| 2010 | EDBT | Anchoring millions of distinct reads on the human genome within seconds. | Tien Huynh, Michail Vlachos, Isidore Rigoutsos |
| 2004 | CIKM | Of parts and relationships: an unending quest. | Isidore Rigoutsos |
| 2001 | CPM | An Output-Sensitive Flexible Pattern Discovery Algorithm. | Laxmi Parida, Isidore Rigoutsos, Daniel E. Platt |
| 2000 | KDD | Knowledge discovery in biological domains (tutorial AM-3). | Aris Floratos, Igor Jurisica, Isidore Rigoutsos |
| 2000 | SODA | Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm. | Laxmi Parida, Isidore Rigoutsos, Aris Floratos, Daniel E. Platt, Yuan Gao |
| 1999 | ISMB | Building Dictionaries of 1D and 3D Motifs by Mining the Unaligned 1D Sequences of 17 Archaeal and Bacterial Genomes. | Isidore Rigoutsos, Yuan Gao, Aris Floratos, Laxmi Parida |
| 1999 | RECOMB | Sequence homology detection through large scale pattern discovery. | Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky, Yuan Gao |
| 1998 | CVPR | Well-Behaved, Tunable 3D-Affine Invariants. | Isidore Rigoutsos |
| 1998 | ICCV | Two-Dimensional Affine Invariants that Distribute Uniformly and can be Tuned to any Convex Feature Domain. | Isidore Rigoutsos |
| 1998 | RECOMB | Motif discovery without alignment or enumeration (extended abstract). | Isidore Rigoutsos, Aris Floratos |
| 1997 | KDD | Automated Discovery of Active Motifs in Three Dimensional Molecules. | Xiong Wang, Jason Tsong-Li Wang, Dennis E. Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos, Kaizhong Zhang |
| 1996 | SEKE | The Impact of Hashing Function Choice on the Load Balancing in Very Large Dartasets. | Isidore Rigoutsos, Alex Delis |
| 1993 | CVPR | FLASH: a fast look-up algorithm for string homology. | Andrea Califano, Isidore Rigoutsos |
| 1993 | CVPR | Distributed Bayesian object recognition. | Isidore Rigoutsos, Robert A. Hummel |
| 1993 | ISMB | FLASH: A Fast Look-Up Algorithm for String Homology. | Andrea Califano, Isidore Rigoutsos |
| 1986 | AAAI | Determining the 3-D Motion of a Rigid Surface Patch Without Correspondence under Perspective Projection. | Yiannis Aloimonos, Isidore Rigoutsos |