A system and method for identification of key driver responsible for bringing changes in a microbial population is provided. The method involves construction of microbial association networks with each microbial taxa as nodes and their associations as edges and subsequent identification of crucial ‘driver’ nodes involved in the studied disease progression. While comparing a particular node between two networks, this method takes individual nodes and their associations into account as well as the identity of their interacting partners. A taxon in the diseased state with an altered set of associations while still being increasingly important for the whole network necessarily holds a key significance in microbial interplay. Using this rationale, this methodology computes a score to quantify this change for each node and calculates its statistical significance. Subsequently, ‘driver’ nodes are identified using the score coupled with other network parameters and a critical score for the ‘driver’ nodes is calculated to quantify its importance.

Biomarkers and methods of using them for aiding diagnosis, prognosis, and treatment of critically ill patients are disclosed. In particular, the invention relates to the use of biomarkers for prognosis of mortality in critically ill patients with sepsis, severe trauma, or burns.

Biomarkers and methods of using them for aiding diagnosis, prognosis, and treatment of critically ill patients are disclosed. In particular, the invention relates to the use of biomarkers for prognosis of mortality in critically ill patients with sepsis, severe trauma, or burns.

The present invention is related to the field of bio/chemical sampling, sensing, assays and applications. Particularly, the present invention is related to how to make the sampling/sensing/assay become simple to use, fast to results, highly sensitive, easy to use, using tiny sample volume (e.g., 0.5 μL or less), operated by a person without any professionals, reading by mobile-phone, or low cost, or a combination of them.

The present invention is related to the field of bio/chemical sampling, sensing, assays and applications. Particularly, the present invention is related to how to make the sampling/sensing/assay become simple to use, fast to results, highly sensitive, easy to use, using tiny sample volume (e.g., 0.5 μL or less), operated by a person without any professionals, reading by mobile-phone, or low cost, or a combination of them.

A method includes performing a nucleic acid amplification of a nucleic acid sample using a detection probe, wherein the nucleic acid amplification occurs over one or more interrogation periods, and, from the nucleic acid amplification, acquiring amplification data that indicates an amount of nucleic acid present for each of the one or more interrogation periods. The method also includes, based on the amplification data, determining a crosstalk correction value associated with a spectral neighbor to the probe to reduce spectral crosstalk from the spectral neighbor; and applying the crosstalk correction value to amplification data collected from multiplex nucleic acid amplifications of nucleic acid samples.

A method includes performing a nucleic acid amplification of a nucleic acid sample using a detection probe, wherein the nucleic acid amplification occurs over one or more interrogation periods, and, from the nucleic acid amplification, acquiring amplification data that indicates an amount of nucleic acid present for each of the one or more interrogation periods. The method also includes, based on the amplification data, determining a crosstalk correction value associated with a spectral neighbor to the probe to reduce spectral crosstalk from the spectral neighbor; and applying the crosstalk correction value to amplification data collected from multiplex nucleic acid amplifications of nucleic acid samples.

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.

Factors affecting the fragmentation pattern of cell-free DNA (e.g., plasma DNA) and the applications, including those in molecular diagnostics, of the analysis of cell-free DNA fragmentation patterns are described. Various applications can use a property of a fragmentation pattern to determine a proportional contribution of a particular tissue type, to determine a genotype of a particular tissue type (e.g., fetal tissue in a maternal sample or tumor tissue in a sample from a cancer patient), and/or to identify preferred ending positions for a particular tissue type, which may then be used to determine a proportional contribution of a particular tissue type.

Embodiments of methods, systems, and tangible non-transitory computer readable medium having instructions are presented. A method includes calculating a plurality of feature values for a number of bioinformatic features of the desired hybridization reaction; and calculating distances between the plurality of feature values and corresponding database rate constant values stored in a database, the database comprising a plurality of hybridization reactions having known rate constants. The method additionally includes calculating a weighted average of a logarithm of the database rate constant values, with larger weights assigned to value instances having values lower in distance to the plurality of feature values of the desired hybridization reaction; and providing the weighted average as a predicted logarithm of the rate constant of the desired hybridization reaction.