| 2020 | RECOMB | PWAS: Proteome-Wide Association Study. | Nadav Brandes, Nathan Linial, Michal Linial |
| 2011 | RECOMB | Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. | Yosef Prat, Menachem Fromer, Michal Linial, Nathan Linial |
| 2008 | ECCB | Connect the dots: exposing hidden protein family connections from the entire sequence tree. | Yaniv Loewenstein, Michal Linial |
| 2008 | ISMB | Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. | Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial |
| 2007 | WABI | When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features. | Roy Varshavsky, Menachem Fromer, Amit Man, Michal Linial |
| 2006 | ISMB | Novel Unsupervised Feature Filtering of Biological Data. | Roy Varshavsky, Assaf Gottlieb, Michal Linial, David Horn |
| 2005 | ISMB | Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains. | Tali Sadka, Michal Linial |
| 2005 | ISPA | COMPACT: A Comparative Package for Clustering Assessment. | Roy Varshavsky, Michal Linial, David Horn |
| 2002 | ISMB | The metric space of proteins-comparative study of clustering algorithms. | Ori Sasson, Nathan Linial, Michal Linial |
| 2002 | WABI | Functional Consequences in Metabolic Pathways from Phylogenetic Profiles. | Yonatan Bilu, Michal Linial |
| 2001 | RECOMB | On the predictive power of sequence similarity in yeast. | Yonatan Bilu, Michal Linial |
| 2000 | RECOMB | Using Bayesian networks to analyze expression data. | Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er |
| 2000 | RECOMB | Probabilities for having a new fold on the basis of a map of all protein sequences. | Elon Portugaly, Michal Linial |
| 1998 | ISMB | A Map of the Protein Space: An Automatic Hierarchical Classification of all Protein Sequences. | Golan Yona, Nathan Linial, Naftali Tishby, Michal Linial |