Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be com...

Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge in molecular biophysics. Network models, such as Markov state models (MSMs), are one potential solution to this problem. MSMs have recently yielded quantitative agreement with experimentally derived structures and folding rates for specific systems, leaving them positioned to potentially provide a d...

Molecular dynamics simulations of biomolecules produce a very high dimensional time-series dataset. Performing analysis necessarily involves projection onto a lower dimensional space. A priori selection of projection coordinates requires (perhaps unavailable) prior information or intuition about the system. At best, such a projection can only confirm the intuition. At worst, a poor projection c...

Markov state models (MSMs)--or discrete-time master equation models--are a powerful way of modeling the structure and function of molecular systems like proteins. Unfortunately, MSMs with sufficiently many states to make a quantitative connection with experiments (often tens of thousands of states even for small systems) are generally too complicated to understand. Here, I present a bayesian ag...

MOTIVATION Comparing tandem mass spectra (MSMS) against a known dataset of protein sequences is a common method for identifying unknown proteins; however, the processing of MSMS by current software often limits certain applications, including comprehensive coverage of post-translational modifications, non-specific searches and real-time searches to allow result-dependent instrument control. Thi...

Abstract Marginal structural models (MSMs) can be used to estimate the causal effect of a potentially time-varying treatment in presence time-dependent confounding via weighted regression. The standard approach using inverse probability weighting (IPTW) sensitive model misspecification and lead high-variance estimates due extreme weights. Various methods have been proposed partially address thi...

Urethral gonorrhoea (UG) dramatically decreased in Paris between 1986 and 1997 as a consequence of safer sexual behaviour. Thus, only 43 cases of gonorrhoea have been collected in our clinic in 1997, the lowest number since the early 1970s. Since 1998, an increase has been observed, as in other STD clinics in France and in the Renago laboratory network. 1–3 Men who have sex with men (MSMs) repr...

BACKGROUND Retrospective studies of haemodialysis patients from large dialysis organizations in the United States have indicated that intravenous vitamin D may be associated with a survival benefit. However, patients prescribed vitamin D are generally healthier than those who are not, suggesting that treatment by indication may have biased previous findings. Additionally, no survival benefit as...

In order to reduce practice variations and offer cancer patients the best treatments according to reference guidelines, therapeutic decisions have to be taken, in France, by "multidisciplinary staff meetings'' (MSMs) as patient-specific care plans which are then implemented by cancer specialists. OncoDoc2 is a CDSS implementing CancerEst guidelines, a "local reference guideline'', on breast can...