Prof. Dr. Tim Conrad

Projects as a project leader

• CH14

  Understanding cell trajectories with sparse similarity learning

  Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte

  Project heads: Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte
  Project members: Nada Cvetkovic
  Duration: 01.06.2017 - 31.12.2019
  Status: running
  Located at: Freie Universität Berlin / Technische Universität Berlin / Konrad-Zuse-Zentrum für Informationstechnik Berlin
  

  Description

  In living organisms, biological cells transition from one state to another. This happens during normal cell development (e.g. aging) or is triggered by events, such as diseases. The time-ordered set of state changes is called a trajectory. Identifying these cell trajectories is a crucial part in bio-medical research to understand changes on a gene and molecular level. It allows to derive biological insights such as disease mechanisms and can lead to new biomedical discoveries and to advances in health-care. With the advent of single cell experiments such as Drop-Seq or inDrop, individual gene expression profiles of thousands of cells can be measured in a single experiment. These large data-sets allow to determine a cell's state based on its gene activity (cell expression profiles, CEPs), which can be expressed as a large feature vector representing its location in some large state space. The main problem with these experiments is that the actual time-information is lost, and needs to be recovered. The state-of-the art solution is to introduce the concept of pseudo-time in which the cells are ordered by CEP similarity. To find robust and biological meaningful trajectories based on CEPs, two main tasks have to be performed: (1) A CEP-based metric has to be learned to define pair-wise distances between CEPs. (2) Given this metric, similar CEP groups and transition paths between those groups should be identified and analysed.
  
  http://medicalbioinformatics.de/research/projects/ecmath-ch14

• CH21

  Data-Driven Modelling of Cellular Processes and beyond

  Prof. Dr. Tim Conrad / Dr. Stefan Klus / Prof. Dr. Christof Schütte

  Project heads: Prof. Dr. Tim Conrad / Dr. Stefan Klus / Prof. Dr. Christof Schütte
  Project members: Dr. Wei Zhang
  Duration: 01.06.2017 - 31.12.2019
  Status: running
  Located at: Konrad-Zuse-Zentrum für Informationstechnik Berlin
  

  Description

  Cellular processes are governed by diffusion, transport, and interactions of its constituents. For many processes the spatial inhomogeneity of cells is of secondary importance; modelling such processes means finding appropriate kinetic models of the underlying cellular reaction networks (CRNs). The availability of such models is key to many areas of the life sciences ranging from computational biology to system medicine and is essential for understanding the fundamentals of cellular behavior, its malfunction under external stress and its restoration by regenerative interventions.
  
  http://medicalbioinformatics.de/research/projects/ecmath-ch21

• CH2

  Sparse compressed sensing based classifiers for -omics mass-data

  Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte

  Project heads: Prof. Dr. Tim Conrad / Prof. Dr. Gitta Kutyniok / Prof. Dr. Christof Schütte
  Project members: Nada Cvetkovic / Martin Genzel
  Duration: -
  Status: completed
  Located at: Freie Universität Berlin / Technische Universität Berlin
  

  Description

  Tumor diseases rank among the most frequent causes of death in Western countries coinciding with an incomplete understanding of the underlying pathogenic mechanisms and a lack of individual treatment options. Hence, early diagnosis of the disease and early relapse monitoring are currently the best available options to improve patient survival. In this project, we aim for the identification of disease specific sets of biological signals that reliably indicate a disease outbreak (or status) in an individual. Such biological signals (e.g. proteomics or genomics data) are typically very large (millions of dimensions), which significantly increases the complexity of algorithms for analyzing the parameter space or makes them even infeasible. However, these types of data usually exhibit a very particular structure, and at the same time, the set of disease specific features is very small compared to the ambient dimension. Such a high-dimensional setting naturally calls for the application of the concept of sparse classifiers, which has been extensively studied in the fields of compressed sensing and statistical learning during the last decade. Our research focuses on both algorithmic improvements of available methods as well as theoretical results such as recovery guarantees for general data models.
  
  http://medicalbioinformatics.de/research/projects/ecmath-ch2

• CH7

  Network-of-Network based -omics data integration

  Prof. Dr. Tim Conrad / Prof. Dr. Christof Schütte

  Project heads: Prof. Dr. Tim Conrad / Prof. Dr. Christof Schütte
  Project members: -
  Duration: -
  Status: completed
  Located at: Freie Universität Berlin
  

  Description

  Project Background

  Pancreatic cancer is the fifth leading cause of cancer death in Germany (see DKFZ Report, 2010). It is estimated that in 2030 it will be the second leading cause of cancer death incurring a cost of about 15,8 Billion US-Dollar worldwide to the public health systems.

  Cancer is a systems disease

  "Cancer is no more a disease of cells than a traffic jam is a disease of cars. A lifetime of study of the internal-combustion engine would not help anyone to understand our traffic problems.'" (Smithers1962). It is accepted that gene mutations are part of the process of cancer, but mutations alone are not enough. Cancer involves an interaction between neoplastic cells and surrounding tissue on many different levels, e.g. interaction of RNA molecules, proteins, and metabolites. But most available models are limited to only one or very few levels of interactions and describe a rather static view.

  From single to multi source: data integration on a systems level

  Current high-throughput -omics technologies have dramatically eased the production of part lists for a variety of organisms. What is still missing are the dynamic interactions among an organism's molecular parts, and the interactions between different biological levels, such as transcriptomics and proteomics. This is pivotal to better understanding of an organism's biology, and - in our case - to understand pancreas cancer.
  
  Therefore, the aim of this project is two-fold: (1) use data acquired in our earlier projects to create a holistic integration of the aforementioned sources and levels for modeling pancreas cancer, which we call Network-of-Networks or short: NoN (in our context networks of different -omics levels, such as genomics, transcriptomics, proteomics and metabolomics. (2) A NoN is a very large and complex object and its structure differs significantly from other biological networks. Thus, new methods for complexity reduction and analyzing NoNs will be developed in this project.

  The goal

  In this project we aim to develop a new method that can be used to solve this task: the identification of minimal, yet robust fingerprints from very high-dimensional, noisy -omics data. Our method will be based on ideas from the areas of compressed sensing and machine learning.
  
  http://medicalbioinformatics.de/research/projects/ecmath-ch7