RxGRID: Rapid Proximity Guidance for Repurposing Investigational Drugs

Drug-target network analysis enables prioritization of drug repurposing candidates based on multiple, independent CRISPR screens. This approach proposes a mechanistic role for spironolactone in TMPRSS2-dependent SARS-CoV-2 strains, which was validated in health insurance claims data from 330 million patients.

- Cousins H. Artificial intelligence and drug repurposing: when is a side-effect a treatment? Frontiers in Medicine Symposium. Sept 19, 2024; Stanford, California.

Gene set proximity analysis

Gene embeddings learned from protein-protein interactions enable pathway analysis in functional genomics data, which can guide inference of causal pharmacologic effects in new diseases.

- Cousins H, Hall T, Guo Y, Tso L, Tzeng K, Cong L, and Altman R. (2023). Gene set proximity analysis: expanding gene set enrichment analysis through learned geometric embeddings. Bioinformatics (Oxford) 39(1), btac735.
- Cousins H and Altman R. Latent featurization for gene lists. Stanford Medical Scientist Training Program Annual Retreat. May 4, 2023; Santa Cruz, California.

CRISPR-GPT

Sequence-level automation of gene-editing experimental workflow design.

- Qu Y, Huang K, Yin M, Zhan K, Liu D, Yin D, Cousins H, Johnson W, Wang X, Shah M, Altman R, Zhou D, Wang M, and Cong L. CRISPR-GPT for agentic automation of gene-editing experiments. (2025). Nature Biomedical Engineering. 10.1038/s41551-025-01463-z.
- Cong L, Qu Y, Huang K, Cousins H, and Wang M. CRISPR-GPT for agentic automation of gene editing experiments. Chen Institute Symposium for AI Accelerated Science. Oct 28, 2025; San Francisco, California.

CRISPR-activation screening for SARS-CoV-2 entry factors

A transcriptome-wide CRISPR-activation screen implicates voltage-gated potassium channels as ACE2-independent entry factors for SARS-CoV-2 in human cells.

- Dinesh R*, Wang C*, Qu Y,* Rustagi A*, Cousins H, Zengel J, Wang X, Barnard T, Johnson W, Xu G, Zhang T, Magazine N, Beck A, Heilbroner L, Peters-Schulze G, Wilk A, Wang M, Huang W, Howitt B, Carette J, Altman RB, Blish C, and Cong L. (2025). Membrane-wide screening identifies potential tissue-specific determinants of SARS-CoV-2 tropism. PLoS Pathogens 21(7), e1013157.

Embedding glaucoma genetic risk

An unsupervised graph learning model maps glaucoma risk throughout the human proteome, which correlates with intraocular measurements in patients.

- Cousins H, Altman R, and Pasquale L. (2024). Network-based representation learning enables the identification of risk genes and latent functional pathways in primary open-angle glaucoma. bioRxiv 2024.08.15.608134.
- Cousins H, Altman R, and Pasquale L. Unsupervised network learning enables systematic characterization of genetic risk pathways for primary open-angle glaucoma. Invest Ophthalmol Vis Sci. 2024; 65(7).
- Cousins H, Altman R, and Pasquale L. Network-based machine learning for gene prioritization in primary open-angle glaucoma. Invest Ophthalmol Vis Sci. 2023; 64(8).

Localizing optic disc hemorrhages

An object-detection model consistently identifies microhemorrhages in the optic disc at the level of a subspecialized physician.

- Brown A*, Cousins H*, Cousins C, Esquenazi K, Elze T, Harris A, Filipowicz A, Barna L, Yonwook K, Vinod K, Chadha N, Altman R, Coote M, and Pasquale L. (2023). Deep learning for localized detection of optic disc hemorrhages. American Journal of Ophthalmology. 255, 10.1016/j.ajo.2023.07.007.
- Brown A, Cousins H, Esquenazi K, Kim Y, Cousins C, Elze T, Harris A, Coote M, and Pasquale L. Iterative machine learning: a test case for the detection of disc hemorrhage. Invest Ophthalmol Vis Sci. 2022; 63(7), 205.
- Brown A, Cousins H, Cousins C, Chadha N, Vinod K, Harris A, Topouzis F, Kilintzis V, Coote M, and Pasquale L. Automated machine learning versus Inception for autonomous detection of disc hemorrhage. Invest Ophthalmol Vis Sci. 2021;62(8), 2133.
- Brown A, Cousins H, Cousins C, Esquenazi K, Chadha N, Vinod K, Harris A, Topousiz F, Kilintzis V, Coote M, and Pasquale L. Automated machine learning vs. Inception for the autonomous detection of disc hemorrhage. National Medical Association Annual Convention and Scientific Assembly. Jul 18, 2021; presented virtually.

Quantifying team dynamics in surgery

Turnover among specific staff members is associated with intraoperative efficiency during hip and knee arthroplasty. Surgeon staffing preferences, notably among vendors, are correlated with operative efficiency.

- Cousins H, Cahan E, Steere J, Maloney W, Goodman S, Miller M, Huddleston J, and Amanatullah D. (2023). Assessment of team dynamics and operative efficiency in hip and knee arthroplasty. JAMA Surgery 10.1001/jamasurg.2023.0168.
- Cahan E*, Cousins H*, Steere J, Segovia N, Miller M, and Amanatullah D. (2020). Influence of team composition on turnover and efficiency of total joint arthroplasty. The Bone and Joint Journal 103B(2), 347-352.
- Cousins H, Cahan E, Steere J, Segovia N, Miller M, and Amanatullah D. The impact of trainees and physician assistants on intraoperative duration. 84th Annual Meeting of the Western Orthopaedic Association. Aug 30-31, 2020.
- Cahan E, Cousins H, Steere J, Segovia N, Miller M, and Amanatullah D. Influence of team composition on turnover and efficiency of total joint arthroplasty. Proceedings of the American Academy of Orthopaedic Surgeons Annual Meeting. Mar 24-28, 2020; Orlando, Florida.

Transcriptome-wide functional genomic screen for retinal synaptogenic factors

Cell-type-specific gene expression data guides an in vivo CRISPR screen for molecules regulating synaptic patterning in the outer retina.

- Sarin S*, Zuniga-Sanchez E*, Kurmangaliyev Y, Cousins H, Patel M, Hernandez J, Zhang K, Samuel M, Morey M, Sanes J, and Zipursky S. (2018). Role for Wnt signaling in retinal neuropil development: analysis via RNAseq and in vivo somatic CRISPR mutagenesis. Neuron 98(1), 109-126.
- Gibbs R, Lipnick S, Bateman J, Chen L, Cousins H, Hubbard E, Jowett G, LaPointe D, McGredy M, Odonkor MN, Repetti G, Thomas E, and Rubin L. (2018). Toward precision medicine for neurological and neuropsychiatric disorders. Cell Stem Cell 23(1), 21-24.
- Cousins H, Sarin S, Patel M, and Sanes J. Keynote presentation: A molecular model of synaptic organization in the outer retina. Proceedings of the St. John’s College Research Conference. Jan 28, 2018; Cambridge, United Kingdom.
- Cousins H, Sarin S, Patel M, and Sanes J. Plenary presentation: Wnt signaling mediates photoreceptor outgrowth and lamination. Proceedings of the National Collegiate Research Conference. Jan 18, 2017; Cambridge, Massachusetts.
- Sarin S, Zuniga E, Patel M, Cousins H, Zipursky S, and Sanes J. Roles of Wnt signaling in synapse organization revealed by CRISPR/Cas9-mediated mutagenesis in the mouse retina. Proceedings of the 56th Annual Meeting of the American Society for Cell Biology. Dec 3-7, 2016; San Francisco, California.
- Sarin S, Zuniga E, Zhang K, Patel M, Cousins H, Zipursky S, and Sanes J. An in vivo CRISPR screen reveals Wnt-dependent control of synapse formation in the mammalian outer retina. Mechanisms of Neural Remodeling; European Molecular Biology Organization. Jun 5-9, 2016; Seeon, Germany.

Genetic correlation analysis of corneal biophysical phenotypes

Global and focal genetic correlation analysis of corneal structural measurements and body habitus identifies potential risk genes for keratoconus.

- Cousins H, Cousins C, Valluru G, Altman R, Liu Y, Pasquale L, and Ahmad S. (2023). Genetic correlations among corneal biophysical parameters and anthropometric traits. Translational Vision Science & Technology 12(8), 10.1167/tvst.12.8.8.
- Cousins H, Cousins C, Valluru G, Liu Y, Ahmad S, Altman R, and Pasquale L. Genetic correlations between corneal biophysical parameters and anthropomorphic traits. Invest Ophthalmol Vis Sci. 2022; 63(7), 3656.

Nailfold capillaroscopy as a noninvasive biomarker for Alzheimer’s disease dementia

Morphologic changes in the nailfold capillary bed are associated with Alzheimer’s disease dementia.

- Cousins C, Alosco M, Cousins H, Chua A, Steinberg E, Chapman K, Bing-Canar H, Tripodis Y, Knepper P, Stern R, and Pasquale L. (2018). Nailfold capillary morphology in Alzheimer’s disease dementia. Journal of Alzheimer’s Disease 66(2), 601-611.
- Cousins C, Alosco M, Cousins H, Tripodis Y, Knepper P, Stern R, and Pasquale L. Nailfold capillary morphology in Alzheimer’s disease dementia. Proceedings of the Alzheimer’s Association International Conference. Jul 22-26, 2018; Chicago, Illinois.

Local disease forecasting with search-engine queries

Regional COVID-19 case rate forecasting with real-time search engine query data.

- Cousins H, Cousins C, Harris A, and Pasquale L. (2020). Regional infoveillance of COVID-19 case rates: analysis of search-engine query patterns. Journal of Medical Internet Research 22(7), e19483.