Author

Marjan Faizi

Harvard UniversityORCID 0000-0002-7170-7762Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1 Genomics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Approach:deep learning· 1 Research Focus:drug response / drug discovery· 1 Organism:human· 1 Assay:long-read sequencing· 1 Assay:proteomics· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Ashwini JambhekariD· 1 shared Bryon DrowniD· 1 shared Cristina LoureiroiD· 1 shared Dan LüiD· 1 shared Galit LahaviD· 1 shared Helen SakharovaiD· 1 shared Helene BorrmanniD· 1 shared Jan ČervenýiD· 1 shared

Activity by Year

2018-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperBioinformatics

Ashwini JambhekarORCID

Mutual co-authors in cluster

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3 papers

Recent·Most cited

A generative language model decodes contextual constraints on codon choice for mRNA design

Marjan Faizi, Helen Sakharova, Helene Borrmann, Mohammad S. Parsa, Liana F. Lareau

This paper introduces Trias, a generative language model that designs mRNAs with high protein output by learning codon usage rules from natural sequences.

bioRxiv · May 13, 2025 · PreprintGenomics

MSModDetector: A Tool for Detecting Mass Shifts and Post-Translational Modifications in Individual Ion Mass Spectrometry Data

Marjan Faizi, Ryan T. Fellers, Dan Lü, Bryon Drown, Ashwini Jambhekar, Galit Lahav, Neil L. Kelleher, Jeremy Gunawardena

MSModDetector identifies PTM patterns in individual ion mass spectrometry data by detecting mass shifts and using linear programming to infer modifications.

Bioinformatics · May 24, 2024Peer-reviewedBioinformatics

A minimal model of protein allocation during phototrophic growth

Marjan Faizi, Tomáš Zavřel, Cristina Loureiro, Jan Červený, Ralf Steuer

The paper develops a minimal kinetic model of cyanobacterial phototrophic growth to study protein allocation trade-offs and derives growth laws similar to heterotrophic organisms with key differences due to light energy and carbon uptake.

Biosystems · Feb 21, 2018Peer-reviewedSystems Biology