Marta Lovino

Marta Lovino is an Assistant Professor in Bioinformatics at the Department of Life Sciences, University of Modena and Reggio Emilia. She received her Ph.D. in Computer and Control Engineering with honors from Politecnico di Torino in 2021, following her B.Sc. and M.Sc. degrees in Biomedical Engineering obtained from the same institution in 2015 and 2017, respectively. Her doctoral research focused on the development of computational tools and pipelines for the analysis of large-scale genomics and proteomics datasets. During her Ph.D. in 2020, she was a visiting researcher at the Institut Curie Center in Paris, working within the Signaling in Development and brain tumors lab for six months.

Dr. Lovino's research expertise lies at the intersection of bioinformatics, biomedical imaging, and artificial intelligence. Her work addresses key computational challenges in these fields, including high data dimensionality, scarcity and uncertainty of annotations, data heterogeneity and bias, and the critical need for model explainability.

Her current research interests include the application of advanced deep learning architectures, such as Graph Neural Networks (GNNs), Transformers (including architectures like BERT for sequence analysis), and Multiple Instance Learning (MIL), to biological and biomedical problems. She focuses on analyzing diverse data modalities, including genomic and RNA sequencing data, and biomedical images like Whole Slide Images (WSI). A significant area of her work involves multimodal learning and data integration to combine information from multiple sources (omics, imaging, clinical data) to gain a more comprehensive understanding of biological systems.

Dr. Lovino applies these cutting-edge AI methodologies to critical problems in cancer research, including prognosis prediction, gene expression and protein prediction from genomic sequences, identifying gene regulatory networks, and analyzing gene fusions. Her goal is to leverage artificial intelligence to uncover novel biomarkers, decipher the molecular mechanisms underlying cancer development, and contribute to the advancement of personalized medicine approaches.

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