Marta Lovino

Marta Lovino is a Postdoctoral Research Fellow at the AImage lab group, having joined in 2022. She obtained her Ph.D. in Computer and Control Engineering with honors from Politecnico di Torino in 2021, after completing a B.Sc. and M.Sc. in Biomedical Engineering at the same university in 2015 and 2017, respectively. Throughout her Ph.D. studies, Marta focused on developing software tools and pipelines for analyzing genomics and proteomics data. In 2020, she also had the opportunity to work as a visiting researcher at the Institute Curie Center in Paris, specifically in the Signaling in Development and brain tumors lab, for a duration of six months.

Marta's research interests primarily revolve around cancer prognosis prediction, gene expression analysis, miRNA target prediction, gene regulatory networks, gene fusions, and multi-omics data integration. She is particularly enthusiastic about leveraging artificial intelligence (AI) in the field of genetics to improve our understanding of cancer biology and enhance patient care.

Marta aims to advance knowledge in her field and apply her expertise to address critical challenges in cancer research. Her interdisciplinary background in computer engineering and biomedical engineering equips her with a unique skill set to bridge the gap between data analysis techniques and biological insights. With a strong focus on genomics and proteomics analysis, Marta strives to uncover new biomarkers, decipher molecular mechanisms underlying cancer development, and develop innovative approaches for personalized medicine.

Research Projects

• DECIDER

Research Activities

• RNA and DNA-Based Gene Fusion Detection: Unveiling Genomic Rearrangements
• Predicting miRNA Targets in Humans: Computational Prediction Approaches
• Integrating Genomics and Transcriptomics: Advancements through Multi-View Approaches
• Advancing Medulloblastoma Research: Genomics and Proteomics Insights from Sample Analysis
• Decoding Gene Expression using DNA Sequence and Exploiting Post-Translational Modifications
• Unleashing the Power of OncoDash: Software for Informed Clinical Decisions
• A Convergence of Histopathology and Genetics for Anticipating Chemotherapy Response in ovarian cancer.
• Identification of AI-Based Biomarkers to Predict HCC Response to Medical Treatment
• Multi-Omic Graph Neural Networks for Cancer Prognosis and Biomarker Identification
• Multimodal Deep Learning Model for cancer prediction

Publications

1	Rausio, H.; Cervera, A.; Heuser, V. D.; West, G.; Oikkonen, J.; Pianfetti, E.; Lovino, M.; Ficarra, E.; Taimen, P.; Hynninen, J.; Lehtonen, R.; Hautaniemi, S.; Carpen, O.; Huhtinen, K. "PIK3R1 fusion drives chemoresistance in ovarian cancer by activating ERK1/2 and inducing rod and ring-like structures" NEOPLASIA, vol. 51, pp. 1 -10 , 2024 | DOI: 10.1016/j.neo.2024.100987 Journal
2	Lovino, M.; Ficarra, E.; Martignetti, L. "Integrated microRNA and proteome analysis of cancer datasets with MoPC" PLOS ONE, vol. 19, pp. 1 -11 , 2024 | DOI: 10.1371/journal.pone.0289699 Journal
3	Cirrincione, G.; Cannata, S.; Cicceri, G.; Prinzi, F.; Currieri, T.; Lovino, M.; Militello, C.; Pasero, E.; Vitabile, S. "Transformer-Based Approach to Melanoma Detection" SENSORS, vol. 23, pp. 5677 -5687 , 2023 | DOI: 10.3390/s23125677 Journal
4	Pianfetti, E.; Lovino, M.; Ficarra, E.; Martignetti, L. "MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge" BMC BIOINFORMATICS, vol. 24, pp. 443 -453 , 2023 | DOI: 10.1186/s12859-023-05560-1 Journal
5	Ghione, G.; Lovino, M.; Ficarra, E.; Cirrincione, G. "BERT Classifies SARS-CoV-2 Variants" Smart Innovation, Systems and Technologies, vol. 360, pp. 157 -163 , 2023 | DOI: 10.1007/978-981-99-3592-5_15 Chapter in Book
6	Bontempo, Gianpaolo; Bartolini, Nicola; Lovino, Marta; Bolelli, Federico; Virtanen, Anni; Ficarra, Elisa "Enhancing PFI Prediction with GDS-MIL: A Graph-based Dual Stream MIL Approach" IMAGE ANALYSIS AND PROCESSING, ICIAP 2023, PT I, vol. 14233, Udine, Italy, pp. 550 -562 , SEP 11-15, 2023, 2023 | DOI: 10.1007/978-3-031-43148-7_46 Conference
7	Stefanini, Matteo; Lovino, Marta; Cucchiara, Rita; Ficarra, Elisa "Predicting gene and protein expression levels from DNA and protein sequences with Perceiver" COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, vol. 234, pp. 107504 -107514 , 2023 | DOI: 10.1016/j.cmpb.2023.107504 Journal
8	Citarrella, Francesca; Bontempo, Gianpaolo; Lovino, Marta; Ficarra, Elisa "FusionFlow: an integrated system workflow for gene fusion detection in genomic samples" European Conference on Advances in Databases and Information Systems - ADBIS 2022 Short Papers, Doctoral Consortium and Workshops: DOING, K-GALS, MADEISD, MegaData, SWODCH, Turin, Italy, September 5–8, 2022, Proceedings, vol. 1652, Torino, Italy, pp. 79 -88 , SEP 05-08, 2022, 2022 | DOI: 10.1007/978-3-031-15743-1_8 Conference
9	Pipoli, Vittorio; Cappelli, Mattia; Palladini, Alessandro; Peluso, Carlo; Lovino, Marta; Ficarra, Elisa "Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers" COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, vol. 225, pp. 107035 -107044 , 2022 | DOI: 10.1016/j.cmpb.2022.107035 Journal
10	Citarrella, F.; Bontempo, G.; Lovino, M.; Ficarra, E. "FusionFlow: An Integrated System Workflow for Gene Fusion Detection in Genomic Samples" Communications in Computer and Information Science, vol. 1652 CCIS, pp. 79 -88 , 2022 | DOI: 10.1007/978-3-031-15743-1_8 Chapter in Book
11	Borgato, S.; Bottino, M.; Lovino, M.; Ficarra, E. "SARS-CoV-2 variants classification and characterization" EPiC Series in Computing, vol. 83, n/a, pp. 66 -75 , 2022, 2022 Conference
12	Lovino, M.; Montemurro, M.; Barrese, V. S.; Ficarra, E. "Identifying the oncogenic potential of gene fusions exploiting miRNAs" JOURNAL OF BIOMEDICAL INFORMATICS, vol. 129, pp. 104057 -N/A , 2022 | DOI: 10.1016/j.jbi.2022.104057 Journal
13	Lovino, Marta; Randazzo, Vincenzo; Ciravegna, Gabriele; Barbiero, Pietro; Ficarra, Elisa; Cirrincione, Giansalvo "A survey on data integration for multi-omics sample clustering" NEUROCOMPUTING, vol. 488, pp. 494 -508 , 2022 | DOI: 10.1016/j.neucom.2021.11.094 Journal
14	Rickert, Daniel; Bartl, Jasmin; Picard, Daniel; Bernardi, Flavia; Qin, Nan; Lovino, Marta; Puget, Stéphanie; Meyer, Frauke-Dorothee; Mahoungou Koumba, Idriss; Beez, Thomas; Varlet, Pascale; Dufour, Christelle; Fischer, Ute; Borkhardt, Arndt; Reifenberger, Guido; Ayrault, Olivier; Remke, Marc "Circular RNA profiling distinguishes medulloblastoma groups and shows aberrant RMST overexpression in WNT medulloblastoma" ACTA NEUROPATHOLOGICA, vol. 141, pp. 975 -978 , 2021 | DOI: 10.1007/s00401-021-02306-2 Journal
15	Lovino, Marta; Bontempo, Gianpaolo; Cirrincione, Giansalvo; Ficarra, Elisa "Multi-omics Classification on Kidney Samples Exploiting Uncertainty-Aware Models" Intelligent Computing Theories and Application, vol. 12464 LNCS, Bari (Online), pp. 32 -42 , October,2020, 2020 | DOI: 10.1007/978-3-030-60802-6_4 Conference
16	Barbiero, Pietro; Lovino, Marta; Siviero, Mattia; Ciravegna, Gabriele; Randazzo, Vincenzo; Ficarra, Elisa; Cirrincione, Giansalvo "Unsupervised Multi-Omic Data Fusion: the Neural Graph Learning Network" LNCS, vol. 12463, Bari (ita), pp. 172 -182 , Ottobre 2020, 2020 | DOI: 10.1007/978-3-030-60799-9_15 Conference
17	Lovino, Marta; Gianvito, Urgese; Enrico, Macii; Santa Di Cataldo, ; Ficarra, Elisa "Predicting the oncogenic potential of gene fusions using convolutional neural networks" Computational Intelligence Methods for Bioinformatics and Biostatistics, vol. 11925, Caparica, pp. 277 -284 , 6 - 8 September 2018, 2020 | DOI: 10.1007/978-3-030-34585-3_24 Conference
18	Lovino, Marta; Bontempo, Gianpaolo; Cirrincione, Giansalvo; Ficarra, Elisa "Multi-omics classification on kidney samples exploiting uncertainty-aware models" LNCS, vol. LNCS, Bari (Online), pp. 32 -42 , Oct 10-11th 2020, 2020 | DOI: 10.1007/978-3-030-60802-6_4 Conference
19	Lovino, Marta; Ciaburri, Maria Serena; Urgese, Gianvito; Di Cataldo, Santa; Ficarra, Elisa "DEEPrior: a deep learning tool for the prioritization of gene fusions" BIOINFORMATICS, vol. 36, pp. 3248 -3250 , 2020 | DOI: 10.1093/bioinformatics/btaa069 Journal
20	Roberti, Ilaria; Lovino, Marta; Di Cataldo, Santa; Ficarra, Elisa; Urgese, Gianvito "Exploiting Gene Expression Profiles for the Automated Prediction of Connectivity between Brain Regions" INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 20, pp. N/A -N/A , 2019 | DOI: 10.3390/ijms20082035 Journal
21	Lovino, Marta; Urgese, Gianvito; Macii, Enrico; Di Cataldo, Santa; Ficarra, Elisa "A Deep Learning Approach to the Screening of Oncogenic Gene Fusions in Humans" INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, vol. 20, pp. 1 -13 , 2019 | DOI: 10.3390/ijms20071645 Journal