Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.

Abstract: Methods, systems, and apparatus for accurately determining a proportion (ratio) of two analytes is provided, as well as provide a concentration of a first analyte from a determined concentration of a second analyte and from a proportion of the analytes to each other. In one aspect, a surface model (called a “dose surface” herein) relating the concentrations of the two analytes to the proportion can be used to obtain accurate values for one of the variables (e.g. a concentration or the proportion) when the other two variables have previously been obtained. The dose surface can be a three-dimensional surface and be non-linear. The dose surface model can include multiple regression functions. For example, measured responses can be individually converted to concentrations using two dose-response curves, and the concentrations can be input to a dose surface function to obtain the proportion.

Abstract: Electronic label processor compares bioinformatic values to determine pharmaco-genomic mutation associated with host. Label display indicates pharmaco-genomic mutation, which is network-accessible for modified medical message. Bioinformatic values are determined preferably at different times.

Abstract: Systems, methods and apparatus for an automated analysis of a collection of melt curves is provided. The analysis can identify certain characteristics of double stranded nucleotide sequences (e.g. DNA or other nucleotide sequences) which were melted. For example, a variation (e.g. a mutation) in the sequences (also called amplicons) may be determined from the analysis. The amplicons may be amplified via any amplification mechanism, such as PCR or Ligase chain reaction (LCR). The automated analysis can include identifying a melt region, normalizing a melt curve, and clustering melt curves.

Abstract: Apparatus and methods for practicing telemedicine in the form of software systems acting over a network and kits containing laboratory supplies and equipment to organize the laboratory operations and interpret the results of molecular diagnostic testing are disclosed. At least two computers in communication over the Internet or other network are used, a remote computer located at a remote site and a central server located at a central site. The remote site may be geographically distant from the central site. A specimen is procured from a patient proximate to the remote site. Laboratory operations are conducted on the specimen at the remote site. The laboratory data resulting from the laboratory operations is interpreted by an expert reviewer who may be located at the central site, and a report is then transmitted back to the remote site.

Abstract: The systems and methods described herein utilize a probabilistic modeling framework for reverse engineering an ensemble of causal models, from data and then forward simulating the ensemble of models to analyze and predict the behavior of the network. In certain embodiments, the systems and methods described herein include data-driven techniques for developing causal models for biological networks. Causal network models include computational representations of the causal relationships between independent variables such as a compound of interest and dependent variables such as measured DNA alterations, changes in mRNA, protein, and metabolites to phenotypic readouts of efficacy and toxicity.

Abstract: Gamete donor selection includes receiving a specification including a phenotype of interest, receiving a genotype of a recipient and a plurality of genotypes of a respective plurality of donors, determining statistical information pertaining to the phenotype of interest based at least in part on different pairings of the genotype of the recipient and a genotype of a donor in the plurality of donors, and identifying a preferred donor among the plurality of donors, based at least in part on the statistical information determined.

Abstract: According to embodiments, techniques for selecting a consistent part of a signal, including a photoplethysmograph (PPG) signal, are disclosed. A pulse oximetry system including a sensor or probe may be used to obtain a PPG signal from a subject. Signal peaks may be identified in the PPG signal. Characteristics of the signal peaks, including the amplitude levels of the signal peaks and/or the time-distance between the signal peaks may be used to determine if the PPG signal is consistent. In an embodiment, signal peaks are processed based on a consistency metric, and the processed signal peaks are compared to the consistency metric to determine if the PPG signal is consistent. If the PPG signal is determined to be consistent, the PPG signal may be further analyzed to determine an underlying signal parameter, including, for example, a patient respiration rate.

Abstract: A method for calculating a sample size for a clinical trial of a first treatment can be provided. The method can include reading a survival curve from a clinical trial for a second treatment, wherein the clinical trial may be selected by a user interacting with a user interface. The method can further include selecting a plurality of points on the survival curve and storing coordinates for each of the plurality of points, wherein the plurality of points are selected so as to capture substantial features of the survival curve. Then, a hazard curve is generated based on the coordinates that were stored, wherein the hazard curve may be a step function. The method can further include calculating a sample size for the clinical trial of the first treatment using a Markov model based on the hazard curve.

Abstract: An analytic apparatus and method is provided for diagnosis, prognosis and biomarker discovery using transcriptome data such as mRNA expression levels from microarrays, proteomic data, and metabolomic data. The invention provides for model-based analysis, especially using kernel-based models, and more particularly similarity-based models. Model-derived residuals advantageously provide a unique new tool for insights into disease mechanisms. Localization of models provides for improved model efficacy. The invention is capable of extracting useful information heretofore unavailable by other methods, relating to dynamics in cellular gene regulation, regulatory networks, biological pathways and metabolism.

Abstract: A system and method for performing similarity searching is disclosed. This includes a programmable logic device configured to include a pipeline that comprises a matching stage, the matching stage being configured to receive a data stream comprising a plurality of possible matches between a plurality of data strings and a plurality of substrings of a query string. The pipeline may further include an ungapped extension prefilter stage located downstream from the matching stage, the prefilter stage being configured to shift through pattern matches between the data strings and the plurality of substrings of a query string and provide a score so that only pattern matches that exceed a user defined score will pass downstream from the prefilter stage. The matching stage may include at least one Bloom filter.

Abstract: Summarizing an aggregate contribution to a characteristic for an individual is disclosed, including determining the characteristic to be evaluated, identifying one or more markers associated with the characteristic, retrieving the measurement of the individual for each of the one or more markers from a database of individuals' markers, retrieving a statistical factor that measures the association between the marker associated with the characteristic and the characteristic for each of the one or more markers from the marker database, and determining the aggregate contribution based at least in part on the retrieved statistical factors.

Abstract: Methods for clustering a data set from a biological assay are provided. Aspects of the methods include applying statistical analyses to bisected subsets of the data at selected cut-of values to identify one or more break points in the data set. In certain aspects, the statistical analyses employed are based on determining the p-values of two-tailed t-tests calculated using the bisected data at each cut-off value. Aspects of the invention further include computer programming and systems which are configured to cluster data sets from biological assays according to the subject methods.

Abstract: According to embodiments, techniques for extracting a signal parameter from a selected region of a generally repetitive signal are disclosed. A pulse oximetry system including a sensor or probe may be used to obtain an original photoplethysmograph (PPG) signal from a subject. A filter transformation may be applied to the original PPG signal to produce a baseline PPG signal. The baseline PPG signal may contain artifacts and/or noise, and a region of the baseline PPG signal suitable for extracting the signal parameter may be selected. A suitable region of the baseline PPG signal may be selected by applying one or more thresholds to the baseline PPG signal, where the values of the thresholds may be set based on derivative values, amplitude-based percentiles, and/or local minima and maxima of the baseline PPG signal. A portion of the original PPG signal corresponding to the selected region may be processed, and the signal parameter may be extracted from the processed region.

Abstract: A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

Abstract: Provided in certain embodiments are methods for pairing patient cells and donor cells to prepare cytotoxic T cells. Such cytotoxic T cells could be administered to the patient for treating certain disorders, such as a cancer (for example, brain cancer).

Abstract: Determining relative relationship includes receiving recombinable deoxyribonucleic acid (DNA) information of a first user and recombinable DNA information of a second user, determining, based at least in part on the recombinable DNA information of the first user and recombinable DNA information of the second user, a predicted degree of relationship between the first user and the second user, and in the event that the expected degree of relationship between the first user and the second user at least meets the threshold, notifying at least the first user about a relative relationship with the second user.

Abstract: The present invention provides methods, systems, and code for accurately classifying whether a sample from an individual is associated with irritable bowel syndrome (IBS). In particular, the present invention is useful for classifying a sample from an individual as an IBS sample using a statistical algorithm and/or empirical data. The present invention is also useful for ruling out one or more diseases or disorders that present with IBS-like symptoms and ruling in IBS using a combination of statistical algorithms and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of IBS and prognostic information useful for guiding treatment decisions.

Abstract: The present invention provides a method for identifying siRNA target motifs in a transcript using a position-specific score matrix approach. The invention also provides a method for identifying off-target genes of an siRNA using a position-specific score matrix approach. The invention further provides a method for designing siRNAs with higher silencing efficacy and specificity. The invention also provides a library of siRNAs comprising siRNAs with high silencing efficacy and specificity.

Abstract: This invention constructs a highly safe system for processing information for providing semantic information and/or information associated with the semantic information useful for each individual organism through effective utilization of differences in nucleotide sequence-related information among individual organisms. This system comprises steps of: (a) obtaining positional information representing a position in a nucleotide sequence in accordance with a request for an object and/or service; and (b) evaluating adequacy of transmission of nucleotide sequence-related information corresponding to the positional information obtained in step (a), based on the flag information associated with the positional information for evaluating adequacy of transmission of nucleotide sequence-related information associated with the positional information representing a position in a nucleotide sequence.