A method of measuring a metabolic activity (MA) of a cell is provided. The method comprising independently measuring in an extracellular environment of the cell, time-dependent acidification profiles due to secretion of: (i) non-volatile soluble metabolic products; (ii) non-volatile soluble metabolic products and volatile soluble metabolic products; and (iii) volatile soluble metabolic products; wherein at least one of the time dependent acidification profiles is indicative of the metabolic activity of the cell. Also provided are clinical methods which make use of the assay.

The present invention provides an approach for the determination of activation state of a plurality of discrete cell populations and/or the state of one or more cellular networks in an individual. The status of a plurality of discrete cell populations and/or the state of one or more cellular networks can be correlated with the diagnosis, prognosis, choice or modification of treatment, and/or monitoring of a condition

The present patent relates to a method for qualitative identification and quantitative prediction of thyroid hormone disrupting chemicals base on the interaction between thyroid hormone receptor and co-regulators (coactivator and corepressor).The method identifies chemicals as passive antagonists, active antagonists and agonists by means of co-regulator involved molecular dynamics simulations, and predicts the relative disrupting potencies by use of binding free energy, therefore, may be used for screening of thyroid hormone disruptors among environmental pollutants. Upon more comprehensive consideration of the functioning mechanism of thyroid hormone receptor, the present invention is able to sufficiently identify thyroid hormone disruptors as agonists and antagonists, and gives more accurate prediction of the disrupting potency. Further, since nuclear receptors, just as thyroid hormone receptor, are strongly associated with co-regulators, the method may be expanded to the screening of nuclear receptor mediated endocrine disruptors.

Systems and methods for targeted therapy based on single-cell stimulus perturbation response. In one embodiment, a method for optimizing stimulus combinations for therapy includes receiving a cell sample, treating the cell sample with a plurality of stimuli by treating a different portion of the cell sample with one of the plurality of stimuli for each of the plurality of stimuli, labeling the cell sample with a plurality of metal-conjugated probes, analyzing the cell sample using a mass spectrometer, obtaining mass spectrometry data from the mass spectrometer, identifying subpopulations within the cell sample using the mass spectrometry data, computing stimulus effects, generating a nested-effects model using the mass spectrometry data, and scoring stimuli combinations using the computing device, wherein the stimulus combinations are combinations made from the plurality of stimuli.

Improved molecular breeding methods include a method in which an association data set is developed by associating the phenotypes of a broad population of individuals with the individual genotypes. The association data set is used in conjunction with a growth model in order to select breeding pairs likely to generate offspring with one or more desirable traits.

Membrane protein expression can be predicted using statistical frameworks to provide an enhanced subset of sequences, out of an initial larger set of potentially expressing sequences, by using features derived from sequences and a model parameterized through a dataset of known expression levels. Also, membrane protein experimentation protocols can be designed using the statistical frameworks in concert known outcomes to identify which laboratory conditions are most likely to produce successful results.

Provided are drug-transport metabolomics profile assessments and therapies.

A method of analyzing biological data containing expression values of a plurality of polypeptides in the blood of a subject. The method comprises: calculating a distance between a segment of a curved line and an axis defined by a direction, the distance being calculated at a point over the curved line defined by a coordinate along the direction. The method further comprises correlating the distance to the presence of, absence of, or likelihood that the subject has, a bacterial infection. The coordinate is defined by a combination of the expression values, wherein at least 90% of the segment is between a lower bound line and an upper bound line.

An embodiment of a system and method for characterizing a Clostridium-associated condition in relation to a user includes: a handling network operable to receive containers including material from a set of users, the handling network including a sequencing system operable to determine microbiome sequences from sequencing the material; a processing system operable to generate a microbiome composition dataset and a microbiome functional diversity dataset based on the microbiome sequences, receive a supplementary dataset associated with the Clostridium-associated condition for the set of users; transform the supplementary dataset and features extracted from the microbiome composition dataset and the microbiome functional diversity dataset into a characterization model for the Clostridium-associated condition; and a therapy system operable to promote a therapy to the user based on characterizing the user in relation to the Clostridium-associated condition using the characterization model.

Provided are a method and a device for selecting a pathway for a target compound by combining biochemical and chemical processes together, wherein an input of at least one pathway for synthesis of a target compound or degradation into a target compound is received, hybrid arrangements of one or more reaction steps included in the at least one pathway are predicted, a pathway feasibility score is computed, and at least one hybrid arrangement is selected based on the pathway feasibility score.