Digital CRO

Digital CRO

Bioinformatics Analysis & Drug Discovery in the era of Artificial Intelligence

Bioinformatics Analysis & Drug Discovery. 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?

They trusted us

Gregg Espiritu Santo Sr. Director of Informatics Systems Atreca, Inc South San Francisco, CA

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.

Martha Carlin CEO The BioCollective The BioCollective Denver, CO, USA

“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.”

Michael Schelle Vice President Research and Operations Acrigen Biosciences Berkeley, CA, USA

“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.”

Robert Feldman CEO and Co-founder COVID-19 Vaccine Corporation (CVC) Auckland City, New Zealand

“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.”

Pawel Fludzinski, PhD CEO AmideBio Louisville, CO, USA

“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.”

Andy Greenstein Director, Translational Science Corcept Therapeutics Menlo Park, CA, USA

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

Lukasz Kuryk, PhD Director, Clinical Science Targovax Oslo, Norway

“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.”

Chris Smith CTO Distributed Bio South San Francisco, USA

“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.”

Dr. Bruno Marchon CTO EpiBiome South San Francisco, USA

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

Dr. Thomas Portmann Director of Neurobiology and Transcriptomics Circuit Therapeutics Menlo Park, CA, USA

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

Dr. Michael W. Rowe Director of Data Sciences HeathTell San Ramon, CA, USA

“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.”