Custom Services

Bioinformatics Analysis & Drug Discovery in the era of Artificial Intelligence

Our team bring 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 Chief Operating Officer

Ardigen enhances Drug Development

From target identification to clinical trials

Target identification

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

Target Validation

  • Computational methods for the creation of KO/KD/KI
  • Computational methods for the creation of disease models
  • In silico prediction of siRNA acting site
  • In silico prediction of sgRNA (CRISPR) acting site
  • Genetic screen perturbation analysis

Hit generation


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

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


  • Prediction of toxicity including immunotoxicity
  • Design of CDx for clinical trials
  • AI-based scoring of whole slide biopsies
  • Evaluation of transcriptome profiles in preclinical models
  • Multi-omic data integration from preclinical studies

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

Discover Our Cutting-Edge Services
and Accelerate Your Drug Discovery Process

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 analyses share common workflow that allows to abstract from technicalities of raw data towards specific biological insights.

At each step technical expertise, diligence and attention to quality is required. Depending on your data, we can conduct a variety of analyses at different levels of detail to suit your specific research needs.

  • Apps and Reports

An image is worth a thousand words, and relevant, explorable data can be worth billions. Explore your data, results and analyses in detailed reports and apps with revealing visualizations.

  • AI Models

Advanced machine learning models help to leverage the wealth of data in biology. Meaningful application of AI models in bioinformatics demands expertise you can find with us.

  • Data Pipelines

The majority of published scientific research is irreproducible in its full form. Data processing pipelines enable the requisite reproducibility application to large data.

See the brochure

Ardigen’s services focused on small molecules integrate the power and efficiency of AI and ML with the accuracy and precision of Computer-Aided Drug Design (CADD) techniques. From computational chemistry and molecular modeling to rational drug design, we turn data into discoveries.


Why partner with us:

  • INTEGRATED EXPERTISE: We combine machine learning proficiency with biology and chemistry expertise and 9+ years of experience on the market to provide relevant scientific value.
  • YOUR DATA, YOUR INSIGHTS: You gain complete ownership of delivered molecules proposed during our collaboration.
  • TRANSPARENCY IN ANALYSIS: We prioritize clarity and interpretability of our models, providing you with the understanding necessary to make informed decisions.

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We help you to discover value in your data by applying our tailored AI methods, automate the workflow and make it usable at scale.

  • Data

We are experts with data modalities critical for life science, laying a robust foundation for model building and leveraging synergies.

  • Model

Our team designs, tunes, and validates algorithms, achieving remarkable improvements in pattern identification and predictive accuracy.

  • Use at scale

By implementing MLOps tools, we ensure that your models are practical and scalable solutions for real-world applications.

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Our SA-AbMILP model transforms the way we assess disease activity, providing a detailed analysis of biopsy samples.


Histopathology Image Analysis:

  • assessment of histologic remission
  • batch effects correction
  • responder/non-responder classification

Radiology Image Analysis

  • segmentation
  • radiomics
  • biomarker discovery

Microscope Image Analysis:

  • custom microscopy image analysis
  • cell segmentation and characterization
  • quality evaluation

Microarrays Image Analysis:

  • image registration
  • grid placement and feature extraction
  • spot detection

See the brochure

Drawing from our past experiences, we have developed a concept of reference architecture to visually guide and simplify discussions about this complex topic. It helps to assess the digital maturity of teams and serves as a reference map for planning new projects.

  • Data Processing and Visualisation
  • Data Governance and Management
  • Cloud Services

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Harnessing the power of automation, scalability and customizability, we’re streamlining how you process and analyze your data. At any stage of your
drug discovery process, we support the transformation of raw data into valuable scientific insights. With our knowledge and expertise, we follow a structured and efficient path from data acquisition to actionable knowledge in research and analysis.

Why partner with us:

INTERDISCIPLINARY EXPERTISE: Our cross-functional teams of software developers, bioinformaticians, and scientists deliver integrated solutions.
GLOBAL COLLABORATIVE NETWORK: Extending capabilities through strategic partnerships with industry leaders like Seqera Labs (Nextflow creators and developers) and AWS.
PROVEN EXCELLENCE: With 9+ years in the field, 400+ successful projects, and a growing team of 20+ Nextflow developers, we set the industry standard.
COMMUNITY CONTRIBUTORS: Active participation in nf-core and OpenPipelines communities, demonstrating our commitment to the advancement of the field.

See the brochure

Download our leaflet to learn more Read more

Ardigen Flexible Engagement Models

How do we work?
  • We focus on partnering, have a collaborative attitude, and always aiming to establish long-term relationships with our clients
  • Client satisfaction and quality of delivery are our priorities
  • We use the Agile approach to projects, ensuring efficient, transparent, and flexible delivery
  • Our delivery team is supported by Excellence Centers and leverages our tools and methodologies to accelerate delivery

How do we collaborate with clients?


They trusted us

“Ardigen provided several teams of high-calibre, multi-disciplined, and proactive individuals to help Genomics England accelerate the transformation of population-scale bioinformatics pipelines. We are delighted with the collaboration and the outstanding results they have delivered. The bioinformatics and software engineering services they provided have helped us reduce project timelines and accelerate our development at a reasonable cost.” 

“Ardigen was instrumental in streamlining our processes with microbiome custom software development. Their deep expertise and unwavering commitment to the project led to significant and measurable improvements in the efficiency and quality of our research efforts. We highly recommend Ardigen for their outstanding and collaborative partnership in facilitating our research project. We are thrilled with the results and are exploring ways to continue our partnership.”

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.”

Know us better

We work with companies from all over the world
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    Years on the market

Watch our webinars:

The AI Advantage: Game – Changing Insights in HCS with Cell Painting
26 October 2023 The AI Advantage: Game – Changing Insights in HCS with Cell Painting Watch the webinar
Navigating Bioinformatics: Transforming Drug Discovery with Innovative Pipeline Solution
11 October 2023 Navigating Bioinformatics: Transforming Drug Discovery with Innovative Pipeline Solution Watch the webinar
Decoding Immuno-Peptidomics: A New Era in Therapeutic Target Identification
15 June 2023 Decoding Immuno-Peptidomics: A New Era in Therapeutic Target Identification Watch the webinar

Read our articles:

Blog Article: AI Brain Slice Segmentation - Innovative Solutions for Precision Diagnostics
5 December 2023 Blog Article: AI Brain Slice Segmentation - Innovative Solutions for Precision Diagnostics Read the article
Blog Article: AI at the Forefront of Modern Radiology Analysis: Brain MRI Use Case
7 November 2023 Blog Article: AI at the Forefront of Modern Radiology Analysis: Brain MRI Use Case Read the article
Publication: Host Factors Associated with Gut Mycobiome Structure
2 March 2023 Publication: Host Factors Associated with Gut Mycobiome Structure Read the article

Excellence Center Directors

  • Marek Kudła, PhD Excellence Center Director of Bioinformatics
  • Tomasz Jetka, PhD Excellence Center Director of Data Science
  • Piotr Faba Excellence Center Director of Software Engineering

Our events

  • Meet us
    10-11 August 2024
    Pennsylvania, US
    BiotechX USA 2024
  • 30 September - 03 October 2024
    Boston, US
    Discovery on Target
  • 15-17 October 2024
    Basel, Switzerland
    Festival of Biologics 2024
  • 05-07 November 2024
    Boston, US
    The 16th PEGS Europe Protein & Antibody Engineering Summit
  • 03-06 June 2024
    Boston, US
    Bio International Convention
  • 27-29 May 2024
    Barcelona, Spain
    SLAS Europe 2024
  • 22-23 May 2024
    Basel, Switzerland
    Discovery Europe 2024
  • 29-30 April 2024
    Hinxton, UK
    Target to Patient
  • 25 April 2024
    Cambridge, UK
    ELRIG: AI in Drug Discovery Forum
  • 23-25 April 2024
    London, United Kingdom
    8th Annual Immuno-Oncology Summit Europe
  • 15-17 April 2024
    Boston, US
    Bio IT
  • 15-17 April 2024
    San Diego, US
    Festival of Biologics San Diego 2024
  • 21-22 March 2024
    Boston, US
    NextGen Omics US 2024
  • 21-22 March 2024
    Boston, US
    Synthetic Biology US
  • 19-21 March 2024
    Boston, US
    Precision Medicine in Inflammatory Bowel Disease Summit
  • 13-14 March 2024
    Basel, Switzerland
    RNA Leaders
  • 11-12 March 2024
    London, United Kingdom
    AI in Drug Discovery
  • 3-7 February 2024
    Boston, US
  • 24 - 26 January 2024
    Santa Clara, US
  • 05 - 08 June 2023
    Boston, USA
    Bio International Convention
  • 31 May - 02 June 2023
    Basel, Switzerland
    Future Labs Live
  • 16 - 18 May 2023
    Boston, MA, USA
  • 24 - 25 April 2023
    Basel, Switzerland
    Swiss Biotech Days
  • 3 - 5 April 2023
    Boston, MA, USA
    TCR-Based Therapies for Solid Tumors Summit
  • 20 - 22 March 2023
    San Diego, USA
    Festival of Biologists
  • 15 - 16 March 2023
    Basel, Switzerland
    RNA Leaders
  • 09 - 10 March 2023
    Boston, MA, USA
    Lab of the Future
  • 25 February - 1 March 2023
    San Diego, USA
  • 25 - 26 January 2023
    London, UK
    Festival of Genomics
  • 25 - 27 January 2023
    Santa Clara, USA
  • 25 November 2022
    Zurich, Switzerland
  • 14 - 15 November 2022
    San Francisco
    Precision In Drug Discovery & Preclinical Summit
  • 8 - 10 November 2022
    BioData World Congress
  • 24 - 25 October 2022
    Wroclaw, Poland
    Central European Technology Forum
  • 18 - 19 October 2022
    Boston, MA, USA
    RNA Leaders
  • 17 October 2022
    Boston, MA, USA & Online
    AI-driven Platform for Target Discovery and Validation
  • 7 October 2022
    Heidelberg, Germany
    BioRN Annual Conference 2022
  • 4 - 5 October 2022
    UK, London
    ELRIG 2022
  • 5 - 6 October 2022
    Munich, Germany
    17th Drug Discovery Innovation Programme
  • 27 - 28 September 2022
    Precision Globe
  • 18 - 20 September 2022
    Boston, USA
  • 26 -28 June
    PMWC 2022
  • 3-5 May 2022
    Bio IT 2022
  • 15-16 February 2022
    Boost your way to successful therapy. AI for Drug Discovery Days”
  • 26 -28 January
    The Festival of Genomics & Biodata
  • 9 - 11 November
    Festival of Biologics
  • 02 - 04 November
    Bio Data World Congress
  • 19-20 October
    Booth D1
  • 23 - 26 June
    SLAS Europe 2021
  • 21- 24 June 2021
  • 14 - 18 June
    PMWC 2021 COVID Virtual
  • 15 - 17 June
    Pharma R&D Week Virtual
  • 7 - 9 June
    Decode AI for Pharmaceuticals
  • 10 - 11 & 14 - 18 June
    BIO Digital 2021
  • 11 - 14 May
    PEGS2021 Boston Virtual Conference & Expo
  • 20 - 23 April
    Digital Nordic Life Science Days
  • 29 March
    Festival of Biologics San Diego 2021
  • 25 - 26 March
    AI in Healthcare & Pharma Virtual Summit
  • 15 March
    Virtual conference AI in drug discovery 2021
  • 27 Febuary
    AI in Drug Discovery Conference
  • 25 January
    SLAS 2021 Conference
  • 18 - 19 October 2022
    Boston, MA, USA
    Discovery on Target

Contact us

    Our Business Development Team
    • Livia Legg Chief Commercial Officer
    • Kaja Milanowska - Zabel, PhD, MBA Business Development Executive
    • Agata Mieżaniec, PhD Senior Business Development Manager
    • Sean Melville Senior Business Development Manager
    • Agnieszka Plociennikowska, PhD Senior Business Development Manager
    • Aneta Kuczewska Business Development Manager
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