Abstract: Systems, methods, and analytical approaches for short read sequence assembly and for the detection of insertions and deletions (indels) in a reference genome. A method suitable for software implementation is presented in which indels may be readily identified in a computationally efficient manner.

Abstract: Methods related to the generation of shape signatures representing molecular shape, and using shape signatures in both ligand-based and receptor-based molecular design. Ray-tracing is used to explore the volume interior to a ligand, or the space exterior to a receptor site. Shape signatures are then probability distributions derived from the ray-traces. Shape signatures provide condensed descriptors of shape properties readily compared to each other to test for shape similarity or complementarity.

Abstract: Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes.

Abstract: Broad-based genetic mutation association gene transcript test and data structure. Genetic mutation considerations for this unique test include a custom set of genetic sequences associated in peer-reviewed literature with various known genetic mutation related to exposure to toxic substances. Such genetic mutations include specific gene sequence alterations based on exposure to diesel fuel, aviation fuel, jet fuel, and many other toxic substances often needed in the aviation and refining industries. The base dataset may be developed through clinical samples obtained by third-parties. Online access of real-time phenotype/genotype associative testing for physicians and patients may be promoted through an analysis of a customized microarray testing service.

Abstract: Gene expression data provides a basis for more accurate identification and diagnosis of lymphoproliferative disorders. In addition, gene expression data can be used to develop more accurate predictors of survival. The present invention discloses methods for identifying, diagnosing, and predicting survival in a lymphoma or lymphoproliferative disorder on the basis of gene expression patterns. The invention discloses a novel microarray, the Lymph Dx microarray, for obtaining gene expression data from a lymphoma sample. The invention also discloses a variety of methods for utilizing lymphoma gene expression data to determine the identity of a particular lymphoma and to predict survival in a subject diagnosed with a particular lymphoma. This information will be useful in developing the therapeutic approach to be used with a particular subject.

Abstract: A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.

Abstract: The present invention provides methods for generating a distribution of optimal answers to a nondeterministic polynomial optimization problem by providing a plurality of solutions comprising input polynucleotides, wherein each solution comprises identical input polynucleotides; and wherein the number of solutions comprising polynucleotides equals a number of data inputs in the problem to be answered, and wherein each input polynucleotide comprises an x segment and a y segment; providing a plurality of solutions comprising connection polynucleotides wherein each solution comprises identical connection polynucleotides; and wherein the number of solutions comprising connection polynucleotides equals a number of unique connections that can be made between the different data inputs, and wherein each polynucleotide in the set of connection polynucleotides is complementary to the x segment of one input polynucleotide and to the y segment of one different input polynucleotide; combining the solutions comprising the i

Abstract: Basis motifs are determined from an input sequence through an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs that are formed by determining sets for selected basis motifs. From these sets, unique intersection sets are determined. This process continues, by selecting additional basis motifs, until all basis motifs have been selected. An apparatus for performing the process is also disclosed.

Abstract: Recombinant polynucleotides and recombinant polypeptides useful for improvement of plants are provided. The disclosed recombinant polynucleotides and recombinant polypeptides find use in production of transgenic plants to produce plants having improved properties.

Abstract: There is provided an identification technique that can consistently maintain a set of information specifying a specimen through all the processes from the amplification process to the detection process of a specific sequence. A base sequence incorporating as a set of decodable information an individual code imparted to the specimen is disposed in an amplifiable region to form an identifier; the identifier is amplified together with the specimen and the presence of the identifier in the amplification product is detected; thus, the individual code of the specimen in the amplification product can be recognized, which specimen the amplification product is derived from can be easily identified, and whether or not the amplification has been carried out satisfactorily can also be simultaneously tested.

Abstract: A 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 is constructed. The method for processing information on a nucleotide sequence comprises: (a) receiving request information for an object and/or service; (b) obtaining positional information in accordance with the request information from a memory having positional information representing a position in a nucleotide sequence memorized therein; and (c) obtaining nucleotide sequence-related information corresponding to the positional information obtained in (b) above, and obtaining semantic information implied by the nucleotide sequence-related information and/or information associated with the semantic information.

Abstract: Systems and methods for selecting factors from a continuous data set of measurements are provided. The measurements include values of factors and/or outcomes. Two or more factors that are jointly associated with one or more outcomes from the data set are identified. Each of the two or more factors are analyzed to determine at least one cooperative interaction among the factors with respect to an outcome. The two or more factors can be a module of factors serving as a single factor participating in a cooperative interaction with another factor or module of factors.

Abstract: An external quality control method, using an external quality control system which comprises an external quality control computer and a plurality of preprocessing devices connected to the external quality control computer via a network, comprising: performing preprocessing operations on preprocessing quality control samples, the preprocessing devices being adapted to prepare samples for measurement of target nucleic acid; measuring preprocessed preprocessing quality control samples to obtain measurement data; providing the measurement data to the external quality control computer over the network; storing the measurement data; and implementing an external quality control process based on the measurement data, is disclosed. An external quality control method for detection of nucleic acid, an external quality control method for preparation of calibration curve, an external quality control computer, a preprocessing device, and a nucleic acid detecting device are also disclosed.

Abstract: A method and system for automated quantitation of tissue micro-array image (TMA) digital analysis. The method and system automatically analyze a digital image of a TMA with plural TMA cores created using a needle to biopsy or other techniques to create standard histologic sections and placing the resulting needle cores into TMA. The automated analysis allows a medical conclusion such as a medical diagnosis or medical prognosis (e.g., for a human cancer) to be automatically determined. The method and system provides reliable automatic TMA core gridding and automated TMA core boundary detection including detection of overlapping or touching TMA cores on a grid.

Abstract: The invention concerns the identification of proteomes of biological fluids and their use in determining the state of maternal/fetal conditions, including maternal conditions of fetal origin, chromosomal aneuploidies, and fetal diseases associated with fetal growth and maturation. In particular, the invention concerns a comprehensive proteomic analysis of human amniotic fluid (AF) and cervical vaginal fluid (CVF), and the correlation of characteristic changes in the normal proteome with various pathologic maternal/fetal conditions, such as intra-amniotic infection, pre-term labor, and/or chromosomal defects. The invention further concerns the identification of biomarkers and groups of biomarkers that can be used for non-invasive diagnosis of various pregnancy-related disorders, and diagnostic assays using such biomarkers.

Abstract: Disclosed is a hierarchical computational method to predict the expression value of genes in time-series microarray data. The method may include the step of first applying a nonlinear independent component analysis (NICA) algorithm that extracts the major components covering all considered genes. An autoregressive exogenous (ARX) model may subsequently be used to quantitatively express the dynamic interactions of all components with each other. Then, using the predicted values for the components, and the nonlinear independent component analysis in the inverse form, the data may be used to predict the expression parameters for individual genes. The method may be used for the analysis of a eukaryotic gene expression throughout the cell cycle.

Abstract: A system and method for identifying high order associations between variables in complex systems that is particularly useful where there is no correlation or weak correlation between variables due to the influence of a third variable, a ternary relationship. The ternary relationship describes how the variation in the pattern of association between a pair of variables, including its sign and strength, is mediated by a third variable. In one embodiment applied to gene expression data, the activity of pairs of correlated genes due to the activity of one or more third genes is shown.

Abstract: To provide a method of accurately and efficiently acquiring a candidate for a set of discrimination elements for identification. Provided is a method of acquiring a set of specific elements on a specific sequence for discriminating the specific sequence from a number of sequences, including the steps of acquiring a group of alignment data in which each of the number of sequences is subjected to alignment processing, and acquiring a set of elements capable of discriminating the specific sequence through computational processing on the group of alignment data.

Abstract: A wellness system monitors the controlled progress of patients under surveillance and includes a server base station which is generally off-site, a web-site interface and a local station at the point-of-use, which is generally a health or fitness center. A unique data base is created for each user and goals and objectives may be set with progress monitored. Typically, the user will respond to a survey or questionnaire to populate his specific database. This is combined with a professional assessment and an automated measurement of vital statistics such as weight, blood pressure and body composition as measured at the local station. Other data may be entered manually such as height, age and the like. In a more comprehensive system the invention is designed to monitor other data such as cholesterol and blood glucose, as well. The locally input data may be updated at will by the user or on behalf of the user by professional personnel.

Abstract: A computer-implemented method for viewing experimental data is provided. In certain embodiments the method comprises: a) inputting genomic array data and cytogenetic data into a computer memory; and b) producing a graphical user interface comprising: i) a chromosomal map of the genomic array data comprising a first positional indicator that indicates a position on the chromosomal map; and ii) a cytogenetic map of the cytogenetic data comprising a second positional indicator that indicates a position on the cytogenetic map.