Papers

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FLIP: Benchmark tasks in fitness landscape inference for proteins

protein-ml · DOI 10.1101/2021.11.09.467890 · bioRxiv (Cold Spring Harbor Laboratory) · 14 citations

proteinbenchmark

Nov 2021

JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations

cell-imaging · DOI 10.1101/2023.03.23.534023 · bioRxiv (Cold Spring Harbor Laboratory) · 108 citations

imagingphenomics

Mar 2023

Universal Cell Embeddings: A Foundation Model for Cell Biology

single-cell · DOI 10.1101/2023.11.28.568918 · bioRxiv (Cold Spring Harbor Laboratory) · 171 citations

single-cellembedding

Nov 2023

Chai-1: Decoding the molecular interactions of life

protein-ml · DOI 10.1101/2024.10.10.615955 · bioRxiv (Cold Spring Harbor Laboratory) · 416 citations

proteinstructure

Oct 2024

Boltz-1 Democratizing Biomolecular Interaction Modeling

protein-ml · DOI 10.1101/2024.11.19.624167 · bioRxiv (Cold Spring Harbor Laboratory) · 472 citations

proteinstructure

Nov 2024

Genome modeling and design across all domains of life with Evo 2

genomics · DOI 10.1101/2025.02.18.638918 · bioRxiv (Cold Spring Harbor Laboratory) · 217 citations

Feb 2025

Scaling Large Language Models for Next-Generation Single-Cell Analysis

single-cell · DOI 10.1101/2025.04.14.648850 · bioRxiv (Cold Spring Harbor Laboratory) · 38 citations

Apr 2025

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

protein-ml · DOI 10.1101/2025.06.14.659707 · bioRxiv (Cold Spring Harbor Laboratory) · 601 citations

proteinstructure

Jun 2025

rbio1 - training scientific reasoning LLMs with biological world models as soft verifiers

single-cell · DOI 10.1101/2025.08.18.670981 · bioRxiv (Cold Spring Harbor Laboratory) · 7 citations

single-cellreasoning

Aug 2025

imAgeScore, a Cell Painting-Based Predictor of Cellular Age for High-throughput Drug Screening Applications

cell-imaging · DOI 10.64898/2026.03.06.710056 · bioRxiv (Cold Spring Harbor Laboratory) · 0 citations

Mar 2026

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