Identifying pathways that are significantly impacted in a given condition is a crucial step in the understanding of the underlying biological phenomena. All approaches currently available for this purpose calculate a p-value that aims to quantify the significance of the involvement of each pathway in the given phenotype. These p-values were previously thought to be independent. Here, we show that this is not the case, and that pathways can affect each other's p-values through a “crosstalk” phenomenon that affects all major categories of existing methods. We describe a novel technique able to detect, quantify, and correct crosstalk effects, as well as identify novel independent functional modules. We assessed this technique on data from four real experiments coming from three phenotypes involving two species.

A method to select a protein target for therapeutic application includes accessing genomic information and protein-protein interaction (PPI) data, computing a thermodynamic measure for each protein node within the network of protein nodes, generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure, generating a PPI subnetwork by applying a topological filtration to the energy landscape data of the PPI data, computing a first Betti number for the PPI subnetwork, sequentially removing a protein node(s) from the PPI subnetwork while replacing the previously removed node(s), computing a new Betti number for the PPI subnetwork with the protein node(s) removed, computing a change between the Betti numbers, and determining, based on the change between the Beti numbers, a most significant protein target within the PPI subnetwork.

A method to select a protein target for therapeutic application includes accessing genomic information and protein-protein interaction (PPI) data, computing a thermodynamic measure for each protein node within the network of protein nodes, generating an energy landscape data corresponding to the network of protein nodes and the thermodynamic measure, generating a PPI subnetwork by applying a topological filtration to the energy landscape data of the PPI data, computing a first Betti number for the PPI subnetwork, sequentially removing a protein node(s) from the PPI subnetwork while replacing the previously removed node(s), computing a new Betti number for the PPI subnetwork with the protein node(s) removed, computing a change between the Betti numbers, and determining, based on the change between the Beti numbers, a most significant protein target within the PPI subnetwork.

The invention relates to an in silico screening method to identify candidate excipients for reducing aggregation of a protein in a formulation. The method combines computational molecular modeling and molecular dynamics simulations to identify sites on a protein where non-specific self-interaction and interaction of different test excipients may occur, determine the relative binding energies of such interactions, and select one or more test excipients that meet specified interaction criteria for use as candidate excipients in empirical screening studies.

The invention relates to an in silico screening method to identify candidate excipients for reducing aggregation of a protein in a formulation. The method combines computational molecular modeling and molecular dynamics simulations to identify sites on a protein where non-specific self-interaction and interaction of different test excipients may occur, determine the relative binding energies of such interactions, and select one or more test excipients that meet specified interaction criteria for use as candidate excipients in empirical screening studies.

A method for generating an immune score, the method comprising the steps of: (i) determining a qualitative and/or quantitative assessment of tumor infiltrating lymphocytes in a sample; (ii) determining a qualitative and/or quantitative assessment of T-cell receptor signaling in the sample; (iii) determining a qualitative and/or quantitative assessment of mutation burden in the sample; (iv) generating, using a predictive algorithm, an immune score based on the determined qualitative and/or quantitative assessment of tumor infiltrating lymphocytes, the determined qualitative and/or quantitative assessment of T-cell receptor signaling, and the determined qualitative and/or quantitative assessment of mutation burden.

A method for generating an immune score, the method comprising the steps of: (i) determining a qualitative and/or quantitative assessment of tumor infiltrating lymphocytes in a sample; (ii) determining a qualitative and/or quantitative assessment of T-cell receptor signaling in the sample; (iii) determining a qualitative and/or quantitative assessment of mutation burden in the sample; (iv) generating, using a predictive algorithm, an immune score based on the determined qualitative and/or quantitative assessment of tumor infiltrating lymphocytes, the determined qualitative and/or quantitative assessment of T-cell receptor signaling, and the determined qualitative and/or quantitative assessment of mutation burden.

A system and method for region-based calling utilizes a probability distribution of a phi-transformed logarithmic ratio to determine a set of possible transition paths through markers and marker states, constructs a local evidence matrix for each of the markers and generates a total per-marker value for each segment in a discrete region.

A medical information processing apparatus according to an embodiment includes processing circuitry. The processing circuitry obtains image data rendering a blood vessel of a patient. The processing circuitry performs a fluid analysis on the obtained image data and calculates an index value related to a blood flow in the blood vessel with respect to each of a plurality of positions in the blood vessel. With respect to the index values to be calculated, the processing circuitry selects a position in which a first value is to be obtained from among the plurality of positions or selects a value serving as the first value from among the index values exhibited in positions. The processing circuitry causes a display to display the first value in a predetermined display region thereof used for displaying the first value.

A medical information processing apparatus according to an embodiment includes processing circuitry. The processing circuitry obtains image data rendering a blood vessel of a patient. The processing circuitry performs a fluid analysis on the obtained image data and calculates an index value related to a blood flow in the blood vessel with respect to each of a plurality of positions in the blood vessel. With respect to the index values to be calculated, the processing circuitry selects a position in which a first value is to be obtained from among the plurality of positions or selects a value serving as the first value from among the index values exhibited in positions. The processing circuitry causes a display to display the first value in a predetermined display region thereof used for displaying the first value.