A functional hierarchical organization of the protein sequence space. - Noam Kaplan; Moriah Friedlich; Menachem Fromer; Michal Linial (BMC Bioinform., 2004)

ProtoNet 4.0: A hierarchical classification of one million protein sequences. - Noam Kaplan; Ori Sasson; Uri Inbar; Moriah Friedlich; Menachem Fromer; Hillel Fleischer; Elon Portugaly; Nathan Linial; Michal Linial (Nucleic Acids Res., 2005)

When Less Is More: Improving Classification of Protein Families with a Minimal Set of Global Features. - Roy Varshavsky; Menachem Fromer; Amit Man; Michal Linial (WABI, 2007)

Dead-end elimination for multistate protein design. - Chen Yanover; Menachem Fromer; Julia M. Shifman (J. Comput. Chem., 2007)

A computational framework to empower probabilistic protein design. - Menachem Fromer; Chen Yanover (ISMB, 2008)

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. - Yaniv Loewenstein; Elon Portugaly; Menachem Fromer; Michal Linial (ISMB, 2008)

An LP View of the M-best MAP problem. - Menachem Fromer; Amir Globerson (NIPS, 2009)

Tradeoff Between Stability and Multispecificity in the Design of Promiscuous Proteins. - Menachem Fromer; Julia M. Shifman (PLoS Comput. Biol., 2009)

Exposing the co-adaptive potential of protein-protein interfaces through computational sequence design. - Menachem Fromer; Michal Linial (Bioinform., 2010)

SPRINT: side-chain prediction inference toolbox for multistate protein design. - Menachem Fromer; Chen Yanover; Amir Harel; Ori Shachar; Yair Weiss; Michal Linial (Bioinform., 2010)

PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. - Nadav Rappoport; Menachem Fromer; Regev Schweiger; Michal Linial (Nucleic Acids Res., 2010)

A probabilistic approach to the design of structural selectivity of proteins (נוספו שער, תקציר ותכן בעברית: גישה הסתברותית לתכנון של סלקטיביות מבנית של חלבונים.). - Menachem Fromer (2010)

Geometric Interpretation of Gene Expression by Sparse Reconstruction of Transcript Profiles. - Yosef Prat; Menachem Fromer; Michal Linial; Nathan Linial (RECOMB, 2011)

Recovering key biological constituents through sparse representation of gene expression. - Yosef Prat; Menachem Fromer; Nathan Linial; Michal Linial (Bioinform., 2011)

zCall: a rare variant caller for array-based genotyping: Genetics and population analysis. - Jacqueline I. Goldstein; Andrew Crenshaw; Jason P. Carey; George B. Grant; Jared Maguire; Menachem Fromer; Colm O'Dushlaine; Jennifer L. Moran; Kimberly Chambert; Christine Stevens; Pamela Sklar; Christina M. Hultman; et al. (Bioinform., 2012)

Transforming Psychiatry into Data-Driven Medicine with Digital Measurement Tools. - Honor Hsin; Menachem Fromer; Bret Peterson; Collin Walter; Mathias S. Fleck; Andrew Campbell; Paul Varghese; Robert M. Califf (npj Digit. Medicine, 2018)