| 2015 | RECOMB | Efficient Alignment Free Sequence Comparison with Bounded Mismatches. | Srinivas Aluru, Alberto Apostolico, Sharma V. Thankachan |
| 2014 | DCC | Alignment Free Sequence Similarity with Bounded Hamming Distance. | Alberto Apostolico, Concettina Guerra, Cinzia Pizzi |
| 2014 | SPIRE | Algorithms for Jumbled Indexing, Jumbled Border and Jumbled Square on Run-Length Encoded Strings. | Amihood Amir, Alberto Apostolico, Tirza Hirst, Gad M. Landau, Noa Lewenstein, Liat Rozenberg |
| 2013 | CPM | Forty Years of Text Indexing. | Alberto Apostolico, Maxime Crochemore, Martin Farach-Colton, Zvi Galil, S. Muthukrishnan |
| 2011 | DCC | Image Compression by 2D Motif Basis. | Alessia Amelio, Alberto Apostolico, Simona E. Rombo |
| 2011 | DCC | Sequence Similarity by Gapped LZW. | Alberto Apostolico, Fabio Cunial |
| 2011 | ISAAC | Range LCP. | Amihood Amir, Alberto Apostolico, Gad M. Landau, Avivit Levy, Moshe Lewenstein, Ely Porat |
| 2010 | SPIRE | A PTAS for the Square Tiling Problem. | Amihood Amir, Alberto Apostolico, Gad M. Landau, Oren Sar Shalom |
| 2010 | SPIRE | Parameterized Searching with Mismatches for Run-Length Encoded Strings - (Extended Abstract). | Alberto Apostolico, Pter L. Erds, Alpr Jttner |
| 2009 | DCC | Probing the Randomness of Proteins by Their Subsequence Composition. | Alberto Apostolico, Fabio Cunial |
| 2008 | DCC | Table Compression by Record Intersections. | Alberto Apostolico, Fabio Cunial, Vineith Kaul |
| 2008 | ITW | Sequence distances based on exhaustive substring composition. | Alberto Apostolico, Olgert Denas |
| 2007 | COCOON | Optimal Offline Extraction of Irredundant Motif Bases. | Alberto Apostolico, Claudia Tagliacollo |
| 2007 | WABI | Incremental Discovery of Irredundant Motif Bases in Time | Alberto Apostolico, Claudia Tagliacollo |
| 2006 | DCC | Textual Compression by Collapsible Tries. | Alberto Apostolico, Yongwook Choi |
| 2006 | ITW | Compressing with Collapsible Tries. | Alberto Apostolico, Yongwook Choi |
| 2005 | COCOON | Monotony and Surprise. | Alberto Apostolico |
| 2005 | DCC | Of Lempel-Ziv-Welch Parses with Refillable Gaps. | Alberto Apostolico |
| 2005 | DCC | Off-Line Compression by Extensible Motifs. | Alberto Apostolico, Matteo Comin, Laxmi Parida |
| 2005 | ISMB | Conservative extraction of over-represented extensible motifs. | Alberto Apostolico, Matteo Comin, Laxmi Parida |
| 2004 | DCC | Motifs in Ziv-Lempel-Welch Clef. | Alberto Apostolico, Matteo Comin, Laxmi Parida |
| 2004 | DIS | Optimal Discovery of Subword Associations in Strings. | Alberto Apostolico, Cinzia Pizzi, Giorgio Satta |
| 2004 | WABI | Monotone Scoring of Patterns with Mismatches: (Extended Abstract). | Alberto Apostolico, Cinzia Pizzi |
| 2003 | DCC | Compression and the Wheel of Fortune. | Alberto Apostolico, Laxmi Parida |
| 2002 | RECOMB | Monotony of surprise and large-scale quest for unusual words. | Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi |
| 2001 | SPIRE | Of Maps Bigger than the Empire (Invited Paper). | Alberto Apostolico |
| 2000 | DCC | Notes on Learning Probabilistic Automata. | Alberto Apostolico |
| 2000 | DCC | Compression of Biological Sequences by Greedy Off-Line Textual Substitution. | Alberto Apostolico, Stefano Lonardi |
| 2000 | RECOMB | Optimal amnesic probabilistic automata or how to learn and classify proteins in linear time and space. | Alberto Apostolico, Gill Bejerano |
| 1999 | DCC | Linear Global Detectors of Redundant and Rare Substrings. | Alberto Apostolico, Mary Ellen Bock, Stefano Lonardi |
| 1998 | DCC | Some Theory and Practice of Greedy Off-Line Textual Substitution. | Alberto Apostolico, Stefano Lonardi |
| 1995 | ICDE | An International Masters in Software Engineering: Experience and Prospects. | Alberto Apostolico, Gianfranco Bilardi, Franco Bombi, Richard A. DeMillo |
| 1994 | STACS | Parallel Detection of all Palindromes in a String. | Alberto Apostolico, Dany Breslauer, Zvi Galil |
| 1992 | ICALP | Optimal Parallel Algorithms for Periods, Palindromes and Squares (Extended Abstract). | Alberto Apostolico, Dany Breslauer, Zvi Galil |