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AI-Driven Precision Medicine for Inflammatory Bowel Disease (IBD)

Scailyte is pioneering an AI-driven approach to revolutionize IBD treatment, moving beyond conventional methods to develop a foundational disease model. By integrating high-resolution multi-omics data from deeply characterized patient cohorts with our proprietary ScaiVision AI platform, we aim to discover predictive biomarkers, unravel resistance mechanisms, and identify novel therapeutic targets. This initiative will empower drug developers to de-risk clinical trials and deliver truly personalized IBD therapies, significantly reducing patient suffering and healthcare costs.

 

The problem:

Up to 70% of IBD Patients Don't Respond to Initial Therapy.

  • Inflammatory Bowel Disease (IBD), encompassing Crohn’s disease and ulcerative colitis, affects millions worldwide, significantly impacting quality of life.

  • Despite advancements, a major challenge persists: current biologic therapies, which are often expensive, fail for up to 70% of patients.

  • This leads to a detrimental and costly trial-and-error approach, where patients endure ineffective treatments, prolonged suffering, and increased risk of disease progression, while healthcare systems face escalating costs.

  • The critical need is for predictive biomarkers that can identify, before treatment begins, which therapy will be most effective for each individual patient.

Scailyte's solution:

Building a Foundational Model for IBD Precision Medicine

At Scailyte, we are transforming the IBD treatment paradigm by developing an AI-driven foundational model of the disease. This model moves beyond broad diagnoses to uncover the precise biological mechanisms driving IBD in individual patients.

Our approach integrates high-resolution multi-omics data with advanced artificial intelligence to:

  • Define novel IBD endotypes: Subgroups of patients characterized by specific molecular pathways.
  • Predict therapy response: Identify which patients will respond to specific biologics.
  • Unravel resistance mechanisms: Understand why therapies fail.
  • Discover novel drug targets: Accelerate the development of next-generation treatments.

Unrivaled Assets: Deep Data, Advanced AI, and Clinical Expertise

World-Class Patient Cohorts:
  • The Swiss IBD Cohort (SIBDC): A meticulously characterized, nationwide, longitudinal cohort (over 2,900 patients) providing a rich history of disease progression and treatment outcomes. Our discovery efforts are anchored in deeply phenotyped subsets from the SIBDC.
  • USZ Prospective Real-World Cohort: Access to an ongoing, real-world cohort at Universitätsspital Zürich (USZ), enabling validation in diverse patient populations and covering a broad spectrum of modern IBD treatments (anti-integrins, anti-IL-12/23, JAKi, S1P modulators).
Cutting-Edge Multi-Omics Data Generation:

We generate high-resolution molecular profiles from patient samples, including single-cell RNA-sequencing (scRNA-seq) from blood and spatial transcriptomics from tissue biopsies. This provides unparalleled insight into disease biology at cellular and tissue-microenvironment levels.

Proprietary AI Platform: ScaiVision:

Our unique explainable AI (xAI) platform excels at uncovering subtle, yet highly predictive, biological signals from complex single-cell and multi-omics data, even from rare cell populations. It doesn’t just predict; it provides mechanistic insights, enabling the discovery of novel biology.

Translational Biomarker Development:

We don’t stop at discovery. We specialize in distilling complex multi-omic signatures into simple, clinically viable assays (e.g., targeted gene panels) for use as predictive companion diagnostics (CDx) or patient stratification tools.

Driving Innovation: The Innosuisse-Funded AIomics Project

  • Scailyte has been awarded a CHF 800,000 Innosuisse grant to execute the AIomics project in collaboration with Prof. Gerhard Rogler’s team at Universitätsspital Zürich.

  • Goal: To create a foundational multi-omics datalake from a well-characterized cohort of IBD patients and apply ScaiVision to discover predictive biomarkers of response to biologics.

  • This project is critical for identifying novel signatures that will transform therapy selection, reduce trial-and-error prescribing, and significantly improve outcomes for IBD patients.

Multi omics data of pre and post immunotherapy treatment

Delivering Transformative Value to IBD Drug Developers

IBD drug developers gain:

  • Predictive Biomarkers (CDx): Clinically actionable tools to identify responders, de-risk clinical trials, and maximize drug efficacy.

  • Deeper Mechanistic Understanding: Uncover the cellular and molecular basis of drug response and resistance, leading to smarter drug development.

  • Novel Target Candidates: Identify new biological pathways and targets for developing next-generation IBD therapies.

  • Patient Stratification: Define granular patient endotypes for more effective trial design and targeted drug positioning.

  • Accelerated Development: Reduce R&D timelines and costs by focusing on the right patients with the right drugs.

Your Partner for IBD Precision Medicine

  • Unique Data Access: Proprietary access to deeply phenotyped, longitudinal IBD cohorts with diverse treatment histories.

  • Leading AI Expertise: Proven track record in biomarker discovery from complex single-cell and spatial omics data.

  • Mechanistic Insights: Our explainable AI goes beyond correlation, delivering biological understanding.

  • Translational Focus: We deliver actionable, verifiable biomarkers, not just scientific insights.

  • Proven Collaboration: Demonstrated success in high-value pharma partnerships (e.g., Sanofi in cell therapy).

Interested in partnering to accelerate your IBD pipeline or understand complex disease mechanisms?
Contact us

Dr. Peter Nestorov

Founder & Chief Executive Officer

Co-founder and Chief Executive Officer of Scailyte. He holds a PhD in genetics from the University of Basel and a degree in Biochemistry from the University of Tübingen.

During his PhD work, Dr. Nestorov pioneered the development and application of methods for single-cell analysis, which sparked his passion for this technology. In 2015, Dr. Nestorov joined Witec AG as Sales Specialist for single-cell and genomics technologies and successfully introduced the first commercial devices for single-cell analysis on the Swiss Life Science market. The interaction with biomedical researchers and the technological insight inspired Dr. Nestorov to start Scailyte and unlock the full clinical potential of single-cell data.

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Dr. Sarah Carl

Lead Data Scientist
is managing the Data Science division of Scailyte. She holds a PhD in Genetics and a Master’s degree in Developmental Biology from the University of Cambridge. Before joining Scailyte she was a post-doc and bioinformatician at the Friedrich Miescher Institute for Biomedical Research in Basel. At Scailyte she is leading the development of new applications and features of the internal data analysis platform, ScaiVision, and the data analysis of the clinical programmes.
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Anna Dimitrova, ACCA

Director Finance & Ops
Is the Director of Finance and Operations at Scailyte. She is an ACCA graduate with a Master’s degree in Finance and Banking from Sofia University. Before joining Scailyte she worked as Senior Audit Assistant at KPMG, Senior Business Consultant at PwC and as Finance Manager in a fast growing company in Bulgaria. At Scailyte she leads the finance, administration and internal operations of the company.

Pascal Winnen

CEO Hemex AG & Scailyte Board of Directors

Pascal is a co-founder and the CEO of HEMEX, a pharmaceutical, biotech and medical device consulting firm with offices in Switzerland, Germany and the USA. He holds a bachelor’s degree in Telecommunication Technologies from the University of Leuven (Belgium) and a master’s degree in Clinical Research from the Donau University in Krems (Austria). Pascal worked in various positions in the pharmaceutical and medtech industry.

From 2011 to 2015, Pascal worked for Finox Biotech, bringing one of the first biosimilar fertility treatments to the market in the EU and leading to the successful acquisition by Gedeon Richter for CHF 190 million. With his consulting firm HEMEX, Pascal has invested in multiple innovative life science startups, where he also advises on regulatory, clinical and marketing strategies, either as a senior consultant or as a board member.

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Dominique Mégret

Head of Swisscom Ventures & Scailyte Board of Directors
Dominique Mégret is head of Swisscom Ventures, which he started in 2007. He joined Swisscom in 2002 as head of the Group Strategy unit. Previously, Dominique Mégret was an entrepreneur in the United Kingdom, a strategy consultant in the European telecom industry and country manager for an IT company in Germany. He currently serves on the boards of Scailyte AG and Bloom SA. He is also an observer on the boards of Sophia Genetics and AVA Women.
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Prof. Dr. Manfred Claassen

Founder & Chief Scientific Advisor AI & Single-Cell Analysis
Co-founder and Chief Scientific Advisor at Scailyte. He holds degrees in both Biochemistry and Computer Science from the University of Tübingen and a PhD in the design and validation of proteome measurements from the ETH Zurich. He continued his academic path as a postdoctoral researcher at Stanford University’s Artificial Intelligence Lab focusing on research in machine learning for high dimensional single-cell biology, he moved back to Switzerland as an Assistant Professor at the ETH. During this time, the idea of establishing a company specialising in digital healthcare was conceived. Dr. Claassen was instrumental in conceptualizing the new company. He is now professor for clinical bioinformatics at the University of Tübingen, Germany in parallel with his role as scientific consultant for Scailyte.
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