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DMCM2021

The 2021 community meeting is hosted by the Department of Systems Biology and Bioinformatics, University of Rostock, Germany.

Location

The DMCM2021 took place online via Zoom.

Abstract submission

The abstract submission is closed.

Registration

The registration is closed.

Invited speakers

Giovanni Scardoni, PhD

Center for BioMedical Computing
University of Verona, Italy

Chris Mungall, PhD

Lawrence Berkeley National Laboratory
Berkeley, United States

Sean O'Donoghue, PhD

School of Biotechnology and Biomolecular Sciences
University of New South Wales, Australia

Joaquin Dopazo, PhD

Clinical Bioinformatics Area, FPS
Hospital Virgen del Rocio Sevilla, Spain

Antonella Di Pizio, PhD

Leibniz-Institute for Food Systems Biology
Technical University of Munich, Germany


Programme

The time is shown for Berlin: Central European Time (CET) – UTC/GMT +1 hour.

Day 1 (November 29, 2021)

8:30 Introductory remark
Olaf Wolkenhauer, University of Rostock, Rostock, Germany


Session 1

8:50 [T1] Reconstruction of a context-specific metabolic model SW620 colorectal cancer cell line to study the metabolic effect of rosemary extract
Jordi Roma Pi, Barcelona Supercomputing Center, Spain

9:15 KEYNOTE Mechanistic models of disease maps for drug discovery and repurposing
Joaquin Dopazo, Head of the Clinical Bioinformatics Area, FPS, Hospital Virgen del Rocio, Sevilla, Spain

10:00 [T2] Inference of an Integrative, Executable Network for Rheumatoid Arthritis Combining Data-Driven Machine Learning Approaches and a State-of-the-Art Mechanistic Disease Map
Anna Niarakis, University of Evry, Paris-Saclay and INRIA Saclay, France

10:25 [T3] Reconstruction of disease mechanisms: update on best practices
Alexander Mazein, Luxembourg Centre for Systems Biomedicine, University of Luxembourg


10:50 Coffee break


11:00 [T4] Leveraging systems biology and machine learning for automatic drug repurposing in the rare disease landscape
Marina Esteban-Medina, Bioinformatics Área, Fundación Progreso y Salud (FPS), Hospital Virgen del Rocío, Sevilla, Spain

11:25 [T5] Interpretation of genomic variation in a cohort of rare mental diseases using a mechanistic approach
Ana M Pérez-Gutiérrez, University of Granada, Spain


Session 2

11:50 KEYNOTE Taste and smell (dys)function from a molecular perspective
Antonella Di Pizio, Leibniz-Institute for Food Systems Biology at the Technical University of Munich


12:35 Lunch Break


13:30 [T6/P8] Systems medicine modelling in Cystic Fibrosis to predict possible drug targets and active compound combinations
Liza Vinhoven, University Medical Center Göttingen, Germany

13:55 [T7] A molecular map of the ageing neuron
Rupert Overall, Humboldt University, Germany

14:20 [T8] A novel Disease Map to link Malnutrition and Sarcopenia through in silico Network Approaches
Matti Hoch, Department of Systems Biology & Bioinformatics, University of Rostock, Germany

14:45 [T9] SIGNOR: a resource of manually curated causal interactions and biological pathways
Livia Perfetto, Fondazione Human Technopole, Italy


15:05 Coffee break


15:20 Poster session

[P1] HCM Clinical: An Interactive Knowledge Resource for HCM Diagnosis, Monitoring, and Treatment
Mila Glavaški, Faculty of Medicine, University of Novi Sad, Serbia

[P2] Network- and Enrichment-based Inference of Phenotypes and Targets from large-scale Disease Maps
Matti Hoch, Department of Systems Biology & Bioinformatics, University of Rostock, Germany

[P3] Understanding crosstalk between tumor and autoimmune diseases using disease map approaches
Krishan P Singh, Department of Systems Biology and Bioinformatics, University of Rostock, Germany

[P4] NaviCenta – The Placenta Specific Disease Map
Julia Scheel, Department of Systems Biology and Bioinformatics, University of Rostock, Germany

[P5] Towards the construction of a psoriasis disease map: the level of intercellular communication
Marcio Luis Acencio, Luxembourg Centre for Systems Biomedicine, University of Luxembourg

[P6] Computational Modeling of the Metabolic Reprogramming in Rheumatoid Arthritis Synovial Fibroblasts
Sahar Aghakhani, GenHotel, Univ. Evry, Univ. Paris-Saclay & Inria Saclay, France

[P7] Network-based comparison of lipid mediator pathways from single-cell RNA-seq data
Matti Hoch, Department of Systems Biology & Bioinformatics, University of Rostock, Germany


16:35 [T10] Systems Medicine in ELIXIR
John Hancock, Institute for Biochemistry, Faculty of medicine, University of Ljubljana, Slovenia

17:00 KEYNOTE Biological Ontologies in the Systems Biology of Human Diseases
Chris Mungall, Head, Biosystems Data Science Department, Lawrence Berkeley National Laboratory, Berkeley


17:45 Closing remarks day 1


Day 2 (November 30, 2021)

Session 3

8:30 The COVID-19 Disease Map
Marek Ostaszewski, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg

9:00 KEYNOTE Using structural modelling to study COVID disease mechanisms
Seán O’Donoghue, Garvan Institute of Medical Research, Australia

9:45 [T11] Initial FAIR assessment of the biological diagrams available in the MINERVA platform within the COVID-19 Disease Map
Irina Balaur, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg

10:10 [T12] Inspecting tissue-specific pathway activities in COVID-19 patients using WikiPathways and the COVID-19 Disease Map
Nhung Pham, Maastricht University, Netherland

10:35 [T13] Discovering potential interactions between rare diseases and COVID-19 by combining mechanistic models of viral infection with statistical modeling
Macarena López-Sánchez, Clinical Bioinformatics Area, FPS; Computational Systems Medicine, IBIS


11:00 Coffee break


Session 4

11:10 [T14] An Integrated Data Analysis of mRNA, miRNA and Signaling Pathways in Oral Cancer
Jyotsna Choubey, Raipur Institute of Technology, Raipur, India

11:35 [T15] Identification of regulatory factors associated with the induction of fetal haemoglobin in β-Thalassaemic patients
Soumya Khare, Raipur Institute of Technology, Raipur, India

12:00 [T16] Intersection—Simple, Yet Effective for Exploring Molecular Mechanisms; Lessons Learned from the HCM Representations
Mila Glavaški, Faculty of Medicine, University of Novi Sad, Serbia


12:25 Lunch Break


13:15 KEYNOTE Integrating experimental data sets in network topological analysis
Giovanni Sardoni, Center for BioMedical Computing, University of Verona, Italy

14:00 [T17] Molecular Interaction Map of TGFβ Induced Epithelial to Mesenchymal Transition in Breast Cancer
Sai Bhavani Gottumukkala, National Institute of Technology Warangal, India

14:25 [T18] The importance of TGF Growth pathway in glaucoma disease progression
Jyoti Kant Choudhari, Department of Biotechnology Raipur Institute of Technology Raipur, Chhattisgarh, India


14:50 Coffee break


15:00 Breakout Session 1
(two topics in parallel)

Topic 1:

Need and approaches to connect various disease maps
Description: Several disease maps are in the public domain providing a comprehensive knowledge base around their indications. The knowledge base available with one disease map can also be used to quickly curate and annotate another disease map. There exist many redundancies in the curated processes and molecular interactions. Systems medicine disease map currently lists 16 disease map projects. A solution to search for cells, molecules, and processes among all Disease Maps (and maybe even other Databases) could improve map curation and connect efforts between different research groups.

Breakout Room 1: GatherTown

Topic 2:

Disease maps from knowledgebase to analysis platform
Description: In most cases, disease maps are in the form of a static knowledge base with linkages to various state-of-the-art databases or mapping of the experimental data in the form of visual overlays. Disease maps should be used not only for the knowledge representation but also as the analysis platform. In this breakout room, we will discuss recent efforts to make disease maps as an analysis platform. We will also discuss potential areas where disease maps can serve as a powerful tool for the generation of data-driven hypotheses.

Breakout Room 2: GatherTown


16:00 Coffee break


16:15 Breakout Session 2
(two topics in parallel)

Topic 3:

Bringing disease maps close to clinics
Description: Ideally, disease maps will eventually be used to stratify patient cohorts and/or predict whether a patient falls into group “disease” or group “control”. Currently, disease maps can serve as a visualization tool for patient data visualization based on patient demographics. Workflows to extend this functionality of disease maps for clinicians have been suggested. In this session, we will discuss recent advances and open tasks to reach this goal.

Breakout Room 3: GatherTown

Topic 4:

Challenges in Disease Maps Curation
Description: There is a certain standard workflow to the curation of disease maps. However, as disease maps are constructed with a certain disease/question in mind, challenges for curators arise, which affect the reusability of disease maps. The different questions disease maps are based on lead to variations of the disease map construction and curation workflow. Presently these deviations are not tracked in an all encompassing navigable manner. Further, standard network analysis workflows are usually based on either using “activity flow” or “process description” SBGN languages. Disease maps often use a mix of the two, making the establishment of adjusted analysis tools/workflows necessary. With time our understanding of disease pathology increases, hence disease maps need constant updates. Currently, this is done manually. As this is both labour and time consuming, a more streamlined solution would be advantageous. Finally, most computational models require experimental validation, before they are accepted by the research community. As of now, no general recommendations for experimental validations are available. This session will be used to exchange ideas and experiences encountered during map curation. Defining a general solution is often not possible. However, it may be beneficial to keep track of experiences and solutions, beyond DMCMs.

Breakout Room 4: GatherTown


17:15 Breakout Summary & Closing remarks of DMCM2021


Organisers

Local organisers

Olaf Wolkenhauer
Matti Hoch
Julia Scheel
Suchi Smita
Shailendra Gupta

Disease Maps Project Coordinators

Alexander Mazein
Marek Ostaszewski
Inna Kuperstein
Anna Niarakis
Andrei Zinovyev
Reinhard Schneider
Emmanuel Barillot
Rudi Balling
Charles Auffray