OmicsML/awesome-foundation-model-single-cell-papers
curated list of foundation-model papers for single-cell omics; the closest external companion to the Foundation Models rows in Papers.md.
Awesome Lists
Community-maintained “awesome lists” and curated bibliographies — living GitHub indexes of papers,
tools, and tutorials. None are cell-ag-specific, but each is a high-signal navigation layer for the
AI / single-cell / bioinformatics literature and tooling that cell-ag work draws on. Star counts and
last-updated dates are fetched from GitHub at build time; the full, current contents live in each
linked repository. The canonical list is AwesomeLists.md.
24 lists across 7 topics · metrics as of Jun 2026
AI & foundation models for single-cell biology
OmicsML/awesome-deep-learning-single-cell-papers
curated list of deep-learning papers for single-cell analysis.
hussius/deeplearning-biology
long-running list of deep-learning applications and implementations across biology.
Single-cell & multi-omics analysis
seandavi/awesome-single-cell
the comprehensive community index of single-cell RNA-seq analysis software.
mdozmorov/scRNA-seq_notes
Mikhail Dozmorov's curated notes on scRNA-seq tools, tutorials, and resources.
crazyhottommy/scRNAseq-analysis-notes
Ming Tang's working notes on scRNA-seq analysis.
mikelove/awesome-multi-omics
Mike Love's list of multi-omics data-integration methods.
crazyhottommy/awesome_spatial_omics
curated spatial-omics methods and tools.
General bioinformatics
danielecook/Awesome-Bioinformatics
broad curated index of bioinformatics software and resources.
j-andrews7/awesome-bioinformatics-benchmarks
curated list of bioinformatics benchmarking studies — useful when selecting methods for cell-ag pipelines.
crazyhottommy/RNA-seq-analysis
RNA-seq analysis notes and resources.
crazyhottommy/ChIP-seq-analysis
ChIP-seq analysis notes and resources.
crazyhottommy/bioinformatics-one-liners
practical command-line one-liners for bioinformatics.
crazyhottommy/getting-started-with-genomics-tools-and-resources
entry-point genomics tooling guide.
davidliwei/awesome-CRISPR
curated list of CRISPR / genome-engineering software, websites, and databases (guide design, off-target analysis, screening).
pansapiens/awesome-protein-design-software
curated collection of protein structure-prediction and design software, with a focus on new deep-learning and transformer-based tools — companion to the protein-engineering tools in Software.md.
lifs-tools/awesome-lipidomics
curated collection of lipidomics tools, databases, and resources for lipid identification and visualization.
Biomedical NLP & information extraction
caufieldjh/awesome-bioie
curated resources for biomedical information extraction — relevant to the literature-mining and agentic-AI layer of cell-ag.
Scientific & biomolecule language models
QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling
curated resources on multi-modal learning that bridges biomolecules (proteins, molecules) and natural language — the companion list to a survey on biomolecule–language cross-modeling.
yuzhimanhua/Awesome-Scientific-Language-Models
comprehensive survey and curated list of scientific large language models across disciplines (mathematics, physics, chemistry, materials, biology, medicine) and modalities.
AI agents for science
AgenticScience/Awesome-Agent-Scientists
curated paper list on AI agents for scientific discovery; the delegation home for the general science-agent literature that Papers.md keeps out of the matrix unless a paper applies an agent to a specific cell-ag problem.
InternScience/Awesome-Scientific-Datasets-and-LLMs
curated collection of papers, datasets, and resources on scientific datasets and large language models, spanning benchmarks and domain LLMs across disciplines.
Biological & protein foundation models
apeterswu/Awesome-Bio-Foundation-Models
collection of biological foundation models across protein, RNA, DNA, gene, and single-cell modalities; a wider-scope companion to the single-cell foundation-model list above.
MachineLearningLifeScience/awesome-protein-foundation-models
curated list of protein foundation models, protein language models (pLMs), and generative models for sequence, structure, and multimodal protein modeling; a focused, if newer, index of the protein-model space that cell-ag protein engineering draws on.
Linked external resources are independent of TUCCA and Tufts University and remain under their own licenses.