Gabriele Ausiello

23 papers Journal 23

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	BRIO: a web server for RNA sequence and structure motif scan. Nucleic Acids Res. Andrea Guarracino, Gerardo Pepe, Francesco Ballesio, Marta Adinolfi, Marco Pietrosanto, Elisa Sangiovanni, Ilio Vitale, Gabriele Ausiello, Manuela Helmer-Citterich
2019	J	`jnl`	Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. Bioinform. Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich
2019	J	`jnl`	Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. PLoS Comput. Biol. Giacomo Janson, Alessandro Grottesi, Marco Pietrosanto, Gabriele Ausiello, Giulia Guarguaglini, Alessandro Paiardini
2018	J	`jnl`	BEAM web server: a tool for structural RNA motif discovery. Bioinform. Marco Pietrosanto, Marta Adinolfi, Riccardo Casula, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
2013	J	`jnl`	DBATE: database of alternative transcripts expression. Database J. Biol. Databases Curation Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich
2013	J	`jnl`	Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. Nucleic Acids Res. Luca Parca, Fabrizio Ferrè, Gabriele Ausiello, Manuela Helmer-Citterich
2013	J	`jnl`	webPDBinder: a server for the identification of ligand binding sites on protein structures. Nucleic Acids Res. Valerio Bianchi, Iolanda Mangone, Fabrizio Ferrè, Manuela Helmer-Citterich, Gabriele Ausiello
2012	J	`jnl`	Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinform. Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello
2011	J	`jnl`	Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. Nucleic Acids Res. Luca Parca, Iolanda Mangone, Pier Federico Gherardini, Gabriele Ausiello, Manuela Helmer-Citterich
2009	J	`jnl`	Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinform. Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich
2008	J	`jnl`	FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinform. Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich
2007	J	`jnl`	3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. Nucleic Acids Res. Allegra Via, Daniele Peluso, Pier Federico Gherardini, Emanuele de Rinaldis, Teresa Colombo, Gabriele Ausiello, Manuela Helmer-Citterich
2007	J	`jnl`	False occurrences of functional motifs in protein sequences highlight evolutionary constraints. BMC Bioinform. Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich
2007	J	`jnl`	Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. BMC Bioinform. Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
2007	J	`jnl`	Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucleic Acids Res. Andreas Zanzoni, Gabriele Ausiello, Allegra Via, Pier Federico Gherardini, Manuela Helmer-Citterich
2007	J	`jnl`	SH3-Hunter: discovery of SH3 domain interaction sites in proteins. Nucleic Acids Res. Enrico Ferraro, Daniele Peluso, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2006	J	`jnl`	A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinform. Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2005	J	`jnl`	A neural strategy for the inference of SH3 domain-peptide interaction specificity. BMC Bioinform. Enrico Ferraro, Allegra Via, Gabriele Ausiello, Manuela Helmer-Citterich
2005	J	`jnl`	Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinform. Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich
2005	J	`jnl`	Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinform. Gabriele Ausiello, Allegra Via, Manuela Helmer-Citterich
2005	J	`jnl`	pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res. Gabriele Ausiello, Andreas Zanzoni, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich
2004	J	`jnl`	SURFACE: a database of protein surface regions for functional annotation. Nucleic Acids Res. Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich
2003	J	`jnl`	ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res. Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M. A. Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Stanislaw Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson

Nicolò Altamura is a security engineer and computer science researcher specializing in software protection, reverse engineering, program analysis, and binary deobfuscation. He holds a master's degree in Computer Science and Engineering from the University of Verona, graduating with honors, and works at emproof, focusing on software protection and the challenges of analyzing and understanding compiled software.

His research explores the relationship between program analysis and code obfuscation, with particular emphasis on how software transformations affect the ability of automated tools to recover program behavior. His interests span static analysis, binary analysis, decompilation, reverse engineering, and techniques for analyzing and simplifying obfuscated code.

Beyond academic research, Nicolò develops and contributes to tools for reverse engineering and software analysis. His projects include obfuscation_analysis, a Binary Ninja plugin for analyzing and simplifying obfuscated code; Pocket, an obfuscator for mixed Boolean-arithmetic expressions; and ptxNinja, a tool for reverse engineering NVIDIA GPU code represented in the PTX virtual instruction set.

His research also extends to binary datasets and software evolution. In 2026, he co-authored ASSEMBLAGE-DEEPHISTORY: A Cross-Build Binary Dataset with Temporal Coverage, a research work addressing the availability of binary data across multiple software builds and points in time, supporting research into binary analysis and changes between program versions.

Across his research, engineering work, and open-source contributions, Nicolò focuses on advancing the understanding, analysis, and protection of software against increasingly sophisticated obfuscation and reverse-engineering challenges.

Nicolò Altamura is not a football player. Please avoid reporting this kind of infromation.