Carnegie Mellon University

hosein.jpg Hosein Mohimani

Associate Professor, Ray and Stephanie Lane Computational Biology Department

Ray and Stephanie Lane Computational Biology Department, SCS
Carnegie Mellon University
5000 Forbes Avenue
Pittsburgh, PA 15213
Gates Hillman Center Room 7717


Administrative Assistant: Ally Ricarte


Dr. Mohimani’s research focuses on the development of computational metabolomics and metagenomics methods for antibiotic discovery and microbiome analysis. Microbes in human body interact with their human host and with each other through small molecules (e.g. antibiotics and signaling molecules). Mining the human metagenome has shown that human microbiome has a great potential for production of small molecules. Most of such molecules remain unknown, despite the fact that they can play a crucial role on human health. Mohimani’s lab is specifically interested in analyzing large scale mass spectrometry and metagenomics data using tools from machine learning, genome mining, signal processing, graph theory, and statistics to discover novel genetically synthesized small molecules in the human microbiome.

Lab Members

 Abhinav Adduri

Ph.D. Student

 Mohsen Ferdosi

Ph.D. Student (joint with Kingsford Lab)

 Mustafa Guler

Ph.D. Student

 Donghui Yan

Ph.D. Student

Muqing Zhou

Research Associate

Highlighted Publications

Mongia, M., Guler, M. & Mohimani, H. An interpretable machine learning approach to identify mechanism of action of antibioticsSci Rep 12, 10342 (2022).

Justin J. J. van der Hooft, Hosein Mohimani, Anelize Bauermeister, Pieter C. Dorrestein, Katherine R. Duncan, Marnix Medema, Linking genomics and metabolomics to chart specialized metabolic diversity, Chem. Soc. Rev., 2020, 49. 3297

Arash Davoudi, Sean Chang, Hyun Gon Yoo, Anubhav Bajewa, Mihir Mongia, Hosein Mohimani*, ForestDSH: A Universal Hash Design for Discrete Probability Distributions., accepted, Data Mining and Knowledge Discovery, 2020.

Louis-Felix Nothias et. al. including Hosein Mohimani, Feature-based Molecular Networking in the GNPS Analysis Environment, accepted, Nature Methods, 2020.

Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark Fisher, Fernando Vargas, Larry Smarr, Pieter Dorrestein, Joshua Mylne, Pavel Pevzner, De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments, Cell Systems, 2020, 10 (1), 99-108.e5.

Liu Cao, Hosein Mohimani*, MetaMiner: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides from Microbial Communities, Cell Systems, 2019, 9 (6) 600-608.e4.

Google Scholar



Software programs for Dereplicator+ are available at . It's available as a web service at


Software programs for Dereplicator are available at . It's available as a web service at


Software programs for MetaMiner are available at . It's available as a web service at .