics: Immunomodulatory roles of platelet-derived extracellular vesicles unveiled by functional testing. J Extracell Vesicles. 2024;13 (10):e12513. doi: 10.1002/jev2.12513. PubMed PMID:39330919 PubMed Central PMC11428872.
  3. Ramessur, R, Saklatvala, J, Budu-Aggrey, A, Ostaszewski, M, Möbus, L, Greco, D et al.. Exploring the Link Between Genetic Predictors of Cardiovascular Disease and Psoriasis. JAMA Cardiol. 2024;9 (11):1009-1017. doi: 10.1001/jamacardio.2024.2859. PubMed PMID:39292496 PubMed Central PMC11411451.
  4. Migliaccio, G, Morikka, J, Del Giudice, G, Vaani, M, Möbus, L, Serra, A et al.. Methylation and transcriptomic profiling reveals short term and long term regulatory responses in polarized macrophages. Comput Struct Biotechnol J. 2024;25 :143-152. doi: 10.1016/j.csbj.2024.08.018. PubMed PMID:39257962 PubMed Central PMC11385784.
  5. Del Giudice, G, Serra, A, Pavel, A, Torres Maia, M, Saarimäki, LA, Fratello, M et al.. A Network Toxicology Approach for Mechanistic Modelling of Nanomaterial Hazard and Adverse Outcomes. Adv Sci (Weinh). 2024;11 (32):e2400389. doi: 10.1002/advs.202400389. PubMed PMID:38923832 PubMed Central PMC11348149.
  6. Möbus, L, Serra, A, Fratello, M, Pavel, A, Federico, A, Greco, D et al.. A Multi-Dimensional Approach to Map Disease Relationships Challenges Classical Disease Views. Adv Sci (Weinh). 2024;11 (30):e2401754. doi: 10.1002/advs.202401754. PubMed PMID:38840452 PubMed Central PMC11321629.
  7. Kynkäänniemi, E, Lindén, J, Ngambundit, S, Saarimäki, LA, Greco, D, Slaba, H et al.. Polyphenol- and Glucuronoxylan-Rich Fiber Extract from Birch ( sp.) Wood Regulates Colonic Barrier Function and Cell Proliferation in Healthy Rats. J Agric Food Chem. 2024;72 (7):3495-3505. doi: 10.1021/acs.jafc.3c07757. PubMed PMID:38343302 PubMed Central PMC11398711.
  8. Federico, A, Möbus, L, Al-Abdulraheem, Z, Pavel, A, Fortino, V, Del Giudice, G et al.. Integrative network analysis suggests prioritised drugs for atopic dermatitis. J Transl Med. 2024;22 (1):64. doi: 10.1186/s12967-024-04879-4. PubMed PMID:38229087 PubMed Central PMC10792836.

Search PubMed

2023

  1. Del Giudice, G, Migliaccio, G, D’Alessandro, N, Saarimäki, LA, Torres Maia, M, Annala, ME et al.. Advancing chemical safety assessment through an omics-based characterization of the test system-chemical interaction. Front Toxicol. 2023;5 :1294780. doi: 10.3389/ftox.2023.1294780. PubMed PMID:38026842 PubMed Central PMC10673692.
  2. Saarimäki, LA, Del Giudice, G, Greco, D. Expanding adverse outcome pathways towards one health models for nanosafety. Front Toxicol. 2023;5 :1176745. doi: 10.3389/ftox.2023.1176745. PubMed PMID:37692900 PubMed Central PMC10485555.
  3. Federico, A, Fratello, M, Pavel, A, Möbus, L, Del Giudice, G, Serra, A et al.. DREAM: an R package for druggability evaluation of human complex diseases. Bioinformatics. 2023;39 (7):. doi: 10.1093/bioinformatics/btad442. PubMed PMID:37471593 PubMed Central PMC10374489.
  4. Valentino, SA, Seidel, C, Lorcin, M, Sébillaud, S, Wolff, H, Grossmann, S et al.. Identification of a Gene Signature Predicting (Nano)Particle-Induced Adverse Lung Outcome in Rats. Int J Mol Sci. 2023;24 (13):. doi: 10.3390/ijms241310890. PubMed PMID:37446067 PubMed Central PMC10341909.
  5. Hautanen, V, Morikka, J, Saarimäki, LA, Bisenberger, J, Toimela, T, Serra, A et al.. The in vitro immunomodulatory effect of multi-walled carbon nanotubes by multilayer analysis. NanoImpact. 2023;31 :100476. doi: 10.1016/j.impact.2023.100476. PubMed PMID:37437691 .
  6. Saarimäki, LA, Fratello, M, Pavel, A, Korpilähde, S, Leppänen, J, Serra, A et al.. A curated gene and biological system annotation of adverse outcome pathways related to human health. Sci Data. 2023;10 (1):409. doi: 10.1038/s41597-023-02321-w. PubMed PMID:37355733 PubMed Central PMC10290716.
  7. Di Lieto, E, Serra, A, Inkala, SI, Saarimäki, LA, Del Giudice, G, Fratello, M et al.. ESPERANTO: a GLP-field sEmi-SuPERvised toxicogenomics metadAta curatioN TOol. Bioinformatics. 2023;39 (6):. doi: 10.1093/bioinformatics/btad405. PubMed PMID:37354497 PubMed Central PMC10313344.
  8. Pavel, A, Del Giudice, G, Fratello, M, Ghemtio, L, Di Lieto, A, Yli-Kauhaluoma, J et al.. KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles. Bioinformatics. 2023;39 (6):. doi: 10.1093/bioinformatics/btad341. PubMed PMID:37225400 PubMed Central PMC10243850.
  9. Maaninka, K, Neuvonen, M, Kerkelä, E, Hyvärinen, K, Palviainen, M, Kamali-Moghaddam, M et al.. OxLDL sensitizes platelets for increased formation of extracellular vesicles capable of finetuning macrophage gene expression. Eur J Cell Biol. 2023;102 (2):151311. doi: 10.1016/j.ejcb.2023.151311. PubMed PMID:36963245 .
  10. Saarimäki, LA, Morikka, J, Pavel, A, Korpilähde, S, Del Giudice, G, Federico, A et al.. Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach. Adv Sci (Weinh). 2023;10 (2):e2203984. doi: 10.1002/advs.202203984. PubMed PMID:36479815 PubMed Central PMC9839874.

Search PubMed

2022

  1. Saarimäki, LA, Morikka, J, Pavel, A, Korpilähde, S, Del Giudice, G, Federico, A et al.. Toxicogenomics Data for Chemical Safety Assessment and Development of New Approach Methodologies: An Adverse Outcome Pathway-Based Approach. Adv Sci (Weinh). 2023;10 (2):e2203984. doi: 10.1002/advs.202203984. PubMed PMID:36479815 PubMed Central PMC9839874.
  2. Federico, A, Pavel, A, Möbus, L, McKean, D, Del Giudice, G, Fortino, V et al.. The integration of large-scale public data and network analysis uncovers molecular characteristics of psoriasis. Hum Genomics. 2022;16 (1):62. doi: 10.1186/s40246-022-00431-x. PubMed PMID:36437479 PubMed Central PMC9703794.
  3. Pavel, A, Saarimäki, LA, Möbus, L, Federico, A, Serra, A, Greco, D et al.. The potential of a data centred approach & knowledge graph data representation in chemical safety and drug design. Comput Struct Biotechnol J. 2022;20 :4837-4849. doi: 10.1016/j.csbj.2022.08.061. PubMed PMID:36147662 PubMed Central PMC9464643.
  4. Wyrzykowska, E, Mikolajczyk, A, Lynch, I, Jeliazkova, N, Kochev, N, Sarimveis, H et al.. Representing and describing nanomaterials in predictive nanoinformatics. Nat Nanotechnol. 2022;17 (9):924-932. doi: 10.1038/s41565-022-01173-6. PubMed PMID:35982314 .
  5. Clerbaux, LA, Albertini, MC, Amigó, N, Beronius, A, Bezemer, GFG, Coecke, S et al.. Factors Modulating COVID-19: A Mechanistic Understanding Based on the Adverse Outcome Pathway Framework. J Clin Med. 2022;11 (15):. doi: 10.3390/jcm11154464. PubMed PMID:35956081 PubMed Central PMC9369763.
  6. Fortino, V, Kinaret, PAS, Fratello, M, Serra, A, Saarimäki, LA, Gallud, A et al.. Biomarkers of nanomaterials hazard from multi-layer data. Nat Commun. 2022;13 (1):3798. doi: 10.1038/s41467-022-31609-5. PubMed PMID:35778420 PubMed Central PMC9249793.
  7. Serra, A, Del Giudice, G, Kinaret, PAS, Saarimäki, LA, Poulsen, SS, Fortino, V et al.. Characterization of ENM Dynamic Dose-Dependent MOA in Lung with Respect to Immune Cells Infiltration. Nanomaterials (Basel). 2022;12 (12):. doi: 10.3390/nano12122031. PubMed PMID:35745370 PubMed Central PMC9228743.
  8. Oláh, P, Szlávicz, E, Kuchner, M, Nemmer, J, Zeeuwen, P, Lefèvre-Utile, A et al.. Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation. J Dermatol Sci. 2022;106 (3):132-140. doi: 10.1016/j.jdermsci.2022.04.007. PubMed PMID:35537882 .
  9. Ribeiro, AI, Fraga, S, Severo, M, Kelly-Irving, M, Delpierre, C, Stringhini, S et al.. Association of neighbourhood disadvantage and individual socioeconomic position with all-cause mortality: a longitudinal multicohort analysis. Lancet Public Health. 2022;7 (5):e447-e457. doi: 10.1016/S2468-2667(22)00036-6. PubMed PMID:35487230 .
  10. Federico, A, Fratello, M, Scala, G, Möbus, L, Pavel, A, Del Giudice, G et al.. Integrated Network Pharmacology Approach for Drug Combination Discovery: A Multi-Cancer Case Study. Cancers (Basel). 2022;14 (8):. doi: 10.3390/cancers14082043. PubMed PMID:35454948 PubMed Central PMC9028433.
  11. Serra, A, Saarimäki, LA, Pavel, A, Del Giudice, G, Fratello, M, Cattelani, L et al.. Nextcast: A software suite to analyse and model toxicogenomics data. Comput Struct Biotechnol J. 2022;20 :1413-1426. doi: 10.1016/j.csbj.2022.03.014. PubMed PMID:35386103 PubMed Central PMC8956870.
  12. Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, JA, Severin, J et al.. Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nat Commun. 2022;13 (1):1200. doi: 10.1038/s41467-022-28758-y. PubMed PMID:35232988 PubMed Central PMC8888638.
  13. Serra, A, Fratello, M, Federico, A, Ojha, R, Provenzani, R, Tasnadi, E et al.. Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation. Brief Bioinform. 2022;23 (1):. doi: 10.1093/bib/bbab507. PubMed PMID:34962256 PubMed Central PMC8769897.
  14. Saarimäki, LA, Melagraki, G, Afantitis, A, Lynch, I, Greco, D. Prospects and challenges for FAIR toxicogenomics data. Nat Nanotechnol. 2022;17 (1):17-18. doi: 10.1038/s41565-021-01049-1. PubMed PMID:34949777 .
  15. Pavel, A, Serra, A, Cattelani, L, Federico, A, Greco, D. Network Analysis of Microarray Data. Methods Mol Biol. 2022;2401 :161-186. doi: 10.1007/978-1-0716-1839-4_11. PubMed PMID:34902128 .
  16. Fratello, M, Cattelani, L, Federico, A, Pavel, A, Scala, G, Serra, A et al.. Unsupervised Algorithms for Microarray Sample Stratification. Methods Mol Biol. 2022;2401 :121-146. doi: 10.1007/978-1-0716-1839-4_9. PubMed PMID:34902126 .
  17. Serra, A, Cattelani, L, Fratello, M, Fortino, V, Kinaret, PAS, Greco, D et al.. Supervised Methods for Biomarker Detection from Microarray Experiments. Methods Mol Biol. 2022;2401 :101-120. doi: 10.1007/978-1-0716-1839-4_8. PubMed PMID:34902125 .
  18. Federico, A, Saarimäki, LA, Serra, A, Del Giudice, G, Kinaret, PAS, Scala, G et al.. Microarray Data Preprocessing: From Experimental Design to Differential Analysis. Methods Mol Biol. 2022;2401 :79-100. doi: 10.1007/978-1-0716-1839-4_7. PubMed PMID:34902124 .
  19. Lefèvre-Utile, A, Saichi, M, Oláh, P, Delord, M, Homey, B, Soumelis, V et al.. Transcriptome-based identification of novel endotypes in adult atopic dermatitis. Allergy. 2022;77 (5):1486-1498. doi: 10.1111/all.15150. PubMed PMID:34689335 .

Search PubMed

2021

  1. Saarimäki, LA, Melagraki, G, Afantitis, A, Lynch, I, Greco, D. Prospects and challenges for FAIR toxicogenomics data. Nat Nanotechnol. 2022;17 (1):17-18. doi: 10.1038/s41565-021-01049-1. PubMed PMID:34949777 .
  2. Lefèvre-Utile, A, Saichi, M, Oláh, P, Delord, M, Homey, B, Soumelis, V et al.. Transcriptome-based identification of novel endotypes in adult atopic dermatitis. Allergy. 2022;77 (5):1486-1498. doi: 10.1111/all.15150. PubMed PMID:34689335 .
  3. Feola, S, Haapala, M, Peltonen, K, Capasso, C, Martins, B, Antignani, G et al.. PeptiCHIP: A Microfluidic Platform for Tumor Antigen Landscape Identification. ACS Nano. 2021;15 (10):15992-16010. doi: 10.1021/acsnano.1c04371. PubMed PMID:34605646 PubMed Central PMC8552492.
  4. Pavel, A, Federico, A, Del Giudice, G, Serra, A, Greco, D. VOLTA: adVanced mOLecular neTwork Analysis. Bioinformatics. 2021;37 (23):4587-4588. doi: 10.1093/bioinformatics/btab642. PubMed PMID:34498028 PubMed Central PMC8687180.
  5. Rintala, TJ, Federico, A, Latonen, L, Greco, D, Fortino, V. A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. Brief Bioinform. 2021;22 (6):. doi: 10.1093/bib/bbab314. PubMed PMID:34396389 PubMed Central PMC8575038.
  6. Alenius, H, Sinkko, H, Moitinho-Silva, L, Rodriguez, E, Broderick, C, Alexander, H et al.. The power and potential of BIOMAP to elucidate host-microbiome interplay in skin inflammatory diseases. Exp Dermatol. 2021;30 (10):1517-1531. doi: 10.1111/exd.14446. PubMed PMID:34387406 .
  7. 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;9 (8):981-993. doi: 10.1158/2326-6066.CIR-20-0814. PubMed PMID:34103348 PubMed Central PMC8974425.
  8. 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.
  9. Scala, G, Delaval, MN, Mukherjee, SP, Federico, A, Khaliullin, TO, Yanamala, N et al.. Multi-walled carbon nanotubes elicit concordant changes in DNA methylation and gene expression following long-term pulmonary exposure in mice. Carbon N Y. 2021;178 :563-572. doi: 10.1016/j.carbon.2021.03.045. PubMed PMID:37206955 PubMed Central PMC10193301.
  10. 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.
  11. 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.
  12. 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 .
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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 .
  20. 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 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 CD4CLA 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 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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2019

  1. Scala, G, Federico, A, Fortino, V, Greco, D, Majello, B. Knowledge Generation with Rule Induction in Cancer Omics. Int J Mol Sci. 2019;21 (1):. doi: 10.3390/ijms21010018. PubMed PMID:31861438 PubMed Central PMC6981587.
  2. Eerola, SK, Santio, NM, Rinne, S, Kouvonen, P, Corthals, GL, Scaravilli, M et al.. Phosphorylation of NFATC1 at PIM1 target sites is essential for its ability to promote prostate cancer cell migration and invasion. Cell Commun Signal. 2019;17 (1):148. doi: 10.1186/s12964-019-0463-y. PubMed PMID:31730483PubMed Central PMC6858710.
  3. Fyhrquist, N, Muirhead, G, Prast-Nielsen, S, Jeanmougin, M, Olah, P, Skoog, T et al.. Microbe-host interplay in atopic dermatitis and psoriasis. Nat Commun. 2019;10 (1):4703. doi: 10.1038/s41467-019-12253-y. PubMed PMID:31619666 PubMed Central PMC6795799.
  4. 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 .
  5. Ilves, M, Kinaret, PAS, Ndika, J, Karisola, P, Marwah, V, Fortino, V et al.. Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation. Part Fibre Toxicol. 2019;16 (1):28. doi: 10.1186/s12989-019-0309-1. PubMed PMID:31277695 PubMed Central PMC6612204.
  6. Göös, H, Fogarty, CL, Sahu, B, Plagnol, V, Rajamäki, K, Nurmi, K et al.. Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy. J Allergy Clin Immunol. 2019;144 (5):1364-1376. doi: 10.1016/j.jaci.2019.06.003. PubMed PMID:31201888 .
  7. Kooter, I, Ilves, M, Gröllers-Mulderij, M, Duistermaat, E, Tromp, PC, Kuper, F et al.. Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model. ACS Nano. 2019;13 (6):6932-6946. doi: 10.1021/acsnano.9b01823. PubMed PMID:31188557 PubMed Central PMC6750904.
  8. Serra, A, Önlü, S, Coretto, P, Greco, D. An integrated quantitative structure and mechanism of action-activity relationship model of human serum albumin binding. J Cheminform. 2019;11 (1):38. doi: 10.1186/s13321-019-0359-2. PubMed PMID:31172382 PubMed Central PMC6551915.
  9. McCrory, C, Leahy, S, Ribeiro, AI, Fraga, S, Barros, H, Avendano, M et al.. Maternal educational inequalities in measured body mass index trajectories in three European countries. Paediatr Perinat Epidemiol. 2019;33 (3):226-237. doi: 10.1111/ppe.12552. PubMed PMID:31090081 .
  10. Scala, G, Serra, A, Marwah, VS, Saarimäki, LA, Greco, D. FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments. BMC Bioinformatics. 2019;20 (1):79. doi: 10.1186/s12859-019-2639-2. PubMed PMID:30767762 PubMed Central PMC6376640.
  11. Marwah, VS, Scala, G, Kinaret, PAS, Serra, A, Alenius, H, Fortino, V et al.. eUTOPIA: solUTion for Omics data PreprocessIng and Analysis. Source Code Biol Med. 2019;14 :1. doi: 10.1186/s13029-019-0071-7. PubMed PMID:30728855 PubMed Central PMC6352382.
  12. Serra, A, Letunic, I, Fortino, V, Handy, RD, Fadeel, B, Tagliaferri, R et al.. INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials. Sci Rep. 2019;9 (1):179. doi: 10.1038/s41598-018-37411-y. PubMed PMID:30655578 PubMed Central PMC6336851.
  13. Uotila, R, Kukkonen, AK, Greco, D, Pelkonen, AS, Mäkelä, MJ. Peanut oral immunotherapy increases IgG4 to Ara h 1, 2, and 6 but does not affect IgG4 to other allergens. Pediatr Allergy Immunol. 2019;30 (2):248-252. doi: 10.1111/pai.13012. PubMed PMID:30561805 .
  14. Karisola, P, Suomalainen, A, Fortino, V, Ottman, N, Vendelin, J, Wolff, HJ et al.. Tape-stripping alters the microbe-host correlations in mouse skin. Allergy. 2019;74 (3):617-621. doi: 10.1111/all.13653. PubMed PMID:30372529 .
  15. Drobin, K, Assadi, G, Hong, MG, Andersson, E, Fredolini, C, Forsström, B et al.. Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci. Inflamm Bowel Dis. 2019;25 (2):306-316. doi: 10.1093/ibd/izy326. PubMed PMID:30358838 PubMed Central PMC6327232.

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2018

  1. Karisola, P, Suomalainen, A, Fortino, V, Ottman, N, Vendelin, J, Wolff, HJ et al.. Tape-stripping alters the microbe-host correlations in mouse skin. Allergy. 2019;74 (3):617-621. doi: 10.1111/all.13653. PubMed PMID:30372529 .
  2. Scala, G, Marwah, V, Kinaret, P, Sund, J, Fortino, V, Greco, D et al.. Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials. Data Brief. 2018;19 :1046-1057. doi: 10.1016/j.dib.2018.05.107. PubMed PMID:30228994PubMed Central PMC6140287.
  3. Laine, MA, Trontti, K, Misiewicz, Z, Sokolowska, E, Kulesskaya, N, Heikkinen, A et al.. Genetic Control of Myelin Plasticity after Chronic Psychosocial Stress. eNeuro. ;5 (4):. doi: 10.1523/ENEURO.0166-18.2018. PubMed PMID:30073192PubMed Central PMC6071195.
  4. Scala, G, Kinaret, P, Marwah, V, Sund, J, Fortino, V, Greco, D et al.. Multi-omics analysis of ten carbon nanomaterials effects highlights cell type specific patterns of molecular regulation and adaptation. NanoImpact. 2018;11 :99-108. doi: 10.1016/j.impact.2018.05.003. PubMed PMID:32140619 PubMed Central PMC7043328.
  5. Oghabian, A, Greco, D, Frilander, MJ. IntEREst: intron-exon retention estimator. BMC Bioinformatics. 2018;19 (1):130. doi: 10.1186/s12859-018-2122-5. PubMed PMID:29642843 PubMed Central PMC5896110.
  6. De Gregorio, R, Pulcrano, S, De Sanctis, C, Volpicelli, F, Guatteo, E, von Oerthel, L et al.. miR-34b/c Regulates Wnt1 and Enhances Mesencephalic Dopaminergic Neuron Differentiation. Stem Cell Reports. 2018;10 (4):1237-1250. doi: 10.1016/j.stemcr.2018.02.006. PubMed PMID:29526736 PubMed Central PMC5998209.
  7. Xu, CJ, Söderhäll, C, Bustamante, M, Baïz, N, Gruzieva, O, Gehring, U et al.. DNA methylation in childhood asthma: an epigenome-wide meta-analysis. Lancet Respir Med. 2018;6 (5):379-388. doi: 10.1016/S2213-2600(18)30052-3. PubMed PMID:29496485 .
  8. Castagné, R, Garès, V, Karimi, M, Chadeau-Hyam, M, Vineis, P, Delpierre, C et al.. Allostatic load and subsequent all-cause mortality: which biological markers drive the relationship? Findings from a UK birth cohort. Eur J Epidemiol. 2018;33 (5):441-458. doi: 10.1007/s10654-018-0364-1. PubMed PMID:29476357 PubMed Central PMC5968064.
  9. Trontti, K, Väänänen, J, Sipilä, T, Greco, D, Hovatta, I. Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression. RNA. 2018;24 (5):643-655. doi: 10.1261/rna.064881.117. PubMed PMID:29445025 PubMed Central PMC5900563.
  10. Marwah, VS, Kinaret, PAS, Serra, A, Scala, G, Lauerma, A, Fortino, V et al.. INfORM: Inference of NetwOrk Response Modules. Bioinformatics. 2018;34 (12):2136-2138. doi: 10.1093/bioinformatics/bty063. PubMed PMID:29425308 .

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2017

  1. Yohannes, DA, Freitag, TL, de Kauwe, A, Kaukinen, K, Kurppa, K, Wacklin, P et al.. Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease. Sci Rep. 2017;7 (1):17977. doi: 10.1038/s41598-017-18137-9. PubMed PMID:29269859 PubMed Central PMC5740085.
  2. Muurinen, M, Hannula-Jouppi, K, Reinius, LE, Söderhäll, C, Merid, SK, Bergström, A et al.. Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children. Sci Rep. 2017;7 (1):15693. doi: 10.1038/s41598-017-16070-5. PubMed PMID:29146936 PubMed Central PMC5691194.
  3. Poon, WL, Alenius, H, Ndika, J, Fortino, V, Kolhinen, V, Meščeriakovas, A et al.. Nano-sized zinc oxide and silver, but not titanium dioxide, induce innate and adaptive immunity and antiviral response in differentiated THP-1 cells. Nanotoxicology. 2017;11 (7):936-951. doi: 10.1080/17435390.2017.1382600. PubMed PMID:28958187 .
  4. Kinaret, P, Marwah, V, Fortino, V, Ilves, M, Wolff, H, Ruokolainen, L et al.. Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo. ACS Nano. 2017;11 (4):3786-3796. doi: 10.1021/acsnano.6b08650. PubMed PMID:28380293 .
  5. Stringhini, S, Carmeli, C, Jokela, M, Avendaño, M, Muennig, P, Guida, F et al.. Socioeconomic status and the 25 × 25 risk factors as determinants of premature mortality: a multicohort study and meta-analysis of 1·7 million men and women. Lancet. 2017;389 (10075):1229-1237. doi: 10.1016/S0140-6736(16)32380-7. PubMed PMID:28159391 PubMed Central PMC5368415.
  6. Kinaret, P, Ilves, M, Fortino, V, Rydman, E, Karisola, P, Lähde, A et al.. Inhalation and Oropharyngeal Aspiration Exposure to Rod-Like Carbon Nanotubes Induce Similar Airway Inflammation and Biological Responses in Mouse Lungs. ACS Nano. 2017;11 (1):291-303. doi: 10.1021/acsnano.6b05652. PubMed PMID:28045493 .
  7. Uotila, R, Kukkonen, AK, Greco, D, Pelkonen, AS, Mäkelä, MJ. Peanut oral immunotherapy decreases IgE to Ara h 2 and Ara h 6 but does not enhance sensitization to cross-reactive allergens. J Allergy Clin Immunol. 2017;139 (4):1393-1396.e6. doi: 10.1016/j.jaci.2016.09.054. PubMed PMID:27916627 .
  8. Muranen, TA, Greco, D, Blomqvist, C, Aittomäki, K, Khan, S, Hogervorst, F et al.. Genetic modifiers of CHEK2*1100delC-associated breast cancer risk. Genet Med. 2017;19 (5):599-603. doi: 10.1038/gim.2016.147. PubMed PMID:27711073 PubMed Central PMC5382131.

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