2019

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 ;30(2)248-252, 2019
PMID

Karisola P, Suomalainen A, Fortino V, Ottman N, Vendelin J, Wolff HJ, Ruokolainen L, Greco D, Fyhrquist N, Alenius H
Tape-stripping alters the microbe-host correlations in mouse skin.
Allergy ;74(3)617-621, 2019
PMID

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 ;20(1)79, 2019
PMID

Marwah VS, Scala G, Kinaret PAS, Serra A, Alenius H, Fortino V, Greco D
eUTOPIA: solUTion for Omics data PreprocessIng and Analysis.
Source Code Biol Med ;2019
PMID

Serra A, Letunic I, Fortino V, Handy RD, Fadeel B, Tagliaferri R, Greco D
INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials.
Sci Rep ;9(1)179, 2019
PMID

Drobin K, Assadi G, Hong MG, Andersson E, Fredolini C, Forsström B, Reznichenko A, Akhter T, Ek WE, Bonfiglio F, Hansen MB, Sandberg K, Greco D, Repsilber D, Schwenk JM, D'Amato M, Halfvarson J
Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci.
Inflamm Bowel Dis ;25(2)306-316, 2019
PMID

2018

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 ;2018
PMID

Scala G, Marwah V, Kinaret P, Sund J, Fortino V, Greco D
Integration of genome-wide mRNA and miRNA expression, and DNA methylation data of three cell lines exposed to ten carbon nanomaterials.
Data Brief ;2018
PMID

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 ;24(5)643-655, 2018
PMID

Oghabian A, Greco D, Frilander MJ
IntEREst: intron-exon retention estimator.
BMC Bioinformatics ;19(1)130, 2018
PMID

Marwah VS, Kinaret PAS, Serra A, Scala G, Lauerma A, Fortino V, Greco D
INfORM: Inference of NetwOrk Response Modules.
Bioinformatics ;34(12)2136-2138, 2018
PMID

De Gregorio R, Pulcrano S, De Sanctis C, Volpicelli F, Guatteo E, von Oerthel L, Latagliata EC, Esposito R, Piscitelli RM, Perrone-Capano C, Costa V, Greco D, Puglisi-Allegra S, Smidt MP, di Porzio U, Caiazzo M, Mercuri NB, Li M, Bellenchi GC
miR-34b/c Regulates Wnt1 and Enhances Mesencephalic Dopaminergic Neuron Differentiation.
Stem Cell Reports ;10(4)1237-1250, 2018
PMID

2017

Muurinen M, Hannula-Jouppi K, Reinius LE, Söderhäll C, Merid SK, Bergström A, Melén E, Pershagen G, Lipsanen-Nyman M, Greco D, Kere J
Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children.
Sci Rep ;7(1)15693, 2017
PMID

Yohannes DA, Freitag TL, de Kauwe A, Kaukinen K, Kurppa K, Wacklin P, Mäki M, Arstila TP, Anderson RP, Greco D, Saavalainen P
Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease.
Sci Rep ;7(1)17977, 2017
PMID

Kinaret P, Marwah V, Fortino V, Ilves M, Wolff H, Ruokolainen L, Auvinen P, Savolainen K, Alenius H, Greco D
Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo.
ACS Nano ;11(4)3786-3796, 2017
PMID

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 ;139(4)1393-1396.e6, 2017
PMID

Poon WL, Alenius H, Ndika J, Fortino V, Kolhinen V, Meščeriakovas A, Wang M, Greco D, Lähde A, Jokiniemi J, Lee JC, El-Nezami H, Karisola P
Nano-sized zinc oxide and silver, but not titanium dioxide, induce innate and adaptive immunity and antiviral response in differentiated THP-1 cells.
Nanotoxicology ;11(7)936-951, 2017
PMID

Kinaret P, Ilves M, Fortino V, Rydman E, Karisola P, Lähde A, Koivisto J, Jokiniemi J, Wolff H, Savolainen K, Greco D, Alenius H
Inhalation and Oropharyngeal Aspiration Exposure to Rod-Like Carbon Nanotubes Induce Similar Airway Inflammation and Biological Responses in Mouse Lungs.
ACS Nano ;11(1)291-303, 2017
PMID

Muranen TA, Greco D, Blomqvist C, Aittomäki K, Khan S, Hogervorst F, Verhoef S, Pharoah PDP, Dunning AM, Shah M, Luben R, Bojesen SE, Nordestgaard BG, Schoemaker M, Swerdlow A, García-Closas M, Figueroa J, Dörk T, Bogdanova NV, Hall P, Li J, Khusnutdinova E, Bermisheva M, Kristensen V, Borresen-Dale AL, Investigators N, Peto J, Dos Santos Silva I, Couch FJ, Olson JE, Hillemans P, Park-Simon TW, Brauch H, Hamann U, Burwinkel B, Marme F, Meindl A, Schmutzler RK, Cox A, Cross SS, Sawyer EJ, Tomlinson I, Lambrechts D, Moisse M, Lindblom A, Margolin S, Hollestelle A, Martens JWM, Fasching PA, Beckmann MW, Andrulis IL, Knight JA, Investigators K, Anton-Culver H, Ziogas A, Giles GG, Milne RL, Brenner H, Arndt V, Mannermaa A, Kosma VM, Chang-Claude J, Rudolph A, Devilee P, Seynaeve C, Hopper JL, Southey MC, John EM, Whittemore AS, Bolla MK, Wang Q, Michailidou K, Dennis J, Easton DF, Schmidt MK, Nevanlinna H
Genetic modifiers of CHEK2*1100delC-associated bre
;
PMID

19(5)
599-603
, 2017 ;
PMID

2016

Kilpinen L, Parmar A, Greco D, Korhonen M, Lehenkari P, Saavalainen P, Laitinen S
Expansion induced microRNA changes in bone marrow mesenchymal stromal cells reveals interplay between immune regulation and cell cycle.
Aging (Albany NY) ;8(11)2799-2813, 2016
PMID

Fortino V, Tagliaferri R, Greco D
CONDOP: an R package for CONdition-Dependent Operon Predictions.
Bioinformatics ;32(20)3199-3200, 2016
PMID

Muranen TA, Blomqvist C, Dörk T, Jakubowska A, Heikkilä P, Fagerholm R, Greco D, Aittomäki K, Bojesen SE, Shah M, Dunning AM, Rhenius V, Hall P, Czene K, Brand JS, Darabi H, Chang-Claude J, Rudolph A, Nordestgaard BG, Couch FJ, Hart SN, Figueroa J, García-Closas M, Fasching PA, Beckmann MW, Li J, Liu J, Andrulis IL, Winqvist R, Pylkäs K, Mannermaa A, Kataja V, Lindblom A, Margolin S, Lubinski J, Dubrowinskaja N, Bolla MK, Dennis J, Michailidou K, Wang Q, Easton DF, Pharoah PD, Schmidt MK, Nevanlinna H
Patient survival and tumor characteristics associated with CHEK2:p.I157T - findings from the Breast Cancer Association Consortium.
Breast Cancer Res ;18(1)98, 2016
PMID

Koli K, Sutinen E, Rönty M, Rantakari P, Fortino V, Pulkkinen V, Greco D, Sipilä P, Myllärniemi M
Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment - A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine.
PLoS One ;11(7)e0159010, 2016
PMID

Penttinen P, Greco D, Muntyan V, Terefework Z, De Lajudie P, Roumiantseva M, Becker A, Auvinen P, Lindström K
Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair.
J Basic Microbiol ;56(6)680-5, 2016
PMID

Hirvinen M, Capasso C, Guse K, Garofalo M, Vitale A, Ahonen M, Kuryk L, Vähä-Koskela M, Hemminki A, Fortino V, Greco D, Cerullo V
Expression of DAI by an oncolytic vaccinia virus boosts the immunogenicity of the virus and enhances antitumor immunity.
Mol Ther Oncolytics ;2016
PMID

2015

Serra A, Fratello M, Fortino V, Raiconi G, Tagliaferri R, Greco D
MVDA: a multi-view genomic data integration methodology.
BMC Bioinformatics ;2015
PMID

Rydman EM, Ilves M, Vanhala E, Vippola M, Lehto M, Kinaret PA, Pylkkänen L, Happo M, Hirvonen MR, Greco D, Savolainen K, Wolff H, Alenius H
A Single Aspiration of Rod-like Carbon Nanotubes Induces Asbestos-like Pulmonary Inflammation Mediated in Part by the IL-1 Receptor.
Toxicol Sci ;147(1)140-55, 2015
PMID

Fortino V, Alenius H, Greco D
BACA: bubble chArt to compare annotations.
BMC Bioinformatics ;2015
PMID

Acevedo N, Reinius LE, Greco D, Gref A, Orsmark-Pietras C, Persson H, Pershagen G, Hedlin G, Melén E, Scheynius A, Kere J, Söderhäll C
Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus.
Hum Mol Genet ;24(3)875-90, 2015
PMID

Fratello M, Serra A, Fortino V, Raiconi G, Tagliaferri R, Greco D
A multi-view genomic data simulator.
BMC Bioinformatics ;2015
PMID

Acevedo N, Reinius LE, Vitezic M, Fortino V, Söderhäll C, Honkanen H, Veijola R, Simell O, Toppari J, Ilonen J, Knip M, Scheynius A, Hyöty H, Greco D, Kere J
Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes.
Clin Epigenetics ;2015
PMID

Palomäki J, Sund J, Vippola M, Kinaret P, Greco D, Savolainen K, Puustinen A, Alenius H
A secretomics analysis reveals major differences in the macrophage responses towards different types of carbon nanotubes.
Nanotoxicology ;9(6)719-28, 2015
PMID

2014

Rydman EM, Ilves M, Koivisto AJ, Kinaret PA, Fortino V, Savinko TS, Lehto MT, Pulkkinen V, Vippola M, Hämeri KJ, Matikainen S, Wolff H, Savolainen KM, Greco D, Alenius H
Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation.
Part Fibre Toxicol ;2014
PMID

Niemelä EH, Oghabian A, Staals RH, Greco D, Pruijn GJ, Frilander MJ
Global analysis of the nuclear processing of transcripts with unspliced U12-type introns by the exosome.
Nucleic Acids Res ;42(11)7358-69, 2014
PMID

Fyhrquist N, Ruokolainen L, Suomalainen A, Lehtimäki S, Veckman V, Vendelin J, Karisola P, Lehto M, Savinko T, Jarva H, Kosunen TU, Corander J, Auvinen P, Paulin L, von Hertzen L, Laatikainen T, Mäkelä M, Haahtela T, Greco D, Hanski I, Alenius H
Acinetobacter species in the skin microbiota protect against allergic sensitization and inflammation.
J Allergy Clin Immunol ;134(6)1301-1309.e11, 2014
PMID

Hannula-Jouppi K, Muurinen M, Lipsanen-Nyman M, Reinius LE, Ezer S, Greco D, Kere J
Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7.
Epigenetics ;9(3)351-65, 2014
PMID

Fortino V, Kinaret P, Fyhrquist N, Alenius H, Greco D
A robust and accurate method for feature selection and prioritization from multi-class OMICs data.
PLoS One ;9(9)e107801, 2014
PMID

Kelhälä HL, Palatsi R, Fyhrquist N, Lehtimäki S, Väyrynen JP, Kallioinen M, Kubin ME, Greco D, Tasanen K, Alenius H, Bertino B, Carlavan I, Mehul B, Déret S, Reiniche P, Martel P, Marty C, Blume-Peytavi U, Voegel JJ, Lauerma A
IL-17/Th17 pathway is activated in acne lesions.
PLoS One ;9(8)e105238, 2014
PMID

Fortino V, Smolander OP, Auvinen P, Tagliaferri R, Greco D
Transcriptome dynamics-based operon prediction in prokaryotes.
BMC Bioinformatics ;2014
PMID