Papers

PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences.

Universal Cell Embeddings: A Foundation Model for Cell Biology

Predicting transcriptional outcomes of novel multigene perturbations with GEARS.

De novo design of protein structure and function with RFdiffusion.

Transfer learning enables predictions in network biology.

Predicting cellular responses to complex perturbations in high-throughput screens.

Genomic benchmarks: a collection of datasets for genomic sequence classification.

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

Evolutionary-scale prediction of atomic-level protein structure with a language model.

Robust deep learning-based protein sequence design using ProteinMPNN.

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning.

ProtGPT2 is a deep unsupervised language model for protein design.

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq.

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans.

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

FLIP: Benchmark tasks in fitness landscape inference for proteins

Highly accurate protein structure prediction with AlphaFold.

Cellpose: a generalist algorithm for cellular segmentation.

The mutational constraint spectrum quantified from variation in 141,456 humans.

Evaluating Protein Transfer Learning with TAPE.

scGen predicts single-cell perturbation responses.

Predicting Splicing from Primary Sequence with Deep Learning.

Deep generative modeling for single-cell transcriptomics.

The Encyclopedia of DNA elements (ENCODE): data portal update.

Continuous Automated Model EvaluatiOn (CAMEO) complementing the critical assessment of structure prediction in CASP12.

The Human Cell Atlas.

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

A global reference for human genetic variation.

PDB-wide collection of binding data: current status of the PDBbind database.