About this Research Topic
Hereby we propose to organize a series of manuscripts related to the topic 'Systems Biology and Bioinformatics in Gastroenterology and Hepatology'. We believe that such series will increase visibility of an innovative scientific discipline connecting clinicians, basic scientists, mathematicians, as well as bioinformatics and will stimulate international networking among them in the field of Gastroenetrology and Hepatology.
Systems biology stands for a comprehensive and integrative approach in life science. During the last decades reductionist approaches, mainly based on molecular biology and biochemistry methods, has successfully identified many central mechanisms and characteristics of e.g. liver and pancreas under physiological and pathological conditions. However, these approaches only offer limited knowledge of how system properties emerge and are disturbed under disease conditions, such as fibrosis, cirrhosis, and cancer development. We believe that the plethora of causes and effects in complex biological networks might be better addressed by measuring time-‐resolved amounts and activity of central components followed by rigorous data integration in elaborative mathematical models. To construct and validate these models and to precisely describe systems' properties, different types of data are needed that are generated by molecular/biochemical analyses, genomics, transcriptomics, proteomics, metabolomics (OMICS) and high- throughput phenotyping.
The relevance of this approach is illustrated by the fact that several federal German programs support this multi-scale approach: HepatoSys (2004) with the aim of modelling the hepatocyte, Virtual Liver Network (VLN, 2010) that develops spatio-temporal models of biological events on the multicellular scale, Systems Medicine of the Liver (LiSyM, 2016) that with the aim to identify and model the common key processes leading to liver diseases.
Work within these initiatives and from other groups significantly increased our understanding of how different liver cells function and communicate to provide a stable environment under normal conditions and how dysfunction participates in the development of diseases. However, opportunities to discuss the diverse facets of systems biology from data generation, utilization of mathematical models, and data integration among experts in the field remain rare. We believe that Frontiers in Physiology would represent an excellent platform for this urgently needed discussion based on a collection of original articles from Hepatology and Gastroenterology with clear focus on systems biology.
Topics to be covered by the Research Topic of Frontiers in Physiology on Systems Biology/Bioinformatics in a state-of-the-art format include:
• The toolbox of systems hepatology/gastroenterology: systems genetics, transcriptomics & proteomics, integrated phenome analysis.
• Applying systems biology at the level of cells, zones, networks, and in regard to systemic consequences.
• Applications to gastrointestinal diseases, including non-alcoholic fatty liver disease, alcoholic hepatitis, viral hepatitis, liver fibrosis, liver cancer, among others.
• Translational medicine: from systems to precision hepatology/gastroenterology.