Kolja Becker

Kolja Becker
Institute of Molecular Biology | IMB · Modelling of Biological Networks

Dr.

About

12
Publications
1,868
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148
Citations
Additional affiliations
December 2018 - January 2019
Institute of Molecular Biology
Position
  • PostDoc Position
August 2013 - April 2016
Institute of Molecular Biology
Position
  • PhD Student

Publications

Publications (12)
Article
Full-text available
TGFβ-signaling regulates cancer progression by controlling cell division, migration, and death. These outcomes are mediated by gene expression changes, but the mechanisms of decision-making toward specific fates remain unclear. Here, we combine SMAD transcription factor imaging, genome-wide RNA sequencing, and morphological assays to quantitatively...
Preprint
Full-text available
TGFβ-signaling regulates cancer progression by controlling cell division, migration and death. These outcomes are mediated by gene expression changes, but the mechanisms of decision making towards specific fates remain unclear. Here, we combine SMAD transcription factor imaging, genome-wide RNA sequencing and morphological assays to quantitatively...
Article
Full-text available
Even though proteins are produced from mRNA, the correlation between mRNA levels and protein abundances is moderate in most studies, occasionally attributed to complex post-transcriptional regulation. To address this, we generate a paired transcriptome/proteome time course dataset with 14 time points during Drosophila embryogenesis. Despite a limit...
Article
Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determi...
Article
Full-text available
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and mRNA expression data and recover the continuous spatio-temporal fields. Rigorous methods are required to ident...
Conference Paper
A common approach for reverse engineering biological networks from data is to deduce the existence of interactions among nodes from information theoretic measures. Estimating these quantities in a multidimensional space is computationally demanding for large datasets. This hampers the application of elaborate algorithms – which are crucial for disc...
Article
Organisms adapt their physiology and behaviour to the 24h day-night cycle to which they are exposed. On a cellular level, this is regulated by intrinsic transcriptional-translational feedback loops important for maintaining the circadian rhythm. These loops are organized by members of the core clock network, which further regulate transcription of...
Article
Full-text available
Author Summary The analysis of pattern-forming gene networks is largely focussed on transcriptional regulation. However, post-transcriptional events, such as translation and regulation of protein stability also play important roles in the establishment of protein expression patterns and levels. In this study, we use a reverse-engineering approach—f...

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