Publications

2021


  1. 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; :. doi: 10.1093/bib/bbaa417. PubMed PMID:33569598 .
  2. 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 .
  3. 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.
  4. 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.
  5. 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.

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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. 2020; :. doi: 10.1111/all.14606. PubMed PMID:33001460 .
  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 .

Search PubMed

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.

Search PubMed

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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