Un-locking 🔐 Data to Transform Biology (part I)
Un-locking 🔐 Data to Transform Biology (part I)
Trends on TechBio: WhiteLab Genomics, Sinopia, Cure51, Owkin, Parallel Bio, PipeBio, Turbine AI, IridescentBio Bio and Peptone
This week’s updates:
Un-locking 🔐 Data to Transform Biology (part I)
Trends on TechBio: WhiteLab Genomics, Sinopia, Cure51, Owkin, Parallel Bio, PipeBio, Turbine AI, IridescentBio Bio and Peptone
Un-locking 🔐 Data to Transform Biology (part II)
Trends on TechBio: Pace Ventures, Giant Ventures, Trisonic Discovery, Thoughtworks, Big_Bets, Cradle Bio, Mercia and Octant Bio
Un-locking 🔐 Data to Transform Biology (part III)
Trends on TechBio: New Atlantis, IPA (BioStrand, Talem), Aging Intervention Foundation, Synthace, Blume VC, Elucidate Bio and Genesis Therapeutics
"Once the cells in a biological machine stop working, it can never be started again. It goes into a cascade of decay, falling toward disorder and randomness. Except in the case of viruses. They can turn off and go dead. Then, if they come in contact with a living system, they switch on and multiply. (194)"
Richard Preston (The Hot Zone: The Terrifying True Story of the Origins of the Ebola Virus
WhiteLab Genomics
At the interface between gene and cell therapy companies, we have the French AI biotech company WhiteLab Genomics (SaaS/Cloud), that provides to the gene and cell therapy companies predictive software simulations to facilitate the design of gene and cell therapies. The company was founded in 2019 by David Del Bourgo, MBA—a former engineer at General Electric Healthcare—and Julien Cottineau, PhD—a geneticist who trained at the Institut Imagine in France—and has a proprietary platform that leverages graph knowledge technology and ML to help scientists discover and design new gene, RNA and cell therapies. The platform offers: target discovery (target expression, profiling, epigenetic signatures identification, protein structure and interaction simulations, cellular biomarker screening), payload design (sequence design, promoter/enhancer choice, chimeric construction, transgene expression modulation) and vector design (viral capsid & envelope design, transduction optimisation, biodistribution prediction, immunoreactivity modulation).
On October 31, 2023, WhiteLab Genomics announced that Laurent van Lerberghe—the former Chief Strategy Officer at Sanofi—joined its Board of Directors. This appointment marked a significant milestone as the company pursues its mission of advancing genomic medicine and healthcare innovation.
In 2023, Sanofi (EPA: SAN), WhiteLab Genomics, the TaRGeT Laboratory at Nantes University and Institut Imagine launched the WIDGeT consortium (Viral Vector Intelligent Design for Gene Therapy) to make France a global leader in gene therapy by accelerating the development of gene therapies using viral vectors derived from adeno-associated viruses (AAV) for the treatment of age-related macular degeneration and hereditary podocytopathies (kidney diseases), leveraging the potential of AI.
🍊 In February 2024, WhiteLab Genomics and Siren Biotechnology—the innovator of universal AAV immuno-gene therapy for cancer—announced a strategic partnership to develop an AI-powered indication discovery platform for AAV immuno-gene therapies for cancer. This collaboration will leverage WhiteLab Genomics’ next generation AI platform and expertise to identify additional target indications for Siren’s immuno-gene therapies, driving their joint vision to discover effective treatments for cancers.
🍊 On April 29, 2024, WhiteLab Genomics, the Vision Institute—an international research center on ophthalmic diseases—and ADLIN Science—which develops a decentralized digital research environment—have entered into a strategic partnership and launched GEAR (Evaluation of Adeno-Associated Virus Vector Gene Therapy for the Retina). The GEAR partnership aims at overcoming barriers and knowledge gaps in retinal dystrophies such as limited access, physical barriers and lack of knowledge of receptors present on retinal cells. GEAR will start with a budget of €4M from BPI France and funds from the Île-de-France region as part of the regional I-demo call for projects of the France 2030 plan.
🍊 On May 6, 2024, WhiteLab Genomics announced its US presence by joining Bayer’s Life Science incubator in Cambridge, MA to leverage Bayer’s (ETR: BAYN) expertise in order to accelerate drug development timelines and mitigate risks through AI-powered genomic analysis, marking a significant step in their mission to deliver life-saving therapies to the market.
WhiteLab Genomics has won numerous awards and is part of French Tech 2030. It was selected in Station F first Future 40 and is currently supported by Future4care incubator created by Capgemini, Generali, Orange and Sanofi. It is also a member of the prestigious American accelerator Y-Combinator. On September 13, 2022, Whitelab Genomics Raised $10M in Series A Funding from Debiopharm Innovation Fund, the strategic investment arm of Swiss biopharmaceutical company Debiopharm, and Omnes Capital.
Sinopia Biosciences Inc
Sinopia Biosciences founded in 2011 in California is enabling the promise of data-driven drug discovery (D4) by applying high-throughput multi-omics data, ML and network analyses and disease models (genome engineered in vitro models and relevant in vivo models). The company is focused on metabolomics. Combining pioneering advances in metabolomics technologies and computational data analysis is enabling Sinopia to study diseases and compounds at an unprecedented level of biomolecular detail using signals (i.e. metabolites) that most closely relate to cellular functions. These advances in multi-omics data generation and ML analysis led to their platform LEADSTM (LEarn And DiScover) that combines high-throughput screening, multi-omics data, AI/ML and network analyses to rapidly identify novel targets and mechanisms.
On April 19, 2023, Sinopia announced that it has selected SB-0110 (a novel proprietary small molecule) after extensive preclinical studies as its lead clinical candidate for Parkinson’s disease and levodopa-induced dyskinesia.
SB-0110 is a novel, proprietary small molecule with a unique mechanism of action. In multiple preclinica studies, SB-0110 has demonstrated a unique and potentially transformative pharmacology for treating both the symptoms of Parkinson’s disease and also the complications of levodopa, (i.e., levodopa-induced dyskinesia). Further, SB-0110 has demonstrated potential for cognitive enhancing effects in non-human primate models of Parkinson’s disease, an area of high unmet need with no approved treatments
🍊 On May 30, 2024, Sinopia Biosciences announced that it has been awarded a Small Business Innovation Research (SBIR) grant from the National Institute of General Medical Sciences (NIGMS) to advance its computational drug discovery LEADS™ platform and explore applications in oncology and immunology.
🍊 On September 12, 2024, Sinopia was awarded a Phase II SBIR grant, totaling $2.2M, from the National Institute of Dental and Craniofacial Research to advance its oral mucositis program to lead discovery and optimization.
Sinopia Biosciences has raised $14.4M and the co-founders are Aarash Bordbar and Bernhard Palsson.
Cure 51
Cure51 (France) is building the first global clinical and molecular database of cancer survivors to discover the biological features that made them "outliers." The aim is to pioneer the creation of the world's first global clinical and molecular database of cancer survivors, by rewriting the narrative of cancer. Rather than focusing on the disease mechanisms, Cure51 studies those individuals who defy statistics and miraculously survive the most aggressive forms of cancer, including metastatic stage pancreatic cancer and glioblastoma.
🍊 On March 20, 2024, Cure51 announced that it had successfully raised €15M in a seed funding round led by Sofinnova Partners. Other investors included: Hitachi Ventures GmbH, Life Extension Ventures, Xavier Niel, and Olivier Pomel, CEO, and co-founder of Datadog.
Cure51 was founded in March 2022 by Nicolas Wolikow and Simon Istolainen, with input and support from Okwin co-founder Thomas Clozel, alongside seasoned entrepreneurs and five world-renowned oncology centers: Gustave Roussy Institute (IGR, Paris - France), Leon Bérard Center (CLB, Lyon - France), Charité Universitätsmedizin (Berlin - Germany), Milan - Italy), the Instituto Europeo di Oncologia (IEO - Milan, Italy) and Vall d'Hebron (VHIO, Barcelona - Spain).
With its Scopus AI search now offered to Scopus customers, Elsevier is stressing its emphasis on responsible use of artificial intelligence.
Owkin Inc
Owkin (2016) is a French-American full-stack AI biotech that identifies novel treatments, optimizes clinical trials and develops diagnostics using histology slides and omics. Owkin is offering solutions for Multimodal patient data, Subgroup discovery, AI drug discovery (BiomarkerPLUS, TargetMATCH and DrugMATCH), AI drug development and AI diagnostics:
Abstra hosts a metadata catalog to enable researchers and data scientists to discover collaborators and datasets, enhancing and expediting AI biomedical research.
Substra is a ready-to-use, open source federated learning (FL) software developed by Owkin, now hosted by the Linux Foundation for AI and Data, that enables the training and validation of ML models on distributed datasets.
MOSAIC is a landmark research project to create a multimodal dataset with spatial transcriptomes from 7,000 patients in 7 cancer types. This is the largest spatial omics atlas to date.
On November 6, 2023, Owkin and 10x Genomics, Inc (Nasdaq: TXG), announced they have entered into an agreement to add 10x Genomics’ spatial omics and single-cell technologies to the MOSAIC project, which has already garnered attention for its pioneering work in tumor analysis for therapeutic discovery (OWKIN Integrates 10x Genomics Spatial Omics and Single-Cell Technologies to the MOSAIC Study).
MSIntuit™ CRC is a CE-marked AI diagnostic that provides a prescreen approach with digital pathology. MSIntuit is used for Microsatellite instability (MSI), genomic biomarker that plays an important role in the treatment of colorectal tumors (CRC) patients, from H&E WSI, and when performed the first successful blind validation confirmed its robustness for clinical applications.
On December 19, 2023, Merck taped Owkin’s AI to boost microsatellite testing of GI cancers.
MSIntuit® CRC V1 for colorectal cancer has already been approved in several European countries.
RlapsRisk™ BC is an AI diagnostic to help pathologists and oncologists determine the right treatment pathway for early breast cancer patients. RlapsRisk BC assesses the risk of distant relapse at 5 years of ER+/HER2- early invasive Breast Cancer patients, post surgery, from HES (hematoxylin-eosin-safran)-stained whole slide images (WSI) and clinical data.
🍊 On February 08, 2024, Owkin announced that they are working with Amazon Web Services (AWS) to transform drug discovery, de-risk and accelerate clinical trials and develop AI diagnostics. More specifically, Owkin selected AWS as its primary cloud provider to develop generative AI applications and accelerate drug discovery and development. The company will leverage AWS’s scalable storage options, enhanced data security measures and robust computing capabilities to empower scientists and researchers to access, analyze, and manage vast amounts of data efficiently and securely in the cloud (TechBio Unicorn Owkin Teams Up with AWS to Advance Generative AI for Precision Medicine). 🍊 On May 23, 2024, Owkin unveiled an innovative drug pipeline in oncology and immunology following an exclusive global licensing agreement with Idorsia (SIX: IDIA) to develop and commercialize OKN4395, a clinic-ready best-in-class dual inhibitor of prostanoid receptors EP2 and EP4 (Owkin Unveils AI-Driven Oncology and Immunology Pipeline, In-Licenses Best-in-Class Asset OKN4395).
Owkin launched on 🍊 February 20, 2024 Bioptimus which is a startup developing a large-language model (LLM), in order to build the first universal AI foundation model for biology to fuel breakthrough discoveries and accelerate innovations in biomedicine and beyond. The French startup was launched with a seed funding of $35M, led by Sofinnova Partners, with Bpifrance Large Venture, and additional funding from top global technology VCs. The world-class team at Bioptimus, led by Professor Jean-Philippe Vert, brings together Google DeepMind alumni and Owkin experts.
In 2021 Sanofi (EPA: SAN) inked a $270M cancer AI deal with Owkin, in order to utilize Owkin’s AI-driven platform for optimization of its clinical trial recruitment processes. In 2022, Sanofi’s Global Head of Partnering Alban de La Sablière headed to Owkin as CBO (Chief Business Officer), and all these after Owkin secured $80M from Bristol Myers Squibb (GILD).
🍊 On March 22 2024, Owkin, announced the expansion of their collaboration with Sanofi to include immunology (Owkin Expands Collaboration with Sanofi).
🍊 On July 03, 2024, Owkin announced its expansion into the DACH region (Germany, Austria and Switzerland) following partnerships with nine of the top centers in the region, including Charité – Universitätsmedizin Berlin, Centre Hospitalier Universitaire Vaudois (CHUV), Universitätsspital Basel, Technische Universität München (TUM), Uniklinikum Erlangen, Universitätsklinikum Leipzig, Inselspital Bern, Universitätsklinik Mannheim-Heidelberg and Medizinische Universität Wien (Owkin, an AI-Biotech Unicorn, Brings Its Cutting-Edge AI to Germany, Austria and Switzerland to Accelerate Research).
Owkin is founder-led by Thomas Clozel, MD, Oncologist, and Gilles Wainrib, PhD, Professor of Machine Learning, is trusted by 8 biopharmas with strategic deals with Sanofi and BMS, is first in class in AI diagnostics and is well-funded with million dollars (a total of $304.1M) raised from leading biopharma companies (Sanofi & BMS) and venture funds (Fidelity, Google Ventures & BPI, among others).
Parallel Bio (Parallel Biosystems, Inc)
Parallel Bio is using immune organoids and AI to design drugs. Founded by Robert M. DiFazio and Juliana L. Hilliard (in the midst of the COVID-19 pandemic) Parallel Bio started with developing an immune organoid to fill a significant gap in disease modeling.
Organoids are small, 3D mini models of human organs (about the size of a pencil eraser) that are the world’s most accurate models of disease, and have recently emerged as a powerful technology for drug discovery. Incredible advances in bioengineering and ML are now allowing scientists to grow organoids at a huge scale and to analyze the hundreds of cells and thousands of molecules that comprise the immune system in a way that humans simply cannot.
Parallel’s platform combines best-in-class human immune organoids with scale and computational methods to generate unprecedented insights into human health and disease. Not only can they rapidly discover new drugs that they know will work in patients from the start, but they know how well a drug performs across an entire population, something not currently possible with existing technology.
🍊 On May 17, 2024, Parallel Bio launched the Clinical Trial in a Dish to predict drug efficacy. The ‘Clinical Trial in a Dish’ to enhance early-stage drug discovery is an innovative approach utilizing human immune organoids and robotics to simulate the biological diversity of a population, potentially offering more accurate predictions of a drug’s safety and efficacy. So far, five pharmaceutical companies have already tested 20 drug candidates, signaling a shift away from traditional animal testing.
🍊 On June 26, 2024, Parallel Bio announced that Ari Gesher has joined as the first head of technology to oversee technical infrastructure and the development of advanced AI and robotics infrastructure to rapidly scale its immune organoid platform for drug discovery (Parallel Bio Appoints Deep Tech Innovator Ari Gesher as Head of Technology). Gesher joins from Insight M (formerly known as Kairos Aerospace), most recently as chief technology officer, where he spent more than seven years developing and growing its wide-area aerial methane detection technology used to manage industrial emissions of the greenhouse gas. Before that, he spent 10 years at Palantir in various engineering and outreach roles, joining in 2006 as one of the first software engineers at the big data software company.
Parallel Bio has raised a total of $4.6M in funding over two rounds.
PipeBio Aps
PipeBio, founded in 2020 in Denmark, is a cloud-based bioinformatics platform for biologics discovery, allowing wet lab scientists to easily analyze antibody and peptide sequences. They offer Antibody Discovery and Antibody Engineering, and they have the following tools for sequence analysis: Sequence storage and powerful querying, Configure workflows and automation by API and a Secure cloud platform.
Founded by Jannick Bendtsen and Owen Bodley, PipeBio now has an ambitious team behind that comes from different backgrounds, ranging from wet-lab biologists to computer engineers, with both academic and industrial experience.
🍊 In April 2024, they presented a study analyzing some single cell Next-generation sequencing (NGS) data and multi-target cross-reactivity assay data from the Beacon B-cell workflow in PipeBio (Bruker Cellular Analysis Beacon® Data in PipeBio Software). They demonstrated that the Beacon system can efficiently recover high quality variable heavy and light chain sequences from cells that have been pre-screened for functional binding. Furthermore, the sequence and assay data can be brought together and analyzed in tandem in the easy-to-use PipeBio platform. The Beacon Optofluidic System from Bruker Cellular Analysis (BCA; formerly Berkeley Lights) is an exciting technology that enables workflows for single cell analysis and functional characterization.
SanaCurrents, LLC is a research & analytics firm tracking market-moving catalysts of biopharmaceutical and medical technology stocks for the investment community.
The company offers its independent research services on a subscription basis, publishing reports on approximately 50 catalyst events every year.
Turbine AI (Turbine Simulated Cell Technologies Ltd)
Turbine’s in silico experiments can test an almost infinite number of interventions on a simulated cell that accurately reflects the molecular diversity of cancer cells. More precisely, Turbine’s core technology, the Simulated Cell™ platform, utilizes ML to understand how human cells make decisions, by mapping and modeling how thousands of signaling proteins interact and by characterizing cellular level cancer behavior and response or resistance to treatment. In other words, Turbine takes laboratory trial and error out of drug discovery and tackles it with scalable power on its servers, all by leveraging AI in an evolving, predictive platform to understand cancer mechanisms and unlock novel therapies with Simulated Cells.
🍊 On May 16, 2024, Accenture (NYSE: ACN) has made a strategic investment, through Accenture Ventures, in Turbine to further extend its capabilities to global biopharma companies that can benefit from Turbine’s ability to uncover hidden biological insights, with the potential to guide and accelerate key drug development workstreams (Accenture Invests in Turbine to Accelerate Use of AI-Powered Cell Simulations for Biopharma Research and Development).
Established in 2016 by Dániel Veres, Kristóf Zsolt Szalay, and Szabolcs Nagy Turbine has partnerships with several firms, including Harmonic Discovery, Bayer (ETR: BAYN), AstraZeneca (LON: AZN), Ginkgo Bioworks (NYSE: DNA) and Ono (TYO: 4528).
🍊 On September 12, 2024, Turbine announced that Ono Pharmaceutical Co., Ltd (Osaka, Japan) has selected multiple targets identified using Turbine’s in silico Simulated Cell™ platform for further development. Turbine will now lead in vitro validation of the identified targets in one of Ono’s priority cancer biology domains, in consultation with Ono (Turbine Achieves Key Milestone in Collaboration with Ono Pharmaceutical).
Additionally, they have three internal programs (Genome instability & mutation, Sustaining proliferative signaling, Deregulating cellular metabolism), a novel kinase program NEK1 in collaboration with Harmonic Discovery, a CDC7 program in collaboration with Cancer Research Horizons (as of February 3, 2023), three programs with Bayer, two programs with AstraZeneca and two more programs with biotech/pharma partners.
The London based Budapest University spinout Turbine AI raised a total $36.79M. Investors of Turbine include Accenture Ventures, MassMutual Ventures, Delin Ventures, XTX Ventures, Accel and 12 more.
IridescentBio: a cloud computational scientist on-demand
IridescentBio (The Netherlands) blends physics and chemistry based predictive modeling with rigorous analytics for antibody hit screening, AI training and antibody patent analysis. Their platform—that leverages Amazon Web Services (AWS) to predict antibody properties at scale—provides insights into binding affinity, target specificity and aggregation risks of antibodies. A typical run generates around 100,000 data points per antibody, within about one hour of compute time in the cloud. Intuitive reports are also generated to guide top-level interpretation of the data, helping biotech professionals to make more informed decisions in their antibody R&D pipelines.
IridescentBio outputs deep data within the space of antibody formulation parameters like pH, temperature, and salt and other excipient concentration. A typical run generates around 100,000 data points per antibody, within about one hour of compute time in the cloud. All AI-ready. Intuitive reports are also generated to guide top-level interpretation of the data, helping biotech professionals to make more informed decisions in their antibody R&D pipelines.
In 2023, Iridescent Bio partnered with The Lens to bring protein patents to life with AI and computational modeling. The Lens—is the flagship project of the social enterprise Cambia—that seeks to source, merge and link diverse open knowledge sets (including scholarly works and patents) to inform discovery, analysis, decision making and partnering on a human-centered user experience built on an open web platform, Lens.org, with toolkits designed to optimize institutional effectiveness in problem solving.
During this collaboration, Iridescent Bio will provide users an augmented view of patented proteins, allowing them to explore the "third dimension" of chemical and physical data that reside behind the printed words in the patent literature. Basically, they mine the IP and patent space of the therapeutic antibodies to enable a better understanding of these biomolecules as potential therapeutics. The user can input a patent number and then receive a report with chemical properties and a 3D visualization of each protein sequence—all created with AI and computational modeling. It’s a bit like a cloud computational scientist on-demand, with a one-hour turn-around time and no expertise required.
The company was co-founded by Aart Bijkerk (also Investor Liaison at We Love SaaS), Johannes (Hans) Fraaije (also Chief Science Advisor at Iridescent) and by Nicholas B. Tito, PhD that is also the Chief Scientific Officer. Nicholas is also the founder of Vanson Viridis—a scientific consultancy and predictive modeling for chemical, formulation and material R&D—and he was the Director of Science at RheoCube, a virtual lab for R&D departments to help scientists predict the physical behavior of complex fluids.
In December 2023, IridescentBio announced that they had closed a pre-seed investment round (Seed $ 377.8K), led by UNIIQ - Finance for the Future and Libertatis Ergo Holding BV.
Peptone Ltd
Peptone—founded in 2018 and born out of 30 years of academic research at the universities of Cambridge, Oxford, ETH Zurich and Groningen—is a translational biophysics company focused on drugging Intrinsically Disordered Proteins. The focal point of their protein therapeutics platform (Oppenheimer) is an intersection of physics, molecular biology and next generation supercomputing.
The proteins in our cells are folded into three-dimensional shapes that enable them to function properly and for some proteins these structures are clearly defined. However, around half the proteins in our cells have significant components with no fixed structure. These intrinsically disordered regions (IDRs) in proteins can have broad functions and implications across a wide range of therapeutic areas. These IDRs, when dysregulated, can induce the formation of toxic multimers via enhanced aggregation, can disrupt protein-protein interactions mediated through disorder contacts or can alter biomolecular condensates and microenvironments essential to correct cell function.
Many intrinsically disordered proteins (Troponin T, Alpha-synuclein, p53) are directly implicated in human pathologies and are very difficult to target with drugs. For this reason, proprietary NMR experiments (Nuclear Magnetic Resonance spectroscopy) coupled with HDX-MS (Hydrogen deuterium exchange mass spectrometry) as well as other experiments are all used to generate ambiguous restraints for modeling of proteins ensembles of Intrinsically Disordered Protein targets.
Then Peptone’s proprietary Molecular Dynamics engine utilizes the experimental restraints to simulate non-canonical behavior of the disordered targets and identify the most plausible drugging sites. Their ML methods generate compact but diverse libraries of high quality protein binders against the best ranking spatial disordered epitopes. Finally, their advanced biophysical laboratory performs lead selection and end to end testing. A data driven decision is made if the binder selection process requires more iterations.
🍊 On June 19, 2024, Deep-learning protein sequence models have shown outstanding performance at de novo protein design and variant effect prediction (Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data). By introducing a second term derived from the models themselves, at Peptone they substantially improved performance without further training or additional experimental data. This term aligns outputs for the task of stability prediction.
On a task to predict variants that increase protein stability, the absolute success probabilities of ProteinMPNN and ESMif are improved by 11% and 5%, respectively.
Peptone—selected as one of Nature Biotechnology’s top academic spinouts in 2023—has raised a total of $42.4M in funding over 2 rounds.