Publications

Journal Papers

Mongia, M., Guler, M. & Mohimani, H. An interpretable machine learning approach to identify mechanism of action of antibiotics. Sci 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 et.al., 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.

Liu Cao, Egor Shcherbin, Hosein Mohimani*, Metabolome-metagenome-wide association network reveals microbial natural products and microbial biotransformations from the human microbiota, mSystems 2019, 4 (4) e00387-19; DOI: 10.1128/mSystems.00387-19.

Dima Meleshko, Hosein Mohimani , Vittorio Tracanna, Iman Hajirasouliha, Marnix Medema, Anton Korobeynikov, Pavel Pevzner, BiosyntheticSPAdes : reconstructing biosynthetic gene clusters from assembly graphs, Genome Research, 2019, doi:10.1101/gr.243477.118.

Hosein Mohimani , Alexey Gurevich, Alexander Shlemov, Alla Mikheenko, Anton Korobeynikov, Liu Cao, Egor Shcherbin, Louis-Felix Nothias, Pieter Dorrestein, Pavel Pevzner, Dereplication of Microbial Natural Products Through Database Search of Mass Spectra, Nature Communications, 2018, 9, 4035.

Alexey Gurevich, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Hosein Mohimani, Pavel Pevzner, Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra, Nature Microbiology, 2018, 3, 319–327.

Daniel McDonald et. al. including Hosein Mohimani, American Gut: an Open Platform for Citizen-Science Microbiome Research, mSystems, 2018, 10.1128/mSystems.00031-18.

Anna Edlund, Neha Garg, Hosein Mohimani, Alexey Gurevich, Xuesong He, Wenyuan Shi, Pieter C. Dorrestein, Jeffrey S. McLean, Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules , mSystems, 2017, 2, e00058-17.

Neha Garg, Yi Zeng, Anna Edlund, Alexey Melnik, Laura Sanchez, Hosein Mohimani, Alexey Gurevich, Vivian Miao, Stefan Schiffler, Yan Wei Lim, Tal Luzzatto-Knaan, Shengxin Kai, Forest Rohwer, Pavel Pevzner, Robert Cichewicz, Theodore Alexandrov, Pieter Dorrestein, The spatial molecular structure of the microbial community of Peltigera Lichen, mSystems, 2016, 1, e00139-16.

Hosein Mohimani, Alexey Gurevich, Alla Mikheenko, Neha Garg, Louis-Felix Nothias, Akihiro Ninomiya, Kentaro Takada, Pieter C. Dorrestein, Pavel A. Pevzner. Dereplication of Peptidic Natural Products Through Database Search of Mass Spectra, Nature Chemical Biology, 2017, 13, 30-37.

Ming Wang et. al. including Hosein Mohimani. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking, Nature Biotechnology, 2016, 34, 828-837.

Hosein Mohimani and Pavel A. Pevzner. Dereplication, Sequencing and Identification of Peptidic Natural Products: from Genome Mining to Peptidogenomics to Spectal Networks, Nat Prod Rep, 2016, 33, 73-86.

Hosein Mohimani, Wei-Ting Liu, Roland Kersten, Bradley Moore, Pieter C. Dorrestein, and Pavel A. Pevzner. NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery, Journal of Natural Products, 2014, 77, 1902-1909.

Hosein Mohimani, Roland D. Kersten, Wei-Ting Liu, Mingxun Wan, Samuel O. Purvine, Si Wu, Heather M. Brewer, Ljiljana Pasa-Tolic, Nuno Bandeira, Bradley S. Moore, Pavel A. Pevzner, and Pieter C. Dorrestein. Automated Genome Mining of Ribosomal Peptide Natural Products, ACS Chemical Biology, 2014, 9, 1545-1551.

Hosein Mohimani, Sangtae Kim, and Pavel A. Pevzner. A new approach to evaluating statistical significance of spectral identifications, Journal of Proteome Research, 2013, 12, 1560-1568.

Hosein Mohimani, Wei-Ting Liu, Joshua S. Mylne, Aaron G. Poth, Michelle Colgrave, Michael Selsted, Pieter C. Dorrestein, and Pavel A. Pevzner. Cycloquest: Identification of cyclopeptides via database search of their mass spectra against genome databases, Journal of Proteome Research, 2011, 10, 4505-4512.

Hosein Mohimani, Yu-Liang Yang, Wei-Ting Liu, Pei-Wen Hsieh, Pieter C. Dorrestein, and Pavel Pevzner. Sequencing Cyclic Peptides by Multistage Mass Spectrometry, Journal of Proteomics, 2011, 11, 3642-50.

Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudenico, William Fenical, Pieter C. Dorrestein, and Pavel Pevzner. Multiplex De Novo Sequencing of Peptide Antibiotics, Journal of Computational Biology, 2011, 18, 1371-1381.

Emily Mevers, Wei-Ting Liu, Niclas Engene, Hosein Mohimani, Tara Byrum, Pavel A. Pevzner, Pieter C. Dorrestein, Carmenza Spadafora, and William H. Gerwick. Cytotoxic veraguamides, alkynyl bromide-containing cyclic depsipeptides from the marine cyanobacterium cf. Oscillatoria margaritifera, Journal of Natural Products, 2011, 74, 928-936.

Massoud Babaie-Zadeh, Christian Jutten, Hosein Mohimani, On the error of estimating the sparsest solution of underdetermined linear systems, IEEE Trans. On Information Theory, 2011, 57, 7840-7855.

Hosein Mohimani, Massoud Babaie-Zadeh and Christian Jutten. A fast approach for over-complete sparse decomposition based on smoothed L0 norm, IEEE Trans. On Signal Processing, 2009, volume 57, 289-301.

Hosein Mohimani, Farid Ashtiani, Adel Javanmard, Mazyiar Hamdi. Mobility Modeling, Spatial Traffic Distribution, and Probability of Connectivity for Sparse and Dense Vehicular Ad-Hoc Networks, IEEE Trans. On Vehicular Technology, 2009, 58, 1998-2007.

Hosein Mohimani, Massoud Babaie-Zadeh, Irina Gorodnitsky, Christian Jutten. SL0 : a convergence analysis, arXiv:1001.5073

Farid Movahedi Naini, Hosein Mohimani, Massoud Babaie-Zadeh and Christian Jutten. Estimating the mixing matrix in Sparse Component Analysis (SCA) based on partial k-dimensional subspace clustering, Neurocomputing, 2008, vol. 71, 10-12, 2330-2343.

Conference Papers

Mohsen Ferdosi, Arash Davoudi, Hosein Mohimani*, Measuring Mutual Information Between All Pairs of Variables in Subquadratic Complexity, AISTAT2020, Palermo, Sicily, Italy.

Mihir Mongia, Benjamin Soudry, Arash Davoudi, Hosein Mohimani*, Efficient Database Search via Tensor Distribution Bucketing, PAKDD2020,
Singapore.

Liu Cao, Egor Shcherbin, Hosein Mohimani*, Metabolome-metagenome-wide association network reveals microbial natural products and microbial biotransformations from the human microbiota, ASMS2019, Atlanta, USA (Oral session).

Hosein Mohimani, Modification-tolerant database search reveals surprising diversity of peptidic natural products, RECOMB2018, Paris, France (Highlight talk).

Hosein Mohimani, Pavel Pevzner. Dereplication, Sequencing and Identification of Peptidic Natural Products: from Genome Mining to Peptidogenomics to Spectal Networks, 3rd International Conference on Circular Proteins (ICCP2015), Moreton Island, Australia, November 1-4 (Invited talk).

Hosein Mohimani, Sangtae Kim, Pavel Pevzner. MS-DPR: An algorithm for computing statistical significance of spectral identifications of non-linear peptides, Workshop on Algorithms in Bioinformatics (WABI2012), Ljubljana, Slovenia, Lecture Notes in Computer Science, Volume 7534, 2012, pp 301-313.

Hosein Mohimani, Wei-Ting Liu, Yu-Liang Yang, Susana P. Gaudenico, William Fenical, Pieter C. Dorrestein, and Pavel Pevzner. Multiplex De Novo Sequencing of Peptide Antibiotics, Vancouver, Research in Computational Molecular Biology (RECOMB2011), Lecture Notes in Computer Science, 2011, Volume 6577, 267-281.

Hosein Mohimani, Wei-Ting Liu, Joshua S. Mylne, Aaron G. Poth, Michelle Colgrave, Michael Selsted, Pieter C. Dorrestein, and Pavel A. Pevzner. Cycloquest: Identification of cyclopeptides via database search of their mass spectra against genome databases, American Society of Pharmacognosy 2011 (ASP2011), San Diego (invited talk).

Jayadev Acharya, Hirakendu Das, Hosein Mohimani, Alon Orlitsky, Shengjun Pan. Exact calculation of pattern probabilities, IEEE International Symposium on Information Theory (ISIT2010), Austin, Texas, June 13 ’18, page 1498-1502.

Massoud Babaie-Zadeh, Hosein Mohimani, Christian Jutten. An upper bound on the estimation error of the sparsest solution of underdetermined linear systems, in Proceedings of SPARS2009, Saint-Malo, France, 2009.

Hosein Mohimani, Massoud Babaie-Zadeh and Christian Jutten. Fast Sparse Representation based on Smoothed L0 norm, 7th International Conference on Independent Component Analysis and Signal Separation (ICA 2007), 9th – 12th September, London, UK, LNCS 4666, pp. 438-445

Hadi Zayyani, Massoud Babaie-Zadeh, Hosein Mohimani, Christian Jutten. Sparse Component Analysis in Presence of Noise Using an Iterative EM-MAP Algorithm, 7th International Conference on Independent Component Analysis and Signal Separation (ICA 2007), 9th – 12th September, London, UK, LNCS 4666, pp. 438-445.

Elham Azizi, Hosein Mohimani, Massoud Babaie-Zadeh. Adaptive Sparse Source Separation With Application To Speech Signals, 2007 IEEE International Conference on Signal Processing and Communications (ICSPC 2007), 24th – 27th November, Dubai, UAE.

Farid Movahedi Naini, Hosein Mohimani, Massoud Babaie-Zadeh, Christian Jutten. Estimating the mixing matrix in Sparse Component Analysis (SCA) based on multidimensional subspace clustering, 14th IEEE International Conference On Telecommunications and 8th IEEE Malaysia International Conference on Communications (ICT-MICC 2007), 14th – 17th May, Penang, Malaysia.

Patents

Eric Stava, Jens Gundlach, Jeffrey Mandell, Kevin Gunderson, Ian Derrington, Hosein Mohimani. Compositions and methods for polynucleotide sequencing, Issued by Illumina Inc, June 4th, 2015.