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Related publications (114)
Employing Batch Reinforcement Learning to Control Gene Regulation Without Explicitly Constructing Gene Regulatory Networks
The goal of controlling a gene regulatory network (GRN) is to generate an intervention strategy, i.e., a control policy, such that by applying the policy the system will avoid undesirable states. In this work, we propose a method to control GRNs by using B ...
AAAI Press2013Batch Mode Reinforcement Learning for Controlling Gene Regulatory Networks and Multi-model Gene Expression Data Enrichment Framework
Over the last decade, modeling and controlling gene regulation has received much attention. In this thesis, we have attempted to solve (i) controlling gene regulation systems and (ii) generating high quality artificial gene expression data problems. For co ...
2013Complete genome sequence of Dehalobacter restrictus PER-K23T
Christof Holliger, Julien Maillard, Hauke Smidt
Dehalobacter restrictus strain PER-K23 (DSM 9455) is the type strain of the species Dehalobacter restrictus. D. restrictus strain PER-K23 grows by organohalide respiration, coupling the oxidation of H2 to the reductive dechlorination of tetra- or trichloro ...
2013TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells
Didier Trono, Adamantia Kapopoulou, Andrea Corsinotti, Helen Mary Rowe, Johan Jakobsson
TRIM28 is critical for the silencing of endogenous retroviruses (ERVs) in embryonic stem (ES) cells. Here, we reveal that an essential impact of this process is the protection of cellular gene expression in early embryos from perturbation by cis-acting act ...
2013Overexpression of the tcp Gene Cluster Using the T7 RNA Polymerase/Promoter System and Natural Transformation-Mediated Genetic Engineering of Vibrio cholerae
The human pathogen and aquatic bacterium Vibrio cholerae belongs to the group of naturally competent bacteria. This developmental program allows the bacterium to take up free DNA from its surrounding followed by a homologous recombination event, which allo ...
Public Library of Science2013Systematic Analysis of Yeast Gene Expression by Synthetic Promoter Libraries
The precise tuning of gene expression levels is essential for optimal performance of transcriptional regulatory networks. Many regulatory components control promoter output, but transcription factor (TF) binding sites are amongst the most prominent. Beside ...
EPFL2013Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue ...
2013Stimulus-induced modulation of transcriptional bursting in a single mammalian gene
Felix Naef, David Michael Suter, Benjamin Zoller, Rosamaria Cannavo
Mammalian genes are often transcribed discontinuously as short bursts of RNA synthesis followed by longer silent periods. However, how these "on" and "off" transitions, together with the burst sizes, are modulated in single cells to increase gene expressio ...
National Academy of Sciences2013Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. The transcription factor Myc is directly induced by serum mitogens and drives a secondary gene expression program tha ...
2012The genome of Dehalobacter restrictus - high gene redundancy for a restricted metabolism
Christof Holliger, Julien Maillard, Aamani Rupakula Boyanapalli, Hauke Smidt
Organohalide respiration (OHR) is a bacterial anaerobic respiratory metabolism dedicated to use halogenated compounds as terminal electron acceptors. OHR bacteria are strictly anaerobic microorganisms which use reductive dehalogenases (RdhA) as key enzymes ...
2012