Sparse signal processing for precision medicine
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About

Immune checkpoint blockade (ICB) is a form of immunotherapy that has resulted in extraordinary gains in clinical response and overall survival in a growing number of cancers. Unfortunately, only a minority of patients respond favorably to these costly and potentially toxic treatments. Molecular biomarkers of different types that predict beforehand who will derive a durable clinical benefit from these revolutionary treatments are urgently needed.
SNR Analytics Inc. (SNRAI) develops sparse signal processing (SSP) techniques that are designed to identify small subsets of molecular variables in big genomic datasets (i.e., sparse signatures) that are predictive of immunotherapeutic response. We have found that sparse signatures discovered by our SSP algorithms are highly enriched for biology associated with the immune status of the tumor microenvironment (TME) and response to immunotherapy.

SNRAI data scientists and software engineers develop data-driven models that leverage the surprising connection between signal sparsity and the immune status of the tumor microenvironment (TME) to better predict how a cancer patient will respond to ICB and other immunotherapies.

SNRAI is developing an internal database of immunological signatures that are likely predictors of ICB response and/or overall survival in multiple cancers based on the analysis of all cancers in The Cancer Genome Atlas using an analysis pipeline based on SSP techniques.

SNRAI is developing a cloud-based version of a SSP pipeline that runs in Jupyter notebooks to facilitate the wider use of SSP techniques in biomarker discovery and predictive modeling of cancer and other complex diseases.

Team

Gordon Okimoto, PhD

President / Chief Scientific Officer

Thomas Wenska, PhD

Data Scientist

Ashkan Zeinalzadeh, PhD

Data Scientist

Michael Vo

Lead Software Engineer

Spencer Long

Software Engineer

Publications

Joint analysis of multiple high-dimensional data types using sparse matrix approximations of rank-1 with applications to ovarian and liver cancer

Okimoto, G., Zeinalzadeh, A., Wenska, T., Loomis, M., Nation, J., Fabre, T., Tiirikainen, M., Hernandez, B., Chan, O., Wong, L. & Kwee, S. (2016)

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A Neural Network Model to Classify Liver Cancer Patients Using Data Expansion and Compression

Zeinalzadeh, A., Wenska, T. & Okimoto, G. (2016)

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The non-invasive diagnosis of lymph-node status based on gene expression profiles of primary breast cancer tumors

Okimoto, G. (2007)

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Initial neural net construction for the detection of cervical intraepithelial neoplasia by fluorescence imaging

Parker, M., Mooradian, G., Okimoto, G., O’Connor, D., Miyazawa, K. & Saggese, S. (2002)

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Principal component analysis in the wavelet domain: New features for underwater object recognition

Okimoto, G. & Lemonds, D. (1999)

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