Top Stories from 2023: Spatial Biology, Innovative Practices, Generative AI, More

January 4, 2024

January 4, 2024 | Spatial biology, large language models, and new informatics tools. Bio-IT is exploring how AI fits into workstreams, still wrangling with data management challenges, and shaping discovery for the new era. Here are the top stories from Bio-IT World as well as thought leaders in the industry. –The Editors

Three Pillars of 10x: Outlook for Single Cell, Spatial and In Situ Platforms

Serge Saxonov, CEO and co-founder of 10x Genomics, gave an overview of the company’s overall progress in its Visium, Chromium, and Xenium platforms at the JP Morgan Healthcare Conference in 2023. Saxonov emphasized the strength of the 10x team, the mergers and acquisitions that have led to the development of the platforms, and the breadth of the company offerings. 

Bio-IT World Names 2023 Innovative Practices Winners

Bio-IT World today announced the 2023 Innovative Practices Awards winners. Six projects were honored. Companies involved in the winning entries included AbbVie, Bayer G4A; Carenostics; City of Hope; Generate Biomedicines; Hackensack Meridian Health; Higher Steaks; Regeneron Pharmaceuticals; SciBite; and Synthace.

Illumina Relaunches Correlation Engine, Banking on Need for ‘Omics Informatics Tools

Illumina relaunched its BaseSpace Correlation Engine—now simply Illumina Correlation Engine—as the sequencing company emphasizes connecting its informatics components together, Mike LeliveIt, VP of Product Management, told Bio-IT World. “What people want now is for the components to talk to each other so they can get work done and they don’t have to build tools. Our shift to Illumina Connected Software really represents the importance of what we’re building.” 

Spatial Biology Poised for Explosion by 2027

Spatial biology is poised for an explosion in the next few years, said Colin Enderlein, a principle at DeciBio Consulting. Speaking in San Diego at the Molecular and Precision Med Tri-Con, Enderlein shared the results of DeciBio’s recent market report on the space. 

Japanese Medical Team Discovers Gut Microbiota to Diagnose and Treat Dementia with Lewy Bodies

A research team from the Nagoya University Graduate School of Medicine (NUSM), Japan, discovered three gut bacteria types that may lead to predicting and treating dementia with Lewy bodies (DLB): Collinsella, Ruminococcus torques, and Bifidobacterium.

Owkin’s Generative AI Vision for Understanding Biology

Generative AI in drug discovery is primarily a patient stratification play, says Thomas Clozel, CEO of Owkin. “People generate new molecules; that’s cool. But I think what you need to generate first with Gen AI is knowledge.” Identifying which group of patients might best respond to a particular drug can still be foggy at best. “Today what AI brings is a new way to characterize certain groups of patients that will see high value and benefits from a drug.” This is the problem Clozel hopes to solve with Owkin, a techbio company he co-founded in 2016. But while he calls Owkin tech-first and his drug discovery platform is in silico, he is prioritizes gathering new knowledge from patient biology. 

NVIDIA and Mitsui Launch Japan’s First Generative AI Supercomputer to Accelerate Drug Discovery

In collaboration with NVIDIA, Mitsui, Japan, recently launched Tokyo-1, a supercomputer designed to boost Japan’s $100B pharmaceutical industry. The project features 16 NVIDIA DGX H100 AI systems—a part of NVIDIA’s NGX enterprise AI platform—to simulate high-resolution molecular dynamics and generate AI models for accelerated drug discovery.

Anastasia Christianson on Pfizer’s Approach to AI, ML, and the Digital Age

At Pfizer, AI plays a key role in every step of the drug discovery process, Anastasia Christianson, Global Head of AI, ML, Analytics, and Data at Pfizer, tells Bio-Team co-founder Stan Gloss on the latest episode of the Trends from the Trenches podcast. And she means it. Christianson lists the areas at Pfizer where AI is in play and for which she has AI/ML responsibility: research and discovery, clinical development, manufacturing supply chain, commercial, medical affairs, human resources, financial departments, and more. Pfizer doesn’t have a digital strategy, Christianson says, turning that buzzword on its head. “Instead, we have a business strategy for a digital world.”

Novel Mouse Avatars Could Advance Personalized Medicine For Cancer

Up to now, mouse avatars haven’t proven to be particularly good tools for forecasting treatment response in human cancer patients. But new models being generated by an international team of researchers are expected to be far more predictive of what is going to happen with different cohorts of clinical trial participants.

Take the DNA Delorean: The Promise of Large Language Models in Genomics

Comment: Elucidating information directly from DNA to understand RNA's and human proteins' downstream structure and function is the holy grail of nearly a century of molecular biology research. The central dogma of the field—that DNA is transcribed into RNA before translation into protein—describes in clear linguistic terms the way our cells function. Today, argues Vanessa Braunstein, NVIDIA, large language models (LLMs) such as GPT-3 and Megatron Turing NLG demonstrate remarkable abilities to interpret, translate, summarize, and generate human languages. Now, we are finally generating the amount of data required to train such models in the language of biology.

‘The Process Is the Product’ Is No Longer Enough. Now, Data Is the Deliverable

Comment: In biomanufacturing, particularly with respect to advanced therapies such as gene and cell therapies, there is a saying: "the process is the product." That insight is still important, but it's also insufficient say Marc Smith and Sadik Kassim of Danaher Corporation. As the industry adapts to increasingly complex manufacturing processes, we'd like to propose a reframe: the data is the deliverable. For personalized medicine to reach its potential, leveraging process data to drive learning will be key.

Discovery To Creation: Highlights from the 2023 Single-Cell and AI in Medicine Symposium

Comment: “Technology and computation are revolutionizing the way we are creating and developing new drugs,” Cellarity CEO Fabrice Chouraqui say. The field of drug discovery is shifting its approach from viewing complex biology as something to be overcome using reductionist principles to something to embrace in a more holistic approach to cell biology.