Elisa Ficarra

Orcid: 0000-0002-8061-2124

According to our database1, Elisa Ficarra authored at least 92 papers between 2002 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
A Graph-Based Multi-Scale Approach With Knowledge Distillation for WSI Classification.
IEEE Trans. Medical Imaging, April, 2024

Enhancing Patch-Based Learning for the Segmentation of the Mandibular Canal.
IEEE Access, 2024

ClusterFix: A Cluster-Based Debiasing Approach without Protected-Group Supervision.
Proceedings of the IEEE/CVF Winter Conference on Applications of Computer Vision, 2024

2023
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge.
BMC Bioinform., December, 2023

Predicting gene and protein expression levels from DNA and protein sequences with Perceiver.
Comput. Methods Programs Biomed., June, 2023

W2WNet: A two-module probabilistic Convolutional Neural Network with embedded data cleansing functionality.
Expert Syst. Appl., 2023

DAS-MIL: Distilling Across Scales for MIL Classification of Histological WSIs.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023, 2023

Neuro-Symbolic Continual Learning: Knowledge, Reasoning Shortcuts and Concept Rehearsal.
Proceedings of the International Conference on Machine Learning, 2023

Buffer-MIL: Robust Multi-instance Learning with a Buffer-Based Approach.
Proceedings of the Image Analysis and Processing - ICIAP 2023, 2023

Enhancing PFI Prediction with GDS-MIL: A Graph-Based Dual Stream MIL Approach.
Proceedings of the Image Analysis and Processing - ICIAP 2023, 2023

2022
Identifying the oncogenic potential of gene fusions exploiting miRNAs.
J. Biomed. Informatics, 2022

A survey on data integration for multi-omics sample clustering.
Neurocomputing, 2022

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers.
Comput. Methods Programs Biomed., 2022

LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.
BMC Bioinform., 2022

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations.
BMC Bioinform., 2022

High Resolution Explanation Maps for CNNs using Segmentation Networks.
Proceedings of the 2022 IEEE Symposium on Visual Languages and Human-Centric Computing, 2022

Catastrophic Forgetting in Continual Concept Bottleneck Models.
Proceedings of the Image Analysis and Processing. ICIAP 2022 Workshops, 2022

FusionFlow: An Integrated System Workflow for Gene Fusion Detection in Genomic Samples.
Proceedings of the New Trends in Database and Information Systems, 2022

2021
Optimizing Quality Inspection and Control in Powder Bed Metal Additive Manufacturing: Challenges and Research Directions.
Proc. IEEE, 2021

Exploration of Convolutional Neural Network models for source code classification.
Eng. Appl. Artif. Intell., 2021

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations: a COVID-19 case-study.
CoRR, 2021

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity.
BMC Bioinform., 2021

FUNGI: FUsioN Gene Integration toolset.
Bioinform., 2021

A Bayesian approach to Expert Gate Incremental Learning.
Proceedings of the International Joint Conference on Neural Networks, 2021

2020
BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis.
Bioinform., 2020

DEEPrior: a deep learning tool for the prioritization of gene fusions.
Bioinform., 2020

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.
Bioinform., 2020

Exploiting "Uncertain" Deep Networks for Data Cleaning in Digital Pathology.
Proceedings of the 17th IEEE International Symposium on Biomedical Imaging, 2020

Multi-omics Classification on Kidney Samples Exploiting Uncertainty-Aware Models.
Proceedings of the Intelligent Computing Theories and Application, 2020

Unsupervised Multi-omic Data Fusion: The Neural Graph Learning Network.
Proceedings of the Intelligent Computing Theories and Application, 2020

Effective Evaluation of Clustering Algorithms on Single-Cell CNA data.
Proceedings of the ICBBE 2020: 7th International Conference on Biomedical and Bioinformatics Engineering, 2020

2018
Predicting the Oncogenic Potential of Gene Fusions Using Convolutional Neural Networks.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2018

geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data.
Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018), 2018

Going Deeper into Colorectal Cancer Histopathology.
Proceedings of the Biomedical Engineering Systems and Technologies, 2018

Colorectal Cancer Classification using Deep Convolutional Networks - An Experimental Study.
Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2018), 2018

2017
FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples.
BMC Bioinform., 2017

A Novel Proof-of-concept Framework for the Exploitation of ConvNets on Whole Slide Images.
Proceedings of the Advances in Intelligent Information Hiding and Multimedia Signal Processing, 2017

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 (BIOSTEC 2017), 2017

2016
ANAlyte: A modular image analysis tool for ANA testing with indirect immunofluorescence.
Comput. Methods Programs Biomed., 2016

isomiR-SEA: an RNA-Seq analysis tool for miRNAs/isomiRs expression level profiling and miRNA-mRNA interaction sites evaluation.
BMC Bioinform., 2016

Automated 3D immunofluorescence analysis of Dorsal Root Ganglia for the investigation of neural circuit alterations: a preliminary study.
Proceedings of the Position Papers of the 2016 Federated Conference on Computer Science and Information Systems, 2016

2015
An automated approach to the segmentation of HEp-2 cells for the indirect immunofluorescence ANA test.
Comput. Medical Imaging Graph., 2015

Unsupervised HEp-2 mitosis recognition in indirect immunofluorescence imaging.
Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2015

2014
Subclass Discriminant Analysis of morphological and textural features for HEp-2 staining pattern classification.
Pattern Recognit., 2014

FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein-Protein Networks.
Genom. Proteom. Bioinform., 2014

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
BMC Syst. Biol., 2014

miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

Dynamic Gap Selector: A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimization.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer.
Proceedings of the BIOINFORMATICS 2014, 2014

Identifying Sub-Network Functional Modules in Protein Undirected Networks.
Proceedings of the BIOINFORMATICS 2014, 2014

2013
Gelsius: A Literature-Based Workflow for Determining Quantitative Associations between Genes and Biological Processes.
IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Integration of Literature with Heterogeneous Information for Genes Correlation Scoring.
ACM J. Emerg. Technol. Comput. Syst., 2013

Acceleration of coarse grain molecular dynamics on GPU architectures.
J. Comput. Chem., 2013

A Novel Pipeline for V(D)J Junction Identification using RNA-Seq Paired-end Reads.
Proceedings of the BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain, 11, 2013

A Preliminary Analysis on HEp-2 Pattern Classification: Evaluating Strategies Based on Support Vector Machines and Subclass Discriminant Analysis.
Proceedings of the Biomedical Engineering Systems and Technologies, 2013

Classification of HEp-2 Staining Patterns in ImmunoFluorescence Images - Comparison of Support Vector Machines and Subclass Discriminant Analysis Strategies.
Proceedings of the BIOINFORMATICS 2013 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Barcelona, Spain, 11, 2013

2012
One Decade of Development and Evolution of MicroRNA Target Prediction Algorithms.
Genom. Proteom. Bioinform., 2012

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots.
Genom. Proteom. Bioinform., 2012

Computer-aided techniques for chromogenic immunohistochemistry: Status and directions.
Comput. Biol. Medicine, 2012

Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.
Bioinform., 2012

Applying textural features to the classification of HEp-2 cell patterns in IIF images.
Proceedings of the 21st International Conference on Pattern Recognition, 2012

Characterization of Coarse Grain Molecular Dynamic Simulation Performance on Graphic Processing Unit Architectures.
Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

A Novel Gaussian Fitting Approach for 2D Gel Electrophoresis Saturated Protein Spots.
Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

A Novel Analysis Flow for Fused Transcripts Discovery from Paired-end RNA-Seq Data.
Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011
Automated Segmentation of Cells With IHC Membrane Staining.
IEEE Trans. Biomed. Eng., 2011

miREE: miRNA Recognition Elements Ensemble.
BMC Bioinform., 2011

Solid state photodetectors for nuclear medical imaging applications.
Proceedings of the Design, Automation and Test in Europe, 2011

Binding Free Energy Calculation via Molecular Dynamics Simulations for a miRNA: mRNA Interaction.
Proceedings of the BIOINFORMATICS 2011, 2011

Improving Latent Semantic Analysis of Biomedical Literature Integrating UMLS Metathesaurus and Biomedical Pathways Databases.
Proceedings of the Biomedical Engineering Systems and Technologies, 2011

A New Latent Semantic Analysis based Methodology for Knowledge Extraction from Biomedical Literature and Biological Pathways Databases.
Proceedings of the BIOINFORMATICS 2011, 2011

Motion Artifact Correction in ASL images: An Improved Automated Procedure.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

A novel framework for chimeric transcript detection based on accurate gene fusion model.
Proceedings of the 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2011

2010
Automated segmentation of tissue images for computerized IHC analysis.
Comput. Methods Programs Biomed., 2010

Achieving the way for automated segmentation of nuclei in cancer tissue images through morphology-based approach: A quantitative evaluation.
Comput. Medical Imaging Graph., 2010

MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation.
Proceedings of the CISIS 2010, 2010

An Automated Tool for Scoring Biomedical Terms Correlation Based on Semantic Analysis.
Proceedings of the CISIS 2010, 2010

GPU acceleration of simulation tool for lipid-bilayers.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

2009
Extraction of Constraints from Biological Data.
Proceedings of the Biomedical Data and Applications, 2009

2008
Joint co-clustering: Co-clustering of genomic and clinical bioimaging data.
Comput. Math. Appl., 2008

Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs. Supervised SVM Classification.
Proceedings of the Biomedical Engineering Systems and Technologies, 2008

Fully-Automated Segmentation of Tumor Areas in Tissue Confocal Images - Comparison between a Custom Unsupervised and a Supervised SVM Approach.
Proceedings of the First International Conference on Biomedical Electronics and Devices, 2008

Segmentation of nuclei in cancer tissue images: Contrasting active contours with morphology-based approach.
Proceedings of the 8th IEEE International Conference on Bioinformatics and Bioengineering, 2008

2007
Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: A Fully Automated Approach.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2007

Gene-Markers Representation for Microarray Data Integration.
Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006
Data mining techniques for genetic information discovery.
PhD thesis, 2006

Data Cleaning and Semantic Improvement in Biological Databases.
J. Integr. Bioinform., 2006

Optimized Technique for Dna Structural Properties Discovering.
Int. J. Artif. Intell. Tools, 2006

Computer-Aided Evaluation of Protein Expression in Pathological Tissue Images.
Proceedings of the 19th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2006), 2006

2005
Automated DNA fragments recognition and sizing through AFM image processing.
IEEE Trans. Inf. Technol. Biomed., 2005

Automatic intrinsic DNA curvature computation from AFM images.
IEEE Trans. Biomed. Eng., 2005

2004
Techniques for Enhancing Computation of DNA Curvature Molecules.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004

2002
Automated DNA sizing in atomic force microscope images.
Proceedings of the 2002 IEEE International Symposium on Biomedical Imaging, 2002


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