BayBifx and Strand Life Sciences at Myriad Genetics

BayBifx and Strand Life Sciences invite you to an evening of talks on Bioinformatics and Big Data at Myriad Genetics!
Simplifying Pipeline Management: From Automation to Infrastructure Setup

Please Register Here: https://forms.gle/n7LCnCR6BAPwkaGJ9

======================= Talk Schedule ============================
Roke Bio: Unlocking advanced protein manufacturing using systems engineering [10 min]
Presenter: Dr. Romel Menacho-Melgar
Abstract: Roke Biotechnologies has developed a systems engineering protein manufacturing platform in E. coli that enables advanced capabilities in protein expression and purification. By decoupling growth from production, the platform delivers standardized, scalable bioprocesses and an autolysis strain that works without tuning across diverse workflows, from high-throughput screening to in-bioreactor purification. Freed from growth-associated boundary conditions, we have also developed advanced tools that drive robust expression of hard-to-express proteins, establishing a versatile foundation for next-generation biomanufacturing.

Strand Life Sciences: Automated Metadata Ingestion and Harmonization in Strand's scRNA-seq Portal and Beyond [20 min]
Presenter: Badri Padhukasahasram, VP of Data Science, Strand Life Sciences
Abstract: Harnessing and standardising metadata from public repositories (like NCBI’s GEO, CellxGene, ArrayExpress etc) can help unlock its potential for a range of research questions. We have developed an automated system based on Retrieval Augmented Generation (RAG) and Large Language Models (LLM) to quickly and accurately (> 95% on average) standardize biomedical terms from
real world paragraphs to standard ontologies. Performance of this pipeline is demonstrated on manually curated ground truths from Strand’s scRNA-seq portal and provides ~3x improvements in turn around time compared to manual curation. The LLM pipeline also provides reliable metrics of quality to enable curators to prioritize manual followup checks and corrections.

Myriad Genetics and Strand Life Sciences: Master Infrastructure Set Up for Multiple Pipeline Integrations in Minimal Residual Disease (MRD) [40 min]
Presenters:
Kirthi Moulika, Software Engineer, Strand Life Sciences
Radhakrishna (RK) Bettadapura, VP, Research Informatics, Strand Life Sciences
Erik Anderson, Staff Software Engineer, Myriad Genetics
Benjamin Vaisvil, Staff Software Engineer, Myriad Genetics
Abstract: This talk will outline the challenges in bioinformatics workflows and our solutions for simplifying day-to-day tasks. It will cover the Strand-Myriad collaboration, which has resulted in a master infrastructure setup, including an ICA computational system using DRAGEN, DNAnexus integration with S3, and configuration of ICA projects for storage on S3, for the easy execution of the complete pipeline.
This infrastructure solution, which facilitates integration with S3 and configuration of analysis pipelines, has resulted in significant cost reductions in terms of storage and computation time, as evident in the MRD assay.
Overall, the audience will take away important strategies for reducing costs, cloud storage, and computation time, as these are essential for the successful launch of production-ready NGS tests.

Castle Biosciences: Genetic Algorithms For High Dimensional Feature Refinement [20 min]
Presenter: Kyle R Covington, Director of Bioinformatics
Abstract: High-throughput biological assays frequently generate extensive feature spaces, posing challenges for downstream analysis, assay cost, and interpretability. Here, we present a versatile framework that employs genetic algorithms (GAs) for constrained feature selection in bioinformatics workflows. This approach evolves compact feature subsets optimized for both predictive performance and practical deployment. We demonstrate how hybridizing GAs with neural network–based predictive modeling can be used to generate robust predictive algorithms that can be deployed within laboratory assay constraints. Key implementation considerations and strategies for preventing overtraining are discussed. This work underscores the utility of GAs as generic optimizers in bioinformatics and provides best practices for their integration into feature‐selection tasks where technical and operational constraints are paramount.

General Announcements

Schedule:
5:00-5:45 - Arrival & Networking
5:45-7:30 - Presentations
7:30-9 - Networking

This event will be available both in person or via Webinar.

Webinar Link:
https://myriad.zoom.us/j/95407735951?pwd=cd2FgTwcrCUjbjm0fXFSXD2TqW78Xy.1
Passcode: 822994
(The webinar and recording will start at 5:45)

The recording of the webinar will be available after the event. If you would like a copy of the recording please contact Jaya Singh (jaya@strandls.com) or Shane Brubaker (shanebrubaker55@gmail.com)

Food and drinks will be provided
Indian Food catered by Varam, Redwood City

Parking will be available in the Nexus garage (next to Myriad) until 9:30 pm