| 2009 | PSB | Master Regulators Used As Breast Cancer Metastasis Classifier. | Wei Keat Lim, Eugenia Lyashenko, Andrea Califano |
| 2009 | PSB | Dissecting the Interface Between Signaling and Transcriptional Regulation in Human B Cells. | Kai Wang, Mariano J. Alvarez, Brygida C. Bisikirska, Rune Linding, Katia Basso, Riccardo Dalla Favera, Andrea Califano |
| 2007 | ISMB | Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. | Wei Keat Lim, Kai Wang, Cline Lefebvre, Andrea Califano |
| 2006 | RECOMB | Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-Independent Conservation Maps. | Nilanjana Banerjee, Andrea Califano |
| 2006 | RECOMB | A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Motifs in Human B Cells. | Cline Lefebvre, Wei Keat Lim, Katia Basso, Riccardo Dalla Favera, Andrea Califano |
| 2006 | RECOMB | Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes. | Kai Wang, Ilya Nemenman, Nilanjana Banerjee, Adam A. Margolin, Andrea Califano |
| 2000 | ISMB | Analysis of Gene Expression Microarrays for Phenotype Classification. | Andrea Califano, Gustavo Stolovitzky, Yuhai Tu |
| 2000 | RECOMB | Systematic and automated discovery of patterns in PROSITE families. | Reece Hart, Ajay K. Royyuru, Gustavo Stolovitzky, Andrea Califano |
| 1998 | ACCV | A High-Dimensional Indexing Scheme for Scalable Fingerprint-Based Identification. | Andrea Califano, Bob Germain, Scott Colville |
| 1993 | CVPR | Systematic design of indexing strategies for object recognition. | Andrea Califano, Rakesh Mohan |
| 1993 | CVPR | FLASH: a fast look-up algorithm for string homology. | Andrea Califano, Isidore Rigoutsos |
| 1993 | ISMB | FLASH: A Fast Look-Up Algorithm for String Homology. | Andrea Califano, Isidore Rigoutsos |
| 1991 | CVPR | Multidimensional indexing for recognizing visual shapes. | Andrea Califano, Rakesh Mohan |
| 1990 | AAAI | Generalized Shape Autocorrelation. | Andrea Califano, Rakesh Mohan |
| 1990 | ICCV | Active 3D object models. | Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Rakesh Mohan |
| 1990 | ICPR | Data and model driven foveation. | Andrea Califano, Rick Kjeldsen, Ruud M. Bolle |
| 1989 | CVPR | Visual recognition using concurrent and layered parameter networks. | Ruud M. Bolle, Andrea Califano, Rick Kjeldsen, Russell W. Taylor |
| 1989 | CVPR | Generalized neighborhoods: a new approach to complex parameter feature extraction. | Andrea Califano, Ruud M. Bolle, Russell W. Taylor |
| 1989 | IJCAI | A Homogeneous Framework for Visual Recognition. | Rick Kjeldsen, Ruud M. Bolle, Andrea Califano, Russell W. Taylor |
| 1988 | AAAI | Feature Recognition Using Correlated Information Contained in Multiple Neighborboods. | Andrea Califano |