Ali Madani
Co-founder and CEO of Profluent; led the ProGen protein language model work at Salesforce AI Research
Ali Madani is a co-founder and the CEO of Profluent, a company that uses AI to design proteins, including gene editors. Profluent's team page describes Madani as a machine learning researcher who, before Profluent, was the architect of the ProGen project at Salesforce AI Research, which showed that language models can generate functional protein sequences.13
Research
At Salesforce AI Research, Madani was the architect of ProGen, which posed protein engineering as an unsupervised sequence generation problem. The 2020 preprint, co-authored with Richard Socher and others, trained a 1.2B-parameter model on about 280 million protein sequences with tags such as molecular function and cellular component.21
The follow-up paper, published in Nature Biotechnology in January 2023 with Madani as first author and affiliations at Salesforce Research and Profluent Bio, reported that large language models generate functional protein sequences across diverse families.3
Profluent
As Profluent's co-founder and CEO, Madani leads a team combining machine learning and biology to design proteins, with the platform first pointed at CRISPR and gene editing. Under its OpenCRISPR initiative the company released OpenCRISPR-1, an AI-created gene editor that keeps a Type II Cas9 architecture while differing from SpCas9 by more than 400 mutations.14
In November 2025 Profluent announced Profluent-E1, retrieval-augmented protein encoder models trained on its Profluent Protein Atlas and released in three sizes for research and commercial use.5
Work
ProGen (external site: arxiv.org)Published research
First author of the 2020 ProGen preprint, which trained a 1.2B-parameter language model on about 280 million protein sequences conditioned on taxonomic and keyword tags, and of the 2023 Nature Biotechnology paper showing that such models generate functional proteins across diverse families.23
OpenCRISPR-1 (external site: profluent.bio)Published research
Leads the company behind OpenCRISPR-1, an AI-generated gene editor that Profluent released under its OpenCRISPR initiative, freely licensed for ethical research and commercial use.41
Profluent-E1Open weights
Leads the company that released Profluent-E1, a family of retrieval-augmented protein encoder models in 150M, 300M and 600M parameter sizes, under a permissive license.51
Profluent-E1 150M (E1-150m)Open weights
Last-listed and corresponding author of the E1 preprint (bioRxiv 2025.11.12.688125), which the Profluent-E1 repository README cites for the model family.675
Profluent-E1 300M (E1-300m)Open weights
Last-listed and corresponding author of the E1 preprint (bioRxiv 2025.11.12.688125), which the Profluent-E1 repository README cites for the model family.675
Profluent-E1 600M (E1-600m)Open weights
Last-listed and corresponding author of the E1 preprint (bioRxiv 2025.11.12.688125), which the Profluent-E1 repository README cites for the model family.675
Career timeline
Other documented roles
Roles the sources document but that are not confirmed as current.
- Researcher; architect of the ProGen project, Salesforce AI Research12
Related people
More sourced profiles at the same organization, in the same field, or from the same school.
- Jeffrey A. RuffoloAlso at Profluent
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- Sarthak JainAlso at Profluent
- Brian HieAI for science
- Clara ShihAlso at Salesforce
- David WaddenLanguage models
- Paul SmithAlso at Salesforce
- Garyk BrixiAI for science
- Hoifung PoonAI for science
- Jakob UszkoreitLanguage models
- Kyunghyun ChoLanguage models
- Liam FedusLanguage models
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