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Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction
We have developed a rapid, simple and general method based on information theory that accurately estimates the level of background mutual information for each pair of positions in a given protein family. Expand
Using information theory to search for co-evolving residues in proteins
MOTIVATION Some functionally important protein residues are easily detected since they correspond to conserved columns in a multiple sequence alignment (MSA). Expand
Mathematical model predicts a critical role for osteoclast autocrine regulation in the control of bone remodeling.
Bone remodeling occurs asynchronously at multiple sites in the adult skeleton and involves resorption by osteoclasts, followed by formation of new bone by osteoblasts. Disruptions in bone remodeling… Expand
Perspectives on the basic reproductive ratio
- J. Heffernan, R. J. Smith, L. Wahl
- Biology, Medicine
- Journal of The Royal Society Interface
- 22 September 2005
The basic reproductive ratio, R0, is defined as the expected number of secondary infections arising from a single individual during his or her entire infectious period, in a population of… Expand
Viral dynamics of primary viremia and antiretroviral therapy in simian immunodeficiency virus infection.
Mathematical modeling of viral replication dynamics, based on sequential measurements of levels of virion-associated RNA in plasma during antiretroviral treatment, has led to fundamental new insights… Expand
Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.
Information theory was used to identify nonconserved coevolving positions in multiple sequence alignments from a variety of protein families. Coevolving positions in these alignments fall into two… Expand
THE PROBABILITY THAT BENEFICIAL MUTATIONS ARE LOST IN POPULATIONS WITH PERIODIC BOTTLENECKS
Abstract Population bottlenecks affect the dynamics of evolution, increasing the probability that beneficial mutations will be lost. Recent protocols for the experimental study of evolution involve… Expand
Reproducibility of Standardized Uptake Value Measurements Determined by 18F-FDG PET in Malignant Tumors
18F-FDG PET is increasingly being used to monitor the early response of malignant tumors to chemotherapy. Understanding the reproducibility of standardized uptake values (SUVs) is an important… Expand
Adherence and drug resistance: predictions for therapy outcome
We combine standard pharmacokinetics with an established model of viral replication to predict the outcome of therapy as a function of adherence to the drug regimen. We consider two types of… Expand
Cytotoxic T lymphocytes and viral turnover in HIV type 1 infection.
- P. Klenerman, R. Phillips, +5 authors M. Nowak
- Biology, Medicine
- Proceedings of the National Academy of Sciences…
- 24 December 1996
To understand the role of the immune system in limiting HIV type 1 replication, it is critical to know to what extent the rapid turnover of productively infected cells is caused by viral… Expand