Company Overview
Introduction
Eclipsebio (legally registered as Eclipse Bioinnovations, Inc.) is a private, venture-backed biotechnology and genomics company specializing in advanced RNA biology, next-generation sequencing (NGS) analytics, and AI-driven sequence design. Founded in 2017 as a university spin-out from Professor Gene Yeo's laboratory at the University of California, San Diego (UCSD), the company is headquartered in San Diego, California, USA.
Eclipsebio operates at the intersection of data science and life sciences, providing an end-to-end framework to support the design, prototyping, manufacturing, and characterization of RNA-focused applications. The company services more than 300 partners across academic institutes, biotechnology firms, and global pharmaceutical corporations?including a vast majority of the top biopharma organizations by revenue. Its principal focus is to accelerate and de-risk the development of safer, more effective RNA therapeutics, vaccines, and gene therapies.
Continue…Core Technology and Approach
The company?s foundation is built upon proprietary, high-throughput NGS assays capable of mapping the "RNA interactome" with single-nucleotide resolution. Unlike traditional quality control and sequencing workflows that fragment molecules or introduce amplification biases via cDNA intermediate conversion, Eclipsebio utilizes sophisticated multi-omic techniques and direct RNA sequencing (such as Oxford Nanopore platforms). This allows the company to study intact, full-length RNA molecules from their 5' start to their 3' end, capturing structural variations, location-specific base modifications, and poly(A) tail dynamics.
By integrating these precision physical assays with artificial intelligence, Eclipsebio utilizes a "lab-in-the-loop" model. Empirical genomic data generated by physical sequencing tests is fed back into machine learning models to iteratively refine, optimize, and synthesize superior RNA drug candidates.
Strategic Platforms
Eclipsebio deploys its capabilities through three foundational commercial platforms, which allow drug developers to transition seamlessly from computational target selection to final product validation.
1. eCOMPASS?
The eCOMPASS platform serves as the company's central, integrated workflow for RNA drug development. It bridges the gap between disconnected vendor services by consolidating sequence design, rapid prototyping, and sequencing-first analytics into a singular iterative loop.
* Design-Make-Characterize Workflow: Each iteration utilizes empirical molecular data to make the subsequent computational candidate better. It assists developers in designing sequence configurations that avoid translational stalling and unintended secondary structures.
* Terrain Bio Acquisition Integration: Enhanced by the strategic acquisition of Terrain Biointelligence (Terrain Bio) in early 2026, eCOMPASS leverages advanced AI sequence design algorithms paired with highly scalable, rapid-response prototyping capabilities.
2. eMERGE?
Launched in mid-2024, eMERGE is an end-to-end analytical platform designed specifically for the deep characterization and optimization of manufactured RNA-based therapeutic products. It assesses therapeutic substance identity and integrity across complex modalities such as messenger RNA (mRNA), circular RNA (circRNA), and self-amplifying RNA (saRNA).
* Functional Measurement: Evaluates translation efficiency, structural stability under varied conditions, and active microRNA (miRNA) regulation.
* Formulation & Storage Impact: Tracks how Lipid Nanoparticle (LNP) packaging modifications and storage timelines affect the secondary structure of the encapsulated RNA.
* eSENSE dsRNA? Module: An expansion module introduced to provide precise quantification and localization of double-stranded RNA (dsRNA) impurities, which are critical triggers for adverse cellular immune reactions.
3. eVERSE?
eVERSE is a comprehensive portfolio of high-quality, highly reproducible, and structured RNA-focused datasets engineered specifically for AI and machine learning model training.
* Data Volume: Built upon millions of proprietary RNA data points compiled across nearly a decade of dedicated RNA research.
* Utility: Provides biopharma companies with clean training data that is absent from public databases, allowing them to train internal algorithms to predict RNA behavior, off-target binding, and cell-type-specific stability profiles.
Products and Proprietary Assays
Eclipsebio provides a diverse portfolio of customizable NGS assays, offered either as a standalone testing service (a la carte) or bundled into comprehensive development partnerships.
RNA Probing and Structural Assays
- eSHAPE: Enhanced SHAPE (Selective 2'-hydroxyl acylation analyzed by primer extension) utilizing a proprietary NAI reagent. It enables researchers to probe structural motifs across the entire length of an RNA molecule, evaluating how modifications or formulation environments alter secondary structures.
- 5' and 3' End-Seq: Specialized sequencing protocols targeting exact transcription start sites and polyadenylation sites. It is vital for characterizing transcript length uniformity, identifying alternative splicing, and verifying transcript isomer distributions.
Translational and Protein-Interaction Mapping
- eCLIP-seq?: The company?s pioneering technology for crosslinking and immunoprecipitation followed by high-throughput sequencing. It is highly efficient at identifying exact protein-binding target maps across the transcriptome, allowing scientists to chart exactly how RNA-binding proteins (RBPs) regulate RNA processing.
- miR-eCLIP-seq: A specialized variation optimized to map miRNA-mRNA interaction networks transcriptome-wide. This assay reveals endogenous microRNA silencing behavior and identifies precise binding regions.
- eRibo?: An advanced method designed to capture and profile ongoing cellular translation. By isolating actively translating ribosomes, eRibo tracks real-time protein expression levels and uncovers specific positions where the translation of an engineered sequence slows down or stalls completely.
Target Modalities and Solutions
Eclipsebio categorizes its technical solutions across five key operational areas, supporting client programs based on their molecule type and overall objectives.
1. RNA Therapeutics & Vaccines
The company supports biopharma clients in creating infectious disease vaccines, personalized cancer vaccines, antibody-encoding RNAs, and protein replacement therapies. The core value lies in ensuring that engineered transcripts maintain optimal stability, precise cellular regulation, and high translational efficiency when delivered in vivo.
2. Small Oligonucleotides
For developers advancing anti-sense oligonucleotides (ASOs), small interfering RNAs (siRNAs), short hairpin RNAs (shRNAs), anti-miRs, and miRNA mimics, Eclipsebio delivers:
* Target Accessibility Analysis: Confirming whether the oligonucleotide can successfully reach and bind its intended structural pocket on target tissue RNAs.
* Off-Target Binding Assays: Multi-omic profiling across the transcriptome to detect unintended hybridization events before clinical trials commence, minimizing toxicities.
3. Small Molecules Targeting RNA
As the pharmaceutical sector increasingly explores small molecules that directly modify or lock RNA structures rather than targeting proteins, Eclipsebio provides:
* Disease-specific target site identification.
* Mechanism-of-action (MoA) validation to confirm structural binding shifts.
* Transcriptome-wide safety evaluations.
4. Basic Research Support
Eclipsebio continues to maintain a specialized business pipeline for academic researchers. These offerings include flexible, single-gene or transcriptome-wide multi-condition comparison studies, helping labs generate publication-grade maps of fundamental cellular mechanisms.
5. AI Training Infrastructure
Catering to modern digital-health and computer-aided drug discovery divisions, this solution utilizes the eVERSE pipeline to supply clean, non-public genomic data packages, validating machine learning inputs for complex biological systems.
