Abstract: A sequence of polymer units in a polymer (3), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore (1), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units (4). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units.

Abstract: A method of administering insulin includes receiving blood glucose measurements of a patient at a data processing device from a glucometer. Each blood glucose measurement is separated by a time interval and includes a blood glucose time associated with a time of measuring the blood glucose measurement. The method also includes receiving patient information at the data processing device and selecting a subcutaneous insulin treatment for tube-fed patients from a collection of subcutaneous insulin treatments. The selection is based on the blood glucose measurements and the patient information. The subcutaneous insulin treatment program for tube-fed patients determines recommended insulin doses based on the blood glucose times. The method also includes executing, using the data processing device, the selected subcutaneous insulin treatment.

Abstract: A method of administering insulin includes receiving blood glucose measurements of a patient at a data processing device from a glucometer. Each blood glucose measurement is separated by a time interval and includes a blood glucose time associated with a time of measuring the blood glucose measurement. The method also includes receiving patient information at the data processing device and selecting a subcutaneous insulin treatment for tube-fed patients from a collection of subcutaneous insulin treatments. The selection is based on the blood glucose measurements and the patient information. The subcutaneous insulin treatment program for tube-fed patients determines recommended insulin doses based on the blood glucose times. The method also includes executing, using the data processing device, the selected subcutaneous insulin treatment.

Abstract: Systems and methods are provided for quality control for biological testing. One embodiment is a system that includes a liquid handler that applies samples of genetic material to a test plate comprising an array of wells, a Polymerase Chain Reaction (PCR) device that amplifies the genetic material, and an analysis device that determines, based on a change in visual appearance of each well, a numerical value indicating whether a corresponding sample is representative of a disease state. The system also includes a quality assurance server that identifies a pattern of the numerical values, and determines a likelihood of the pattern. In an event that the likelihood is less than a threshold value, the quality assurance server flags the test plate as potentially contaminated, and in an event that the likelihood exceeds the threshold value, the quality assurance server refrains from flagging the test plate as potentially contaminated.

Abstract: A method and system for optimizing insulin dosages for diabetic subjects which includes a processor for calculating basal and bolus dosages to be recommended for meal types including breakfast, lunch, dinner, snack, or at miscellaneous times. The bolus calculations are specifically directed to time periods which are taken from either pre-meal, post-meal, bedtime, mid-sleep or miscellaneous times. The processor calculates an optimized bolus for a specific time period and meal type based upon prior basal dosages, prior glucose doses, hypoglycemia thresholds, mid-point of target ranges, and subject insulin sensitivity factors. A display is provided to the subject for sensing the optimized insulin dosage recommended at a specific time period and for a specific meal type.

Abstract: A method of administering insulin includes receiving scheduled glucose time intervals and obtaining glucose data of a patient that includes glucose measurements, glucose times, and insulin dosages previously administered by the patient. The method also includes applying a set of filters to identify which of the glucose measurements associated with at least one of the scheduled time intervals are usable and which of the glucose measurements associated with the at least one scheduled time interval are unusable. The method also includes aggregating the glucose measurements associated with the at least one scheduled time interval identified as usable to determine a representative aggregate glucose measurement and determining a next recommended insulin dosage for the patient based on the representative aggregate glucose measurement and the insulin dosages previously administered by the patient.

Abstract: Computational methods used for large scale scaffolding of a genome assembly are provided. Such methods may include a step of applying a location clustering model to a test set of contigs to form two or more location cluster groups, each location cluster group comprising one or more location-clustered contigs; a step of applying an ordering model to each of the two or more location cluster groups to form an ordered set of one or more location-clustered contigs within each cluster group; and a step of applying an orienting model to each ordered set of one or more location-clustered contigs to assign a relative orientation to each of the location-clustered contigs within each location cluster group. In some aspects, the test set of contigs are generated from aligning a set of reads generated by a chromosome conformation analysis technique (e.g., Hi-C) with a draft assembly, a reference assembly, or both.

Abstract: The invention relates a method and an apparatus of predicting or planning a temperature distribution (52) in a body. The method comprises the steps of: a) obtaining a model of the body (50) related to a temperature transport mechanism or temperature distribution (52) in the body; b) simulating an application of heat to at least a part of the body such as targeted tissue; c) determining and/or predicting the temperature (52) or heat distribution in at least a part of the body using the model of the body (50).

Abstract: Systems and methods to automatically de novo assemble a set of unordered read sequences into one or more, larger nucleotide sequences are presented. The method involves first creating two identical sets of the reads, dividing each read in both sets into smaller sorted mer sequences and then comparing the mers for each read in set 1 to the mers from each read in set 2 to exhaustively identify overlapping segments. Overlap information is used to construct a modified assembly string graph, traversal of which produces a sorted string graph layout file consisting of all the reads ordered left to right including their approximate starting offset position. The sorted string graph layout file is then processed by a novel multiple sequence alignment system that uses mer matches between all the overlapping reads at a given position to place matching individual bases from each read into columns from which an overall consensus sequence is determined.

Abstract: The present invention relates to methods for evaluating the probability that a patient's diagnosis may be treated with a particular clinical regimen or therapy.

Abstract: Described herein are improved methods for the detection of endometriosis. Generally, the methods include, but are not limited to, applying machine learning algorithm to miRNA levels in order to detect, predict, diagnose, or monitor the presence or absence of endometriosis.

Abstract: Techniques to identify a mechanism of action of a compound using network dysregulation are disclosed herein. An example method can include selecting at least a first interaction involving at least a first gene, determining a first n-dimensional probability density of gene expression levels for the first gene and one or more genes in a control state, determining a second n-dimensional probability density of gene expression levels for the first gene and one or more genes following treatment using at least one compound, estimating changes between the first probability density and the second probability density, and determining whether the estimated changes are statistically significant.

Abstract: A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

Abstract: An amount of mitochondrial DNA molecules relative to an amount of nuclear DNA molecules is determined in a biological sample, and the relative amount is used for various purposes, e.g., screening, detection, prognostication or monitoring of various physiological and pathological conditions. As examples, an amount of mitochondrial DNA can be used to estimate a concentration of DNA of a tissue type, such as a fetal DNA concentration, tumor DNA concentration, or a concentration of DNA in the biological sample derived from a non-hematopoietic tissue source. Sequencing techniques can be used to determine a mitochondrial DNA concentration in a sample for an accurate detection of a level of cancer. A level of an auto-immune disease is also determined using a relative amount of mitochondrial DNA molecules compared nuclear DNA molecules.

Abstract: System and methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Additionally, various embodiments of an interactive graphical user interface (GUI) may provide an end-user with ready analysis of large sets of data representing a plurality of samples. In various embodiments of an interactive GUI, an end-user may be provided with a synchronized display of tabular and graphical sample data determined by an initial analysis according to a statistical model of a PDF.

Abstract: This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

Abstract: A method and system for optimizing insulin dosages for diabetic subjects which includes a processor for calculating basal and bolus dosages to be recommended for meal types including breakfast, lunch, dinner, snack, or at miscellaneous times. The bolus calculations are specifically directed to time periods which are taken from either pre-meal, post-meal, bedtime, mid-sleep or miscellaneous times. The processor calculates an optimized bolus for a specific time period and meal type based upon prior basal dosages, prior blood glucose doses, hypoglycemia thresholds, mid-point of target ranges, and subject insulin sensitivity factors. A display is provided to the subject for sensing the optimized insulin dosage recommended at a specific time period and for a specific meal type.

Abstract: Endonucleases play an essential role in genetic engineering and molecular biology. A major barrier to the clinical adoption of nucleases and engineered nucleases remain the overall lack of specificity and activity. Off-site cleavage, cleavage at loci other than the target loci, typically occurs resulting in mutations, unexpected gene-knockouts, or translocations. Provided herein are systems and methods for identifying the off-site cleavage loci and predicting the activity of engineered endonucleases for a given genome. It is expected that these tools and methods will be useful for designing nucleases and other related DNA binding domains (e.g. TAL effectors) for genomic therapy and engineering.

Abstract: A method of administering insulin includes receiving scheduled blood glucose time intervals and obtaining blood glucose data of a patient that includes blood glucose measurements, blood glucose times, and insulin dosages previously administered by the patient. The method also includes applying a set of filters to identify which of the blood glucose measurements associated with at least one of the scheduled time intervals are usable and which of the blood glucose measurements associated with the at least one scheduled time interval are unusable. The method also includes aggregating the blood glucose measurements associated with the at least one scheduled time interval identified as usable to determine a representative aggregate blood glucose measurement and determining a next recommended insulin dosage for the patient based on the representative aggregate blood glucose measurement and the insulin dosages previously administered by the patient.

Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads) comprising repeating sequences, methods for building reference sequence constructs comprising repeating sequences, and systems that can be used to align reads comprising repeating sequences. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long. The methods and systems can additionally account for variability within a repeating sequence, or near to a repeating sequence, due to genetic mutation.