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- 1From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedA systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain...
- 2From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedAccurate predictions of orthology and paralogy relationships are necessary to infer human molecular function from experiments in model organisms. Previous genome-scale approaches to predicting these relationships have...
- 3From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedA significant number of human X-linked genes escape X chromosome inactivation and are thus expressed from both the active and inactive X chromosomes. The basis for escape from inactivation and the potential role of the X...
- 4From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedReinforcement learning theorizes that strengthening of synaptic connections in medium spiny neurons of the striatum occurs when glutamatergic input (from cortex) and dopaminergic input (from substantia nigra) are...
- 5From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedMembers of the vascular endothelial growth factor (VEGF) family of proteins are critical regulators of angiogenesis. VEGF concentration gradients are important for activation and chemotactic guidance of capillary...
- 6From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedLast summer, the Student Council of the International Society for Computational Biology prompted an Editorial, "Ten Simple Rules for Getting Published" [1]. The interest in that piece (it has been downloaded 14,880 times...
- 7From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedThe prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a...
- 8From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-Reviewed"Many scientists and engineers spend much of their lives writing, debugging, and maintaining software, but only a handful have ever been taught how to do this effectively: after a couple of introductory courses, they are...
- 9From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedThe aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the...
- 10From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedObservations on the relationship between cardiac work rate and the levels of energy metabolites adenosine triphosphate (ATP), adenosine diphosphate (ADP), and phosphocreatine (CrP) have not been satisfactorily explained...
- 11From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedRecent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors...
- 12From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedText-mining algorithms make mistakes in extracting facts from natural-language texts. In biomedical applications, which rely on use of text-mined data, it is critical to assess the quality (the probability that the...
- 13From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedOur investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the...
- 14From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedThe initial coupling between ligand binding and channel gating in the human α7 nicotinic acetylcholine receptor (nAChR) has been investigated with targeted molecular dynamics (TMD) simulation. During the simulation,...
- 15From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-Reviewed
Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice.
In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing... - 16From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedDiscrete stochastic simulations are a powerful tool for understanding the dynamics of chemical kinetics when there are small-to-moderate numbers of certain molecular species. In this paper we introduce delays into the...
- 17From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedLive-virus vaccines activate both humoral and cell-mediated immunity, require only a single boosting, and generally provide longer immune protection than killed or subunit vaccines. However, growth of live-virus...
- 18From: PLoS Computational Biology. (Vol. 2, Issue 9) Peer-ReviewedThe intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether cytochrome c released from...