Elisa Ficarra

Elisa Ficarra graduated in Electrical Engineering at the University of Bologna, Italy, in March 2001. In 2006 she got an International Ph.D. of excellence in Systems and Computer Science at the Politecnico di Torino, Italy. She was a visiting scientist at the Computer Science Dept. of Stanford University (CA, USA) in 2002 and at the Integrated System Laboratory of EPFL, Lausanne, Switzerland, from Jan. to Dec. 2005. She worked at Politecnico di Torino as an Associate Professor in Bioinformatics until 2021.

Since 2021, she has been a Full Professor at the University of Modena and Reggio Emilia in the Department of Engineering "Enzo Ferrari". 

TBD

Curriculum vitae:

Keywords: 

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Teaching Activities

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Research Projects

• DECIDER
• Fit for Medical Robotics
• Human monoclonal antibodies against Shigella (ShiMabs), for therapy and vaccine acceleration

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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.
• Studying host-pathogen interaction via microscopy and Deep Learning: application to antimicrobial resistant bacteria and monoclonal antibodies discovery

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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	Lumetti, Luca; Pipoli, Vittorio; Bolelli, Federico; Ficarra, Elisa; Grana, Costantino "Enhancing Patch-Based Learning for the Segmentation of the Mandibular Canal" IEEE ACCESS, pp. 1 -12 , 2024 Journal
4	Bontempo, Gianpaolo; Bolelli, Federico; Porrello, Angelo; Calderara, Simone; Ficarra, Elisa "A Graph-Based Multi-Scale Approach with Knowledge Distillation for WSI Classification" IEEE TRANSACTIONS ON MEDICAL IMAGING, vol. 43, pp. 1412 -1421 , 2024 | DOI: 10.1109/TMI.2023.3337549 Journal
5	Capitani, Giacomo; Bolelli, Federico; Porrello, Angelo; Calderara, Simone; Ficarra, Elisa "ClusterFix: A Cluster-Based Debiasing Approach without Protected-Group Supervision" 2024 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), Waikoloa, Hawaii, pp. 4858 -4867 , Jan 4-8, 2024 | DOI: 10.1109/WACV57701.2024.00480 Conference
6	Ponzio, F.; Macii, E.; Ficarra, E.; Di Cataldo, S. "W2WNet: A two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality" EXPERT SYSTEMS WITH APPLICATIONS, vol. 214, pp. 1 -10 , 2023 | DOI: 10.1016/j.eswa.2022.119121 Journal
7	Marconato, E.; Bontempo, G.; Ficarra, E.; Calderara, S.; Passerini, A.; Teso, S. "Neuro-Symbolic Continual Learning: Knowledge, Reasoning Shortcuts and Concept Rehearsal" Proceedings of Machine Learning Research, vol. 202, Honolulu, USA, pp. 23915 -23936 , 2023, 2023 Conference
8	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
9	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
10	Bontempo, G.; Lumetti, L.; Porrello, A.; Bolelli, F.; Calderara, S.; Ficarra, E. "Buffer-MIL: Robust Multi-instance Learning with a Buffer-Based Approach" Image Analysis and Processing – ICIAP 2023, vol. 14234, Udine, Italy, pp. 1 -12 , Sep 11-15, 2023 | DOI: 10.1007/978-3-031-43153-1_1 Conference
11	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
12	Marconato, Emanuele; Bontempo, Gianpaolo; Ficarra, Elisa; Calderara, Simone; Passerini, Andrea; Teso, Stefano "Neuro Symbolic Continual Learning: Knowledge, Reasoning Shortcuts and Concept Rehearsal" 2023 | DOI: 10.48550/arxiv.2302.01242 Other
13	Bontempo, Gianpaolo; Porrello, Angelo; Bolelli, Federico; Calderara, Simone; Ficarra, Elisa "DAS-MIL: Distilling Across Scales for MILClassification of Histological WSIs" Medical Image Computing and Computer Assisted Intervention – MICCAI 2023, PT I, vol. 14220, Vancouver, can, pp. 248 -258 , OCT 08-12, 2023, 2023 | DOI: 10.1007/978-3-031-43907-0_24 Conference
14	Bontempo, Gianpaolo; Lumetti, Luca; Porrello, Angelo; Bolelli, Federico; Calderara, Simone; Ficarra, Elisa "Buffer-MIL: Robust Multi-instance Learning with a Buffer-based Approach" Image Analysis and Processing – ICIAP 2023, Udine, Italy, pp. 1 -12 , Sep 11-15, 2023 Conference
15	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
16	Mascolini, A.; Ponzio, F.; Macii, E.; Ficarra, E.; Di Cataldo, S. "High Resolution Explanation Maps for CNNs using Segmentation Networks" Proceedings of IEEE Symposium on Visual Languages and Human-Centric Computing, VL/HCC, vol. 2022-, ita, 2022, 2022 | DOI: 10.1109/VL/HCC53370.2022.9833004 Conference
17	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
18	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
19	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
20	Mascolini, Alessio; Cardamone, Dario; Ponzio, Francesco; Di Cataldo, Santa; Ficarra, Elisa "Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations" BMC BIOINFORMATICS, vol. 23, pp. 295 -312 , 2022 | DOI: 10.1186/s12859-022-04845-1 Journal
21	Marconato, E.; Bontempo, G.; Teso, S.; Ficarra, E.; Calderara, S.; Passerini, A. "Catastrophic Forgetting in Continual Concept Bottleneck Models" Lecture Notes in Computer Science, vol. 13374, 23 May 2022through 27 May 2022Code, pp. 539 -547 , 2022, 2022 | DOI: 10.1007/978-3-031-13324-4_46 Conference
22	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
23	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
24	Winkler, J.; Urgese, G.; Ficarra, E.; Reinert, K. "LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences" BMC BIOINFORMATICS, vol. 23, pp. 1 -22 , 2022 | DOI: 10.1186/s12859-021-04532-7 Journal
25	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
26	Montemurro, M.; Grassi, E.; Pizzino, C. G.; Bertotti, A.; Ficarra, E.; Urgese, G. "PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity" BMC BIOINFORMATICS, vol. 22, pp. 1 -21 , 2021 | DOI: 10.1186/s12859-021-04277-3 Journal
27	Cervera, Alejandra; Rausio, Heidi; Kähkönen, Tiia; Andersson, Noora; Partel, Gabriele; Rantanen, Ville; Paciello, Giulia; Ficarra, Elisa; Hynninen, Johanna; Hietanen, Sakari; Carpén, Olli; Lehtonen, Rainer; Hautaniemi, Sampsa; Huhtinen, Kaisa "FUNGI: FUsioN Gene Integration toolset" BIOINFORMATICS, vol. 37, pp. 3353 -3355 , 2021 | DOI: 10.1093/bioinformatics/btab206 Journal
28	Mieuli, V.; Ponzio, F.; Mascolini, A.; Macii, E.; Ficarra, E.; Di Cataldo, S. "A Bayesian approach to Expert Gate Incremental Learning" Proceedings of the International Joint Conference on Neural Networks, vol. 2021-, chn, pp. 1 -7 , 18-22 July 2021, 2021 | DOI: 10.1109/IJCNN52387.2021.9534204 Conference
29	Di Cataldo, Santa; Vinco, Sara; Urgese, Gianvito; Calignano, Flaviana; Ficarra, Elisa; Macii, Alberto; Macii, Enrico "Optimizing Quality Inspection and Control in Powder Bed Metal Additive Manufacturing: Challenges and Research Directions" PROCEEDINGS OF THE IEEE, vol. 109, pp. 326 -346 , 2021 | DOI: 10.1109/JPROC.2021.3054628 Journal
30	Barchi, F.; Parisi, E.; Urgese, G.; Ficarra, E.; Acquaviva, A. "Exploration of Convolutional Neural Network models for source code classification" ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE, vol. 97, pp. 1 -13 , 2021 | DOI: 10.1016/j.engappai.2020.104075 Journal
31	Alessio, Mascolini; Puzzo, S.; Incatasciato, G.; Ponzio, F.; Ficarra, E.; Di Cataldo, S. "A Novel Proof-of-concept Framework for the Exploitation of ConvNets on Whole Slide Images" Progresses in Artificial Intelligence and Neural Systems, vol. 184, pp. 125 -136 , 2021 | DOI: 10.1007/978-981-15-5093-5_12 Chapter in Book
32	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
33	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
34	Desvignes, Thomas; Loher, Phillipe; Eilbeck, Karen; Ma, Jeffery; Urgese, Gianvito; Fromm, Bastian; Sydes, Jason; Aparicio-Puerta, Ernesto; Barrera, Victor; Espin, Roderic; Londin, Eric; Telonis, Aristeidis G; Ficarra, Elisa; Friedlander, Marc R; Postlethwait, John H; Rigoutsos, Isidore; Hackenberg, Michael; Vlachos, Ioannis S; Halushka, Marc K.; Pantano, Lorena "Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API" BIOINFORMATICS, vol. 36, pp. 698 -703 , 2020 | DOI: 10.1093/bioinformatics/btz675 Journal
35	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
36	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
37	Ponzio, Francesco; Deodato, Giacomo; Macii, Enrico; Di Cataldo, Santa; Ficarra, Elisa "Exploiting "uncertain" deep networks for data cleaning in digital pathology" 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), vol. 2020-, Coralville (USA), pp. 1139 -1143 , 3-7 Aprile 2020, 2020 | DOI: 10.1109/ISBI45749.2020.9098605 Conference
38	Montemurro, Marilisa; Urgese, Gianvito; Grassi, Elena; Pizzino, Carmelo Gabriele; Bertotti, Andrea; Ficarra, Elisa "Effective evaluation of clustering algorithms on single-cell CNA data" Proceedings of ACM 7th International Conference on Biomedical and Bioinformatics Engineering (ICBBE 2020), Kyoto, 06-09 novembre 2020, 2020 Conference
39	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
40	Ciglieri, Elisa; Vacca, Maurizia; Ferrini, Francesco; Atteya, Mona A; Aimar, Patrizia; Ficarra, Elisa; Di Cataldo, Santa; Merighi, Adalberto; Salio, Chiara "Cytoarchitectural analysis of the neuron-to-glia association in the dorsal root ganglia of normal and diabetic mice" JOURNAL OF ANATOMY, vol. 237, pp. 988 -997 , 2020 | DOI: 10.1111/joa.13252 Journal
41	Urgese, Gianvito; Parisi, Emanuele; Scicolone, Orazio; Di Cataldo, Santa; Ficarra, Elisa "BioSeqZip: a collapser of NGS redundant reads for the optimisation of sequence analysis" BIOINFORMATICS, pp. N/A -N/A , 2020 | DOI: 10.1093/bioinformatics/btaa051 Journal
42	Montemurro, Marilisa; Grassi, Elena; Urgese, Gianvito; Gabriele Pizzino, Carmelo; Bertotti, Andrea; Ficarra, Elisa "Single-cell DNA Sequencing Data: a Pipeline for Multi-Sample Analysis" Titolo volume non avvalorato, Roma, 16-18 September 2019, 2019 Conference Abstract
43	Marilisa, Montemurro; Grassi, Elena; Urgese, Gianvito; Emanuele, Parisi; Gabriele Pizzino, Carmelo; Bertotti, Andrea; Ficarra, Elisa "Single-cell DNA Sequencing Data: a Pipeline for Multi-Sample Analysis" Titolo volume non avvalorato, Bergamo, 4-6 September 2019, 2019 Conference
44	Padella and, Antonella; Simonetti and, Giorgia; Paciello and, Giulia; Giotopoulos and, George; Baldazzi and, Carmen; Righi and, Simona; Ghetti and, Martina; Stengel and, Anna; Guadagnuolo and, Viviana; De Tommaso and, Rossella; Papayannidis and, Cristina; Robustelli and, Valentina; Franchini and, Eugenia; Ghelli Luserna di Rorà and, Andrea; Ferrari and, Anna; Fontana and Maria, Chiara; Bruno and, Samantha; Ottaviani and, Emanuela; Soverini and, Simona; Storlazzi and Clelia, Tiziana; Haferlach and, Claudia; Sabattini and, Elena; Testoni and, Nicoletta; Iacobucci and, Ilaria; Huntly and Brian, J. P.; Ficarra, Elisa; Martinelli and, Giovanni "Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia" CANCERS, vol. 11, pp. N/A -N/A , 2019 | DOI: 10.3390/cancers11121951 Journal
45	Ponzio, Francesco; Macii, Enrico; Ficarra, Elisa; Di Cataldo, Santa "Going Deeper into Colorectal Cancer Histopathology" International Joint Conference on Biomedical Engineering Systems and Technologies, vol. 1024, pp. 114 -131 , 2019 | DOI: 10.1007/978-3-030-29196-9_7 Chapter in Book
46	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
47	Ponzio, Francesco; Urgese, Gianvito; Ficarra, Elisa; Di Cataldo, Santa "Dealing with Lack of Training Data for Convolutional Neural Networks: The Case of Digital Pathology" ELECTRONICS, vol. 8, pp. N/A -N/A , 2019 | DOI: 10.3390/electronics8030256 Journal
48	Simonetti, Giorgia; Padella, Antonella; do Valle, Italo Farìa; Fontana, Maria Chiara; Fonzi, Eugenio; Bruno, Samantha; Baldazzi, Carmen; Guadagnuolo, Viviana; Manfrini, Marco; Ferrari, Anna; Paolini, Stefania; Papayannidis, Cristina; Marconi, Giovanni; Franchini, Eugenia; Zuffa, Elisa; Laginestra, Maria Antonella; Zanotti, Federica; Astolfi, Annalisa; Iacobucci, Ilaria; Bernardi, Simona; Sazzini, Marco; Ficarra, Elisa; Hernandez, Jesus Maria; Vandenberghe, Peter; Cools, Jan; Bullinger, Lars; Ottaviani, Emanuela; Testoni, Nicoletta; Cavo, Michele; Haferlach, Torsten; Castellani, Gastone; Remondini, Daniel; Martinelli, Giovanni "Aneuploid acute myeloid leukemia exhibits a signature of genomic alterations in the cell cycle and protein degradation machinery" CANCER, vol. 125, pp. 712 -725 , 2019 | DOI: 10.1002/cncr.31837 Journal
49	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
50	L’Abbate, Alberto; Iacobucci, Ilaria; Lonoce, Angelo; Turchiano, Antonella; Ficarra, Elisa; Paciello, Giulia; Cattina, Federica; Ferrari, Anna; Imbrogno, Enrica; Agostinelli, Claudio; Zinzani, Pierluigi; Martinelli, Giovanni; Derenzini, Enrico; Storlazzi, Clelia Tiziana "RALE051: a novel established cell line of sporadic Burkitt lymphoma" LEUKEMIA & LYMPHOMA, vol. 59, pp. 1252 -1255 , 2018 | DOI: 10.1080/10428194.2017.1372580 Journal
51	Mancini, Manuela; Monaldi, Cecilia; De Santis, Sara; Papayannidis, Cristina; Rondoni, Michela; Bavaro, Luana; Martelli, Margherita; Maria Chiara, Abbenante; Curti, Antonio; Ficarra, Elisa; Paciello, Giulia; Chiara Fontana, Maria; Zanotti, Roberta; Bonifacio, Massimiliano; Scaffidi, Luigi; Pagano, Livio; Criscuolo, Marianna; Albano, Francesco; Ciceri, Fabio; Elena, Chiara; Tosi, Patrizia; Delledonne, Massimo; Avanzato, Carla; Xumerle, Luciano; Valent, Peter; Martinelli, Giovanni; Cavo, Michele; Soverini, Simona "MDM2 and Aurora Kinase a Contribute to SETD2 Loss of Function in Advanced Systemic Mastocytosis: Implications for Pathogenesis and Treatment" BLOOD, vol. 132, pp. 1779 -1779 , 2018 | DOI: 10.1182/blood-2018-99-113278 Abstract in Journal
52	Goddi, A; Ponzio, F; Ficarra, E; di Cataldo, S; Roatta, S. "Low-cost pupillometry for human-computer interface" Le Tecnologie Assistive nell'Età Adulta: realtà europee e nuovi approcci riabilitativi, un tema multidisciplinare., Torino, 13-14 Aprile 2018, 2018 Other
53	Scicolone, ORAZIO MARIA; Paciello, Giulia; Ficarra, Elisa "geneEX a novel tool to assess differential expression from gene and exon sequencing data" BIOINFORMATICS 2018 - 9th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 11th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2018, vol. 3, Funchal - Madeira, Portugal, pp. 174 -181 , 19-21 January, 2018, 2018 | DOI: 10.5220/0006657501740181 Conference
54	Ponzio, Francesco; Macii, Enrico; Ficarra, Elisa; Di Cataldo, Santa "Colorectal Cancer Classification using Deep Convolutional Networks. An Experimental Study" Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING, vol. 2, Funchal Madeira, Portugal, pp. 58 -66 , 19-21 January 2018, 2018 | DOI: 10.5220/0006643100580066 Conference
55	Ciglieri, Elisa; Vacca, Maurizia; Ferrini, Francesco; Di Cataldo, Santa; Ficarra, Elisa; Salio, Chiara "Spatial distribution of peptidergic and non-peptidergic nociceptors in mouse dorsal root ganglia: a cluster story" Titolo volume non avvalorato, Roma (ITA), 25-26 Maggio 2017, 2017 Conference Abstract
56	Isella, Claudio; Brundu, FRANCESCO GAVINO; Bellomo, Sara E.; Galimi, Francesco; Zanella, Eugenia; Consalvo Petti, Roberta; Fiori, Alessandro; Orzan, Francesca; Senetta, Rebecca; Boccaccio, Carla; Ficarra, Elisa; Marchionni, Luigi; Trusolino, Livio; Medico, Enzo; Bertotti, Andrea "Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer" NATURE COMMUNICATIONS, vol. 8, pp. 1 -16 , 2017 | DOI: 10.1038/ncomms15107 Journal
57	DI CATALDO, Santa; Ficarra, Elisa "Mining textural knowledge in biological images: applications, methods and trends" COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, vol. 15, pp. 56 -67 , 2017 | DOI: 10.1016/j.csbj.2016.11.002 Journal
58	Urgese, Gianvito; Paciello, Giulia; Macii, Enrico; Acquaviva, Andrea; Ficarra, Elisa "isomiR-SEA: miRNA and isomiR expression level detection in seven RNA-Seq datasets" Titolo volume non avvalorato, Prague, 21-25 July 2017, 2017 | DOI: 10.7490/f1000research.1114698.1 Other
59	Paciello, Giulia; Ficarra, Elisa "FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples" BMC BIOINFORMATICS, vol. 18, pp. 1 -12 , 2017 | DOI: 10.1186/s12859-016-1450-6 Journal
60	Ponzio, Francesco; Macii, Enrico; Ficarra, Elisa; DI CATALDO, Santa "A multi-modal brain image registration framework for US-guided neuronavigation systems. Integrating MR and US for minimally invasive neuroimaging" Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 2: BIOIMAGING, (BIOSTEC 2017), vol. 2017-, Porto, Portugal, pp. 114 -121 , 21-23 February 2017, 2017 | DOI: 10.5220/0006239201140121 Conference
61	Andrea, Bertotti; Claudio, Isella; Sara E., Bellomo; Brundu, FRANCESCO GAVINO; Francesco, Galimi; Ficarra, Elisa; Livio, Trusolino; Enzo, Medico "Unsupervised analysis of cancer-cell intrinsic transcriptional traits defines a new classification system for colorectal cancer with improved predictive and prognostic value" CANCER RESEARCH, vol. 76, pp. 107 -107 , 2016 | DOI: 10.1158/1538-7445.AM2016-107 Abstract in Journal
62	Simona, Soverini; Caterina De, Benedittis; Michela, Rondoni; Cristina, Papayannidis; Ficarra, Elisa; Paciello, Giulia; Marco, Manfrini; Manuela, Mancini; Roberta, Zanotti; Luigi, Scaffidi; Giorgina, Specchia; Francesco, Albano; Serena, Merante; Chiara, Elena; Livio, Pagano; Domenica, Gangemi; Patrizia, Tosi; Luana, Bavaro "The Genomic and Transcriptomic Landscape of Systemic Mastocytosis" BLOOD, vol. 128, 2016 | DOI: 10.1182/blood.V128.22.3136.3136 Abstract in Journal
63	Antonella, Padella; Giorgia, Simonetti; Anna, Ferrari; Paciello, Giulia; Elisa, Zago; Carmen, Baldazzi; Viviana, Guadagnuolo; Cristina, Papayannidis; Valentina, Robustelli; Enrica, Imbrogno; Nicoletta, Testoni; Massimo, Delledonne; Ilaria, Iacobucci; Tiziana Clelia, Storlazzi; Ficarra, Elisa; Pier Luigi, Lollini; Giovanni, Martinelli "Novel fusion transcripts identified by RNAseq cooperate with somatic mutations in the pathogenesis of acute myeloid leukemia" CANCER RESEARCH, vol. 76, pp. 113 -113 , 2016 | DOI: 10.1158/1538-7445.AM2016-113 Abstract in Journal
64	Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa "isomiR-SEA: An RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation" BMC BIOINFORMATICS, vol. 17, pp. N/A -N/A , 2016 | DOI: 10.1186/s12859-016-0958-0 Journal
65	Paciello, Giulia; Pighi, C.; Ficarra, Elisa; Zamo', A. "Detection of rearranged light chain sequences by RNA-Seq in B-cell lymphomas and reactive lymphadenopathies" EAHP: Book of Abstracts, Basilea, 3-8 Sept. 2016, 2016 Conference Abstract
66	DI CATALDO, Santa; Tonti, Simone; Ciglieri, Elisa; Ferrini, Francesco; Macii, Enrico; Ficarra, Elisa; Salio, Chiara "Automated 3D immunofluorescence analysis of Dorsal Root Ganglia for the investigation of neural circuit alterations: a preliminary study" Position Papers of the 2016 Federated Conference on Computer Science and Information Systems, vol. 9, Gdansk, pp. 65 -70 , 11-14 September 2016, 2016 | DOI: 10.15439/2016F569 Conference
67	DI CATALDO, Santa; Tonti, Simone; Bottino, ANDREA GIUSEPPE; Ficarra, Elisa "ANAlyte: a modular image analysis tool for ANA testing with Indirect Immunofluorescence" COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, vol. 128, pp. 86 -99 , 2016 | DOI: 10.1016/j.cmpb.2016.02.005 Journal
68	Natale, Massimo; Caiazzo, Alfonso; Ficarra, Elisa "A novel gaussian extrapolation approach for 2-D gel electrophoresis saturated protein spots" 2-D PAGE MAP ANALYSIS: METHODS AND PROTOCOLS, vol. 1384, pp. 203 -211 , 2016 | DOI: 10.1007/978-1-4939-3255-9_12 Chapter in Book
69	A., Padella; G., Simonetti; Paciello, Giulia; A., Ferrari; E., Zago; C., Baldazzi; V., Guadagnuolo; C., Papayannidis; V., Robustelli; E., Imbrogno; N., Testoni; M., Cavo; M., Delledonne; I., Iacobucci; Ct, Storlazzi; Ficarra, Elisa; G., Martinelli "A COMBINED APPROACH TO DETECT RARE FUSION EVENTS IN ACUTE MYELOID LEUKEMIA" Haematologica, journal of the European Hematology Association and the Ferrata Storti Foundation, HAEMATOLOGICA, vol. 101, Copenhagen, Denmark, pp. 666 -667 , June 9–12, 2016, 2016 Conference
70	Crescenzo, R.; Abate, F.; Lasorsa, E.; Tabbo', F.; Gaudiano, M.; Chiesa, N.; Di Giacomo, F.; Spaccarotella, E.; Barbarossa, L.; Ercole, E.; Todaro, M.; Boi, M.; Acquaviva, A.; Ficarra, E.; Novero, D.; Rinaldi, A.; Tousseyn, T.; Rosenwald, A.; Kenner, L.; Cerroni, L.; Tzankov, A.; Ponzoni, M.; Paulli, M.; Weisenburger, D.; Chan, W. C.; Iqbal, J.; Piris, M. A.; Zamo', A.; Ciardullo, C.; Rossi, D.; Gaidano, G.; Pileri, S.; Tiacci, E.; Falini, B.; Shultz, L. D.; Mevellec, L.; Vialard, J. E.; Piva, R.; Bertoni, F.; Rabadan, R.; Inghirami, G. "Erratum to Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma [Cancer Cell 27, 516-532] April 13, 2015 10.1016/j.ccell.2015.04.014" CANCER CELL, vol. 27, pp. 744 -744 , 2015 | DOI: 10.1016/j.ccell.2015.04.014 Journal
71	Paciello, Giulia; Acquaviva, Andrea; Chiara, Pighi; Alberto, Ferrarini; Macii, Enrico; Alberto, Zamò; Ficarra, Elisa "VDJSeq-Solver: In Silico V(D)J Recombination Detection tool" PLOS ONE, vol. 10, pp. 1 -26 , 2015 | DOI: 10.1371/journal.pone.0118192 Journal
72	Tonti, Simone; DI CATALDO, Santa; Macii, Enrico; Ficarra, Elisa "Unsupervised HEp-2 mitosis recognition in Indirect Immunofluorescence Imaging" Proceedings of 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Milano, pp. 8135 -8138 , 25-29 August, 2015, 2015 | DOI: 10.1109/EMBC.2015.7320282 Conference
73	Padella, A.; Simonetti, G.; Paciello, Giulia; Ferrari, A.; Zago, E.; Baldazzi, C.; Guadagnuolo, V.; Papayannidis, C.; Robustelli, V.; Imbrogno, E.; Testoni, N.; Musuraca, G.; Soverini, S.; Delledonne, M.; Iacobucci, I.; Storlazzi, C. T.; Ficarra, Elisa; Martinelli, G. "RNA Sequencing Reveals Novel and Rare Fusion Transcripts in Acute Myeloid Leukemia" BLOOD, vol. 126, pp. 3627 -3627 , 2015 Abstract in Journal
74	Urgese, Gianvito; Paciello, Giulia; Ficarra, Elisa; Macii, Enrico; Acquaviva, Andrea "On the relevance of a complete characterisation of miRNAs, isomiRs and miRNA-mRNA interaction sites through miRNA-specific alignment tools" Titolo volume non avvalorato, Oxford (UK), 24-26 March 2015, 2015 Conference Abstract
75	Cantini, Laura; Isella, Claudio; Petti, Consalvo; Picco, Gabriele; Chiola, Simone; Ficarra, Elisa; Caselle, Michele; Medico, Enzo "MicroRNA/mRNA interactions underlying colorectal cancer molecular subtypes" NATURE COMMUNICATIONS, vol. 6, pp. 1 -12 , 2015 | DOI: 10.1038/ncomms9878 Journal
76	Ramona, Crescenzo; Francesco, Abate; Elena, Lasorsa; Fabrizio, Tabbo’; Marcello, Gaudiano; Nicoletta, Chiesa; Filomena Di, Giacomo; Elisa, Spaccarotella; Luigi, Barbarossa; Elisabetta, Ercole; Maria, Todaro; Michela, Boi; Acquaviva, Andrea; Ficarra, Elisa; Domenico, Novero; Andrea, Rinaldi; Thomas, Tousseyn; Andreas, Rosenwald; Lukas, Kenner; Lorenzo, Cerroni; Alexander, Tzankov; Maurilio, Ponzoni; Marco, Paulli; Dennis, Weisenburger; Wing C., Chan; Javeed, Iqbal; Miguel A., Piris; Alberto, Zamo’; Carmela, Ciardullo; Davide, Rossi; Gianluca, Gaidano; Stefano, Pileri; Enrico, Tiacci; Brunangelo, Falini; Leonard D., Shultz; Laurence, Mevellec; Jorge E., Vialard; Roberto, Piva; Francesco, Bertoni; Raul, Rabadan; Giorgio, Inghirami "Convergent Mutations and Kinase Fusions Lead to Oncogenic STAT3 Activation in Anaplastic Large Cell Lymphoma" CANCER CELL, vol. 27, pp. 516 -532 , 2015 | DOI: 10.1016/j.ccell.2015.03.006 Journal
77	Ciglieri, Elisa; Ferrini, Francesco; Tonti, Simone; DI CATALDO, Santa; Ficarra, Elisa; Salio, Chiara "An integrated approach for morphofunctional analysis of DRGs in normal and diabetic mice" Titolo volume non avvalorato, Cagliari, Italy, October 8th -11th, 2015., 2015 Conference Abstract
78	Tonti, Simone; Di Cataldo, Santa; Bottino, Andrea Giuseppe; Ficarra, Elisa "An automated approach to the segmentation of HEp-2 cells for the indirect immunofluorescence ANA test" COMPUTERIZED MEDICAL IMAGING AND GRAPHICS, vol. 40, pp. 62 -69 , 2015 | DOI: 10.1016/j.compmedimag.2014.12.005 Journal
79	F., Abate; M., Todaro; J. A., van der Krogt; M., Boi; I., Landra; R., Machiorlatti; F., Tabbò; K., Messana; A., Barreca; D., Novero; M., Gaudiano; S., Aliberti; F., Di Giacomo; T., Tousseyn; E., Lasorsa; R., Crescenzo; L., Bessone; Ficarra, Elisa; Acquaviva, Andrea; A., Rinaldi; M., Ponzoni; Dl, Longo; S., Aime; M., Cheng; B., Ruggeri; Pp, Piccaluga; S., Pileri; E., Tiacci; B., Falini; B., Pera Gresely; L., Cerchietti; J., Iqbal; Wc, Chan; Ld, Shultz; I., Kwee; R., Piva; I., Wlodarska; R., Rabadan; F., Bertoni; G., Inghirami; The European T., cell Lymphoma Study Group "A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation" LEUKEMIA, vol. 29, pp. 1390 -1401 , 2015 | DOI: 10.1038/leu.2014.347 Journal
80	DI CATALDO, Santa; Bottino, ANDREA GIUSEPPE; UL-ISLAM, Ihtesham; FIGUEIREDO VIEIRA, Tiago; Ficarra, Elisa "Subclass Discriminant Analysis of Morphological and Textural Features for HEp-2 Staining Pattern Classification" PATTERN RECOGNITION, vol. 47, pp. 2389 -2399 , 2014 | DOI: 10.1016/j.patcog.2013.09.024 Journal
81	Abate, Francesco; Sakellarios, Zairis; Ficarra, Elisa; Acquaviva, Andrea; Chris H., Wiggins; Veronique, Frattini; Anna, Lasorella; Antonio, Iavarone; Giorgio, Inghirami; Raul, Rabadan "Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer" BMC SYSTEMS BIOLOGY, vol. 8, pp. 1 -14 , 2014 | DOI: 10.1186/s12918-014-0097-z Journal
82	Antonella, Padella; Giorgia, Simonetti; Viviana, Guadagnuolo; Emanuela, Ottaviani; Anna, Ferrari; Elisa, Zago; Francesca, Griggio; Marianna, Garonzi; Paciello, Giulia; Simona, Bernardi; Carmen, Baldazzi; Cristina, Papayannidis; Maria Chiara, Abbenante; Francesca, Volpato; Raffaele, Calogero; Nicoletta, Testoni; Ficarra, Elisa; Alberto, Ferrarini; Massimo, Delledonne; Ilaria, Iacobucci; Giovanni, Martinelli "Next-Generation Sequencing Analysis Revealed That BCL11B Chromosomal Translocation Cooperates with Point Mutations in the Pathogenesis of Acute Myeloid Leukemia" BLOOD, vol. 124, 2014 Abstract in Journal
83	Natale, Massimo; Benso, Alfredo; DI CARLO, Stefano; Ficarra, Elisa "Indentifying sub-network functional modules in protein undirected networks" Proceedings of BIOINFORMATICS 2014, Eseo, Angers, France, 3-6 March 2014, 2014 Conference
84	Natale, Massimo; Benso, Alfredo; Di Carlo, Stefano; Ficarra, Elisa "Identifying sub-network functional modules in protein undirected networks" BIOINFORMATICS 2014 - 5th Int. Conf. on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 7th Int. Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2014, Angers, Loire Valley, fra, pp. 149 -155 , MAR 03-06, 2014, 2014 Conference
85	Natale, M.; Benso, Alfredo; DI CARLO, Stefano; Ficarra, Elisa "FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks" GENOMICS, PROTEOMICS & BIOINFORMATICS, vol. 12, pp. 178 -186 , 2014 | DOI: 10.1016/j.gpb.2014.05.002 Journal
86	Urgese, Gianvito; Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Graziano, Mariagrazia; Zamboni, Maurizio "Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation" Proceedings of 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2014), vol. 2, Granada, pp. 1347 -1358 , April 7-9 2014, 2014 Conference
87	Paula H., Reyes Herrera; Ficarra, Elisa "Computational Methods for CLIP-seq Data Processing" BIOINFORMATICS AND BIOLOGY INSIGHTS, vol. 8, pp. 199 -207 , 2014 | DOI: 10.4137/BBI.S16803 Journal
88	UL-ISLAM, Ihtesham; DI CATALDO, Santa; Bottino, ANDREA GIUSEPPE; Macii, Enrico; Ficarra, Elisa "A Preliminary Analysis on HEp-2 Pattern Classification: Evaluating Strategies Based on Support Vector Machines and Subclass Discriminant Analysis" Biomedical Engineering Systems and Technologies, vol. 452, pp. 176 -190 , 2014 | DOI: 10.1007/978-3-662-44485-6_13 Chapter in Book
89	Paciello, Giulia; Acquaviva, Andrea; Consalvo, Petti; Claudio, Isella; Enzo, Medico; Ficarra, Elisa "A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer" BIOINFORMATICS 2014 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, ESEO, Angers, Loire Valley, France, 3-6 March, 2014, Angers, Loire Valley, fra, pp. 142 -148 , 3-6 March 2014, 2014 | DOI: 10.5220/0004799401420148 Conference
90	Shkurti, Ardita; Mario, Orsi; Acquaviva, Andrea; Ficarra, Elisa; Macii, Enrico; Sophia, Wheeler; Jonathan W., Essex "Optimization of Molecular Dynamics Simulations from a High Performance Computing Viewpoint" Titolo volume non avvalorato, Nottingham, United Kingdom, 25-27 March 2013, 2013 Other
91	Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Macii, Enrico "Integration of Literature with Heterogeneous Information for Genes Correlation Scoring" ACM JOURNAL ON EMERGING TECHNOLOGIES IN COMPUTING SYSTEMS, vol. 9, 2013 | DOI: 10.1145/2504728 Journal
92	Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Piva, R.; Macii, Enrico "Gelsius: A Literature-Based Workflow for Determining Quantitative Associations between Genes and Biological Processes" IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, vol. 10, pp. 619 -631 , 2013 | DOI: 10.1109/TCBB.2013.11 Journal
93	UL-ISLAM, Ihtesham; DI CATALDO, Santa; Bottino, ANDREA GIUSEPPE; Ficarra, Elisa; Macii, Enrico "Classification of HEp-2 staining patterns in ImmunoFluorescence images. Comparison of Support Vector Machines and Subclass Discriminant Analysis strategies" Proc. of BIOINFORMATICS 2013, Barcelona, esp, pp. 53 -61 , 11-14 February 2013, 2013 Conference
94	Shkurti, Ardita; Mario, Orsi; Macii, Enrico; Ficarra, Elisa; Acquaviva, Andrea "Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures" JOURNAL OF COMPUTATIONAL CHEMISTRY, vol. 34, pp. 803 -818 , 2013 | DOI: 10.1002/jcc.23183 Journal
95	Paciello, Giulia; Ficarra, Elisa; Alberto, Zamò; Chiara, Pighi; Carmelo, Foti; Abate, Francesco; Macii, Enrico; Acquaviva, Andrea "A novel pipeline for V(D)J junction identification using RNA-Seq paired-end reads" Titolo volume non avvalorato, Barcelona, Spain, pp. 185 -189 , 11-14 February 2013, 2013 Conference
96	Abate, F.; Paciello, G.; Acquaviva, A.; Ficarra, E.; Ferrarini, A.; Delledonne, M.; Macii, E. "A novel analysis flow for fused transcripts discovery from paired-end RNA-SEQ data" BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, prt, pp. 331 -334 , FEB 01-04, 2012, 2012 | DOI: 10.5220/0003789003310334 Conference
97	Shkurti, Ardita; Acquaviva, Andrea; Ficarra, Elisa; Orsi, M.; Macii, Enrico; Essex, J. W. "Towards Low Cost Virtual Biological Laboratories: Molecular Modelling Simulation on Commodity Hardware" Titolo volume non avvalorato, Londra, Novembre 2012, 2012 Other
98	Terzo, Olivier; Mossucca, L; Acquaviva, Andrea; Abate, Francesco; Ficarra, Elisa; Provenzano, R. "Reverse Engineering of TopHat: Splice Junction Mapper for Improving Computational Aspect" Titolo volume non avvalorato, Kota Kinabalu, mys, pp. 171 -176 , 8 – 10 February 2012, 2012 | DOI: 10.1109/ISMS.2012.76 Conference
99	Terzo, Olivier; Mossucca, L; Acquaviva, Andrea; Abate, Francesco; Ficarra, Elisa; Provenzano, R. "Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure" Titolo volume non avvalorato, Shanghai, 17-20 My 2012, 2012 Conference
100	Paula H., Reyes Herrera; Ficarra, Elisa "One Decade of Development and Evolution of MicroRNA Target Prediction Algorithms" GENOMICS, PROTEOMICS & BIOINFORMATICS, vol. 10, pp. 254 -263 , 2012 | DOI: 10.1016/j.gpb.2012.10.001 Journal
101	Valentini, S.; Natale, Massimo; Ficarra, Elisa; Barmaz, A. "New Software for the Identification and Characterization of Peptides Generated during Fontina Cheese Ripening Using Mass Spectrometry Data" JOURNAL OF CHEMISTRY AND CHEMICAL ENGINEERING, vol. 6, pp. 323 -326 , 2012 Journal
102	Deriu, Marco Agostino; Shkurti, Ardita; Paciello, Giulia; Bidone, Tamara Carla; Morbiducci, Umberto; Ficarra, Elisa; Audenino, Alberto; Acquaviva, Andrea "Multiscale Modelling of Cellular Actin Filaments: From Atomistic Molecular to Coarse Grained Dynamics" PROTEINS, vol. 80, pp. 1598 -1609 , 2012 | DOI: 10.1002/prot.24053 Journal
103	Di Cataldo, Santa; Ficarra, Elisa; Macii, Enrico "Computer-aided techniques for Chromogenic Immunohistochemistry: Status and Directions" COMPUTERS IN BIOLOGY AND MEDICINE, vol. 42, pp. 1012 -1025 , 2012 | DOI: 10.1016/j.compbiomed.2012.08.004 Journal
104	Shkurti, Ardita; Acquaviva, Andrea; Ficarra, Elisa; Orsi, Mario; Macii, Enrico "CHARACTERIZATION OF COARSE GRAIN MOLECULAR DYNAMIC SIMULATION PERFORMANCE ON GRAPHIC PROCESSING UNIT ARCHITECTURES" BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, prt, pp. 339 -342 , 1-4 Feb 2012, 2012 | DOI: 10.5220/0003790703390342 Conference
105	Abate, Francesco; Acquaviva, Andrea; Paciello, Giulia; Foti, Carmelo; Ficarra, Elisa; Ferrarini, A.; Delle donne, M.; Iacobucci, I.; Soverini, S.; Martinelli, G.; Macii, Enrico "Bellerophontes: a RNA-seq data analysis framework tor chimeric transcripts discovery base on accurate fusion model" BIOINFORMATICS, vol. 28, pp. 2114 -2121 , 2012 | DOI: 10.1093/bioinformatics/bts334 Journal
106	Di Cataldo, Santa; Bottino, Andrea Giuseppe; Ficarra, Elisa; Macii, Enrico "Applying Textural Features to the Classification of HEp-2 Cell Patterns in IIF images" Proc. of 21st International Conference on Pattern Recognition (ICPR 2012), Tsukuba, jpn, pp. 3349 -3352 , November 11-15, 2012, 2012 Conference
107	F., Tabbó; A., Barreca; R., Piva; G., Inghirami; R., Bruna; D., Corino; D., Cortese; R., Crescenzo; G., Cuccuru; F., Di Giacomo; A., Fioravanti; M., Ladetto; I., Landra; K., Messana; R., Machiorlatti; B., Martinoglio; E., Medico; M., Mossino; E., Pellegrino; M., Todaro; P., Campisi; L., Chiusa; A., Chiappella; D., Novero; U., Vitolo; Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; R., Freilone; M., Chilosi; A., Zamó; F., Facchetti; S., Lonardi; A., De Chiara; F., Fulciniti; C., Doglioni; M., Ponzoni; L., Agnelli; A., Neri; K., Todoerti; C., Agostinelli; P. P., Piccaluga; S., Pileri; B., Falini; E., Tiacci; P., Van Loo; T., Tousseyn; C., De Wolf Peeters; E., Geissinger; H. K., Muller Hermelink; A., Rosenwald; M. A., Pirisand; M. E., Rodriguez; F., Bertoni; M., Boi; I., Kwee "ALK signaling and target therapy in anaplastic large cell lymphoma" FRONTIERS IN ONCOLOGY, vol. 2, pp. N/A -N/A , 2012 | DOI: 10.3389/fonc.2012.00041 Journal
108	Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa "A novel Gaussian fitting approach for 2D gel electrophoresis saturated protein spots" Titolo volume non avvalorato, Vilamoura, Algarve, Portugal, pp. 335 -338 , 1-4 Feb. 2012, 2012 | DOI: 10.5220/0003789803350338 Conference
109	Natale, Massimo; Caiazzo, A.; Bucci, E. M.; Ficarra, Elisa "A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots" GENOMICS, PROTEOMICS & BIOINFORMATICS, vol. 10, pp. 336 -344 , 2012 | DOI: 10.1016/j.gpb.2012.06.005 Journal
110	Abate, F.; Ficarra, E.; Acquaviva, A.; Macii, E. "Improving Latent Semantic Analysis of Biomedical Literature Integrating UMLS Metathesaurus and Biomedical Pathways Databases" Communications in Computer and Information Science, vol. 273, Rome, ita, pp. 173 -187 , 2011, 2011 | DOI: 10.1007/978-3-642-29752-6 Conference
111	Paciello, G.; Acquaviva, A.; Ficarra, E.; Deriu, M. A.; Grosso, A.; Macii, E. "Binding free energy calculation via molecular dynamics simulations for a miRNA:mRNA interaction" BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Rome, ita, pp. 318 -321 , JAN 26-29, 2011, 2011 Conference
112	Abate, F.; Acquaviva, A.; Ficarra, E.; Macii, E. "A new latent semantic analysis based methodology for knowledge extraction from biomedical literature and biological pathways databases" BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Rome, ita, pp. 66 -74 , 2011, 2011 Conference
113	Mazzillo, M.; Fallica, P. G.; Ficarra, Elisa; Messina, A.; Romeo, M.; Zafalon, R. "Solid state photodetectors for nuclear medical imaging applications" 2011 DESIGN, AUTOMATION & TEST IN EUROPE (DATE), Grenoble, fra, pp. 511 -512 , 14-18 March, 2011, 2011 Conference
114	DI CATALDO, Santa; Ficarra, Elisa; Acquaviva, Andrea; Macii, Enrico "Motion artifact correction in ASL images: an improved automated procedure" Titolo volume non avvalorato, Atlanta, GA, usa, pp. 410 -413 , 12-15 Nov. 2011, 2011 | DOI: 10.1109/BIBM.2011.106 Conference
115	REYES HERRERA, PAULA HELENA; Ficarra, Elisa; Acquaviva, Andrea; Macii, Enrico "miREE: miRNA Recognition Elements Ensemble" BMC BIOINFORMATICS, vol. 12, pp. N/A -N/A , 2011 | DOI: 10.1186/1471-2105-12-454 Journal
116	Ficarra, Elisa; Di Cataldo, Santa; Acquaviva, Andrea; Macii, Enrico "Automated Segmentation of Cells with IHC Membrane Staining" IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, vol. 58, pp. 1421 -1429 , 2011 | DOI: 10.1109/TBME.2011.2106499 Journal
117	Terzo, Olivier; Mossucca, L.; Ruiu, Pietro; Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Macii, Enrico "An effective grid infrastructure for efficiently support high throughput sequencing analysis" Titolo volume non avvalorato, Orlando (USA), March 27th - 30th, 2011, 2011 Conference
118	Abate, Francesco; Acquaviva, Andrea; Ficarra, Elisa; Paciello, Giulia; Macii, Enrico; A., Ferrarini; M., Delledonne; S., Soverini; G., Martinelli "A novel framework for chimeric transcript detection based on accurate gene fusion model" Titolo volume non avvalorato, Atlanta, GA, usa, pp. 34 -41 , 12-15 Nov. 2011, 2011 | DOI: 10.1109/BIBMW.2011.6112352 Conference
119	Paciello, Giulia; Acquaviva, Andrea; Ficarra, Elisa; Deriu, Marco Agostino; Macii, Enrico "A Molecular Dynamics study of a miRNA:mRNA interaction" JOURNAL OF MOLECULAR MODELING, vol. 17, pp. 2895 -2906 , 2011 | DOI: 10.1007/s00894-011-0991-x Journal
120	Reyes-Herrera, P. H.; Acquaviva, A.; Ficarra, E.; Macii, E. "MicroRNA target prediction and exploration through candidate binding sites generation" CISIS 2010 - The 4th International Conference on Complex, Intelligent and Software Intensive Systems, Krakow, pol, pp. 683 -688 , 2010, 2010 | DOI: 10.1109/CISIS.2010.129 Conference
121	Orsi, M.; Shkurti, A.; Acquaviva, A.; Ficarra, E.; Macii, E.; Ruggiero, M. "GPU acceleration of simulation tool for lipid-bilayers" 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2010, HongKong, chn, pp. 849 -850 , 2010, 2010 | DOI: 10.1109/BIBMW.2010.5703940 Conference
122	Di Cataldo, Santa; Ficarra, Elisa; Acquaviva, Andrea; Macii, Enrico "Automated segmentation of tissue images for computerized IHC analysis" COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE, vol. 100, pp. 1 -15 , 2010 | DOI: 10.1016/j.cmpb.2010.02.002 Journal
123	Abate, Francesco; Ficarra, Elisa; Acquaviva, Andrea; Macii, Enrico "An Automated Tool for Scoring Biomedical Terms Correlation Based on Semantic Analysis" Complex, intelligent and software intensive systems (CISIS), 2010 international conference on, Krakow, Poland, pp. 700 -705 , February 15th - 18th, 2010 | DOI: 10.1109/CISIS.2010.126 Conference
124	DI CATALDO, Santa; Ficarra, Elisa; Acquaviva, Andrea; Macii, E. "Achieving the Way for Automated Segmentation of Nuclei in Cancer Tissue Images through Morphology-Based Approach: a Quantitative Evaluation" COMPUTERIZED MEDICAL IMAGING AND GRAPHICS, vol. 34, pp. 453 -461 , 2010 | DOI: 10.1016/j.compmedimag.2009.12.008 Journal
125	REYES HERRERA, PAULA HELENA; Acquaviva, Andrea; Ficarra, Elisa; Macii, Enrico "Novel Method for MicroRNA Target Prediction Using a Genetic Algorithm" 7th Annual Rocky Mountain Bioinformatics conference, vol. 1, Aspen, Colorado - USA, pp. 50 -51 , December 10th - 12th, 2009 Conference
126	Apiletti, Daniele; Bruno, Giulia; Ficarra, Elisa; Baralis, Elena Maria "Extraction of Constraints from Biological Data" Biomedical Data and Applications., vol. 224, pp. 169 -186 , 2009 | DOI: 10.1007/978-3-642-02193-0_7 Chapter in Book
127	Ficarra, Elisa; DE MICHELI, G; Yoon, S; Benini, L; Macii, Enrico "Joint co-clustering: co-clustering of genomic and clinical bioimaging data" COMPUTERS & MATHEMATICS WITH APPLICATIONS, vol. 55, pp. 938 -949 , 2008 | DOI: 10.1016/j.camwa.2006.12.102 Journal
128	Baralis, Elena Maria; Bruno, Giulia; Ficarra, Elisa "Temporal Association Rules for Gene Regulatory Networks" Titolo volume non avvalorato, vol. 3, Varna, bgr, pp. 12-2 -12-7 , September 6-8, 2008, 2008 | DOI: 10.1109/IS.2008.4670511 Conference
129	DI CATALDO, Santa; Ficarra, Elisa; Acquaviva, Andrea; Macii, Enrico "Segmentation of Nuclei in Cancer Tissue Images: Contrasting Active Contours with Morphology-Based Approach" BIBE, Athens, grc, October 8-10, 2008, 2008 | DOI: 10.1109/BIBE.2008.4696793 Conference
130	DI CATALDO, Santa; Ficarra, Elisa; Macii, Enrico "Fully-Automated Segmentation of Tumor Areas in Tissue Confocal Images" BIOSIGNALS (1), vol. 1, Madeira, Portugal, pp. 116 -123 , January 28-31, 2008, 2008 Conference
131	Di Cataldo, Santa; Ficarra, Elisa; Macii, Enrico "Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs Supervised SVM Classification" Biomedical Engineering Systems and Technologies, vol. 25, pp. 344 -356 , 2008 | DOI: 10.1007/978-3-540-92219-3_26 Chapter in Book
132	DI CATALDO, Santa; Ficarra, Elisa; Macii, Enrico "Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: a Fully-Automated Approach" BIBM, vol. 0, Fremont, CA, usa, pp. 390 -398 , November 2-4, 2007, 2007 | DOI: 10.1109/BIBM.2007.10 Conference
133	Baralis, ELENA MARIA; Ficarra, Elisa; Fiori, Alessandro; Macii, Enrico "Gene-Markers Representation for Microarray Data Integration" Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, vol. 2, Boston, pp. 1056 -1060 , 14-17 October 2007, 2007 | DOI: 10.1109/BIBE.2007.4375688 Conference
134	Masotti, D; Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G. "Optimized Techniques for DNA structural properties investigation" INTERNATIONAL JOURNAL ON ARTIFICIAL INTELLIGENCE TOOLS, vol. 15, pp. 695 -709 , 2006 | DOI: 10.1142/S0218213006002886 Journal
135	Apiletti, Daniele; Bruno, Giulia; Ficarra, Elisa; Baralis, ELENA MARIA "Data Cleaning and Semantic Improvement in Biological Databases" JOURNAL OF INTEGRATIVE BIOINFORMATICS, vol. 3(2):40, 2006 Journal
136	Ficarra, Elisa; Macii, Enrico; Benini, L; DE MICHELI, G. "Computer-aided evaluation of protein expression in pathological tissue images" Titolo volume non avvalorato, vol. 2006, Salt Lake City, UT, usa, pp. 413 -418 , June 2006, 2006 | DOI: 10.1109/CBMS.2006.71 Conference
137	Ficarra, Elisa; Yoon, S; Benini, L; Macii, E; DE MICHELI, G. "Clinical bioimaging and functional genomics" FIMA International Conference on "Models and Methods for Human Genomics", Ayas-Champoluc, Aosta Valley, ITALY, pp. 37 -37 , January 23-27, 2006, 2006 Conference
138	Ficarra, E.; DE MICHELI, G.; Yoon, S.; Benini, L.; Macii, E. "Bioimaging and Clinical Genomics" Proceedings of pHealth IEEE International workshop on wearable micro and nanosystems for personalized Health, Luzern, Switzerland, pp. S.6.5 - , 30 Jan. - 01 Feb. 2006, 2006 Conference
139	Ficarra, Elisa; Masotti, D; Benini, L; Macii, Enrico; Zuccheri, G; Samori, B. "Automatic Intrinsic DNA Curvature Computation from AFM Images" IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING, vol. 52, pp. 2074 -2086 , 2005 | DOI: 10.1109/TBME.2005.857666 Journal
140	Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G. "Automated DNA Fragments Recognition and Sizing through AFM Image Processing" IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, vol. 9, pp. 508 -517 , 2005 | DOI: 10.1109/TITB.2005.855546 Journal
141	Masotti, D; Ficarra, Elisa; Macii, Enrico; Benini, L. "Techniques for Enhancing Computation of DNA Curvature Molecules" Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering, Taichung, twn, pp. 22 -29 , May 19-21, 2004, 2004 | DOI: 10.1109/BIBE.2004.1317321 Conference
142	Ficarra, Elisa; Benini, L; Macii, Enrico; Zuccheri, G. "A Robust Algorithm for Automated Analysis of DNA Molecules in AFM Images" Titolo volume non avvalorato, Innsbruck, aut, pp. 213 -218 , February 2004, 2004 Conference
143	Ficarra, Elisa "Automated DNA sizing in atomic force microscope images" Proceedings - International Symposium on Biomedical Imaging, vol. 2002-, Ritz-Carlton Hotel, usa, pp. 453 -456 , 2002, 2002 | DOI: 10.1109/ISBI.2002.1029292 Conference

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