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53 entries in Genomics

Showing 48 of 53

AlphaFoldDBLiteFoldAlphaFoldDB prediction index — open database of predicted protein 3D structures with confidence scores, providing structural coverage for known protein sequences at scale.Predicted StructuresExplore
ATBAllTheBacteriaAllTheBacteria: a comprehensive collection of ~2 million bacterial genome assemblies from public sequence databases, standardized for large-scale genomic analysis.Microbial GenomicsExplore
Bac-Corpus-dna-intergenic-sequences-high-diversityAllTheBacteriaHigh-diversity corpus of bacterial intergenic DNA sequences for training DNA language models on non-coding regulatory regions.Microbial GenomicsExplore
Bac-Corpus-protein-sequences-high-diversityAllTheBacteriaHigh-diversity corpus of bacterial protein sequences derived from the ATB collection, filtered for maximum sequence diversity to support protein language model pretraining.Microbial GenomicsExplore
BFDLiteFoldBFD source archive index — clustered UniProt + metagenomic protein sequences, the standard database for AlphaFold-style homology search and MSA construction.Protein SequencesExplore
bioreason-pro-sft-reasoning-datawanglabReasoning trace dataset used to supervised-fine-tune BioReason-Pro — multimodal biological problems with rationales over genomic variants and pathway data.Biological Reasoning CorpusExplore
Botanic1-pretrainingliving-modelsThe genomic sequence corpus used to pre-train the Botanic1 plant genome models — 7.2M training windows of 8,192 bp spanning 320 embryophyte species, roughly 59B effective base pairs.Genomic SequencesExplore
carbon-pretraining-corpusHuggingFaceBioCarbon pretraining corpus — the curated DNA sequence dataset used to train the Carbon-500M / 3B / 8B genomic foundation models.Genomic Pretraining CorpusExplore
CATHLiteFoldCATH domain classification — hierarchical classification of protein domain structures by class, architecture, topology, and homologous superfamily.Domain ClassificationExplore
clinvar-vepHuggingFaceBioClinVar variants annotated with VEP (Variant Effect Predictor) — formatted for benchmarking genomic-LLM pathogenicity classification.Clinical VariantsExplore
EmeraldBaytahoebioEmerald Bay — single-cell perturbation dataset of 1.8M+ transcriptomic profiles spanning 52 cell lines × 91 drug treatments (plus combinations), generated on Tahoe’s MOSAIC high-throughput platform with paired transcriptional and drug-phenotype readouts over a five-day culture.Single-Cell PerturbationExplore
ESMAtlasLiteFoldHub mirror of the ESM Metagenomic Atlas — large-scale predicted metagenomic protein structures generated with ESMFold, packaged as webdataset shards.Predicted StructuresExplore
ESMC-SAE-FeaturesbiohubFeature table for the 16,384-feature sparse autoencoder trained on layer 60 of ESMC-6B — supports mechanistic-interpretability research on protein language models.InterpretabilityExplore
EvolutionaryLiteFoldPrecomputed evolutionary sequence-alignment data (MMseqs2-style) packaged for the Hub — drop-in MSA features for protein-LM and structure-prediction pipelines.MSA / Training CorpusExplore
genomic-niahHuggingFaceBioGenomic Needle-in-a-Haystack — long-context evaluation for genomic LLMs, measuring retrieval and reasoning over long DNA sequences.Long-Context BenchmarkExplore
GOLiteFoldGene Ontology terms — structured controlled vocabulary for describing gene-product functions, biological processes, and cellular components across organisms.OntologyExplore
GOALiteFoldGene Ontology Annotation (UniProt) — high-quality evidence-coded GO annotations for UniProtKB proteins, RNAs, and protein complexes.OntologyExplore
HumanProteinAtlasLiteFoldHuman Protein Atlas — gene and protein expression across tissues, cells, organs, pathology, and subcellular locations for human proteins.Protein AnnotationExplore
img_virus_plasmidwanglabCombined IMG/VR (uncultivated virus genomes) and IMG/PR (plasmids from genomes and metagenomes) catalog with rich functional, taxonomic, and ecological metadata.Microbial GenomicsExplore
InterProLiteFoldInterPro entries — integrated protein family, domain, repeat, and functional-site signatures across multiple member databases for sequence classification.Protein AnnotationExplore
keggwanglabKEGG pathway entries paired with variant annotations for training and evaluating multimodal biological reasoning models (used by the BioReason work).Biological ReasoningExplore
MgnifyLiteFoldMGnify protein catalogues — microbiome-derived protein sequences from EBI’s MGnify platform with train/test splits for downstream metagenomic protein tasks.MetagenomicsExplore
multi_species_genomesInstaDeepAIWhole-genome sequences for 850 species spanning bacteria, fungi, plants, and animals — the pre-training corpus for the Nucleotide Transformer model family.GenomicsExplore
NCBILiteFoldNCBI RefSeq protein shard index — curated non-redundant protein subset of NCBI’s Reference Sequence collection, packaged as parquet for efficient loading.Protein SequencesExplore
NTv3_benchmark_datasetInstaDeepAIBenchmark dataset with functional tracks and genome annotations across 7 species.GenomicsExplore
nucleotide_transformer_downstream_tasksInstaDeepAI18 genomic prediction benchmark tasks covering histone marks, regulatory regions, splice sites, and promoter activity across human and multi-species genomes.GenomicsExplore
OGtattabioOpen Genomes (OG) — curated genome-sequence corpus from Tatta Bio for genomic ML pretraining and benchmarking.Genomic CorpusExplore
OMGtattabioOpen Mixed Genomes (OMG) — large mixed-organism nucleotide corpus underpinning Tatta Bio’s gLM2 genomic foundation models.Genomic CorpusExplore
opengenome2arcinstituteCurated collection of prokaryotic and eukaryotic genomic sequences for training and benchmarking large-scale biological foundation models.GenomicsExplore
OpenProteinSetLiteFoldOpenProteinSet — open-source MSA training corpus released by the OpenFold team (Ahdritz et al., NeurIPS 2023) reproducing AlphaFold-style training data.MSA / Training CorpusExplore
PATHOS-PLM-EMBEDDINGSDSIMBPATHOS protein language-model embeddings — precomputed feature representations supporting pathogenicity prediction and downstream macromolecular ML on protein sequences.Protein EmbeddingsExplore
PDBLiteFoldHub-packaged index over the Protein Data Bank mmCIF entries — the global archive of experimentally-determined 3D structures of biological macromolecules.Protein StructureExplore
Perturb-SapiensarcinstituteLarge-scale human single-cell perturbation dataset used in the STACK foundation-model lineage — paired baseline and perturbed expression profiles for genetic perturbation screens.Single-Cell PerturbationExplore
perturbation-benchHuggingFaceBioGenetic perturbation benchmark — evaluates how well genomic foundation models predict perturbation responses across cell states.Genomic BenchmarkExplore
PfamLiteFoldPfam — protein family and domain annotation built from curated multiple sequence alignments and profile HMMs, mirrored to the Hub as JSONL.Protein FamiliesExplore
plant-genomic-benchmarkInstaDeepAIPlant genomics benchmark spanning gene expression, chromatin accessibility, and agronomic trait prediction tasks across multiple crop and model plant species.Plant GenomicsExplore
protenix-dataLiteFoldTraining data for Protenix — ByteDance’s open-source PyTorch reproduction of AlphaFold3 handling proteins, DNA, RNA, ligands, ions, and modifications.Structure PredictionExplore
replogle-nadig-de-rhaistertahoebioDifferential-expression summary statistics for the Replogle-Nadig genome-scale CRISPR screen (4 cell lines × ~2,000 gene knockdowns: HepG2, Jurkat, K562, RPE1) — per-gene fold changes, significance, and pseudobulk deltas used to train Rhaister.CRISPR Differential ExpressionExplore
Replogle-Nadig-PreprintarcinstituteReplogle-Nadig single-cell perturbation dataset (preprint release) — Perturb-seq screens used in the STATE single-cell embedding work for perturbation-response modelling.Single-Cell PerturbationExplore
SE-167M-Humanarcinstitute167M human single-cell RNA expression profiles across diverse tissues and cell types, used for training STACK and SE single-cell foundation models.Single-Cell BiologyExplore
SPIREAllTheBacteriaSearchable Planetary-scale mIcrobiome REsource: a large-scale metagenomics resource aggregating environmental microbiome samples from diverse global habitats.Microbial GenomicsExplore
Stack-CellxGene45Marcinstitute45M curated single-cell profiles drawn from the CellxGene corpus, standardised for in-context learning and cross-study perturbation analysis.Single-Cell BiologyExplore
State-Tahoe-FilteredarcinstituteFiltered Tahoe-100M slice used in the STATE workflow — high-quality single-cell perturbation profiles for training and benchmarking cross-study cell-state models.Single-Cell PerturbationExplore
Tahoe-100MtahoebioGiga-scale perturbation atlas with 100M+ single-cell profiles from 50 cancer cell lines and 1,100 drugs.Single-Cell BiologyExplore
Tahoe-x1-embeddingstahoebioPre-computed cell and gene embeddings from the Tahoe-x1 foundation model.Single-Cell BiologyExplore
TCGA_virtual_spatial_transcriptomics_atlasratschlabPopulation-scale virtual spatial transcriptomics atlas generated with DeepSpot-M by computationally augmenting TCGA retrospective histopathology archives — 28,664 whole-slide images from 10,865 patients across 32 cancer types.Spatial TranscriptomicsExplore
traitgymHuggingFaceBioTraitGym — multi-task benchmark for evaluating genomic foundation models on trait prediction across diverse phenotypes.Trait Prediction BenchmarkExplore
true-cds-protein-tasksInstaDeepAICoding sequence and protein function prediction benchmark tasks.Protein TasksExplore

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