Ali Madani

Biochemistry, Genetics and Molecular Biology · Life Sciences

21h-index4.8kcitations44works26.62yr avg
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Research Topics

RNA and protein synthesis mechanisms(14), Machine Learning in Bioinformatics(12), Protein Structure and Dynamics(9), COVID-19 diagnosis using AI(7), Genomics and Phylogenetic Studies(5)

Publications44 total

FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications
2026Open Access
E1: Retrieval-Augmented Protein Encoder Models
2025· 3 citedOpen Access
Design of highly functional genome editors by modelling CRISPR–Cas sequences
Nature·2025· 45 citedOpen Access
Scaling Unlocks Broader Generation and Deeper Functional Understanding of Proteins
2025· 26 citedOpen Access
Engineering of CRISPR-Cas PAM recognition using deep learning of vast evolutionary data
2025· 4 citedOpen Access
Function-Guided Conditional Generation Using Protein Language Models with Adapters
arXiv (Cornell University)·2024Open Access
Adapting protein language models for structure-conditioned design
2024· 23 citedOpen Access
Deep Learning for Geothermal Reservoir Characterization: Estimating Rock Properties from Seismic Data Using Convolutional Neural Networks
2024
Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences
2024· 82 citedOpen Access
Designing proteins with language models
Nature Biotechnology·2024· 82 cited
Towards Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion
arXiv (Cornell University)·2023· 2 citedOpen Access
ProGen2: Exploring the boundaries of protein language models
Cell Systems·2023· 367 citedOpen Access
Generated sequences and fitness data for ProGen2
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
Generated sequences and fitness data for ProGen2
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
Large language models generate functional protein sequences across diverse families
Nature Biotechnology·2023· 926 citedOpen Access
A language model beats alphafold2 on orphans
Nature Biotechnology·2022· 54 citedOpen Access
Deep Extrapolation for Attribute-Enhanced Generation
Neural Information Processing Systems·2021
FLIP: Benchmark tasks in fitness landscape inference for proteins
2021· 14 citedOpen Access
Deep neural language modeling enables functional protein generation across families
2021· 43 citedOpen Access
Deep Extrapolation for Attribute-Enhanced Generation
arXiv (Cornell University)·2021· 12 citedOpen Access
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Frequent Co-authors

Jeffrey A. Ruffolo(12), Mohammad R. K. Mofrad(8), Aadyot Bhatnagar(8), Richard Socher(7), Nikhil Naik(7), Stephen Nayfach(5), Joel Beazer(5), Ben Krause(4), Mehdi Moradi(4), Tanveer Syeda-Mahmood(4), Joseph P. Gallagher(4), Emily Hill(4), Caiming Xiong(3), James S. Fraser(3), Ramy Arnaout(3), Rima Arnaout(3), Erik Nijkamp(3), Eli N. Weinstein(3), Nitish Shirish Keskar(3), Riffat Hussain(3)