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- Search Terms:ISSN: 1553734XAndISSN: 15537358AndVolume Number: 3AndIssue Number: 3AndStart Page: e57AndDate: 2007 Revise Search
- 1From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedMost tissues in metazoans undergo continuous turnover due to cell death or epithelial shedding. Since cellular replication is associated with an inherent risk of mutagenesis, tissues are maintained by a small group of...
- 2From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedEscherichia coli bacteria respond to DNA damage by a highly orchestrated series of events known as the SOS response, regulated by transcription factors, protein-protein binding, and active protein degradation. We present...
- 3From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedProteins interact with each other in a highly specific manner, and protein interactions play a key role in many cellular processes; in particular, the distortion of protein interfaces may lead to the development of many...
- 4From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedThe aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice...
- 5From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedUncovering pathways underlying drug-induced toxicity is a fundamental objective in the field of toxicogenomics. Developing mechanism-based toxicity biomarkers requires the identification of such novel pathways and the...
- 6From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedRecent analyses indicate that differences in protein concentrations are only 20%-40% attributable to variable mRNA levels, underlining the importance of posttranscriptional regulation. Generally, protein concentrations...
- 7From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedMicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional...
- 8From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedHIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as for supporting...
- 9From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedScientific research has always been a collaborative undertaking, and this is particularly true today. For example, between 1981 and 2001, the average number of coauthors on a paper for the Proceedings of the National...
- 10From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedComputational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription...
- 11From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedThe analysis of methylation patterns is a promising approach to investigate the genealogy of cell populations in an organism. In a stem cell-niche scenario, sampled methylation patterns are the stochastic outcome of a...
- 12From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedIn metabolic networks, metabolites are usually present in great excess over the enzymes that catalyze their interconversion, and describing the rates of these reactions by using the Michaelis--Menten rate law is...
- 13From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedMetrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the...
- 14From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedDirected cell migration in response to chemical cues, also known as chemotaxis, is an important physiological process involved in wound healing, foraging, and the immune response. Cell migration requires the simultaneous...
- 15From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedTranscription factor (TF) proteins recognize a small number of DNA sequences with high specificity and control the expression of neighbouring genes. The evolution of TF binding preference has been the subject of a number...
- 16From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedMost ab initio gene predictors use a probabilistic sequence model, typically a hidden Markov model, to combine separately trained models of genomic signals and content. By combining separate models of relevant genomic...
- 17From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedDrug molecules not only interact with specific targets, but also alter the state and function of the associated biological network. How to design drugs and evaluate their functions at the systems level becomes a key...
- 18From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedAlternative splicing (AS) and gene duplication (GD) both are processes that diversify the protein repertoire. Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD....
- 19From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedWhen searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search...
- 20From: PLoS Computational Biology. (Vol. 3, Issue 3) Peer-ReviewedIt is well-known that weakly electric fish can exhibit extreme temporal acuity at the behavioral level, discriminating time intervals in the submicrosecond range. However, relatively little is known about the spatial...