publications

2025

  1. Systems and Algorithms for Convolutional Multi-Hybrid Language Models at Scale
    Jerome Ku*, Eric Nguyen*, David W Romero*, and 13 more authors
    arXiv preprint arXiv:2503.01868, 2025
  2. Genome modeling and design across all domains of life with Evo 2
    Garyk Brixi*, Matthew G Durrant*, Jerome Ku*, and 49 more authors
    bioRxiv, 2025

2024

  1. Protein language models learn evolutionary statistics of interacting sequence motifs
    Zhidian Zhang*, Hannah K Wayment-Steele*, Garyk Brixi, and 3 more authors
    Proceedings of the National Academy of Sciences, 2024
  2. Transferrin receptor targeting chimeras for membrane protein degradation
    Dingpeng Zhang, Jhoely Duque-Jimenez, Francesco Facchinetti, and 5 more authors
    Nature, 2024
  3. Sequence modeling and design from molecular to genome scale with Evo
    Eric Nguyen*, Michael Poli*, Matthew G Durrant*, and 8 more authors
    Science, 2024

2023

  1. Directed differentiation of human iPSCs to functional ovarian granulosa-like cells via transcription factor overexpression
    Merrick D Pierson Smela*, Christian C Kramme*, Patrick RJ Fortuna, and 8 more authors
    Elife, 2023
  2. Human Germ Cell Specification via Combinatorial Expression of Prioritized Transcription Factors
    Christian Kramme*, Merrick Smela*, Bennett Wolf, and 8 more authors
    2023
  3. Understanding and Predicting Polycystic Ovary Syndrome through Shared Genetic Architecture with Testosterone, SHBG, and Inflammatory Markers
    Lillian Kay Petersen*, Garyk Brixi*, Jun Li, and 8 more authors
    medRxiv, 2023
  4. SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders
    Garyk Brixi*, Tianzheng Ye*, Lauren Hong*, and 8 more authors
    Communications Biology, 2023
  5. Investigating the utility of protein language models for modeling isoforms
    Zhidian Zhang*, Hannah Wayment-Steele*, Brixi Garyk, and 1 more author
    In PROTEIN SCIENCE, 2023

2022

  1. Design of peptide-based protein degraders via contrastive deep learning
    Kalyan Palepu*, Manvitha Ponnapati*, Suhaas Bhat, and 5 more authors
    bioRxiv, 2022

2021

  1. Ready-to-use therapeutic food (RUTF) containing low or no dairy compared to standard RUTF for children with severe acute malnutrition: a systematic review and meta-analysis
    Isabel Potani, Carolyn Spiegel-Feld, Garyk Brixi, and 5 more authors
    Advances in Nutrition, 2021

2019

  1. Developing Local Treatments for Acutely Malnourished Children in Sub-Saharan Africa: A Novel Optimization Approach Automatically Ensuring Protein Quality (FS14-06-19)
    Garyk Brixi
    Current Developments in Nutrition, 2019

2018

  1. Innovative optimization of ready to use food for treatment of acute malnutrition
    Garyk Brixi
    Maternal & Child Nutrition, 2018