Blank Bio Raises $7.2M in Seed Funding and Strategic Collaboration with PacBio

The company plans to use the funding to continue developing its models, expand collaborations with pharmaceutical and diagnostic companies, and build new long-read RNA-seq datasets. These efforts will support applications in biomarkers, clinical trial design and diagnostics.

Blank Bio is developing RNA foundation models that analyze the molecular complexity of tumor transcriptomes. The goal is to improve patient-level predictions in oncology.

In collaboration with PacBio, Blank Bio will generate PacBio HiFi long-read bulk RNA sequencing data from up to 100 fresh-frozen tumor samples across multiple cancer types. The sequencing will be conducted at Seattle Children’s Research Institute, using automated Kinnex RNA library preparation on the SPTLabtech firefly®+ platform.

Blank Bio will use this dataset to train and evaluate its oncology models, focusing on improving patient stratification, biomarker discovery and clinical interpretation by incorporating RNA-level signals.

Bulk RNA-seq is widely used in oncology research, drug development, and clinical care because it measures tumor biology at a scale that is practical for real world use. However, most standard analysis methods reduce the data to simple gene-level counts, which can miss important details such as isoform structure, mutations and patient-specific tumor complexity.

“PacBio HiFi long-read sequencing was built to resolve biology that other technologies miss, and nowhere is that more consequential than in the complex transcriptomes of patient tumors,” said David Miller, Global Vice President of Marketing at PacBio. “Blank Bio’s foundation models demonstrate how high-resolution RNA data and machine learning can advance the next generation of precision oncology applications, from biomarkers and diagnostics to clinical trial design.”

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“Bulk RNA-seq is one of the most clinically accessible and information-rich assays in oncology, but much of its signal is still reduced to simplified gene-level summaries,” said Jonathan Hsu, CEO and Co-Founder of Blank Bio. “Blank Bio was founded to apply foundation models to the full molecular detail contained in each patient’s tumor transcriptome and turn that information into more precise, clinically useful predictions. This financing will support continued model development and partnership expansion. At the same time, our collaboration with PacBio will generate the high-resolution long-read RNA data needed to further train and evaluate these models in patient tumor samples.”

“Blank Bio is building at the intersection of two major shifts in biology: the expanding clinical use of RNA-seq and the emergence of foundation models capable of learning complex biological patterns at scale,” said Sahir Raoof, TechBio advisor to SignalFire. “The company brings together deep scientific and technical expertise in RNA biology, machine learning, and oncology, with a platform that has the potential to turn transcriptomic data into a more powerful layer of patient-level insight for drug development and diagnostics.”

About Blank Bio

Founded by Philip Fradkin, Ruian Shi, and Jonathan Hsu, Blank Bio is an applied AI research lab building foundation models that study patient differences using transcriptome data. The company focuses on extracting patient-level insights from bulk RNA-seq that traditional gene-count methods often miss. Blank Bio also works with pharmaceutical and diagnostic companies to help identify suitable patient populations for therapies, predict disease progression and support RNA-seq–based clinical diagnostics.

About PacBio

Founded in 2004, PacBio is a life science technology company that develops advanced DNA sequencing tools for researchers and clinicians. Its technologies, including HiFi long read sequencing, help solve complex genetic problems across areas such as human genetics, plant and animal research, infectious disease, microbiology, oncology and other emerging fields.

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