Elisa Ficarra

发表

Automated DNA sizing in atomic force microscope images

Luca Benini, Bruno Riccò, Elisa Ficarra, 2002, Proceedings IEEE International Symposium on Biomedical Imaging.

Exploiting “Uncertain” Deep Networks for Data Cleaning in Digital Pathology

Enrico Macii, Elisa Ficarra, Francesco Ponzio, 2020, 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI).

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

Andrea Acquaviva, Elisa Ficarra, Gianvito Urgese, 2016, BMC Bioinformatics.

Acceleration of coarse grain molecular dynamics on GPU architectures

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2013, J. Comput. Chem..

Applying textural features to the classification of HEp-2 cell patterns in IIF images

Enrico Macii, Elisa Ficarra, Andrea Bottino, 2012, Proceedings of the 21st International Conference on Pattern Recognition (ICPR2012).

One Decade of Development and Evolution of MicroRNA Target Prediction Algorithms

Elisa Ficarra, Paula Helena Reyes-Herrera, E. Ficarra, 2012, Genom. Proteom. Bioinform..

Techniques for enhancing computation of DNA curvature molecules

Luca Benini, Enrico Macii, Elisa Ficarra, 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

Low-cost pupillometry for human-computer interface.

Elisa Ficarra, Francesco Ponzio, A Goddi, 2018 .

Automated 3D immunofluorescence analysis of Dorsal Root Ganglia for the investigation of neural circuit alterations: a preliminary study

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2016, FedCSIS.

Fully-Automated Segmentation of Tumor Areas in Tissue Confocal Images - Comparison between a Custom Unsupervised and a Supervised SVM Approach

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2008, BIOSIGNALS.

Segmentation of nuclei in cancer tissue images: Contrasting active contours with morphology-based approach

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

Computer-Aided Evaluation of Protein Expression in Pathological Tissue Images

Luca Benini, Giovanni De Micheli, Enrico Macii, 2006, 19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06).

Dynamic Gap Selector: a Smith Waterman Sequence Alignment Algorithm with Affine Gap Model Optimisation Dynamic Gap Selector: a Smith Waterman Affine Gap Model Optimisation

Mariagrazia Graziano, Maurizio Zamboni, Andrea Acquaviva, 2022 .

A Preliminary Analysis on HEp-2 Pattern Classification: Evaluating Strategies Based on Support Vector Machines and Subclass Discriminant Analysis

Enrico Macii, Elisa Ficarra, Andrea Bottino, 2013, BIOSTEC.

Optimized Technique for Dna Structural Properties Discovering

Luca Benini, Enrico Macii, Elisa Ficarra, 2006, Int. J. Artif. Intell. Tools.

DEEPrior: a deep learning tool for the prioritization of gene fusions

Elisa Ficarra, Gianvito Urgese, Santa Di Cataldo, 2020, Bioinform..

Colorectal Cancer Classification using Deep Convolutional Networks - An Experimental Study

Enrico Macii, Elisa Ficarra, Francesco Ponzio, 2018, BIOIMAGING.

Optimization of Molecular Dynamics Simulations from a High Performance Computing Viewpoint

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2013 .

An effective grid infrastructure for efficiently support high throughput sequencing analysis

Enrico Macii, Andrea Acquaviva, Olivier Terzo, 2011 .

Mining textural knowledge in biological images: Applications, methods and trends

Elisa Ficarra, Santa Di Cataldo, E. Ficarra, 2016, Computational and structural biotechnology journal.

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Karen Eilbeck, Xavier Bofill-De Ros, Elisa Ficarra, 2020, Bioinform..

Repository ISTITUZIONALE

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2022 .

MicroRNA Target Prediction and Exploration through Candidate Binding Sites Generation

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2010, 2010 International Conference on Complex, Intelligent and Software Intensive Systems.

Dealing with Lack of Training Data for Convolutional Neural Networks: The Case of Digital Pathology

Elisa Ficarra, Gianvito Urgese, Francesco Ponzio, 2019, Electronics.

miRTOP: An open source community project for the development of a unified format file for miRNA data

Karen Eilbeck, Elisa Ficarra, Gianvito Urgese, 2018 .

Multi-omics Classification on Kidney Samples Exploiting Uncertainty-Aware Models

Giansalvo Cirrincione, Elisa Ficarra, Marta Lovino, 2020, ICIC.

Computational tools for the interactive exploration of proteomics data and automatic bio-networks reconstruction

Enrico Macii, Elisa Ficarra, E. Macii, 2015 .

Binding Free Energy Calculation via Molecular Dynamics Simulations for a miRNA: mRNA Interaction

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, BIOINFORMATICS.

miR-SEA: miRNA Seed Extension based Aligner Pipeline for NGS Expression Level Extraction

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2014, IWBBIO.

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Karen Eilbeck, Elisa Ficarra, Gianvito Urgese, 2018, bioRxiv.

Data Cleaning and Semantic Improvement in Biological Databases

Elena Baralis, Daniele Apiletti, Giulia Bruno, 2006, J. Integr. Bioinform..

GPU acceleration of simulation tool for lipid-bilayers

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Data Cleaning and Semantic Improvement in Biological Databases

Elena Baralis, Daniele Apiletti, Giulia Bruno, 2006, J. Integr. Bioinform..

Automated segmentation of tissue images for computerized IHC analysis

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2022 .

ANAlyte: A modular image analysis tool for ANA testing with indirect immunofluorescence

Elisa Ficarra, Andrea Bottino, Santa Di Cataldo, 2016, Comput. Methods Programs Biomed..

Integration of Literature with Heterogeneous Information for Genes Correlation Scoring

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2013, JETC.

A Novel Proof-of-concept Framework for the Exploitation of ConvNets on Whole Slide Images

Elisa Ficarra, Francesco Ponzio, Santa Di Cataldo, 2017, IIH-MSP.

Joint co-clustering: Co-clustering of genomic and clinical bioimaging data

Luca Benini, Giovanni De Micheli, Enrico Macii, 2008, Comput. Math. Appl..

Novel Method for MicroRNA Target Prediction Using a Genetic Algorithm

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2009 .

A Novel Gaussian Extrapolation Approach for 2-D Gel Electrophoresis Saturated Protein Spots.

Elisa Ficarra, Massimo Natale, Alfonso Caiazzo, 2016, Methods in molecular biology.

Characterization of Coarse Grain Molecular Dynamic Simulation Performance on Graphic Processing Unit Architectures

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2012, BIOINFORMATICS.

An Automated Tool for Scoring Biomedical Terms Correlation Based on Semantic Analysis

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2010, 2010 International Conference on Complex, Intelligent and Software Intensive Systems.

A novel framework for chimeric transcript detection based on accurate gene fusion model

Enrico Macii, Andrea Acquaviva, Giovanni Martinelli, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

geneEx - A Novel Tool to Assess Differential Expression from Gene and Exon Sequencing Data

Elisa Ficarra, Giulia Paciello, Orazio M. Scicolone, 2018, BIOINFORMATICS.

A Novel Pipeline for V(D)J Junction Identification using RNA-Seq Paired-end Reads

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2013, BIOINFORMATICS.

Going Deeper into Colorectal Cancer Histopathology

Enrico Macii, Elisa Ficarra, Francesco Ponzio, 2018, BIOSTEC.

A Deep Learning Approach to the Screening of Oncogenic Gene Fusions in Humans

Enrico Macii, Elisa Ficarra, Gianvito Urgese, 2019, International journal of molecular sciences.

Achieving the way for automated segmentation of nuclei in cancer tissue images through morphology-based approach: A quantitative evaluation

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2010, Comput. Medical Imaging Graph..

Towards Low Cost Virtual Biological Laboratories: Molecular Modelling Simulation on Commodity Hardware

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2012 .

An automated approach to the segmentation of HEp-2 cells for the indirect immunofluorescence ANA test

Elisa Ficarra, Andrea Bottino, Santa Di Cataldo, 2015, Comput. Medical Imaging Graph..

miREE: miRNA recognition elements ensemble

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, BMC Bioinformatics.

Gene-Markers Representation for Microarray Data Integration

Elena Baralis, Enrico Macii, Elisa Ficarra, 2007, 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering.

Subclass Discriminant Analysis of morphological and textural features for HEp-2 staining pattern classification

Elisa Ficarra, Andrea Bottino, Ihtesham Ul Islam, 2014, Pattern Recognit..

Automatic intrinsic DNA curvature computation from AFM images

Luca Benini, Enrico Macii, Elisa Ficarra, 2005, IEEE Transactions on Biomedical Engineering.

Automated DNA fragments recognition and sizing through AFM image processing

Luca Benini, Enrico Macii, Elisa Ficarra, 2005, IEEE Transactions on Information Technology in Biomedicine.

FuGePrior: A novel gene fusion prioritization algorithm based on accurate fusion structure analysis in cancer RNA-seq samples

Elisa Ficarra, Giulia Paciello, G. Paciello, 2017, BMC Bioinformatics.

BIBE 2004 TABLE OF CONTENTS

Yaw-Ling Lin, Enrico Macii, Elisa Ficarra, 2004 .

Extraction of Constraints from Biological Data

Elena Baralis, Daniele Apiletti, Giulia Bruno, 2009, Biomedical Data and Applications.

FunMod: A Cytoscape Plugin for Identifying Functional Modules in Undirected Protein–Protein Networks

Alfredo Benso, Stefano Di Carlo, Elisa Ficarra, 2014, Genom. Proteom. Bioinform..

Optimizing Splicing Junction Detection in Next Generation Sequencing Data on a Virtual-GRID Infrastructure

Andrea Acquaviva, Olivier Terzo, Lorenzo Mossucca, 2012 .

A New Latent Semantic Analysis based Methodology for Knowledge Extraction from Biomedical Literature and Biological Pathways Databases

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, BIOINFORMATICS.

A Novel Analysis Flow for Fused Transcripts Discovery from Paired-end RNA-Seq Data

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2012, BIOINFORMATICS.

Identifying Sub-Network Functional Modules in Protein Undirected Networks

Alfredo Benso, Stefano Di Carlo, Elisa Ficarra, 2014, BIOINFORMATICS.

BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis

Elisa Ficarra, Gianvito Urgese, Santa Di Cataldo, 2020, Bioinform..

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

Enrico Macii, Andrea Acquaviva, Giovanni Martinelli, 2012, Bioinform..

Exploration of Convolutional Neural Network models for source code classification

Andrea Acquaviva, Elisa Ficarra, Francesco Barchi, 2021, Eng. Appl. Artif. Intell..

A Multi-modal Brain Image Registration Framework for US-guided Neuronavigation Systems - Integrating MR and US for Minimally Invasive Neuroimaging

Enrico Macii, Elisa Ficarra, Francesco Ponzio, 2017, BIOIMAGING.

A Novel Gaussian Fitting Approach for 2D Gel Electrophoresis Saturated Protein Spots

Elisa Ficarra, Massimo Natale, Enrico M. Bucci, 2012, BIOINFORMATICS.

Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs. Supervised SVM Classification

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2008, BIOSTEC.

Improving Latent Semantic Analysis of Biomedical Literature Integrating UMLS Metathesaurus and Biomedical Pathways Databases

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, BIOSTEC.

Automated Segmentation of Cells With IHC Membrane Staining

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, IEEE Transactions on Biomedical Engineering.

Predicting the Oncogenic Potential of Gene Fusions Using Convolutional Neural Networks

Enrico Macii, Elisa Ficarra, Gianvito Urgese, 2018, CIBB.

Classification of HEp-2 Staining Patterns in ImmunoFluorescence Images - Comparison of Support Vector Machines and Subclass Discriminant Analysis Strategies

Enrico Macii, Elisa Ficarra, Andrea Bottino, 2013, BIOINFORMATICS.

Exploiting Gene Expression Profiles for the Automated Prediction of Connectivity between Brain Regions

Elisa Ficarra, Gianvito Urgese, Ilaria Roberti, 2019, International journal of molecular sciences.

A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Elisa Ficarra, Massimo Natale, Enrico M. Bucci, 2012, Genom. Proteom. Bioinform..

Gelsius: A Literature-Based Workflow for Determining Quantitative Associations between Genes and Biological Processes

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Unsupervised Multi-omic Data Fusion: The Neural Graph Learning Network

Giansalvo Cirrincione, Elisa Ficarra, Vincenzo Randazzo, 2020, ICIC.

Motion Artifact Correction in ASL images: An Improved Automated Procedure

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

Selection of Tumor Areas and Segmentation of Nuclear Membranes in Tissue Confocal Images: A Fully Automated Approach

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2007, 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007).

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

Chris Wiggins, Andrea Acquaviva, Elisa Ficarra, 2014, BMC Systems Biology.

A Novel Pipeline for Identification and Prioritization of Gene Fusions in Patient-derived Xenografts of Metastatic Colorectal Cancer

Andrea Acquaviva, Elisa Ficarra, Giulia Paciello, 2014, BIOINFORMATICS.

Unsupervised HEp-2 mitosis recognition in indirect immunofluorescence imaging

Enrico Macii, Elisa Ficarra, Santa Di Cataldo, 2015, 2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Next Generation Sequencing on Hybrid Grid Cloud Infrastructure

Enrico Macii, Andrea Acquaviva, Olivier Terzo, 2011, WCE 2011.

Optimizing Quality Inspection and Control in Powder Bed Metal Additive Manufacturing: Challenges and Research Directions

Enrico Macii, Alberto Macii, Sara Vinco, 2021, Proceedings of the IEEE.

A Bayesian approach to Expert Gate Incremental Learning

Enrico Macii, Elisa Ficarra, Francesco Ponzio, 2021, 2021 International Joint Conference on Neural Networks (IJCNN).

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity

Elisa Ficarra, Gianvito Urgese, Andrea Bertotti, 2021, BMC Bioinformatics.

FUNGI: FUsioN Gene Integration toolset

Elisa Ficarra, Gabriele Partel, Johanna Hynninen, 2021, Bioinform..

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

Elisa Ficarra, Francesco Ponzio, Santa Di Cataldo, 2021, ArXiv.

MicroRNA–mRNA interactions underlying colorectal cancer molecular subtypes

Elisa Ficarra, Laura Cantini, Claudio Isella, 2015, Nature Communications.

Selective analysis of cancer-cell intrinsic transcriptional traits defines novel clinically relevant subtypes of colorectal cancer

Elisa Ficarra, Alessandro Fiori, Luigi Marchionni, 2017, Nature Communications.

VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool

Enrico Macii, Andrea Acquaviva, Elisa Ficarra, 2015, PloS one.

Computational Methods for CLIP-seq Data Processing

Elisa Ficarra, E. Ficarra, Paula H Reyes-Herrera, 2014, Bioinformatics and biology insights.

A Robust Algorithm for Automated Analysis of DNA Molecules in AFM Images

Luca Benini, Enrico Macii, Elisa Ficarra, 2004 .

Multiscale modeling of cellular actin filaments: From atomistic molecular to coarse‐grained dynamics

Andrea Acquaviva, Elisa Ficarra, Umberto Morbiducci, 2012, Proteins.