Benjamin Auerbach Email & Phone Number

San Francisco, California, United States

Building DNA language models.

San Francisco Bay Area

Worked as a computational biologist for an NK cell therapy platform

Cambridge, Massachusetts, United States

Consulting for an early-stage venture-backed biotech. Leveraging computational approaches to inform target selection and pipeline strategy for a bifunctional platform.

Boston, Massachusetts, United States

Paris, France

Philadelphia, Pennsylvania, United States

• Led computational analysis of scRNA-seq data to study vascular smooth muscle cell phenotypic switching in atherosclerosis and to identify therapeutic targets. Used deep learning autoencoder-based approaches for cell.
• Led project (idea conception, model design, model validation) to build an algorithm using Bayesian variational inference to estimate cell circadian timing in cell populations from scRNA-seq data.
• Led project (idea conception, experimental design, data analysis) to study the effect of night-time lighting on aortic circadian transcription, and how this effect differs by sex, using scRNA-seq. Coordinated and.
• Led project (idea conception, experimental design, data analysis) to assess the influence of circadian time on cell fate decisions made by vascular smooth muscle cells upon exposure to atherogenic stimuli. Coordinated.
• Applied B-variational autoencoder algorithm to identify latent factors explaining gene expression in spatial transcriptomics data that have semantic meaning (e.g. morphogen tissue gradients).
• Collaborated with radiologists to analyze the utility of existing biomarkers for glioblastoma prognosis.

St Louis, Missouri, United States

• Developed device to objectively measure skin scratching with applications in pharmaceutical development and clinical care. Responsible for development of SVM classification algorithm and data collection pipeline.
• Pitched product to potential pharma partners.

Boston, Massachusetts, United States

• Developed an application for internal querying and analysis of CRISPR screen results.

St Louis, Missouri, United States

San Francisco, California, United States

New York, New York, United States

New Haven, Connecticut, United States

Doctor Of Philosophy (Ph.D.), Genomics & Computational Biology

Activities and Societies: Wharton Innovation Fund investor, Penn HealthX Startup Incubator, Upward Bound Math and Science Program mentor.

Master Of Arts - Ma, Statistics

Bachelor’S Degree, Computer Science; Bioinformatics Minor

Activities and Societies: Olin Venture Fund (co-founder), Club Squash Team (co-captain), Pikers A Cappella (treasurer; assistant music.

Education record

Activities and Societies: Harmonaires A Cappella Group (head), Baseball, Squash, Elementary School Tutoring, Senior Fellow, School Newspaper