Bioinformatics & Data Science

With a unique combination of biological knowledge and IT expertise we effectively support Life Science professionals in their research and development efforts. Our bioinformatics experts have significant expertise in applying their skills and knowledge both in the pharmaceutical and medical areas, as well as in the computational and structural biology field. Each problem we approach is analysed individually. We build our solutions based on the protocols used by renowned research institutions.

At Ardigen we provide customized professional services to accommodate your research in the new bioinformatics environment. We implement peer reviewed protocols as well as state of the art solutions to satisfy the needs of your organization. To gain an edge and improve accuracy and specificity of the results we apply deep learning algorithms and make them ready at your fingertips.

We will process your data, apply quality measures, test your hypotheses and provide professional reports in your favourite form, whether it’s PDF, dynamic website or presentation slides. All in order to help you achieve your goal.

Once the perfect processing setup is achieved we will wrap it up in an easy to use pipeline you can execute using command line or dedicated graphical interface. With user friendly web interface you will be able to comfortably switch between analyses variants.

If you seek discovery in metagenomics data, changes in gene regulation networks underlying diseases, integration of expression results from different platforms, application of NGS to precision medicine… we are there for you.

Detailed offer

Next Generation Sequencing:
  • quality control and pre-processing
  • alignment to reference genome
  • functional annotation
  • Whole Genome Sequencing
  • RNA-seq - gene expression, non-coding RNA, gene fusions
  • ChIP-seq - protein interaction regions analysis
  • RRBS (Reduced Representation Bisulfide Sequencing) - methylation analysis
Microarray data analysis:
  • (Affymetrix, Agilent, Illumina, home-made)
  • Gene expression
  • Genotyping
PCR:
  • DNA profiling, including barcoding and other species identification methods
  • Primer design

Biological and medical information extraction and inference

  • Integration of genomics, transcriptomics, proteomics and metabolomics data
  • Experimental effects
  • Pathway and network analysis
  • Evaluate and refine hypotheses
  • Integration of external data sources into analysis
  • Drug targets analysis
  • Application of Structural Bioinformatics approach
  • Time-series analysis
  • Statistical and Multivariate Analyses
  • Clustering methods to evaluate the data structure
  • Reduce data complexity
  • Phylogenetics analysis

Complementary informatics services

  • Analytical pipelines
  • Building and managing databases
  • Data extraction from public databases
  • Integration of internal data sources
  • Information consolidation
  • User interface design
  • Data visualization
  • Specialized platforms design, building and management
  • Big Data management and processing
  • Cloud computing and HPC

Ardigen offers a spectrum of services considering protein bioinformatics. We help with mass spectrometry as well as sequence data analysis. Your proteins need wider context. That’s why we integrate information from public databases and other types of experiments regarding your samples and field of study. We calculate the catalytic properties of your enzyme and present its other family members. Finally we model the protein structure and its various possible interactions and properties.

Detailed offer

Data integration and sequence analysis
  • Integration of genomics, transcriptomics, proteomics and metabolomics data
  • MS analysis
  • Phylogenetic analysis
  • Enzyme sub-families identification
  • Integration of proteomics data with other experiments
  • Integration of information from public data bases
Analysis of protein properties
  • Molecular modeling of antibody-antigen complexes
  • Loop modeling
  • Analysis of receptor-ligand interactions
  • Binding free energy calculations
  • In silico alanine scanning
  • Epitope prediction
Modeling and engineering of proteins
  • Homology modeling
  • Protein-protein docking
  • In silico mutagenesis
  • Protein modifications
  • Protein structure refinement
  • Molecular dynamics simulations

Biological and medical information extraction and inference

  • Experimental effects
  • Pathway and network analysis
  • Evaluate and refine hypotheses
  • Integration of external data sources into analysis
  • Drug targets analysis
  • Application of Structural Bioinformatics approach
  • Time-series analysis
  • Statistical and Multivariate Analyses
  • Clustering methods to evaluate the data structure
  • Reduce data complexity
  • Phylogenetics analysis

Complementary informatics services

  • Analytical pipelines
  • Building and managing databases
  • Data extraction from public databases
  • Integration of internal data sources
  • Information consolidation
  • User interface design
  • Data visualization
  • Specialized platforms design, building and management
  • Big Data management and processing
  • Cloud computing and HPC

Metabolomics is at the moment the cutting edge of integrated omics experiments. Enriching your research with seamlessly integrated metabolome information enables systems biology approach. At Ardigen we help to analyze your metabolomics data and combine it with genomics, transcriptomics and proteomics information. Complex analysis of various types of metabolites subgroups will help you focus your view on the target of your research. On the other hand full fingerprinting and statistical analyses will keep your perspective in place. Combining your research with the information from public sources will strengthen the results. If you are looking for a dedicated cancer metabolism bioinformatics services you have come to the right place.

Detailed offer

  • Integration of genomics, transcriptomics, proteomics and metabolomics data
  • Full metabolome analysis
  • Next-generation lipidomics
  • Dynamics of biochemical levels
  • Statistical and Multivariate Analyses
  • Clustering methods
  • Discovery of biochemical relationships (network analysis)
  • Metabolic pathways changes
  • Metabolic fingerprinting
  • Integration of information from public data bases
  • Structural similarity of metabolites
  • Changes in energy utilization and oxidative stress
  • Prognostic metabolomic biomarkers:
    • amino acid metabolites, altered pyruvate kinase regulation, NADH redox states, level of tocopherols

Biological and medical information extraction and inference

  • Experimental effects
  • Pathway and network analysis
  • Evaluate and refine hypotheses
  • Integration of external data sources into analysis
  • Drug targets analysis
  • Application of Structural Bioinformatics approach
  • Time-series analysis
  • Statistical and Multivariate Analyses
  • Clustering methods to evaluate the data structure
  • Reduce data complexity

Complementary informatics services

  • Analytical pipelines
  • Building and managing databases
  • Data extraction from public databases
  • Integration of internal data sources
  • Information consolidation
  • User interface design
  • Data visualization
  • Specialized platforms design, building and management
  • Big Data management and processing
  • Cloud computing and HPC

Immunomics field has reached the high-throughput era with various techniques providing stream of information. Using these data sources we aim to deconvolute the network of interactions in your experiment to provide you with as much evidence as possible to answer your research questions. We enable your platform with deep machine learning algorithms to transform it into question answering tool and make complex analysis simple and reliable. Furthermore we combine your data with the relevant public resources and visualize the results appropriate for your needs whether it is research or immunotherapy selection.

Detailed offer

  • Large-scale studies of immune system regulation and response to cancer
  • Analysis of immunome-wide gene expression patterns in different tumors and hematological malignancies that correlate with antigen-induced activation or anergy in cancer eg. PD-L1, PD-1, CD3, CD4, CD8, CD45RO, CD57, CD68, Granzyme B, FOXP3, and OX-40 levels
  • Uniplex IHC and multiple immunofluorescence (IF) methodologies
  • Quantification using image analysis systems (Aperio, Vectra and MultiOmyx)
  • Integration of genomic level information from other experiments
  • Integration with public data bases
  • Application of deep machine learning algorithms

Biological and medical information extraction and inference

  • Experimental effects
  • Pathway and network analysis
  • Evaluate and refine hypotheses
  • Integration of external data sources into analysis
  • Drug targets analysis
  • Application of Structural Bioinformatics approach
  • Time-series analysis
  • Statistical and Multivariate Analyses
  • Clustering methods to evaluate the data structure
  • Reduce data complexity

Complementary informatics services

  • Analytical pipelines
  • Building and managing databases
  • Data extraction from public databases
  • Integration of internal data sources
  • Information consolidation
  • User interface design
  • Data visualization
  • Specialized platforms design, building and management
  • Big Data management and processing
  • Cloud computing and HPC

Experts at Ardigen are ready to cope with large volumes of unstructured data coming from various sources, streamed at high velocity or stored in massive clusters. We create the link from data to your business goal by selecting the right environment and algorithms for your problem, experimenting with data and optimizing the analysis process. By applying individual approach and top class solutions Ardigen helps data-driven organizations thrive. With your data we can collect evidence to help with the decisions you need to make or we can help monetize your data by creating data products.

Detailed offer

  • Machine learning on large data sets
  • Topological Data Analysis method
  • Deep learning
  • Stream analysis
  • Recommender systems
  • Predictive maintenance
  • User behavior and preferences reports
  • Marketing campaign response measurement and optimization

Complementary informatics services

  • Analytical pipelines
  • Building and managing databases
  • Data extraction from public databases
  • Integration of internal data sources
  • Information consolidation
  • User interface design
  • Data visualization
  • Specialized platforms design, building and management
  • Big Data management and processing
  • Cloud computing and HPC
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Contact

Address

Ardigen S.A.
tel.: +48 12 340 20 40
mail: ardigen@ardigen.com


West Coast US
1001 Bayhill Drive, Suite 245
San Bruno CA, 94066
USA


Headquarters
ul. Bobrzyńskiego 14
30-348 Kraków
POLAND

Software Development Center
ul. Litewska 8
35-302 Rzeszów
POLAND