User profiles for Mattias Rydenfelt

Mattias Rydenfelt

Charité Universitätsmedizin Berlin
Verified email at charite.de
Cited by 550

[HTML][HTML] The transcription factor titration effect dictates level of gene expression

…, FM Weinert, HG Garcia, D Song, M Rydenfelt… - Cell, 2014 - cell.com
Models of transcription are often built around a picture of RNA polymerase and transcription
factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between …

[HTML][HTML] Classification of gene signatures for their information value and functional redundancy

…, L Calzone, L Martignetti, M Rydenfelt… - NPJ systems biology …, 2017 - nature.com
Gene signatures are more and more used to interpret results of omics data analyses but
suffer from compositional (large overlap) and functional (correlated read-outs) redundancy. …

SPEED2: inferring upstream pathway activity from differential gene expression

M Rydenfelt, B Klinger, M Klünemann… - Nucleic acids …, 2020 - academic.oup.com
Extracting signalling pathway activities from transcriptome data is important to infer mechanistic
origins of transcriptomic dysregulation, for example in disease. A popular method to do …

Scaling of gene expression with transcription-factor fugacity

FM Weinert, RC Brewster, M Rydenfelt, R Phillips… - Physical review …, 2014 - APS
The proteins associated with gene regulation are often shared between multiple pathways
simultaneously. By way of contrast, models in regulatory biology often assume these …

Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration

M Rydenfelt, RS Cox III, H Garcia, R Phillips - Physical Review E, 2014 - APS
Transcription factors (TFs) with regulatory action at multiple promoter targets is the rule rather
than the exception, with examples ranging from the cAMP receptor protein (CRP) in E. coli …

[HTML][HTML] The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli

M Rydenfelt, HG Garcia, RS Cox III, R Phillips - PLoS one, 2014 - journals.plos.org
The ability to regulate gene expression is of central importance for the adaptability of living
organisms to changes in their external and internal environment. At the transcriptional level, …

Oncogenic β-catenin and PIK3CA instruct network states and cancer phenotypes in intestinal organoids

P Riemer, M Rydenfelt, M Marks, K van Eunen… - Journal of Cell …, 2017 - rupress.org
Colorectal cancer is driven by cooperating oncogenic mutations. In this study, we use
organotypic cultures derived from transgenic mice inducibly expressing oncogenic β-catenin and/…

The cancer cell proteome and transcriptome predicts sensitivity to targeted and cytotoxic drugs

M Rydenfelt, M Wongchenko, B Klinger… - Life Science …, 2019 - life-science-alliance.org
Tumors of different molecular subtypes can show strongly deviating responses to drug
treatment, making stratification of patients based on molecular markers an important part of …

Tracking Price Trends Using User–Product Interaction Data From a Price Comparison Service

M Rydenfelt - International Conference on Applied Economics, 2021 - Springer
Using online prices has made it possible to estimate inflation rates at a larger scale and
higher time resolution than were previously possible. In this chapter, we introduce a daily …

[BOOK][B] The Combinatorics of Transcriptional Regulation

M Rydenfelt - 2014 - search.proquest.com
The ability to regulate gene expression is of central importance for the adaptability of living
organisms to changes in their internal and external environment. At the transcriptional level, …