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Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs. [ABSTRACT FROM PUBLISHER]

Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

We hypothesize that our ability to track objects through occlusions is mediated by timely assistance from gaze in the form of "rescue saccades"-eye movements to tracked objects that are in danger of being lost due to impending occlusion. Observers tracked 2-4 target sharks (out of 9) for 20 s as they swam through a rendered 3D underwater scene. Targets were either allowed to enter into occlusions (occlusion trials) or not (no occlusion trials). Tracking accuracy with 2-3 targets was ≥ 92% regardless of target occlusion but dropped to 74% on occlusion trials with four targets (no occlusion trials remained accurate; 83%). This pattern was mirrored in the frequency of rescue saccades. Rescue saccades accompanied approximatlely 50% of the Track 2-3 target occlusions, but only 34% of the Track 4 occlusions. Their frequency also decreased with increasing distance between a target and the nearest other object, suggesting that it is the potential for target confusion that summons a rescue saccade, not occlusion itself. These findings provide evidence for a tracking system that monitors for events that might cause track loss (e.g., occlusions) and requests help from the oculomotor system to resolve these momentary crises. As the number of crises increase with the number of targets, some requests for help go unsatisfied, resulting in degraded tracking.