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Our AI approach to single-cell genomics

Artificial Intelligence driving insight in single-cell genomics, biomedical research and personalized medicine

The Life Sciences and the modern Medicine are currently experiencing a dramatic development fueled by the genomic revolution of single-cell genomics. The technological achievement of single-cell RNA sequencing (or short scRNA-seq) allows for the first time in history to analyze the genetic expression of single cells. Thereby it has opened the door for a completely new market of personalized and precision medicine, which is estimated to reach a volume of five billion US$ by 2025. The Comma Soft AG as a strong partner and expert in Data Science and solutions in the field of Artificial Intelligence (AI) is actively taking part in this market. Furthermore, Comma Soft is building bridges between academia and industry and, thus, fosters translation and promotes knowledge transfer across sectors.

For the first time in history, it is possible to study the genetic expression of single cells

Every single of the approximately 37 trillion cells in our body carries the same genetic information. Yet, every cell is unique. They divide into many different cell classes and types – nerve cells, muscle cells, skin cells, immune cells and more – each of which with specific morphologies and tasks within our body. On top of that, there are a plethora of subtypes and cell states that are still not understood and which only became observable with help of single-cell genomics.

The root cause for the vast amount of different cell types – despite of them having the same underlying genetic information – lies in the expression of this genetic information. In fact, many if not most of the 25,000 human genes remain inactive within one cell and only the set of active genes defines the so-called phenotype, which is the set of observable individual traits and characteristics of a cell. Single-cell genomics now makes it possible to detect and analyze the genetic expression of each single cell. This enables deep insights into the composition of tissue, the interaction between cells, and into the evolution of dynamic biochemical processes on the resolution of single cells.

FASTGenomics features

  • Intuitive analysis environment with cloud access from everywhere
  • Support of multiple data formats (mtx, rds, hdf5, h5ad, loom, csv, tsv)
  • R and Python: use Seurat and ScanPy with full support of their associated data objects
  • Data management: share your data and metadata with colleagues, coworkers or publish
  • State-of-the-art analytics: constantly growing number of analyses from renowned working groups
  • Interactive analyses using Jupyter notebooks
  • Showcase of results: make your analysis available to the community
  • Reproducibility and reusability of your results through dockerized environments

Artificial Intelligence by FASTGenomics and Comma Soft in the Life Sciences

In recent years we have seen a dramatic technical development in the field of single-cell sequencing. It is now possible to analyze millions of cells in a single experiment [Svensson et al., 2019]. Along with this technical development in single-cell sequencing comes an exponential growth of the data volume, which cannot be handled with classical algorithms from genomics research. As Prof. Joachim Schultze, head of the Department for Genomics & Immunoregulation at the LIMES Institute of the University of Bonn explains in his keynote at the annual Petersberger Gespräche 2018 hosted by Comma Soft AG:

“The understanding of the fundamental units of life can only be achieved with artificial intelligence.“

Already in 2014 and as the first German company, Comma Soft – as an expert in AI and with years of experience in data preparation, handling, and analysis in many industrial sectors – realized that a revenue-generating analysis of such complex, noisy and highly-connected data is only possible through an extensive dialog and transfer between the associated disciplines: On the one hand single-cell sequencing requires a specialized lab of experience biologists, and on the other hand the application of problem-adapted AI-based methods requires experts in the field of computer science and mathematics. In order to enable such interdisciplinary application Comma Soft, together with the LIMES Institute, developed the AI-analytics platform FASTGenomics. In 2016, this project received funding by the German Federal Ministry of Economic Affairs and Energy for three years. FASTGenomics is now an open platform for single-cell genomics bridging the disciplines and thereby provides an innovative and high-performance tool for biomedical research.

Fundamental insights and large growth potential based on the connection of single-cell genomics and AI

It is now common sense that the developments in AI and biotechnology will shape our future [see Dickten et al., 2019, for an overview]. Both market analysts and research experts estimate an enormous growth potential for single-cell genomics with the possibility to generate fundamental biomedical insights. Results based on single-cell genomics have recently been awarded the Science Breakthrough of the Year 2018. It is expected that single-cell genomics will revolutionize the landscape of cancer genomics, immunology and whole-organism science [Shapiro et al., 2013] and that it will create a new global market of personalized and precision medicine that is estimated to reach more than $5 billion by 2025. Due to its early involvement in the field the Comma Soft AG has gained much experience in the necessary competences and has created a broad network of players. Thus, Comma Soft has the potential to actively shape this new market.

FASTGenomics: Building bridges between academia and industry

The Comma Soft AG is an active member in several national and European research consortia. Additionally, Comma Soft collaborates closely with industrial partners. For example, Comma Soft leads a multi-faceted research project in the field of immunology and pulmonology for a large pharma company. The projects led by Comma Soft span across sectors and include sampling of probes in the hospital, genetic sequencing, academic and AI-based analysis of the data, up to the identification of pharmaceutical relevant biomarker candidates. The success of these projects is deeply rooted in the close collaboration with and transfer between academic, clinical and industrial partners in connection with the application of state-of-the-art AI-analytics. The Comma Soft AG has such acquired a central position and is building bridges between the disciplines thereby fostering translation and an effective and quick transfer of knowledge from research to product.

From this central position and as a connector between AI and biology, Comma Soft offers problem-adapted services to enable biologists and medical doctors to apply complex AI-based algorithms to their specific topic and research question. For that matter, the FASTGenomics platform and scientific consulting services provide the necessary framework for sustainable insights regarding new biochemical processes and their translation into the industrial context to generate new applications and therapies.