Statistical Biophysics Blog: FAQ on Trajectory Ensembles

Statistical Biophysics Blog: “Proof ” of the Hill Relation Between Probability Flux and Mean First- Passage Time

Preprint Déjà Vu: an FAQ

This commentary originally appeared in the EMBO Journal. It benefited significantly from editorial supervision, and is reposted here with permission (and minor updates). The introduction provides some overall context. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 FAQ 1: Why d...

Empirically Defining Trajectories of Late-Life Cognitive and Functional Decline

BACKGROUND Alzheimer's disease (AD) is associated with variable cognitive and functional decline, and it is difficult to predict who will develop the disease and how they will progress. OBJECTIVE This exploratory study aimed to define latent classes from participants in the Alzheimer's Disease Neuroimaging Initiative (ADNI) database who had similar growth patterns of both cognitive and functi...

DCU@FIRE2012: Monolingual and Crosslingual SMS-based FAQ Retrieval

This paper presents results for DCU’s second participation in the SMS-based FAQ Retrieval task at FIRE. For FIRE 2012, we submitted runs for the monolingual English and Hindi and the crosslingual English to Hindi subtasks. Compared to our experiments for FIRE 2011, our system was simplified by using a single retrieval engine (instead of three) and using a single approach for detecting out-of-do...

ENCORE: Software for Quantitative Ensemble Comparison

There is increasing evidence that protein dynamics and conformational changes can play an important role in modulating biological function. As a result, experimental and computational methods are being developed, often synergistically, to study the dynamical heterogeneity of a protein or other macromolecules in solution. Thus, methods such as molecular dynamics simulations or ensemble refinemen...