Predicting how a cell's transcriptome shifts when a gene is silenced: a solo entry to the Virtual Cell Challenge 2026, built in the open.
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Nov 5, 2026 - Python
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crispri
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Zero-shot CRISPRi perturbation response prediction in unseen cell lines, with evaluated uncertainty. Virtual Cell Challenge 2026 entry
python benchmark machine-learning bioinformatics transfer-learning single-cell zero-shot model-evaluation anndata virtual-cell crispri perturb-seq perturbation-prediction virtual-cell-challenge cell-eval
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Nov 5, 2026 - Python
🌱 Designing CRISPRi experiments in bacteria
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May 14, 2026 - Python
What a genome-scale CRISPRi screen can and cannot discover. 50 Hallmark programs x 9,837 knockdowns in K562. Four evaluations, three negative, all four reported.
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Sep 16, 2026 - HTML
Unified genetic engineering platform: CRISPR, protein engineering, synthetic biology, gene therapy, genomics, metabolic engineering, AI/ML, biosecurity. 331 tests, TDD, OSS.
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Oct 5, 2026 - Python
Adversarial-debate LLM agent for predicting CRISPRi perturbation effects on gene expression (Genentech MLGenX BioReasoning Challenge)
bioinformatics computational-biology gene-expression kaggle-competition crispri vllm llm-agents agentic-ai perturbation-biology
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Oct 9, 2026 - Python
Computational design and adversarial validation of synthetic gene circuits targeting PDAC transcription factors, trained from scratch on real public genomics data
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Aug 10, 2026 - Python
Reproducible uncertainty-aware multicriteria prioritization of MALAT1 CRISPRi guides in A549 cells.
bioinformatics reproducible-research uncertainty-quantification decision-analysis smaa multicriteria-decision-analysis crispri
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Oct 9, 2026 - Python
Reproducible CRISPRi/Perturb-seq analysis of an ENTPD1/CD39 T-cell program in rheumatoid arthritis and methotrexate treatment
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Jul 28, 2026 - Python
Phenotypic screening of a CRISPRi strain library [Smith et 2017, Mol Syst Biol (2017)13:913] for acetic acid tolerance targeting essential and respiratory essential genes in Saccharomyces cerevisiae
yeast phenomics high-throughput-screening saccharomyces-cerevisiae stress-tolerance essential-genes scan-o-matic bioscreen acetic-acid crispri
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Oct 9, 2021 - R
AI-assisted platform for designing CRISPR experiments — from target selection to bench-ready protocols
python bioinformatics crispr gradio base-editing gene-editing guide-rna research-tools crispri prime-editing crispor crispra
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Apr 13, 2026 - Python
A Triangulated Causal Machine Learning Framework Decodes Super-Enhancer Regulatory Networks and Actionable Vulnerabilities in Triple-Negative Breast Cancer
machine-learning cancer-genomics causal-inference single-cell-genomics super-enhancers explainable-ai gene-regulatory-networks triple-negative-breast-cancer crispri perturb-seq
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Nov 4, 2026 - Jupyter Notebook
Repository containing the code and methods for Bosch & DeJesus et al. 2021
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Sep 8, 2025 - R
Virtual cell: predicting transcriptional responses to unseen gene knockdowns (PerturbFormer + conditional flow matching) - biomedical informatics course project
bioinformatics pytorch transformer single-cell virtual-cell crispri flow-matching perturb-seq perturbation-prediction
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Nov 10, 2026 - Python
Figure code and data for Johnson et al. 2021, J Am Chem Soc 143(31):12003-12013, doi:10.1021/jacs.1c02622. CRISPRi chemical genomics identifying IleRS as the target of thiomarinol
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Aug 8, 2026 - R
Arc Institute Virtual Cell Challenge 2026 实战仓库：零样本预测 CRISPRi 扰动后的单细胞基因表达原始计数，包含竞赛资料、模型审计和可运行教程。
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Oct 5, 2026 - Jupyter Notebook
PyTorch classifier predicting CRISPRi guide identity from single-cell expression (Adamson et al. 2016 Perturb-seq)
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Nov 11, 2026 - Python
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