Domenica D'Elia
Socio Ordinario
Ricercatore
CNR - Istituto di Tecnologie Biomediche
Contact Information
phone
+ 39 080 5929674
fax
+ 39 080 5929690
RESEARCH AREA
biological data integration,knowledge base management,network systems,sequence analysis
RESEARCH ACTIVITY
Research interests: Bioinformatics, Functional Genomics & Transcriptomics, Post-Transcriptional Regulation of Gene Expression, non-coding RNAs, micro RNAs.
Bioinformatics research expertise in the development of biological databases, data integration and analysis tools.
Databases developed: MitBASE, Human MitBase, KeyNet, MitoDrome, MitoRes, UTRminer, the LIBI Grid platform, Molecular Biodiversity Laboratory DB, ComiRNet, NonCode aReNA DB.
Research activity
Since 2009 she has been collaborating with the Department of Computer Sciences of the University of Bari to develop data mining tools for discovering non-coding RNA molecular mechanisms and functional roles. The first approach was for the discovery of miRNA regulatory modules by using data of validated and predicted miRNAs:mRNAs interactions. The scientific aim of this research line was to clarify the mechanisms and functions of miRNAs in human disease that can open new possibilities for using them as therapeutic targets and non-invasive biomarkers of diseases and therapy responses. Another work she realised in collaboration with the Department of Computer Sciences of the University of Bari is represented by a machine-learning algorithm that has been proven to be fundamental for the computational discovery of miRNA regulatory networks when using large-scale prediction data. Data produced by the application of these data-mining tools have been collected and published in the ComiRNet database. More recent developments are represented by two new tools, one predicting causal associations between ncRNAs and diseases exploiting Multi-Type Hierarchical Clustering and the other for gene network reconstruction by positive unlabeled link prediction via transfer learning.
Dr Domenica D’Elia has also been collaborating on a project based at the Institute for Biomedical Technologies in Bari, developing a bioinformatics suite for the classification and analysis of the non-coding RNA component of transcriptome sequence data from different NGS platforms (Roche 454, Illumina and Solid)(First InterOmics Flagship Project). This platform has been designed to include also tools for providing gene expression profiles of ncRNAs in total RNA-seq and small RNA- seq experiments (Arena-Idb).
Another research area she is investigating is the potential role of exogenous plant miRNAs, acquired through food, on the expression level of human genes in cancer and neurological diseases. In the nutrigenomics field, she is investigating the molecular basis of the Mediterranean diet’s benefits in healthy subjects. She is collaborating with the Council for Agricultural Research and Economics (CREA) to investigate the effect of grapes on the gene expression profile of healthy subjects. The collaboration inside the ml4microbiome COST Action also expects further developments in the nutrigenomics research field.
Projects (2019-2023)
COST Action ML4Microbiome (CA18131): Statistical and machine learning techniques in human microbiome studies
COST Action CHARME (CA15110): Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research
Scientific Project Coordinator: Flagship Project InterOmics “Scouting cross-kingdom
transfer: effect of exogenous plant microRNA on the expression of human genes involved in ageing-related diseases (SCKT)
InterOmics Flagship Project - Development of an integrated platform for the application of “omics” sciences to biomarker definition and theranostic, predictive and diagnostic profiles
Bioinformatics research expertise in the development of biological databases, data integration and analysis tools.
Databases developed: MitBASE, Human MitBase, KeyNet, MitoDrome, MitoRes, UTRminer, the LIBI Grid platform, Molecular Biodiversity Laboratory DB, ComiRNet, NonCode aReNA DB.
Research activity
Since 2009 she has been collaborating with the Department of Computer Sciences of the University of Bari to develop data mining tools for discovering non-coding RNA molecular mechanisms and functional roles. The first approach was for the discovery of miRNA regulatory modules by using data of validated and predicted miRNAs:mRNAs interactions. The scientific aim of this research line was to clarify the mechanisms and functions of miRNAs in human disease that can open new possibilities for using them as therapeutic targets and non-invasive biomarkers of diseases and therapy responses. Another work she realised in collaboration with the Department of Computer Sciences of the University of Bari is represented by a machine-learning algorithm that has been proven to be fundamental for the computational discovery of miRNA regulatory networks when using large-scale prediction data. Data produced by the application of these data-mining tools have been collected and published in the ComiRNet database. More recent developments are represented by two new tools, one predicting causal associations between ncRNAs and diseases exploiting Multi-Type Hierarchical Clustering and the other for gene network reconstruction by positive unlabeled link prediction via transfer learning.
Dr Domenica D’Elia has also been collaborating on a project based at the Institute for Biomedical Technologies in Bari, developing a bioinformatics suite for the classification and analysis of the non-coding RNA component of transcriptome sequence data from different NGS platforms (Roche 454, Illumina and Solid)(First InterOmics Flagship Project). This platform has been designed to include also tools for providing gene expression profiles of ncRNAs in total RNA-seq and small RNA- seq experiments (Arena-Idb).
Another research area she is investigating is the potential role of exogenous plant miRNAs, acquired through food, on the expression level of human genes in cancer and neurological diseases. In the nutrigenomics field, she is investigating the molecular basis of the Mediterranean diet’s benefits in healthy subjects. She is collaborating with the Council for Agricultural Research and Economics (CREA) to investigate the effect of grapes on the gene expression profile of healthy subjects. The collaboration inside the ml4microbiome COST Action also expects further developments in the nutrigenomics research field.
Projects (2019-2023)
COST Action ML4Microbiome (CA18131): Statistical and machine learning techniques in human microbiome studies
COST Action CHARME (CA15110): Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research
Scientific Project Coordinator: Flagship Project InterOmics “Scouting cross-kingdom
transfer: effect of exogenous plant microRNA on the expression of human genes involved in ageing-related diseases (SCKT)
InterOmics Flagship Project - Development of an integrated platform for the application of “omics” sciences to biomarker definition and theranostic, predictive and diagnostic profiles
SELECTED PUBLICATIONS
- Hollmann S, Regierer B, Bechis J, Tobin L, D’Elia D. Ten simple rules on how to develop a stakeholder engagement plan. PLoS Comput Biol. 2022 Oct 13;18(10):e1010520. doi: 10.1371/journal.pcbi.1010520.
- Susanne Hollmann, Babette Regierer, Domenica D’Elia, Annamaria Kisslinger, Giovanna L. Liguori (2022) Toward the definition of common strategies for improving reproducibility, standardisation, management, and overall impact of academic research. Advances in Biomembranes and Lipid Self-Assembly. Academic Press,ISSN 2451-9634, https://doi.org/10.1016/bs.abl.2022.05.001
- Balech B, Brennan L, Carrillo de Santa Pau E et al. The future of food and nutrition in ELIXIR [version 1; peer review: 1 approved with reservations]. F1000Research 2022, 11(ELIXIR):978. https://doi.org/10.12688/f1000research.51747.1
- Ibrahimi et al. (2022) Report of the ML4Microbiome workshop 2021 - Statistical and Machine Learning Techniques for Microbiome Data Analysis. EMBnet.journal 27, e1012 http://dx.doi.org/10.14806/ej.27.0.1012
- Hollmann S, Kremer A, Baebler S, Trefois C, Gruden C, Rudnicki WR, Tong W, Gruca A, Bongcam-Rudloff E, Evelo CT, Nechyporenko A, Frohme M, Safranek D, Regierer B, D’Elia D (2021) The need for standardisation in life science research - an approach to excellence and trust. F1000Research, 9:1398. https://doi.org/10.12688/f1000research.27500.2
- Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pasic L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truica CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ ] (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology 12:277. https://doi.org/10.3389/fmicb.2021.635781
- Hollmann S, Frohme M, Endrullat C, Kremer A, D'Elia D, Regierer B, Nechyporenko A; Cost Action CA15110. Ten simple rules on how to write a standard operating procedure. PLoS Comput Biol. 2020 Sep 3;16(9):e1008095. https://doi.org/10.1371/journal.pcbi.1008095
- Marzano F, Caratozzolo MF, Consiglio A, Licciulli F, Liuni S, Sbisà E, D'Elia D, Tullo A, Catalano D. Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. Front Genet. 2020 Sep 18;11:552490. doi: 10.3389/fgene.2020.552490.
- Barracchia EP, Pio G, D’Elia D, Ceci M (2020) Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. BMC Bioinformatics 21:70. https://doi.org/10.1186/s12859-020-3392-2
- Milella RA, GasparroM, Alagna F, Cardone MF, Rotunno S, Ammollo CT, Semeraro F, Tullo A, Marzano F, Catalano D, Antonacci D, Colucci M, D’Elia D (2020) Microarray data and pathway analyses of peripheral blood mononuclear cells from healthy subjects after a three weeks grape-rich diet. Data in Brief 29, 105278. https://doi.org/10.1016/j.dib.2020.105278
- Milella RA, GasparroM, Alagna F, Cardone MF, Rotunno S, Ammollo CT, Semeraro F, Tullo A, Marzano F, Catalano D, Antonacci D, Colucci M, D’Elia D (2020) Gene expression signature induced by grape intake in healthy subjects reveals wide-spread beneficial effects on peripheral blood mononuclear cells. Journal of Functional Food, 64: 103705. https://doi.org/10.1016/j.jff.2019.103705.
- Mignone P, Pio G, D’Elia D, Ceci M. (2019) Exploiting Transfer Learning for the Reconstruction of the Human Gene Regulatory Network. Bioinformatics, Oct 14. pii: btz781. doi:10.1093/bioinformatics/btz781
- Efthimiadou A, Papakonstantinou E, Vlachakis D, D’Elia D, Bongcam-Rudloff E (2019) Big Data analysis and reproducibility: new challenges and needs of the post-genomics era. In Springer Communications in Computer and Information Science book series. ICT Innovations 2019 Web proceedings: 253-257. ISSN 1857-7288.
- Papakonstantinou E, Bacopoulou F, Brouzas D, Megalooikonomou V, D’Elia D, Bongcam-Rudloff E, Vlachakis D. (2019) NOTCH3 and CADASIL syndrome: a genetic and structural overview. EMBnet J. 2019;24. pii: e921. doi: 10.14806/ej.24.0.921. PMID: 31218211
- Susanne Hollmann , Babette Regierer , Domenica D’Elia , Kristina Gruden , Špela Baebler , Marcus Frohme , Juliane Pfeil , Ugur Sezerman , Chris T Evelo , Friederike Ehrhart , Berthold Huppertz , Erik Bongcam-Rudloff , Christophe Trefois , Aleksandra Gruca , Deborah A. Duca , Gianni Colotti , Roxana Merino-Martinez , Christos Ouzounis , Oliver Hunewald , Feng He and Andreas Kremer (2018) Standardisation in Life-science Research - Making the Case for Harmonization to Improve Communication and Sharing of Data amongst Researchers. Web proceedings papers. Springer in Communications in Computer and Information Science Series (CCIS), ISSN: 1865:0929, vol. 13:149-159
- Susanne Hollmann, Teresa K. Attwood, Erik Bongcam-Rudloff, Deborah Duca, Domenica D’Elia, Christoph Endrullat, Marcus Frohme, Katrin Messerschmidt, Babette Regierer. Standardization and Quality Assurance in Life-Science Research - Crucially Needed or Unnecessary and Annoying Regulation?I n: Kalajdziski S., Ackovska N. (eds) ICT Innovations 2018. Engineering and Life Sciences. ICT 2018. Communications in Computer and Information Science, vol. 940. Springer, Cham. https://doi.org/10.1007/978-3-030-00825-3_2
- Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D’Elia, Nicola Bombieri, Flavio Licciulli, Rosalba Giugno (2018) Arena-Idb: a platform to build human non-coding RNA interaction networks. BMC Bioinformatics201819 (Suppl 10) :350
https://doi.org/10.1186/s12859-018-2298-8
- D'Elia, D., Barreto Hernandez, E., Klucar, L., & Bongcam-Rudloff, E. (2017). 2016 EMBnet Annual General Meeting – Executive Board Report. EMBnet.Journal, 22, e887. doi:http://dx.doi.org/10.14806/ej.22.0.887
- Romano P, Hofestädt R, Lange M, D’Elia D (2017) The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. BMC Bioinformatics, 18(Suppl 5): 101. doi: 10.1186/s12859-017-1532-0
- Domenica D'Elia, Lubos Klucar, Rafael Jimenez, Axel Thieffry (2015) 2015 EMBnet Annual General Meeting – Publicity and Public Relations Project Committee report. EMBnet.journal 21:e857. DOI: http://dx.doi.org/10.14806/ej.21.0.857
- Pio G, Michelangelo Ceci, Donato Malerba, Domenica D’Elia (2015) ComiRNet: a web- based system for the analysis of miRNA-gene regulatory networks. BMC Bioinformatics 16(Suppl 9):S7. doi:10.1186/1471-2105-16-S9-S7
- Domenica D’Elia, Vicky Schneider-Gricar, Rubina Karla, Cesar Bonavides-Martinez, Rafael Jimenez (2014) 2014 Annual General Meeting: Publicity & Public Relations Project Committee Report. EMBnet.journal 20, e758. http://dx.doi.org/10.14806/ej.20.0.800
- G. Pio, M. Ceci, D. D’Elia, D. Malerba (2014) Network Reconstruction for the Identification of miRNA:mRNA Interaction Networks. Chapter in Book “Machine Learning and Knowledge Discovery in Databases”, ECML PKDD 2014, Part III, LNCS 8726, pp. 508–511. T. Calders et al. (Eds.): Springer-Verlag Berlin Heidelberg 2014. DOI 10.1007/978-3-662-44845-8
- Gianvito Pio, Michelangelo Ceci, Domenica D’Elia and Donato Malerba (2014) Learning to Combine miRNA Target Predictions: a Semi-supervised Ensemble Learning Approach (Discussion Paper) in Proceedings of SEDB 2014. http://www.sebd2014.unina.it/content/accepted-papers
- Susanne Hollmann, Babette Regierer, Domenica D’Elia, Annamaria Kisslinger, Giovanna L. Liguori (2022) Toward the definition of common strategies for improving reproducibility, standardisation, management, and overall impact of academic research. Advances in Biomembranes and Lipid Self-Assembly. Academic Press,ISSN 2451-9634, https://doi.org/10.1016/bs.abl.2022.05.001
- Balech B, Brennan L, Carrillo de Santa Pau E et al. The future of food and nutrition in ELIXIR [version 1; peer review: 1 approved with reservations]. F1000Research 2022, 11(ELIXIR):978. https://doi.org/10.12688/f1000research.51747.1
- Ibrahimi et al. (2022) Report of the ML4Microbiome workshop 2021 - Statistical and Machine Learning Techniques for Microbiome Data Analysis. EMBnet.journal 27, e1012 http://dx.doi.org/10.14806/ej.27.0.1012
- Hollmann S, Kremer A, Baebler S, Trefois C, Gruden C, Rudnicki WR, Tong W, Gruca A, Bongcam-Rudloff E, Evelo CT, Nechyporenko A, Frohme M, Safranek D, Regierer B, D’Elia D (2021) The need for standardisation in life science research - an approach to excellence and trust. F1000Research, 9:1398. https://doi.org/10.12688/f1000research.27500.2
- Moreno-Indias I, Lahti L, Nedyalkova M, Elbere I, Roshchupkin G, Adilovic M, Aydemir O, Bakir-Gungor B, Santa Pau EC, D'Elia D, Desai MS, Falquet L, Gundogdu A, Hron K, Klammsteiner T, Lopes MB, Marcos-Zambrano LJ, Marques C, Mason M, May P, Pasic L, Pio G, Pongor S, Promponas VJ, Przymus P, Saez-Rodriguez J, Sampri A, Shigdel R, Stres B, Suharoschi R, Truu J, Truica CO, Vilne B, Vlachakis D, Yilmaz E, Zeller G, Zomer AL, Gómez-Cabrero D, Claesson MJ ] (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology 12:277. https://doi.org/10.3389/fmicb.2021.635781
- Hollmann S, Frohme M, Endrullat C, Kremer A, D'Elia D, Regierer B, Nechyporenko A; Cost Action CA15110. Ten simple rules on how to write a standard operating procedure. PLoS Comput Biol. 2020 Sep 3;16(9):e1008095. https://doi.org/10.1371/journal.pcbi.1008095
- Marzano F, Caratozzolo MF, Consiglio A, Licciulli F, Liuni S, Sbisà E, D'Elia D, Tullo A, Catalano D. Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. Front Genet. 2020 Sep 18;11:552490. doi: 10.3389/fgene.2020.552490.
- Barracchia EP, Pio G, D’Elia D, Ceci M (2020) Prediction of new associations between ncRNAs and diseases exploiting multi-type hierarchical clustering. BMC Bioinformatics 21:70. https://doi.org/10.1186/s12859-020-3392-2
- Milella RA, GasparroM, Alagna F, Cardone MF, Rotunno S, Ammollo CT, Semeraro F, Tullo A, Marzano F, Catalano D, Antonacci D, Colucci M, D’Elia D (2020) Microarray data and pathway analyses of peripheral blood mononuclear cells from healthy subjects after a three weeks grape-rich diet. Data in Brief 29, 105278. https://doi.org/10.1016/j.dib.2020.105278
- Milella RA, GasparroM, Alagna F, Cardone MF, Rotunno S, Ammollo CT, Semeraro F, Tullo A, Marzano F, Catalano D, Antonacci D, Colucci M, D’Elia D (2020) Gene expression signature induced by grape intake in healthy subjects reveals wide-spread beneficial effects on peripheral blood mononuclear cells. Journal of Functional Food, 64: 103705. https://doi.org/10.1016/j.jff.2019.103705.
- Mignone P, Pio G, D’Elia D, Ceci M. (2019) Exploiting Transfer Learning for the Reconstruction of the Human Gene Regulatory Network. Bioinformatics, Oct 14. pii: btz781. doi:10.1093/bioinformatics/btz781
- Efthimiadou A, Papakonstantinou E, Vlachakis D, D’Elia D, Bongcam-Rudloff E (2019) Big Data analysis and reproducibility: new challenges and needs of the post-genomics era. In Springer Communications in Computer and Information Science book series. ICT Innovations 2019 Web proceedings: 253-257. ISSN 1857-7288.
- Papakonstantinou E, Bacopoulou F, Brouzas D, Megalooikonomou V, D’Elia D, Bongcam-Rudloff E, Vlachakis D. (2019) NOTCH3 and CADASIL syndrome: a genetic and structural overview. EMBnet J. 2019;24. pii: e921. doi: 10.14806/ej.24.0.921. PMID: 31218211
- Susanne Hollmann , Babette Regierer , Domenica D’Elia , Kristina Gruden , Špela Baebler , Marcus Frohme , Juliane Pfeil , Ugur Sezerman , Chris T Evelo , Friederike Ehrhart , Berthold Huppertz , Erik Bongcam-Rudloff , Christophe Trefois , Aleksandra Gruca , Deborah A. Duca , Gianni Colotti , Roxana Merino-Martinez , Christos Ouzounis , Oliver Hunewald , Feng He and Andreas Kremer (2018) Standardisation in Life-science Research - Making the Case for Harmonization to Improve Communication and Sharing of Data amongst Researchers. Web proceedings papers. Springer in Communications in Computer and Information Science Series (CCIS), ISSN: 1865:0929, vol. 13:149-159
- Susanne Hollmann, Teresa K. Attwood, Erik Bongcam-Rudloff, Deborah Duca, Domenica D’Elia, Christoph Endrullat, Marcus Frohme, Katrin Messerschmidt, Babette Regierer. Standardization and Quality Assurance in Life-Science Research - Crucially Needed or Unnecessary and Annoying Regulation?I n: Kalajdziski S., Ackovska N. (eds) ICT Innovations 2018. Engineering and Life Sciences. ICT 2018. Communications in Computer and Information Science, vol. 940. Springer, Cham. https://doi.org/10.1007/978-3-030-00825-3_2
- Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D’Elia, Nicola Bombieri, Flavio Licciulli, Rosalba Giugno (2018) Arena-Idb: a platform to build human non-coding RNA interaction networks. BMC Bioinformatics201819 (Suppl 10) :350
https://doi.org/10.1186/s12859-018-2298-8
- D'Elia, D., Barreto Hernandez, E., Klucar, L., & Bongcam-Rudloff, E. (2017). 2016 EMBnet Annual General Meeting – Executive Board Report. EMBnet.Journal, 22, e887. doi:http://dx.doi.org/10.14806/ej.22.0.887
- Romano P, Hofestädt R, Lange M, D’Elia D (2017) The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. BMC Bioinformatics, 18(Suppl 5): 101. doi: 10.1186/s12859-017-1532-0
- Domenica D'Elia, Lubos Klucar, Rafael Jimenez, Axel Thieffry (2015) 2015 EMBnet Annual General Meeting – Publicity and Public Relations Project Committee report. EMBnet.journal 21:e857. DOI: http://dx.doi.org/10.14806/ej.21.0.857
- Pio G, Michelangelo Ceci, Donato Malerba, Domenica D’Elia (2015) ComiRNet: a web- based system for the analysis of miRNA-gene regulatory networks. BMC Bioinformatics 16(Suppl 9):S7. doi:10.1186/1471-2105-16-S9-S7
- Domenica D’Elia, Vicky Schneider-Gricar, Rubina Karla, Cesar Bonavides-Martinez, Rafael Jimenez (2014) 2014 Annual General Meeting: Publicity & Public Relations Project Committee Report. EMBnet.journal 20, e758. http://dx.doi.org/10.14806/ej.20.0.800
- G. Pio, M. Ceci, D. D’Elia, D. Malerba (2014) Network Reconstruction for the Identification of miRNA:mRNA Interaction Networks. Chapter in Book “Machine Learning and Knowledge Discovery in Databases”, ECML PKDD 2014, Part III, LNCS 8726, pp. 508–511. T. Calders et al. (Eds.): Springer-Verlag Berlin Heidelberg 2014. DOI 10.1007/978-3-662-44845-8
- Gianvito Pio, Michelangelo Ceci, Domenica D’Elia and Donato Malerba (2014) Learning to Combine miRNA Target Predictions: a Semi-supervised Ensemble Learning Approach (Discussion Paper) in Proceedings of SEDB 2014. http://www.sebd2014.unina.it/content/accepted-papers
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