Workshop 1
Integrative data handling for improved human health research

Organizers
Katarzyna Bozek - CMMC-Lab. of Data Science of Bioimages
Philipp Antczak- CMMC-Lab. of Computational Biology of Aging

University Hospital Cologne (UHC) with over 340,000 patients annually, with 60,300 of them receiving inpatient care, is not only a key medical facility but also a huge hub for biomedical research. Research at the UHC spans a wide range of human health relevant projects and involves several large human cohorts. The vast amount of data generated at the UHC is often used uniquely within their specific projects and insufficiently explored to tackle challenges in other areas of biomedical research. Integrative data analyses, in conjunction with personalized medicine, offer the potential to extract novel understanding of the biological systems and provide a new perspective on human health, patient stratification and welfare.

In this workshop we will learn about diverse clinical and experimental data flows that exist at the UHC, the data management practices that are implemented across the labs and clinical departments, and the practical reasons behind exploiting these to improve human health. With the goal of achieving an integrated analytical system at the UHC we will hold an in-depth discussion on improving data depositing and internal reporting as well as knowledge exchange across research fields and departments. Inherent to our discussion will be the removal of boundaries throughout the organization to inspire new integrative research projects and comprehensive (re)use of the rich biomedical datasets developed at the UHC. Institution-wide communication and inter-departmental links will contribute to an improved, integrative patient care and biomedical research.

Interactive Workshop via Zoom Meeting
Katarzyna Bozek and Philipp Antczak (organizers) are pleased to welcome the on-site workshop participants (see below) and the participants who will join the workshop via Go-To-Meeting.

Participants of the roundtable discussions:

• Thomas Benzing - Clinic II of Internal Medicine and NephroLab Cologne - Kidney Research Center Cologne
• Reinhard Büttner - Insitute for Pathology
• Katrin Bohl - Team Member of the NephroLab Cologne - Kidney Research Center Cologne
• Konstantina Charmpi - Team Member of the CellNet Group
• Alexander Dilthey - CECAD Biofinformatics Core Facility
• Florian Erger - Institute of Human Genetics
• Roman-Ulrich Müller -NephroLab Cologne - Kidney Research Center Cologne
• Astrid Schauss - CECAD Imaging Facility

Background information:
A) General publications introducing the topic:

• Data integration in the era of omics: current and future challenges - https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-8-S2-I1
  published by Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, Ballestar E, Bongcam-Rudloff E, Conesa A, Tegnér: J. BMC Syst Biol. 2014;8 Suppl 2(Suppl 2):I1. doi: 10.1186/1752-0509-8-S2-I1. Epub 2014 Mar 13.
   
• A selective review of multi-level omics data integration using variable selection - https://www.mdpi.com/2571-5135/8/1/4
  published by by Cen Wu, Fei Zhou, Jie Ren, Xiaoxi Li, Yu Jiang and Shuangge Ma: High-Throughput 2019, 8(1), 4

B) Interesting publications of the organizers

• Identifying robust biomarkers of infection through an omics-based meta-analysis
  Ashleigh C M, Perkins S, Rushton D, Jonathan D, Spencer P, Jones A R, Antczak P( 2020)BIOINFORMATICS (under review)
   
• Towards dense object tracking in a 2D honeybee hive.
  Bozek K, Hebert L, Mikheyev AS, Stephens GJ. Computer Vision and Pattern Recognition 2018 -  https://arxiv.org/abs/1712.08324
   
• Towards dense object tracking in a 2D honeybee hive.
  Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto, M, Tomita M, Pääbo S, Sherwood, CC, Hof PR, Ely Towards dense object tracking in a 2D honeybee hive. , Y Li, D Steinhauser, L Willmitzer, P Giavalisco, P Khaitovich. Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque and mouse tissues. Neuron 2015 - https://pubmed.ncbi.nlm.nih.gov/25661180/ s
   
• Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.
  K Bozek, Y Wei, Z Yan, X Liu, J Xiong, M Sugimoto, M Tomita, S Pääbo, R Pieszek, CC Sherwood, PR Hof, JJ Ely, D Steinhauser, L Willmitzer, J Bangsbo, O Hansson, J Call, P Giavalisco, P Khaitovich.  PLoS Biol 2014 - https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001871
   
• The COPD knowledge base: Enabling data analysis and computational simulation in translational COPD research.
  Cano I, Tényi A, Schueller C, Wolff M, Huertas Migueláñez MM, Gomez-Cabrero D, Antczak P, Roca J, Cascante M, Falciani, F and Maier D (2014). Journal of Translational Medicine 2014 - 12( Suppl 2):S6 - 2014 - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255911/
   
• A systems biology approach reveals alLink between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD.
  ”Davidsen,P K, Herbert J M, Antczak P, Clarke K, Ferrer E, Peinado V I, Gonzalez C, Roca J, Egginton S, Barberá J A, Falciani F, and others. (2014) Genome Medicine 2014 - 6(8):59. - https://pubmed.ncbi.nlm.nih.gov/25228925/