PDZBase: a protein?Cprotein interaction database for PDZ-domains. - Thijs Beuming; Lucy Skrabanek; Masha Y. Niv; Piali Mukherjee; Harel Weinstein (Bioinform., 2005)

Modeling activated states of GPCRs: the rhodopsin template. - Masha Y. Niv; Lucy Skrabanek; Marta Filizola; Harel Weinstein (J. Comput. Aided Mol. Des., 2006)

Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation. - Shu Cheng; Masha Y. Niv (J. Chem. Inf. Model., 2010)

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping. - Avraham Ben-Shimon; Masha Y. Niv (PLoS Comput. Biol., 2011)

BitterDB: a database of bitter compounds. - Ayana Wiener; Marina Shudler; Anat Levit; Masha Y. Niv (Nucleic Acids Res., 2012)

Predicting GPCR Promiscuity Using Binding Site Features. - Anat Levit; Thijs Beuming; Goran Krilov; Woody Sherman; Masha Y. Niv (J. Chem. Inf. Model., 2014)

Biomimetic Sensors for the Senses: Towards Better Understanding of Taste and Odor Sensation. - Chunsheng Wu; Ya-Wen Du; Liquan Huang; Yaron Ben-Shoshan Galeczki; Ayana Dagan-Wiener; Michael Naim; Masha Y. Niv; Ping Wang (Sensors, 2017)

BitterDB: taste ligands and receptors database in 2019. - Ayana Dagan-Wiener; Antonella Di Pizio; Ido Nissim; Malkeet Singh Bahia; Nitzan Dubovski; Eitan Margulis; Masha Y. Niv (Nucleic Acids Res., 2019)

Validity of machine learning in biology and medicine increased through collaborations across fields of expertise. - Maria Littmann; Katharina Selig; Liel Cohen-Lavi; Yotam Frank; Peter Hönigschmid; Evans Kataka; Anja Mösch; Kun Qian 003; Avihai Ron; Sebastian Schmid 002; Adam Sorbie; Liran Szlak; et al. (Nat. Mach. Intell., 2020)

BitterMatch: recommendation systems for matching molecules with bitter taste receptors. - Eitan Margulis; Yuli Slavutsky; Tatjana Lang; Maik Behrens; Yuval Benjamini; Masha Y. Niv (J. Cheminformatics, 2022)