When Bio met Tech 💘
When Bio met Tech 💘
AI/ML Revolutionizing Drug Discovery
“What is mathematics? It is only a systematic effort of solving puzzles posed by nature”.
By Shakuntala Devi
✳️ News ❇️
🥦 The Simons Foundation and Simons Foundation International are now accepting applications for the next class of Pivot Fellows. The program provides funding for today’s brightest minds to apply their talent and expertise to a new field in mathematics or the natural sciences.
🥬 Join Nucleate Summit Partnering Day on March 13th, to learn about their mission, hear from their 2023 Summit partners and explore 2024 Summit partnership opportunities.
🥑 Join NVIDIA at the 2024 GTC AI conference.
🫛 FB1006: AI-discovered drug advances to clinical trials for ALS
🫑 Microsoft and 1910 Genetics to enable AI-driven drug discovery
🌽 hubXchange’s Augmented Intelligence in Drug Discovery Xchange Philadelphia 2024, is bringing together executives from pharma and biotech to address and find solutions to the key issues faced in AI-led drug discovery. Discussion topics will cover Data Quality, Target Identification, Lead Generation & Lead Optimization and Drug Response Prediction.
BioStrand: LLMs and Antibodies
BioStrand—founded in Belgium and acquired in 2022 by ImmunoPrecise Antibodies/IPA in Canada 🍁 for €20M—is a company at the intersection of biotech discovery, biotherapeutics and AI. Biostrand has a patented LENSai™ Integrated Intelligence Technology powered by HYFTs®, that seamlessly integrates massive data from diverse data sources, to enhance LLMs and accelerate antibody discovery.
In particular, by analyzing diverse data sources LENSai can identify new antibody targets and predict binding affinities, as well as design and optimize antibody sequences and predict potential side effects, immunogenicity and therapeutic applications. Then, the HYFT technology (their proprietary transversal language) powered by ML and NLP, uncovers meaningful patterns, sequences, connections and insights from data, empowering scientists to make faster and more informed decisions. Moreover, HYFT BioStrand’s universal language for biological data, can unify, organize and standardize all omics data, which enables scientists to collaborate and perform more efficient and accurate analyses.
Their HYFT language uniquely captures sequence, function and protein structure info in a single multi-dimensional knowledge graph with over 25B+ relations. The platform continuously enriches its knowledge base through data looping, while NLP provides instant access to 33 million abstracts from the PubMed database, expanding the network. Their platform, LENSᵃⁱ, seamlessly integrates: Sequence (DNA-RNA-Protein), Structure (AlphaFold, ESM-2, Rosetta Fold, Cryo-EM, Crystallography) and Text (Peer-Reviewed Literature, Patents, Clinical Trials).
In a case study of Validating LENSai in silico antibody epitope binning against classical wet lab binning, LENSai was used for epitope binning—a crucial step used to characterize the binding of monoclonal antibodies to target a protein—performed on 29 antibodies sequences directed against a transmembrane protein. Then the results were compared with classical wet lab binning indicating that BioStrand's AI accurately predicted antibody-antigen binding interactions. Moreover, the AI identified similar antibodies that shared epitopes, aiding in grouping them together. This case study demonstrates how BioStrand's AI technology:
can significantly improve the epitope binning process for a faster, more accurate and cost-effective development of therapeutic antibodies,
and offers also a green environmentally friendly solution, that is safer for the planet, by reducing lab waste from unnecessary wet lab experiments.
On November 13, 2023, IPA announced that its subsidiary BioStrand has published a preprint of its groundbreaking white paper titled, "New Paradigm for Biological Sequence Retrieval Inspired by Natural Language Processing and Database Research" on bioRχiv. In the manuscript, they present their novel search algorithm involving an indexing scheme based on patterns discovered by natural language processing, i.e., short strings of nucleotides or amino acids, akin to standard k-mers, but mined from cumulative cross-species omic data repositories. Their results suggest that the HYFT-indexing and searching is a good alternative and a static, alignment-free method to retrieve homologous sequences down to 50% sequence identity.
✴️ Patterns ✴️
Regarding patterns, LLMs and search algorithms, BioStrand is a company on its way to potentially solve the Information Integration Dilemma in systems biology (Cracking the Information Integration Dilemma (IID) in systems biology) by learning how to to integrate, standardize and curate “ALL data omics complexity” into one comprehensive, contextual, scalable data matrix that will change forever the way we do research.
Information integration is the merging of information from heterogeneous sources with differing conceptual, contextual and typographical representations. It is used in data mining and consolidation of data from unstructured or semi-structured resources.
When it comes to omics data and biology, cracking the Information Integration Dilemma means finding this “something” that connects the genetic code with the transcriptome and the proteome in the realm of mathematics, physics and information science, beyond chemistry and beyond biology.
Think of this “something” like a “shadow code”—like the theater of shadows 👤👥 where a beam of light behind the actors (for example the mRNAs) will place them in silhouette so the audience will only see their outline (2D structure)—but in actual reality this “something” works like a software in a higher dimension (3D or 4D or even 5D) that actually runs a manufacturing site allowing our cells to produce, in a highly sophisticated and hierarchical way, all the mRNAs at any given time and space point (decoding randomness for more).
This “shadow code” (or data matrix) orchestrates the entire manufacturing line from transcription to translation, and goes back to our origins, where probably nothing happened randomly.
“From where we stand the rain seems random. If we could stand somewhere else, we would see the order in it.”
Tony Hillerman, Coyote Waits
Ingrid Brands is the co-founder and former CEO of BioStrand, which was founded in 2019, and now holds the position of General Manager guiding the company's path towards becoming a global leader in the genetic research domain. The biotech startup is a family affair since the husband and wife duo Dr Dirk Van Hyfte and Dr. Ingrid Brands developed this technology.
BioGeneration Ventures (BGV)
BioGeneration Ventures (BGV) is the early-stage strategy of the Forbion-BGV platform of funds, which also includes Forbion Ventures and Forbion Growth. BGV—that focuses on company creation, seed and series A rounds—has been located with Forbion in Naarden NL 🌷 since inception. BGV invests in partnerships with other professional investors in life sciences and has built strategic relationships with various academic institutions and leading healthcare companies as well as venture capital investors in the Netherlands, the EU and the US. Since their inception in 2006, BGV has managed over €400M across four funds.
On July 13, 2023, BGV announced the closing of BGV V at €150M, its largest fund since launching its first fund in 2006. BGV V was oversubscribed, with strong demand from both existing and new investors, with existing investors Eli Lilly and Company, Novo Holdings and Bristol Myers Squibb further strengthening BGV’s investor base of strategic life sciences and institutional investors. Of the new investors in the fund, 78% were of US origin, all of whom are either large financial institutions or global life sciences companies. The managing partners are Edward van Wezel and Oskar Slotboom and BGV invests into 🧚:
Dunad Therapeutics (UK, 2021) that focuses on the development of next-generation targeted protein degradation therapies.
Fibrocor Therapeutics (Canada, 2020) is developing therapeutics based on a discovery platform for novel fibrosis targets.
Scenic Biotech (The Netherlands, 2017) develops a technology platform to discover disease suppressor genes.
Tiga TX (US, 2020) develops an IgA therapeutic monoclonal antibody platform for the treatment of solid tumors. And
Synaffix BV (The Netherlands, 2013) develops a next generation anti-body drug conjugate platform. In 2023 Lonza acquired Synaffix.
As I mentioned earlier, BGV is part of the Forbion-BGV platform of funds, which also includes Forbion Ventures and Forbion Growth. More specifically, Forbion (Series A-B rounds) that operates a joint venture with BGV, was born out of ABN AMRO Capital Life Sciences and currently manages €3 bn across ten funds. As of October 2022, Forbion holds 43 active portfolio companies bringing its investments to 95 companies to date with 46 employees.
Forbion’s investors include the European Investment Fund (EIF), notably through its European Recovery Programme (ERP), LfA, the Dutch Venture Initiative (DVI) and AMUF facilities, and the Kreditanstalt für Wiederaufbau (KFW) through the ERP – Venture Capital Fondsfinanzierung facility.
Forbion invests into 🧚♀️:
AAVantgarde Bio in Italy 🍕has two proprietary, AAV-based large gene delivery platforms. The first leveraging DNA recombination, named dual hybrid and the second, a protein trans-splicing, named AAV intein.
Orbis’ platform in Switzerland 🧀 is the first to systematically explore the macrocycle chemical space using a unique combination of high-throughput chemical synthesis and large-scale assaying, supported by ML.
Rampart Bioscience in the US is developing a novel non-viral gene therapy platform based on a proprietary HALO DNA technology that has been designed to deliver genetic medicines effectively and durably, and to overcome key limitations and safety concerns of viral and early non-viral gene therapy approaches.
Bluebird Bio in the US is developing innovative gene therapies for severe genetic disorders from a broadly applicable gene therapy platform. Bluebird bio has two later stage clinical products in development for childhood cerebral adrenoleukodystrophy and beta-thalassemia/ sickle cell anemia. The company was formerly known as Genetix Pharmaceuticals.
With offices in The Netherlands, Germany and Singapore Forbion is managed by Sander Slootweg.
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Advanced Machine Learning for Innovative Drug Discovery, the AIDD project
The prime goal of the AIDD project is to train and prepare a new generation of scientists who have skills both in ML and in chemistry and can advance medicinal chemistry. This project is funded by Horizon2020 research and innovation programme under the Marie Skłodowska-Curie actions and the final AIDD School will be taking place in Berlin, from 04.03 until 13.03. 2024. The agenda and Zoom link/s for the lectures can be found on the Lectures page.
Lectures 👨🏫👩🏫 that are going to be open to the public are:
Monday 4th March, Lecture by John O'Donnell (Bayer)
Integrated Structural Biology: everything but the kitchen sink.
Monday 4th March, Lecture by Thomas Löhr (AstraZeneca)
Navigating the Maize: Computational chemistry workflows with cycles and conditions.
Wednesday 6th March, Workshop by Gilles Marcou (UNISTRA)
Intro to KNIME and Standardization of Molecules in KNIME.
KNIME the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform.
Wednesday 6th March, Workshop by Alex Tropsha (UNC Eshelman School of Pharmacy)
Rigor and reproducibility of Chemoinformatics models: from data curation to experimental validation.
Wednesday 6th March, Practical Session by David Winkler (La Trobe University)
Choosing an algorithm, descriptors and approach for diverse applications of AI and ML.
Thursday 7th March, Lecture by Alexandre Tkatchenko (ULUX)
Navigating Chemical Compound Space Directly and Inversely.
Thursday 7th March, Lecture by Robin Winter (Pfizer)
Multi-Objective Optimization in Continuous Latent Spaces.
Monday 11th March
GPU Programming Workshop by NVIDIA.
Tuesday 12th March, Lecture by Geemi Wellawatte (EPFL)
XAI for Chemistry.
Tuesday 12th March, Lecture by Mike Preuss (ULEI)
Monte Carlo tree search and multi-objective variants.
Decktopus AI is an AI-powered presentation generator.
Verdane Investment Firm
Verdane based in Oslo is a specialist growth investment firm that partners with tech-enabled and sustainable European businesses. Verdane can invest as a minority or majority investor, either in single companies or through portfolios of companies, and looks to deploy inside two core growth themes; digitalisation and decarbonisation.
Verdane funds hold over €5.7 billion in total commitments and have made over 300 investments in fast-growing businesses since 2003. Verdane’s team of over 140 investment professionals and operating experts, based out of Berlin, Munich, Copenhagen, Helsinki, London, Oslo and Stockholm, is dedicated to being the preferred growth partner to tech-enabled and sustainable businesses in Europe.
The firm has just successfully closed its newest fund Edda III at €1.1 billion doubling its predecessor fund, and has invested into 👛:
ams makes sensor solutions that make devices smarter, safer, convenient and more environment-friendly. They offer sensors (including optical sensors), interfaces and related software for consumer, communications, industrial, medical and automotive markets.
AquaGen is a breeding company which develops, produces and delivers genetic material 🧬 to the global aquaculture 🐟 farming industry. Through market-oriented research and development AquaGen has achieved a leading position as a provider of fertilized eggs of Atlantic salmon and rainbow trout.
CRF Health is a top-three global provider of electronic patient reporting solutions. The company's strength on the global market made it well-positioned to capitalize on the strong market potential of the Clinical Outcome Assessment (COA) market.
Scientists aghast at bizarre AI rat with huge genitals in peer-reviewed article
It's unclear how such egregiously bad images made it through peer-review. 🙀
Flagship Biosciences
Flagship Biosciences is a leader in supporting drug development through biomarker analytics and the application of spatial biology technologies. They provide a comprehensive biomarker solutions service that encompasses broad testing capabilities using their AI enabled pathology platform to deliver the most accurate and informative data available. Areas of Flagship expertise using ML and computer science to analyze and interpret data include Image Analysis and Genomics:
They offer spatially resolved data (transcriptomics and proteomics) using appropriate computational methods. By utilizing a combination of expert image analyst guidance, pathologist review and ML they ensure the best quality data from any tissue sample from scanning through final results.
Flagship has partnered with Genomenon® (a Genomic Intelligence company for Genetic Disease & Cancer) to provide its customers with access to Genomenon’s rare disease and oncology genetics library.
On January 23, 2024, Flagship Biosciences—considered a leader 🎖️ in spatial biology and biomarker analytics services—and Offspring Biosciences—a preclinical contract research service—announced their partnership in order to advance precision drug development with a complete biomarker offering from discovery to companion diagnostics development.
Founded in 2009 by David Young, Flagship Biosciences has raised a total of $15.3M.
For more: When Tech met Bio 💘 (2nd part).
Until next time 🏵️