• AI & Bioinformatics Custom Services

AI & Bioinformatics Custom Services

Bioinformatics Analysis & 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

  • 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

Preclinical

  • 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
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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

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

  • Synthetic lethality-based gene pairs identification
  • Genetic landscape characterization
  • Prediction of similarities in drug effects
  • Differential gene expression analysis
  • Translation analysis with ribosome profiling
  • Functional characterisation of affected gene sets
  • Literature data mining for target evidence and mechanism of action

Comprehensive computational approaches to validate the early stages of the drug discovery process in-silico.

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

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

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

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

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.)
  • High-content phenotypic screening (HCS) with superior image-based compound fingerprints
  • Robust image processing aimed at improving prediction properties
  • Advanced Computer Vision pipelines with diverse applications in biomedical imaging
  • Automated assessment of pathological changes outperforming human experts
  • 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)
  • In-house AI-based RMAT technology for accurate prediction of compound properties

Custom solutions based on in-house PRISM technology:

  • Working with any protein type
  • Prediction and optimization for properties, such as binding, stability, immunogenicity, interactions, etc.
  • Recommendation of 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

  • Comprehensive life science computing support
  • End-to-end cloud-native systems development
  • MLOps solutions for Al projects
  • Security & legal compliance
  • 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

Find out More

  • Data architecture consulting
  • Data ingestion & engineering
  • Big data analytics
  • Bioinformatics workflows engineering
  • Data capture & storage systems
  • Harmonization & FAIRification pipelines
  • Reporting & dashboard solutions
  • Self-service data marts
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 agile approach to projects to ensure 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?

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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
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    Projects

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    PhD (25%)

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    Partners

Learn more: Watch our videos

Leveraging Single-Cell Transcriptomics for the Discovery of New Therapeutic
6 December 2022 Leveraging Single-Cell Transcriptomics for the Discovery of New Therapeutic Watch the webinar
Latest developments in the Nextflow ecosystem – Reproducible omics pipelines in a cloudy world
22 October 2022 Latest developments in the Nextflow ecosystem – Reproducible omics pipelines in a cloudy world Watch the webinar
Webinar: Computer Vision for Precision Medicine
30 August 2022 Webinar: Computer Vision for Precision Medicine Watch the webinar

Learn more: Read our articles

Publication: Host Factors Associated with Gut Mycobiome Structure
2 March 2023 Publication: Host Factors Associated with Gut Mycobiome Structure Read the article
Publication: ProtoMIL: Multiple Instance Learning with Prototypical Parts for Whole-Slide Image Classification
2 February 2023 Publication: ProtoMIL: Multiple Instance Learning with Prototypical Parts for Whole-Slide Image Classification Read the article
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
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Excellence Center Directors

  • https://ardigen.com/wp-content/uploads/2023/01/Marek-Kudla-2-modified.png Marek Kudła, PhD Excellence Center Director of Bioinformatics
  • https://ardigen.com/wp-content/uploads/2023/01/Tomasz_Jetka-3-modified.png Tomasz Jetka, PhD Excellence Center Director of Data Science
  • https://ardigen.com/wp-content/uploads/2023/01/DSC01673-modified.png Piotr Faba Excellence Center Director of Software Engineering

Our events

  • Meet 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
    BIOIT
  • 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
    SLAS
  • 25 - 26 January 2023
    London, UK
    Festival of Genomics
  • 25 - 27 January 2023
    Santa Clara, USA
    PMWC
  • 25 November 2022
    Zurich, Switzerland
    hubXchange
  • 14 - 15 November 2022
    San Francisco
    Precision In Drug Discovery & Preclinical Summit
  • 8 - 10 November 2022
    Basel
    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
    Frankfurt
    Precision Globe
  • 18 - 20 September 2022
    Boston, USA
    SBI2
  • 26 -28 June
    PMWC 2022
  • 3-5 May 2022
    Bio IT 2022
  • 15-16 February 2022
    digital
    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
    DRUG DISCOVERY 2021
  • 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
  • 18 - 19 October 2022
    Boston, MA, USA
    Discovery on Target

Contact us

Digital CRO services?

    Our Business Development Team
    • https://ardigen.com/wp-content/uploads/2021/05/Group-115@2x.jpg Agata Mieżaniec, PhD Senior Business Development Manager
    • https://ardigen.com/wp-content/uploads/2023/01/MG_7531-modified.png Claudio Rota, PhD Senior Business Development Manager
    • https://ardigen.com/wp-content/uploads/2023/01/DSC01813-modified.png Aneta Kuczewska Business Development Manager
    • https://ardigen.com/wp-content/uploads/2023/02/Agnieszka_Plociennikowska1-1.png Agnieszka Plociennikowska, PhD Program Director
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