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- 1From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-Reviewed
Transcriptional regulation: effects of promoter proximal pausing on speed, synchrony and reliability
Recent whole genome polymerase binding assays in the Drosophila embryo have shown that a substantial proportion of uninduced genes have pre-assembled RNA polymerase-II transcription initiation complex (PIC) bound to... - 2From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThe entanglement of lignin polymers with cellulose and hemicellulose in plant cell walls is a major biological barrier to the economically viable production of biofuels from woody biomass. Recent efforts of reducing...
- 3From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedNeurons spike when their membrane potential exceeds a threshold value. In central neurons, the spike threshold is not constant but depends on the stimulation. Thus, input-output properties of neurons depend both on the...
- 4From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedBistability plays a central role in the gene regulatory networks (GRNs) controlling many essential biological functions, including cellular differentiation and cell cycle control. However, establishing the network...
- 5From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThe modular organization of networks of individual neurons interwoven through synapses has not been fully explored due to the incredible complexity of the connectivity architecture. Here we use the modularity-based...
- 6From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThe self-organization of peptides into amyloidogenic oligomers is one of the key events for a wide range of molecular and degenerative diseases. Atomic-resolution characterization of the mechanisms responsible for the...
- 7From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedIn prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes. A toolbox model of evolution was recently proposed to explain this...
- 8From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedInferring regulatory and metabolic network models from quantitative genetic interaction data remains a major challenge in systems biology. Here, we present a novel quantitative model for interpreting epistasis within...
- 9From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedSpatiotemporal pattern formation in neuronal networks depends on the interplay between cellular and network synchronization properties. The neuronal phase response curve (PRC) is an experimentally obtainable measure...
- 10From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThe interplay between hippocampus and prefrontal cortex (PFC) is fundamental to spatial cognition. Complementing hippocampal place coding, prefrontal representations provide more abstract and hierarchically organized...
- 11From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedInstrumental responses are hypothesized to be of two kinds: habitual and goal- directed, mediated by the sensorimotor and the associative cortico-basal ganglia circuits, respectively. The existence of the two...
- 12From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThe cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being...
- 13From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedA common theoretical view is that attractor-like properties of neuronal dynamics underlie cognitive processing. However, although often proposed theoretically, direct experimental support for the convergence of neural...
- 14From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedMany projects in computational biology lead to the creation of a small application program or collection of scripts that can be of use to other scientists. A natural progression is to make this tool available via a Web...
- 15From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedThis PLoS Computational Biology tutorial was presented at ISMB 2010. Introduction Identification of differentially expressed pathways from expression data is an important problem because it allows us to gain...
- 16From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedHammerhead ribozymes are small self-cleaving RNAs that promote strand scission by internal phosphoester transfer. Comparative sequence analysis was used to identify numerous additional representatives of this ribozyme...
- 17From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedMammalian embryogenesis is a dynamic process involving gene expression and mechanical forces between proliferating cells. The exact nature of these interactions, which determine the lineage patterning of the...
- 18From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedOverexpression of the xenotoxin transporter P-glycoprotein (P-gp) represents one major reason for the development of multidrug resistance (MDR), leading to the failure of antibiotic and cancer therapies. Inhibitors of...
- 19From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedBiological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. Here...
- 20From: PLoS Computational Biology. (Vol. 7, Issue 5) Peer-ReviewedCellular electrophysiology experiments, important for understanding cardiac arrhythmia mechanisms, are usually performed with channels expressed in non myocytes, or with non-human myocytes. Differences between cell...