Abstract: The methods of the present invention described herein may be carried out to reduce unintended binding of probes to target and/or template nucleic acids, to increase the accuracy and efficiency in nucleic acid assays, nucleic acid synthesis and multiplex amplification reactions. The present invention relates to at least three methods: (i) methods of reducing noise and increasing efficiency in nucleic acid assays; (ii) methods of increasing efficiency and accuracy of nucleic acid synthesis; and (iii) methods of reducing noise, increasing efficiency and accuracy of multiplex amplification. By increasing efficiency, it is meant that the reaction time to achieve a given signal is reduced and the signal strength and uniformity may be increased in nucleic acid assays, greater copy numbers of accurate nucleic acids are produced in shorter periods of time in nucleic acid synthesis, and the sequencing time to sequence large genomes is reduced in multiplex amplification.

Abstract: Methods, computer-readable media, and systems for providing disease management. In one implementation, a system develops a treatment recommendation for a patient based on patient data. The system may receive patient data, execute a basic model of the physiological system of the patient to generate a modified model for the patient based on the patient data, perform a statistical analysis of the patient data to detect data excursions of the parameter values; use the modified model to determine factors causing the data excursions; and use the model to develop a treatment recommendation to ameliorate negative effects of the disease.

Abstract: A method of improving signal-to-noise performance of a probe. A probe or set of probes is provided for hybridization with a sample. The probe or set of probes is hybridized with the sample at a first hybridization stringency over a first hybridization time period. Following the hybridization over the first hybridization time period, the probe or set of probes is hybridized with the sample at a second hybridization stringency over a second hybridization time period. A method of improving signal-to-noise performance of probes on an array includes providing a sample containing sequences that provide perfect complementary matches to sequences contained on at least some of said probes; and hybridizing the probes with the sample, while cycling the stringency of hybridization conditions during the hybridization.

Abstract: The methods of the present invention described herein may be carried out to reduce unwanted binding of probes or other nucleic acids, and thereby reduce noise (i.e., improve signal-to-noise characteristics of signals read from these probes for their intended targets) or interference in nucleic acid assays and nucleic acid synthesis reactions. The time such assays or reactions take to complete is also reduced. The present invention relates to at least two methods: (i) methods of reducing noise and increasing efficiency in nucleic acid assays; and (ii) methods of increasing efficiency and accuracy of nucleic acid synthesis. By increasing efficiency in assays, it is meant that the reaction time to achieve a given signal is reduced and the signal strength may be increased. By increasing efficiency in nucleic acid synthesis, it is meant that greater copy numbers of accurate nucleic acids are produced in shorter periods of time.

Abstract: Methods, systems and recordable media for using expression data characterizing protein pathways of diseases to produce phase relationships between treatment responses of diseased tissues to treatments applied thereto and expression profiles of the diseased tissues as measured when untreated. Methods, systems and recordable media for augmenting an original or existing treatment or treatment combination with one or more treatments that cover gene activity of a disease not addressed by the original/existing treatment.

Abstract: Methods, systems and recordable media for accurately reading and identifying high quality signals from a microarray feature. Signals may be identified and used regardless of their geographic/geometric locations and patterns within the feature zone. High quality signals may be read, identified and outputted from a microarray feature in a geometrically independent manner, such that the best quality signals are identified and useable, regardless of the locations or patterns in the region from which the best quality signals are outputted.

Abstract: Methods, systems and computer readable media for selecting probes for design of a chemical array. A first set of candidate probes is provided for hybridization with a sample at a first hybridization stringency and a second set of candidate probes identical to the first set is provided for hybridization with the sample at a second hybridization stringency. After hybridizing the first set with the sample at the first hybridization stringency and the second set with the sample at the second hybridization stringency higher than the first hybridization stringency, the relative change in signal extracted from a probe in the first set relative to the same probe in the second set is calculated, and this calculation is carried out for each of a plurality of (up to and including all) other probes in the first set and same probes in the second set, respectively.

Abstract: Methods, systems and computer readable media for producing a metric to characterize a chemical array. Effects of terms impacting results of measurement of an output generated from analysis of the array or a procedure performed using the array, are quantified by performing ANOVA analysis and calculating sums of squares quantities attributable to each of the terms respectively. A metric is derived from at least two of the calculated sum of squares quantities. Methods systems and computer readable media for characterizing one or more chemical arrays may perform the steps of querying a database storing sums of squares quantities quantifying effects of terms impacting results of measurements of outputs generated from a plurality of chemical arrays; selecting sums of squares quantities based on the querying; and generating a metric based on the at least two sums of squares quantities.

Abstract: Systems methods and recordable media for predicting multi-variable outcomes based on multi-variable inputs. Additionally, the models described can be used to predict the multi-variable inputs themselves, based on the multi-variable inputs, providing a smoothing function, acting as a noise filter. Both multi-variable inputs and multi-variable outputs may be simultaneously predicted, based upon the multi-variable inputs. The models find a critical subset of data points, or “tent poles” to optimally model all outcome variables simultaneously to leverage communalities among outcomes.

Abstract: Methods, systems and computer readable media for imposing monotonic consistency among results of multiple platforms measuring the same specific property for the same/equivalent series of samples, to provide viable comparisons of sensitivity and precision among the platforms as well as provide useful conversion formulas among the platforms to ensure equivalent quantitation.

Abstract: Methods, systems and computer readable media for calibrating a device for which it is not possible to provide another device having a higher degree of precision to be used as a standard against which the device to be calibrated can be compared to perform the calibration. Metrology for interpreting the input and output fields and monitoring and supervising tasks of the device, and having sufficient accuracy, may be used to facilitate calibration.

Abstract: Methods, systems and computer readable media for imposing monotonic consistency among results of multiple platforms measuring the same specific property for the same/equivalent series of samples, to provide viable comparisons of sensitivity and precision among the platforms as well as provide useful conversion formulas among the platforms to ensure equivalent quantitation.

Abstract: Systems methods and recordable media for predicting multi-variable outcomes based on multivariable inputs. Additionally, the models described can be used to predict the multi-variable inputs themselves, based on the multi-variable inputs, providing a smoothing function, acting as a noise filter. Both multi-variable inputs and multi-variable outputs may be simultaneously predicted, based upon the multi-variable inputs. The models find a critical subset of data points, or “tent poles” to optimally model all outcome variables simultaneously to leverage communalities among outcomes.

Abstract: Systems, methods and computer readable media for evaluating profiles of multi-variable data values. Systems, methods and computer readable media for removing nuisance distortions from data to provide “cleaner”, more reliable data.

Abstract: A system and method for dynamically identifying clusters of related data in a database uses a probe to identify the clusters. These clusters, also known as density patterns, are identified by launching the probe from an initial position in a data space associated with the data comprised of a plurality of data points. Each of the data points attracts the probe to itself. Distant data points attract the probe to a lesser extent than do proximate data points. In this manner, the probe is drawn along a trajectory toward an equilibrium point. Once the equilibrium point is reached, a cluster is identified and its location optionally stored. Additional probes are launched from different initial positions in the data space to identify other clusters that may exist in the data space until no unique clusters are identified. The collection of identified clusters is representative of a number and, in some embodiments of the present invention, a general location of related data within the data space.

Abstract: A computer-implemented statistical technique is provided for normalizing the response curves of multiple measurement methods. The end result is a group of response curves, one for each measurement method under consideration, which depend on a common independent variable—the actual physical property being measured by the methods. The results are provided as a collection of equations, curves, and/or tables (a “nomogram”) to facilitate conversion of measured values from one method to measured values from a second method. In the technique, data is provided for each of the methods being normalized. The input data includes measured values from common samples which are analyzed by two or more of the methods under consideration. The technique also requires assumptions or approximations of the true physical property values for each of the samples used to generate the data. Still further, the technique requires assumptions of the mathematical form of the response curves (e.g., linear, sigmoidal, etc.

Abstract: Methods, software, and systems for evaluating the response of a patient afflicted with a disease to a therapeutic regimen for the disease are described. In one aspect, the present methods, systems, and software are provided for evaluating the utility of a treatment regimen for treating a patient afflicted with a disease. In one embodiment of this aspect, the value of at least one diagnostic variable relating to a statistical model describing the utility of the treatment regimen is determined. The statistical model is derived using a robustified similarity metric least squares (SMILES) analysis of the response to the treatment regimen which has been adapted to include discriminant and logistical analysis. The value of the diagnostic variable is then applied to the model to provide an estimated utility of the treatment regimen in treating the patient.