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- 1From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedEncounters between human neutrophils and zymosan elicit an initially protrusive cell response that is distinct from the thin lamella embracing antibody-coated targets. Recent experiments have led us to hypothesize that...
- 2From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedDespite many experimental and computational studies of the gating transition of pentameric ligand-gated ion channels (pLGICs), the structural basis of how ligand binding couples to channel gating remains unknown. By...
- 3From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedChromosomal gains and losses comprise an important type of genetic change in tumors, and can now be assayed using microarray hybridization-based experiments. Most current statistical models for DNA copy number estimate...
- 4From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedA scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection,...
- 5From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedGetting a promotion or a new position are important parts of the scientific career process. Ironically, a committee whose membership has limited ability to truly judge your scholarly standing is often charged with...
- 6From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedUnderstanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled...
- 7From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedFollowing recent advances in high-throughput mass spectrometry (MS)-based proteomics, the numbers of identified phosphoproteins and their phosphosites have greatly increased in a wide variety of organisms. Although a...
- 8From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedWe studied the global relationship between gene expression and neuroanatomical connectivity in the adult rodent brain. We utilized a large data set of the rat brain "connectome" from the Brain Architecture Management...
- 9From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedRecently, we presented a study of adult neurogenesis in a simplified hippocampal memory model. The network was required to encode and decode memory patterns despite changing input statistics. We showed that additive...
- 10From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedWe present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses. We use statistical mechanics to analyze the competition that...
- 11From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedNeurons transform time-varying inputs into action potentials emitted stochastically at a time dependent rate. The mapping from current input to output firing rate is often represented with the help of phenomenological...
- 12From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedPharmacodynamic modeling has been increasingly used as a decision support tool to guide dosing regimen selection, both in the drug development and clinical settings. Killing by antimicrobial agents has been...
- 13From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedWe introduce a novel dynamic model of stem cell and tissue organisation in murine intestinal crypts. Integrating the molecular, cellular and tissue level of description, this model links a broad spectrum of...
- 14From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedThe complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells. However, insufficient or excessive complement activation will lead to immune-related...
- 15From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedIn many applications, one is interested in determining which of the properties of a network module change across conditions. For example, to validate the existence of a module, it is desirable to show that it is...
- 16From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedThe nematode Caenorhabditis elegans, with information on neural connectivity, three-dimensional position and cell linage, provides a unique system for understanding the development of neural networks. Although C....
- 17From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedDetermining the forces that conserve amino acid positions in proteins across species is a fundamental pursuit of molecular evolution. Evolutionary conservation is driven by either a protein's function or its...
- 18From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedElectrophysiological studies of the human heart face the fundamental challenge that experimental data can be acquired only from patients with underlying heart disease. Regarding human atria, there exist sizable gaps in...
- 19From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedVirtually every molecular biologist has searched a protein or DNA sequence database to find sequences that are evolutionarily related to a given query. Pairwise sequence comparison methods--i.e., measures of similarity...
- 20From: PLoS Computational Biology. (Vol. 7, Issue 1) Peer-ReviewedMicrobial diversity is typically characterized by clustering ribosomal RNA (SSU-rRNA) sequences into operational taxonomic units (OTUs). Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect...