This webpage is dedicated to the tool RE:IN, providing information on the latest version available.
PhD Position Available: Exploring motif-based design patterns for biological computation
Software design patterns provide abstract, reusable solutions to frequently encountered problem. In this project, we will explore whether biology also exploits design patterns in the regulatory programs controlling cellular behaviours. We will focus on the role of small regulatory motifs that are known to be enriched in living systems, and which cluster in specific ways, and employ formal methods to understand how structure gives rise to function in these motifs. A new regulatory system based on engineered RNA interactions will be developed to allow for the reliable creation of large regulatory circuits, which will then be used to implement novel regulatory programs from motif-based design rules.
4-year PhD Scholarship, Supervisor: Dr Thomas Gorochowski (School of Biological Sciences, University of Bristol, UK) Co-supervisors: Dr Boyan Yordanov, Dr Sara-Jane Dunn (Biological Computation Group, Microsoft Research Cambridge, UK) and Lucia Marucci (Engineering Mathematics, University of Bristol, UK).
Find out more information here.
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There is computational interface with notebooks for the underlying Reasoning Engine on Github.
- The network governing naive pluripotency in mouse embryonic stem cells. This corresponds to the initial set of components, interactions and constraints that we encoded.
- Identifying the minimal transcriptional network governing naive pluripotency. In this example, use the 'Find Minimal Models' functionality.
- A yeast cell cycle example, based on a Boolean network model published by Li et al. (2004).
- An example from cardiac development, based on a Boolean network model published by Herrmann et al. (2012).
- An example from myeloid progenitor differentiation, based on a Boolean network model published by Krumsiek et al. (2011).
- The 0.782 cABN. This is the cABN that was used to generate the initial set of predictions concerning the dynamics of EpiSC resetting.
- The 0.717 cABN. This is the final, refined set of models that was also used to predict the dynamics of reprogramming from MEFs.
Windows bug-testing software cracks stem cell programs – New Scientist
Minimal toolkit for stem cell self-renewal – The Scientist
Theorem prover sheds new light on stem cell behaviour – Inside Microsoft Research
<!--[panel header="Prepared Examples"]The following links navigate to examples from the indicated publications. The files used to generate these can be saved directly from the tool for examination, or further editing and exploration.Austin Smith (Wellcome-MRC Cambridge Stem Cell Institute) and Graziano Martello (University of Padova), we developed RE:IN to uncover the transcriptional program governing naive pluripotency in mouse ESCs. The following links correspond to the investigations presented in this publication.
Christoph M. Wintersteiger
Research Software Development Engineer