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CompCancer Colloquium - 20.04.2023 - Stefan Legewie

We are glad to have Stefan Legewie from the University of Stuttgart in our Colloquium with his talk entitled "Alternative splicing by the numbers"

 

Thursday, 20.04.2023 at 10 am

Maud-Menten Hall, Phillipstr. 13, House 18, 3rd floorPoster for the colloquium

Short bio:

Stefan Legewie studied biochemistry at the University of Witten / Herdecke. During his studies, showed interest in the field of systems biology (still young then), in which mathematical tools are used to interpret experimental data. He did his PhD in Biophysics at the Humboldt University in Berlin under the supervision of Hanspeter Herzel and in 2008 he received his doctorate with distinction (summa cum laude). In his dissertation he examined cellular information networks that transmit hormonal signals from the cell surface to the cell nucleus, and was able to derive design principles that give these networks robustness and switch-like decision-making behavior. The dissertation was awarded the MTZ Prize for Medical Systems Biology and the Reinhart Heinrich Prize for Theoretical Biology. After a short stay at the German Cancer Research Center, Stefan moved to the newly founded Institute for Molecular Biology (IMB) in Mainz as a group leader in 2010. There he was able to expand his work on the robustness and heterogeneity of biological systems and also deal with the question of how the activity of genes can be reliably controlled. He has been Professor of Systems Biology at the University of Stuttgart since September 1, 2020.

CompCancer Seminar 12.04.2023 - Kenji Kamimoto

For the seminar on the 12th of April am Melanie Fatohi invited Kenji Kamimoto from the Morris Lab (Washington University in St. Louis, Missouri, USA), to give us a talk on his recent work about CellOracle, a computational tool that infers gene regulatory networks for in silico gene perturbations for elucidation of cell identity dynamics.. If you are interested in joining write an e-Mail to compcancer at charite dot de to receive the zoom link.

Because of the time difference, the literature seminar will take place virtually on zoom at 5 pm.

Colloquium 23.03.2023 - Martin Schäfer

We are pleased to announce our first speaker in our Colloquium 2023!

Martin Schäfer from the Istituto Europeo di Oncologia in Milano will give a presentation entitled "Selection in tumor genome and epigenome evolution"

When?     March 23 starting at 4 pm

Where?   Maud-Menten-Hall
                  Philippstraße 13
                  Haus 18 (3rd floor)
                  10115 Berlin

 

Martin Schäfer and his lab members are interested how alterations of the DNA transform a healthy into a malignant cell. Recent efforts uncovered a large number of genetic or epigenetic alterations in cancer patients, but it is difficult to tell which of those contribute to disease progression.

As the process of cancer development often takes many years, they are studying the evolutionary principles and try to understand how the environment modulates cancer evolution.

Additionally, with newly developed methods using tools from network and systems biology they try to better understand the interplay between different alterations in cancer genomes and epigenomes.

 

Workshop on IT in health and cancer

Monday, 23.1.2023, 14:00-17:30

Berlin-Mitte, Philipstr. 13, Haus 18 (Leonor Michaelis Haus), 3rd floor, Maud Menten Hall

Programme:

14.00   Ulf Leser: Welcome
14.10   Dieter Beule: Local and national systems for omics data mangement
14.50   Bert Arnrich: Connected Healthcare: Paving the Way for a User-Centered and Preventive Healthcare Model
15.30   Break
16.00   Meike Zehlike: Beyond Incompatibility in Algorithmic Fairness -- A FAir Interpolation Method
16.40   Fabian Praßer: Sharing data for translational research: privacy-enhancing approaches
17.20   Wrap Up
17:30  End of workshop

 

Invitation

Dieter Beule: Local and national systems for omics data mangement
Scientists employing large-scale omics in life science research face challenges in modeling of multi-assay studies, recording of relevant parameters, and managing resulting large data volumes with complex metadata. We introduce SODAR, the system for omics data access and retrieval, that helps to address some of these challenges. Furthermore, we discuss emerging national infrastructures for sharing data omics data across sites.

Bert Arnrich: Connected Healthcare: Paving the Way for a User-Centered
and Preventive Healthcare Model


Connected Healthcare aims to pave the way for transforming healthcare systems from purely managing illness to maintaining wellness. Ubiquitous sensing and computing technologies are foreseen as the key enabler for pushing the paradigm shift from the established provider-centric healthcare model to a user-centered and preventive overall lifestyle health management that is available everywhere, anytime and to anyone. In this talk we will provide examples of the three pillars of success: unobtrusive sensing technology, adequate data processing and modeling, and persuasive human-computer interfaces.

Meike Zehlike: Beyond Incompatibility in Algorithmic Fairness -- A FAir Interpolation Method

Trustworthy AI becomes ever more important, both in machine learning and in the law. One important consequence is that decision makers must seek to guarantee a `fair', i.e., non-discriminatory, algorithmic decision procedure. However, there are several competing notions of algorithmic fairness that have been shown to be mutually incompatible under realistic factual assumptions. This concerns, for example, the widely used fairness measures of ‘calibration within groups’ and ‘balance for the positive/negative class’. Indeed, the COMPAS algorithm, which predicts recidivism risk of criminal offenders, exhibits racial bias according to the balance metrics, but not regarding calibration.
In this talk, I present a novel algorithm (FAIM) for continuously interpolating between these three fairness criteria. Thus, an initially unfair prediction can be remedied to at least partially meet a desired, weighted combination of the respective fairness conditions. The algorithm relies on methods from the mathematical theory of optimal transport. We demonstrate the effectiveness of our algorithm when applied to synthetic data, the COMPAS data set, and a new, real-world data set from the e-commerce sector. Finally, I discuss to what extent FAIM can be harnessed to comply with conflicting legal obligations. The analysis suggests that it may operationalize duties in traditional legal fields, such as credit scoring and criminal justice proceedings, but also for the latest AI regulation put forth in the EU, like the recently enacted Digital Markets Act.

Fabian Praßer: Sharing data for translational research: privacy-enhancing approaches

Data sharing and the re-use of health data for secondary purposes have become a core elements of biomedical research, resulting in complex privacy challenges. Ideally, generic solutions would allow researchers to integrate and process biomedical data on a large scale, while citizens and patients can exercise their right to privacy and control what happens to their personal data. However, there are inherent trade-offs and technical solutions typically require balancing conflicting objectives: (1) privacy protection and (2) usefulness. Both objectives can be broken down into several further aspects. First, the term "privacy protection" can relate to a wide variety of different guarantees or degrees of control that can be provided. Second, the term "usefulness" may refer to the quality of data or results, to the flexibility with which users can perform analyses or to the scalability of platforms. In this talk, we will provide an overview of different properties that translational research data platforms can have and analyze common approaches.

CompCancer Seminar 07.12.2022 - Pauline Hiort

For the seminar on the 7th of December at 11 am Sofya Marchenko invited Pauline Hiort (PhD student from Prof. Dr. Bernhard Renard Group at the HPI) to talk about her research. If you are interested in joining write an e-Mail to compcancer at charite dot de to receive the zoom link.

 

DrDimont: explainable drug response prediction from differential analysis of multi-omics networks

The recent publication explained a novel method for condition-specific molecular networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks, which allows to predict drug responses. To demonstrate the efficiency the method, it is applied to breast cancer patients’ samples containing transcriptomics, proteomics, phosphosites and metabolomics measurements and compares drug response between estrogen receptor positive and receptor negative patients. 

The paper

 

 

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About

The research training group CompCancer (RTG2424) is a DFG funded PhD programme in Berlin, focussing on computational aspects of cancer research.

Contact: compcancer at charite dot de