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<!DOCTYPE html>
<html lang="en">
<!-- Head -->
<head> <!-- Metadata, OpenGraph and Schema.org -->
<!-- Standard metadata -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title>Giulio Ermanno Pibiri | Publications</title>
<meta name="author" content="Giulio Ermanno Pibiri" />
<meta name="description" content="Assistant Professor of Computer Science at Ca' Foscari University of Venice
" />
<meta name="keywords" content="jekyll, jekyll-theme, academic-website, portfolio-website" />
<!-- Bootstrap & MDB -->
<link href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.1/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY=" crossorigin="anonymous">
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</head>
<!-- Body -->
<body class="fixed-top-nav ">
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<header>
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<nav id="navbar" class="navbar navbar-light navbar-expand-sm fixed-top">
<div class="container">
<a class="navbar-brand title font-weight-lighter" href="https://jermp.github.io/"><span class="font-weight-bold">Giulio Ermanno</span> Pibiri</a>
<!-- Navbar Toggle -->
<button class="navbar-toggler collapsed ml-auto" type="button" data-toggle="collapse" data-target="#navbarNav" aria-controls="navbarNav" aria-expanded="false" aria-label="Toggle navigation">
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<!-- About -->
<li class="nav-item ">
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<!-- Other pages -->
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<a class="nav-link" href="/contact">Contact</a>
</li>
<li class="nav-item active">
<a class="nav-link" href="/publications">Publications<span class="sr-only">(current)</span></a>
</li>
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<a class="nav-link" href="/service">Service</a>
</li>
<li class="nav-item ">
<a class="nav-link" href="/software">Software</a>
</li>
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<a class="nav-link" href="/talks">Talks</a>
</li>
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<a class="nav-link" href="/teaching">Teaching</a>
</li>
<!-- Toogle theme mode -->
<div class="toggle-container">
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</header>
<!-- Content -->
<div class="container mt-5">
<!-- page.html -->
<div class="post">
<header class="post-header">
<h2 class="post-title">Publications</h2>
<p class="post-description"></p>
</header>
<article class="content">
<!-- _pages/publications.md -->
<div class="publications">
<h2 class="year">2025</h2>
<ol class="bibliography"><li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">S&P</abbr></div>
<!-- Entry bib key -->
<div id="calzavara2025verifiable" class="col-sm-8">
<!-- Title -->
<div class="title">Verifiable Boosted Tree Ensembles</div>
<!-- Author -->
<div class="author">Stefano Calzavara, Lorenzo Cazzaro, Claudio Lucchese, and <em>Giulio Ermanno Pibiri</em>
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In The 46th IEEE Symposium on Security and Privacy</em>, 2025
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/SP2025.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li></ol>
<h2 class="year">2024</h2>
<ol class="bibliography">
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">bioRXiv24</abbr></div>
<!-- Entry bib key -->
<div id="groot2024openclosed" class="col-sm-8">
<!-- Title -->
<div class="title">The open-closed mod-minimizer algorithm</div>
<!-- Author -->
<div class="author">Ragnar Groot Koerkamp, Daniel Liu, and <em>Giulio Ermanno Pibiri</em>
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>bioRXiv</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/2024.11.02.621600v1.full.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">JCB</abbr></div>
<!-- Entry bib key -->
<div id="Campanelli2024" class="col-sm-8">
<!-- Title -->
<div class="title">Where the patterns are: repetition-aware compression for colored de Bruijn graphs</div>
<!-- Author -->
<div class="author">Alessio Campanelli,
<em>Giulio Ermanno Pibiri</em>, Jason Fan, and Rob Patro
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>Journal of Computational Biology</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/JCB2024.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">WABI</abbr></div>
<!-- Entry bib key -->
<div id="groot2024mod" class="col-sm-8">
<!-- Title -->
<div class="title">The mod-minimizer: a simple and efficient sampling algorithm for long k-mers</div>
<!-- Author -->
<div class="author">Ragnar Groot Koerkamp, and <em>Giulio Ermanno Pibiri</em>
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In 24-th International Workshop on Algorithms in Bioinformatics</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/WABI2024.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">ESA</abbr></div>
<!-- Entry bib key -->
<div id="hermann2024phobic" class="col-sm-8">
<!-- Title -->
<div class="title">PHOBIC: Perfect Hashing with Optimized Bucket Sizes and Interleaved Coding</div>
<!-- Author -->
<div class="author">Stefan Hermann, Hans-Peter Lehmann,
<em>Giulio Ermanno Pibiri</em>, Peter Sanders, and Stefan Walzer
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In 32nd Annual European Symposium on Algorithms</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/ESA2024-full-version.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">BIOINF</abbr></div>
<!-- Entry bib key -->
<div id="karami2024designing" class="col-sm-8">
<!-- Title -->
<div class="title">Designing efficient randstrobes for sequence similarity analyses</div>
<!-- Author -->
<div class="author">Moein Karami, Aryan Soltani Mohammadi, Marcel Martin, Barış Ekim, Wei Shen, Lidong Guo, Mengyang Xu,
<em>Giulio Ermanno Pibiri</em>, Rob Patro, and Kristoffer Sahlin
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>Bioinformatics</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/BIOINF2024.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">AMB</abbr></div>
<!-- Entry bib key -->
<div id="fulgor2024algomb" class="col-sm-8">
<!-- Title -->
<div class="title">Fulgor: A fast and compact k-mer index for large-scale matching and color queries</div>
<!-- Author -->
<div class="author">Jason Fan, Noor Pratap Singh, Jamshed Khan,
<em>Giulio Ermanno Pibiri</em>, and Rob Patro
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>Algorithms for Molecular Biology</em>, 2024
</div>
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<div class="links">
<a href="/assets/pdf/papers/ALGOMB2024.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">RECOMB</abbr></div>
<!-- Entry bib key -->
<div id="Pibiri2024meta" class="col-sm-8">
<!-- Title -->
<div class="title">Meta-colored compacted de Bruijn graphs</div>
<!-- Author -->
<div class="author">
<em>Giulio Ermanno Pibiri</em>, Jason Fan, and Rob Patro
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In 28-th International Conference on Research in Computational Molecular Biology</em>, 2024
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/RECOMB2024.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
</ol>
<h2 class="year">2023</h2>
<ol class="bibliography">
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">CCS</abbr></div>
<!-- Entry bib key -->
<div id="calzavara2023verifiable" class="col-sm-8">
<!-- Title -->
<div class="title">Verifiable Learning for Robust Tree Ensembles</div>
<!-- Author -->
<div class="author">Stefano Calzavara, Lorenzo Cazzaro,
<em>Giulio Ermanno Pibiri</em>, and Nicola Prezza
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In 2023 ACM SIGSAC Conference on Computer and Communications Security</em>, 2023
</div>
<!-- Links/Buttons -->
<div class="links">
<a href="/assets/pdf/papers/CCS2023.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">TKDE</abbr></div>
<!-- Entry bib key -->
<div id="Pibiri2023TKDE" class="col-sm-8">
<!-- Title -->
<div class="title">Parallel and External-Memory Construction of Minimal Perfect Hash
Functions with PTHash</div>
<!-- Author -->
<div class="author">
<em>Giulio Ermanno Pibiri</em>, and Roberto Trani
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>IEEE Transactions on Knowledge and Data Engineering</em>, 2023
</div>
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<a href="/assets/pdf/papers/TKDE2023.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">AMB</abbr></div>
<!-- Entry bib key -->
<div id="pibiri2023algomb" class="col-sm-8">
<!-- Title -->
<div class="title">On Weighted k-mer Dictionaries</div>
<!-- Author -->
<div class="author">
<em>Giulio Ermanno Pibiri</em>
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>Algorithms for Molecular Biology</em>, 2023
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<a href="/assets/pdf/papers/ALGOMB2023.pdf" class="btn btn-sm z-depth-0" role="button">.pdf</a>
</div>
</div>
</div>
</li>
<li>
<!-- _layouts/bib.html -->
<div class="row">
<div class="col-sm-2 abbr"><abbr class="badge">WABI</abbr></div>
<!-- Entry bib key -->
<div id="pibiri2023wabi" class="col-sm-8">
<!-- Title -->
<div class="title">Fulgor: A fast and compact k-mer index for large-scale matching and color queries</div>
<!-- Author -->
<div class="author">Jason Fan, Noor Pratap Singh, Jamshed Khan,
<em>Giulio Ermanno Pibiri</em>, and Rob Patro
</div>
<!-- Journal/Book title and date -->
<!----><div class="periodical">
<em>In 23-rd International Workshop on Algorithms in Bioinformatics</em>, 2023
</div>
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<div class="col-sm-2 abbr"><abbr class="badge">RECOMB</abbr></div>
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<div class="title">Spectrum preserving tilings enable sparse and modular reference indexing</div>
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<div class="author">Jason Fan, Jamshed Khan,
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<em>In 27-th International Conference on Research in Computational Molecular Biology</em>, 2023
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<div class="col-sm-2 abbr"><abbr class="badge">ISMB</abbr></div>
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<div class="title">Locality-Preserving Minimal Perfect Hashing of k-mers</div>
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<em>Giulio Ermanno Pibiri</em>, Yoshihiro Shibuya, and Antoine Limasset
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<em>Bioinformatics</em>, 2023
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<div class="col-sm-2 abbr"><abbr class="badge">GBIO</abbr></div>
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<div class="title">Matchtigs: minimum plain text representation of k-mer sets</div>
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<div class="author">Sebastian Schmidt, Shahbaz Khan, Jarno Alanko,
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<em>Genome Biology</em>, 2023
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<h2 class="year">2022</h2>
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<div class="title">On Weighted k-mer Dictionaries</div>
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<em>Giulio Ermanno Pibiri</em>
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<em>In 22-nd International Workshop on Algorithms in Bioinformatics</em>, 2022
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<div class="title">Sparse and Skew Hashing of k-mers</div>
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<em>Bioinformatics</em>, 2022
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<h2 class="year">2021</h2>
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<div class="title">Techniques for Inverted Index Compression</div>
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<em>Giulio Ermanno Pibiri</em>, and Rossano Venturini
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<em>ACM Computing Surveys</em>, 2021
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<div class="title">Rank/select queries over mutable bitmaps</div>
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<em>Information Systems</em>, 2021
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<em>Software: Practice and Experience</em>, 2021
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<div class="title">Compressed Indexes for Fast Search of Semantic Data</div>
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<em>IEEE Transactions on Knowledge and Data Engineering</em>, 2021
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<em>In 31st Data Compression Conference</em>, 2021
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<div class="title">Compressed Indexes for Fast Search of Semantic Data (Extended Abstract)</div>
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<em>In 37th IEEE International Conference on Data Engineering</em>, 2021
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<div class="title">PTHash: Revisiting FCH Minimal Perfect Hashing</div>
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<em>In 44th International ACM SIGIR Conference on Research
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<div class="title">TSXor: A Simple Time Series Compression Algorithm</div>
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<div class="author">Andrea Bruno, Franco Maria Nardini,
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<em>In 28th International Symposium on String Processing and Information Retrieval</em>, 2021
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<h2 class="year">2020</h2>
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<div class="title">On Optimally Partitioning Variable-Byte Codes</div>
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<em>IEEE Transactions on Knowledge and Data Engineering</em>, 2020
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<em>In 43rd International ACM SIGIR conference on
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<div class="title">Succinct Dynamic Ordered Sets with Random Access</div>
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<em>arXiv</em>, 2020
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<h2 class="year">2019</h2>
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<div class="title">On Implementing the Binary Interpolative Coding Algorithm</div>
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<em>Tech. Report</em>, 2019
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<div class="title">Handling Massive N-Gram Datasets Efficiently</div>
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<em>Giulio Ermanno Pibiri</em>, and Rossano Venturini
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