Digital CRO

Drug Discovery in the era of Artificial Intelligence

The digital CRO team brings together scientists and engineers with diverse skill sets, ranging from biology and chemistry to statistics and machine learning. We work with both small startups and big pharmas to leverage digital power in order to enable the development of new therapies. We contribute to the entire drug discovery process, from target identification and validation, to compound design and clinical trials. We make bioinformatic workflows and software with human-readable code, as well as machine learning models that “understand” biological data and provide cutting-edge solutions for Precision Medicine.

Łukasz Nowak COO, General Director of Digital CRO Unit

Ardigen enhances Drug Development

From target identification to clinical trials

Target identification

  • Identification of protein-DNA interaction sites
  • Identification of off-target binding sites
  • Prediction of protein-protein interaction sites
  • Prediction of similarities in drug effect and mode of action
  • Identification of genetic and epigenetic variability
  • Profiling of gene expression, protein, and metabolite abundances
  • Dimensionality reduction and clustering in single cell analysis
  • Natural Language Processing for information retrieval
  • Machine Learning-based binding pocket search
  • Data mining for target identification
  • Computer Vision for medical image analysis

Target Validation

  • Computational methods for the creation of KO/KD/KI
  • Computational methods for the creation of disease models

Hit generation

  • RNAi-based therapeutics
  • Machine Learning-based virtual screening
  • Computer Vision for high-content screening
  • Drug repurposing

Hit to Lead optimization

  • Peptide structure modelling and optimization
  • Prediction of druggability
  • Deep learning generative models for compound design
  • Machine Learning-based prioritization of molecules
  • Property and affinity prediction
  • Prediction of ADME/T properties
  • Prediction of protein properties
  • Protein optimization

Preclinical

  • Prediction of toxicity including immunotoxicity
  • Design of CDx for clinical trials

Clinical Trials

  • Biomarker-based patient stratification and survival analysis
  • Statistical inference on experimental data
  • Computer Vision for medical image analysis
  • Prediction, monitoring, and analysis of treatment response
  • Biomarker Discovery, including on multi-omics datasets
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Learn more about our services

Our power lies in the mix of three digital skills: bioinformatics, AI & Data Science and Software Engineering. Read more about our skills and projects.

Bioinformatics

Our broad range of expertise in bioinformatics and machine learning allows for efficient, multi-evidence identification and stratification of leading candidate targets.

  • Prediction of similarities in drug effects
  • Protein-DNA and protein-RNA interaction analysis
  • Differential gene expression analysis
  • Translation analysis with mass-spectrometry and ribosome profiling
  • Functional characterisation of affected gene sets
  • Literature data mining for target evidence and mechanism of action

Biomarker signatures of a patient’s response to the treatment to improve statistical power of trial.

  • Patient stratification associated with overall survival
  • Prediction of response and survival
  • Publication and reporting
  • Discovery of novel biomarkers
  • Surrogate markers for safety and efficacy
  • Better understanding of biology

Ardigen’s disease model design enables preclinical studies of pharmacological properties.

  • Experimental design
  • Data management
  • Indication suggestion
  • Meta-analyses
  • Biomarker identification

Biomarker signatures of a patient’s response to the treatment to improve statistical power of trial.

  • Patient stratification associated with overall survival
  • Prediction of response and survival
  • Publication and reporting
  • Discovery of novel biomarkers
  • Surrogate markers for safety and efficacy
  • Better understanding of biology

AI & Data Science

  • Custom methods leveraging AI/Data Science in your challenging R&D projects
  • Broad applications: Biomarker Discovery, NLP for knowledge extraction, MLOps for production and experimental AI pipelines, etc.
  • Research in collaboration with renowned academic groups on the development and application of novel deep learning methods (adversarial networks, semi-supervised learning, graph-representation learning, etc.)
  • Advanced Computer Vision pipelines with diverse applications in biomedical imaging
  • Automated assessment of pathological changes outperforming human experts
  • High-content phenotypic screening (HCS) with superior image-based compound fingerprints
  • Robust image processing aimed at improving prediction properties
  • Interpretability, quality control, automatic segmentation of tissues
  • In-house COPTIC technology for molecule property prediction and optimization
  • Based on cutting-edge research (presented at NeurIPS 2019 and 2020)
  • Validated in vitro Flexible (custom rules and constraints on the chemical space)
  • Augments your medicinal chemists’ efforts with quick iterations
  • Custom solutions based on our PRISM technology
  • Works with any protein type to address your specific challenges
  • Protein property prediction and optimization for properties, such as binding, stability, immunogenicity, interactions, etc.
  • Suggests changes in the amino-acid sequence with custom constraints
  • Collaboration scenarios tailored to your needs (optimization iterations and/or web application for cloud computing)

Software Engineering

  • Design, implementation, and tuning of data processing algorithms
  • Custom tools for data processing and visualization
  • Design and tuning of domain specific databases
  • Data lakes and FAIR experimental data management systems
  • Large scale, automated production pipelines for RNA-Seq, DNA-Seq, single cell, etc.
  • Robust research oriented pipelines
  • Pipeline benchmarking and optimization
  • High quality and reproducible pipelines
  • Kubernetes and Docker-based solutions
  • Serverless architectures and microservice-based systems
  • MLOps for production and experimental machine learning pipelines
  • Cloud based and hybrid systems maintenance and cost optimization
  • Technical consulting, systems integration and migration of legacy solutions
  • Technical support and maintenance
  • User interface and user experience (UX) design
  • Security and legal compliance – FDA, HIPAA, HITECH, CLIA
Gene Regulation platform Read more

How we work

AGILE for Life Sciences

We work according to Agile methodology, which we adopted for Life Science projects. It accelerates the delivery of business value. Through a process of continuous planning and feedback we are able to constantly maximize value throughout the research or development process

Why using agile methodology?

Face to face interaction with customer Quick delivery of a good quality version of the product High flexibility and simplicity Self-organizing team Sprint-based project Feature brings positive effects to the entire project

They trusted us

At Atreca, Ardigen has established themselves as a comprehensive service providing a multi-disciplined team that manages all aspects of our Informatics needs. We have been impressed with their flexibility to grow teams and add new specializations on-demand at a reasonable cost.

“Ardigen hit a grand slam for us! Their expertise and mastery of microbiome data mining and predictive analytics found important and unique biomarkers in our data where others had failed. The team was amazing and I would work with them again in a heartbeat.”

“Ardigen has been a great bioinformatics partner for Acrigen Biosciences. They were able to develop a custom bioinformatics workflow and wrap it in a web application, allowing easy access for our scientists.”

“CVC is excited to be working with Ardigen who are at the forefront of T-cell epitope design. The collaboration gives us the best chance of our product inducing an effective T-cell response against SARS-Cov-2.”

“The PRISM pipeline has dramatically improved our discovery efforts and uncovered new unexpected lead candidates. In addition, the deployment on cloud computing resources has allowed our discovery team to explore possibilities that would be untenable under traditional settings.”

“Working with Ardigen has enabled us to apply precision bioinformatics and machine learning to our most pressing problems.”

“We at Targovax have been impressed and delighted with Ardigen’s expertise, professional attitude, attention to details and flexibility. We also highly value their individual approach when working with clients, and last but not least, their result delivery is on time. Generated results represent a key component of our clinical pipeline readouts.”

“Our strategic partnership with Ardigen has enabled us to not only keep pace with, but vastly exceed the expectations of our diverse and rapidly expanding user base of over 40 major pharmas and biotechs.”

“We’re extremely happy with Ardigen’s level of responsiveness, attention to details and overall technical insight.”

“Ardigen’s deep understanding of the complexities of molecular biology work flows and data has made them our partner of choice.”

“I’ve been really impressed with their expertise and communication skills. When we give them an analysis task, they go beyond what we’ve asked for and suggest and test new methods.”

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Know us better

We work with companies from all over the world
  • +

    People

  • PhD (30%)

  • +

    Partners

Learn more: Watch our videos

Conference presentation: Gene Regulation Platform
29 April 2021 Conference presentation: Gene Regulation Platform Watch the movie
Taming terabytes – life beyond text files in Life Science research
12 November 2020 Taming terabytes – life beyond text files in Life Science research Watch the webinar

Learn more: Read our articles

Publication: Kernel Self-Attention for Weakly-supervised Image Classification using Deep Multiple Instance Learning
5 March 2021 Publication: Kernel Self-Attention for Weakly-supervised Image Classification using Deep Multiple Instance Learning Read the article
Publication: Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
12 February 2021 Publication: Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction Read the article
Publication: Mol-CycleGAN - a generative model for molecular optimization
6 February 2021 Publication: Mol-CycleGAN - a generative model for molecular optimization Read the article
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Competence Centers Directors

  • https://ardigen.com/wp-content/uploads/2021/05/Mask-Group-32@2x-1.png Marek Piątek, PhD DIrector of Bioinformatics
  • https://ardigen.com/wp-content/uploads/2021/05/Mask-Group-32234@2x.png Jan Kaczmarczyk, PhD Director of Data Science
  • https://ardigen.com/wp-content/uploads/2021/05/Mask-Group-32543@2x.png Piotr Radkowski Director of Software Engineering

Meet us at upcoming events

  • Coming soon
    23 - 26 June
    digital
    SLAS Europe 2021
  • 21- 24 June 2021
    BIOTRINITY 2021
  • 14 - 18 June
    digital
    PMWC 2021 COVID Virtual
  • 15 - 17 June
    digital
    Pharma R&D Week Virtual
  • 7 - 9 June
    digital
    Decode AI for Pharmaceuticals
  • 10 - 11 & 14 - 18 June
    digital
    BIO Digital 2021
  • 11 - 14 May
    digital
    PEGS2021 Boston Virtual Conference & Expo
  • 20 - 23 April
    digital
    Digital Nordic Life Science Days
  • 29 March
    digital
    Festival of Biologics San Diego 2021
  • 25 - 26 March
    digital
    AI in Healthcare & Pharma Virtual Summit
  • 15 March
    digital
    Virtual conference AI in drug discovery 2021
  • 27 Febuary
    digital
    AI in Drug Discovery Conference
  • 25 January
    digital
    SLAS 2021 Conference

Contact us

Digital CRO services?

    Our Business Development Team
    • https://ardigen.com/wp-content/uploads/2021/05/Mask-Group-115@2x.jpg Łukasz Nowak General Director of Digital CRO
    • https://ardigen.com/wp-content/uploads/2021/05/Group-115@2x.jpg Agata Mieżaniec, PhD Business Development Manager
    • https://ardigen.com/wp-content/uploads/2021/05/Mask-Group-122@2x.jpg Monika Maślanka Business Development Manager
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