| 2007 | RECOMB | Framework for Identifying Common Aberrations in DNA Copy Number Data. | Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Brresen-Dale, Zohar Yakhini |
| 2005 | RECOMB | Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. | Doron Lipson, Yonatan Aumann, Amir Ben-Dor, Nathan Linial, Zohar Yakhini |
| 2004 | PSB | Multiplexing Schemes for Generic SNP Genotyping Assays. | Roded Sharan, Amir Ben-Dor, Zohar Yakhini |
| 2004 | WABI | Joint Analysis of DNA Copy Numbers and Gene Expression Levels. | Doron Lipson, Amir Ben-Dor, Elinor Dehan, Zohar Yakhini |
| 2003 | PSB | Methods for Analysis and Visualization of SNP Genotype Data for Complex Diseases. | Anya Tsalenko, Amir Ben-Dor, Nancy Cox, Zohar Yakhini |
| 2003 | RECOMB | Towards optimally multiplexed applications of universal DNA tag systems. | Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini |
| 2002 | RECOMB | Discovering local structure in gene expression data: the order-preserving submatrix problem. | Amir Ben-Dor, Benny Chor, Richard M. Karp, Zohar Yakhini |
| 2002 | RECOMB | The restriction scaffold problem. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir |
| 2001 | RECOMB | Class discovery in gene expression data. | Amir Ben-Dor, Nir Friedman, Zohar Yakhini |
| 2000 | RECOMB | Tissue classification with gene expression profiles. | Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michl Schummer, Zohar Yakhini |
| 2000 | RECOMB | Universal DNA tag systems: a combinatorial design scheme. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Zohar Yakhini |
| 1999 | CPM | On the Complexity of Positional Sequencing by Hybridization. | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan |
| 1999 | RECOMB | Clustering gene expression patterns. | Amir Ben-Dor, Zohar Yakhini |
| 1998 | RECOMB | From four-taxon trees to phylogenies (preliminary report): the case of mammalian evolution. | Amir Ben-Dor, Benny Chor, Dan Graur, Ron Ophir, Dan Pelleg |
| 1997 | CPM | Banishing Bias from Consensus Sequences. | Amir Ben-Dor, Giuseppe Lancia, Jennifer Perone, R. Ravi |
| 1997 | RECOMB | On constructing radiation hybrid maps (extended abstract). | Amir Ben-Dor, Benny Chor |
| 1994 | PODC | Potential Function Analysis of Greedy Hot-Potato Routing. | Amir Ben-Dor, Shai Halevi, Assaf Schuster |