Abstract: A method, computer product, and computer system of minimizing surprisal data comprising: at a source, reading and identifying characteristics of a genetic sequence of an organism; receiving an input of rank of at least two identified characteristics of the genetic sequence of the organism; generating a hierarchy of ranked, identified characteristics based on the rank of the at least two identified characteristics of the genetic sequence of the organism; comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and if at least one reference genome from the repository matches the hierarchy of ranked, identified characteristics, breaking the matched reference genomes into pieces, combining pieces associated with the identified characteristics from at least one matched reference genome to form a filter pattern to be compared to the nucleotides of the genetic sequence of the organism, to obtain differences and create surprisal data.

Abstract: Methods and compositions for the identification of breast cancer grade signatures are provided. The signature profiles are identified based upon multiple sampling of reference breast tissue samples from independent cases of breast cancer and provide a reliable set of molecular criteria for identification of cells as being in one or more particular stages and/or grades of breast cancer.

Abstract: A computer product and system of minimizing surprisal data comprising: at a source, reading and identifying characteristics of an organism's background associated with a genetic sequence of the organism; receiving an input of rank of at least two identified characteristics of the genetic sequence; generating a hierarchy of ranked, identified characteristics based on the rank of the identified characteristics; comparing the hierarchy of ranked, identified characteristics to a repository of reference genomes; and if at least one reference genome from the repository matches the ranked characteristics, breaking the matched reference genomes into pieces, combining pieces associated with the identified characteristics from the matched reference genome to form a filter pattern to be compared to the nucleotides of the genetic sequence of the organism. The differences from the comparison are used to create surprisal data representing an entire genome of the organism.

Abstract: The present invention is directed to computer based pharmacokinetics systems, such as. web-based pharmacokinetics systems, and their use to predict a dose and a dosing interval for a patient in need of a clotting factor therapy.

Abstract: An aberration in a fetal genome can be identified by analyzing a sample of fetal and maternal DNA. Classifications of whether an aberration (amplification or deletion) exists in a subchromosomal region are determined using count-based and size-based methods. The count classification and the size classification can be used in combination to determine whether only the fetus or only the mother, or both, have the aberration in the subchromosomal region, thereby avoiding false positives when the mother has the aberration and the fetus does not.

Abstract: Techniques are disclosed relating to assay configuration. Assay devices are often used to determine characteristics of test samples, e.g., using polymerase chain reaction (PCR) or Deoxyribonucleic Acid (DNA) melt techniques. Various disclosed techniques allow detailed specification of assay parameters. This may allow user modification of assays and/or assay development by third parties. In embodiments in which assay parameters are specified using a separate device, these techniques may reduce validation requirements resulting from modified assays. In some embodiments, assay configuration information that may be added/removed/modified may include: a sequence of operations, parameters for the sequence of operations, data processing parameters, call logic rules/dependencies, and/or reporting rules.

Abstract: Described embodiments enable identification of family networks using combinations of DNA analysis and genealogical information. Genealogical data is provided by users of a genealogical research service or collected from other sources and used to create family trees for each user. DNA samples are also received from the users. By analyzing the DNA samples, potential genetic relationships can be identified between some users. Once these DNA-suggested relationships have been identified, common ancestors can be sought in the respective trees of the potentially related users. Where these common ancestors exist, an inference is drawn that the DNA-suggested relationship accurately represents a familial overlap between the individuals in question. People descended from the same common ancestor are each members of a family network. Members of a family network not in a user's tree may be identified for the user, enabling the user to discover additional ancestors that might otherwise have remained unknown.

Abstract: Displaying a comparison of genetic data is disclosed, including receiving an indication of a first individual, receiving an indication of a second individual, retrieving the genotypic information for the first individual and the second individual, comparing the genotypic information of the first individual and the second individual, displaying an indication of the comparison of the genotypic information of the first individual and the second individual graphically. A first graphical symbol is used to display an indication of the genome regions for which the first individual and the second individual are identical. A second graphical symbol is used to display an indication of the genome regions for which the first individual and the second individual are half identical.

Abstract: A method for detection of at least one reversibly photo-convertible fluorescent species, comprises the following steps: a) illumination of a sample comprising said or at least one of the reversibly photo-convertible fluorescent species by a periodically modulated illuminating light; and b) detection of fluorescent emission emitted by the sample thus illuminated; wherein the method further comprises the following step: c) extraction of the amplitude of the intensity component of the fluorescent emission exhibiting the same periodicity as the periodically modulated illuminating light and a phase quadrature with respect to the same; and wherein the mean intensity of the illuminating light and the modulation frequency of the same are chosen to maximize the amplitude of the intensity component of the fluorescent emission.

Abstract: Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.

Abstract: Methods and systems for evaluating biological dataset profiles relating to toxic agents including candidate pharmaceuticals, environmental agents, biowarfare and chemical warfare agents are provided, where datasets comprising information for multiple cellular parameters are compared and identified, and used in the evaluation of candidate agents.

Abstract: The present invention describes a bioinformatic method that can be used in the estimation of an individual's susceptibility to cancer through an evaluation of that individual's personal genome sequence. More specifically, this invention is a continuation-in-part of the methodology described in patent application Ser. No. 14/154,303 for the early detection of cancer. Said method is based upon an analysis of the structure of the repetitive DNA sequences surrounding and within the various cancer-linked regions of the individual's genome being evaluated. Said analysis of said individual's genome is then compared to the same analysis conducted for one or more reference genomes and/or genes for which cancer susceptibility has been previously determined. Said analysis can also be used to estimate the respective likelihoods that each cancer-linked genomic region will be damaged in the potential formation of a tumor.

Abstract: Methods are provided for diagnosing pregnancy-associated disorders, determining allelic ratios, determining maternal or fetal contributions to circulating transcripts, and/or identifying maternal or fetal markers using a sample from a pregnant female subject. Also provided is use of a gene for diagnosing a pregnancy-associated disorder in a pregnant female subject.

Abstract: The present disclosure presents methods, systems, and devices for identifying new molecules directly from biological sequence information, with at least one of a desired bioactivity profile, functional attribute, biochemical reactivity, biological impact, pharmacological characteristic or therapeutic effect. The present disclosure further includes analyzing, at the processor, data features of biological sequence information and other data sources, including a feature-definition set by processing, using one or more bioinformatic techniques, computational algorithms, or methods of statistical machine learning, data sources relating to biological or chemical molecules, including biomolecules, including but not limited to peptides, having desired physical or chemical characteristics, bioactivities, functional attributes, biological impacts, pharmacologic properties or therapeutic effects.

Abstract: Described herein are systems and methods that receive as input a DNA or RNA sequence, extract features, and apply layers of processing units to compute one ore more condition-specific cell variables, corresponding to cellular quantities measured under different conditions. The system may be applied to a sequence containing a genetic variant, and also to a corresponding reference sequence to determine how much the condition-specific cell variables change because of the variant. The change in the condition-specific cell variables are used to compute a score for how deleterious a variant is, to classify a variant's level of deleteriousness, to prioritize variants for subsequent processing, and to compare a test variant to variants of known deleteriousness.

Abstract: Contemplated systems and methods employ chimeric reference sequences that include a plurality of viral genome sequences to identify/quantify integration and co-amplification events. Most typically, the viral genome sequences are organized in the chimeric reference sequences as single chromosomes and the chimeric reference sequences are in BAM format.

Abstract: A system and method for converting static/still medical images of a particular patient into dynamic and interactive images interacting with medical tools including medical devices by coupling a model of tissue dynamics and tool characteristics to the patient specific imagery for simulating a medical procedure in an accurate and dynamic manner.

Abstract: A system and method for converting static/still medical images of a particular patient into dynamic and interactive images interacting with medical tools including medical devices by coupling a model of tissue dynamics and tool characteristics to the patient specific imagery for simulating a medical procedure in an accurate and dynamic manner.

Abstract: The present invention relates to a method for classifying genotype or subtype of query sequence. More particularly, the present invention is directed to a method for classifying genotype or subtype of query sequence, comprising: (i) selecting base sequences of various viruses of which genotypes or subtypes are known as reference sequences and obtaining a distance matrix by calculating distances between sequences in a multiple alignment of said reference sequences; and (ii) developing a discriminant equation which may classify the reference sequences by performing discriminant analysis for a cluster obtained by clustering said reference sequences through multidimensional scaling of the distance matrix, followed by classifying genotype or subtype of a query sequence according to said discriminant equation.

Abstract: Methods of deconvolving a feature profile of a physical system are provided herein. The present method may include: optimizing a regression between a) a feature profile of a first plurality of distinct components and b) a reference matrix of feature signatures for a second plurality of distinct components, wherein the feature profile is modeled as a linear combination of the reference matrix, and wherein the optimizing includes solving a set of regression coefficients of the regression, wherein the solution minimizes 1) a linear loss function and 2) an L2-norm penalty function; and estimating the fractional representation of one or more distinct components among the second plurality of distinct components present in the sample based on the set of regression coefficients. Systems and computer readable media for performing the subject methods are also provided.