Abstract: A method of diagnosing, predicting, or prognosticating about a disease that includes obtaining experimental data, wherein the experimental data is high dimensional data, filtering the data, reducing the dimensionality of the data through use of one or more methods, training a supervised pattern recognition method, ranking individual data points from the data, wherein the ranking is dependent on the outcome of the supervised pattern recognition method, choosing multiple data points from the data, wherein the choice is based on the relative ranking of the individual data points, and using the multiple data points to determine if an unknown set of experimental data indicates a diseased condition, a predilection for a diseased condition, or a prognosis about a diseased condition.

Abstract: In one aspect, a system for implementing a copy number variation analysis method, is disclosed. The system can include a nucleic acid sequencer and a computing device in communications with the nucleic acid sequencer. The nucleic acid sequencer can be configured to interrogate a sample to produce a nucleic acid sequence data file containing a plurality of nucleic acid sequence reads. In various embodiments, the computing device can be a workstation, mainframe computer, personal computer, mobile device, etc. The computing device can comprise a sequencing mapping engine, a coverage normalization engine, a segmentation engine and a copy number variation identification engine. The sequence mapping engine can be configured to align the plurality of nucleic acid sequence reads to a reference sequence, wherein the aligned nucleic acid sequence reads merge to form a plurality of chromosomal regions.

Abstract: Embodiments of computer systems for visualizing information and data from samples, such as nucleic acids, proteins, or other bio-polymers, are disclosed. One embodiment of a method comprises displaying first and second display areas on a display, displaying an axis dividing the first display area into first and second sub-areas, and displaying first and second axes, wherein the axes are substantially perpendicular to each other. The method further comprises displaying a plurality of bar graphs in the first display area, wherein a length of each bar graph in the first sub-area corresponds to the scalar data information of a first biological sample, and a length of each bar graph in the second sub-area corresponds to the scalar data information of a second biological sample; displaying, in the second display area, a plurality of markers, wherein each marker is related to one of the bar graphs.

Abstract: Epitope prediction models are described herein. By way of example, a system for predicting epitope information relating to a epitope can include a classification model (e.g., logistic regression model). The trained classification model can illustratively operatively execute one ore logistic functions on received protein data, and incorporate one or more of hidden binary variables and shift variables that when processed represent the identification (e.g., prediction) of one or more desired epitopes. The classification model can be configured to predict the epitope information by processing data including various features of an epitope, MHC, MHC supertype, and Boolean combinations thereof.

Abstract: Methods using mass spectral data analysis and a classification algorithm provide an ability to determine whether a non-small-cell lung cancer patient, head and neck squamous cell carcinoma or colorectal cancer patient has likely developed a non-responsiveness to treatment with a drug targeting an epidermal growth factor receptor pathway. As the methods of this disclosure require only simple blood samples, the methods enable a fast and non-intrusive way of measuring when drugs targeting the EGFR pathway cease to be effective in certain patients. This discovery represents the first known example of true personalized selection of these types of cancer patients for treatment using these classes of drugs not only initially, but during the course of treatment.

Abstract: Methods for comparing a first DNA profile with a second DNA profile are provided. The likelihood ratio for one hypothesis relative to another, as to the sources of the DNA, is conditioned on quantity of DNA in the test sample providing the first DNA profile and/or another sample providing the second DNA profile.

Abstract: Methods using mass spectral data analysis and a classification algorithm provide an ability to determine whether a non-small-cell lung cancer patient, head and neck squamous cell carcinoma or colorectal cancer patient has likely developed a non-responsiveness to treatment with a drug targeting an epidermal growth factor receptor pathway. As the methods of this disclosure require only simple blood samples, the methods enable a fast and non-intrusive way of measuring when drugs targeting the EGFR pathway cease to be effective in certain patients. This discovery represents the first known example of true personalized selection of these types of cancer patients for treatment using these classes of drugs not only initially, but during the course of treatment.

Abstract: The present invention provides methods for diagnosis and prognosis of lung cancer using expression analysis of one or more groups of genes, and a combination of expression analysis with bronchoscopy. The methods of the invention provide far superior detection accuracy for lung cancer when compared to any other currently available method for lung cancer diagnostic or prognosis. The invention also provides methods of diagnosis and prognosis of other lung diseases, particularly in individuals who are exposed to air pollutants, such as cigarette or cigar smoke, smog, asbestos and the like air contaminants or pollutants.

Abstract: The invention relates a method of quantifying CD64 and CD163 expression in leukocytes and, specifically to a kit for use with a flow cytometer including a suspension of quantitative fluorescent microbead standards, fluorescent labeled antibodies directed to CD64 and CD163, and analytical software. The software is used to take information on the microbead suspension and fluorescent labeled antibodies from a flow cytometer and analyse data, smooth curves, calculate new parameters, provide quality control measures and notify of expiration of the assay system.

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: The present invention concerns a method for prediction and identification of microRNA precursors (pre-microRNA) and microRNA molecules using data processing programs and databases. The invention also pertains to the isolated form of these pre-microRNAs, microRNA molecules and derived nucleic acids there of. The invention also relates to recombinant vector, host cell, support, pharmaceutical composition or kit comprising such microRNA molecules or there of derivated molecules. The invention also applies to the use of such microRNA molecules and/or their identified targets in research, prognostic, diagnostic tools/methods as well as for therapeutic applications.

Abstract: The present invention relates to a method for indexing nucleic acid sequences to aid computer based searching of nucleic acid sequences by indexing a nucleotide sequence by the presence of unique Kmers in the sequence. The method of the present invention comprises utilizing an algorithm to automatically index a nucleic acid sequence.

Abstract: The present invention provides, among other things, new methods for optimizing comparative genomic hybridization (CGH) data analysis. In particular, the methods of the invention provide increased sensitivity and specificity due to the implemented individual chromosome-based GC-wave correction. In certain embodiments, the log ratios of probes derived from each chromosome are corrected based on the chromosome's GC content slope, and certain selected chromosomes undergo chromosomal median adjustment. As a result, the log ratios of the probes on the array are normalized to be closer to zero (0) for diploid regions and thus, the GC waves are substantially reduced, resulting in a reduced false positive rate. Systems, computer readable media, and kits for use in the optimized CGH methods also are provided.

Abstract: There is provided a resonator sensor useful for detecting polymorphisms and mutations in DNA. The resonator sensor has a capture molecule immobilised on its surface, the capture molecule being either a probe DNA containing a reference sequence, or a mismatch binding molecule, and being capable of forming a probe DNA/target DNA/mismatch binding molecule complex on the surface of the resonator. A method for detecting mutations in a target DNA, including single nucleotide polymorphisms, is also provided.

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: 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: The present invention relates to generation (e.g., synthesis) of proteins. In particular, the present invention provides methods to predict miRNA targets using sequence similarity and thermodynamic stability of miRNA-bridges across both 3? and 5? UTR. Such methods find use in research, diagnostic and therapeutic settings (e.g., to discover targets, drugs, diagnostic products, etc.).

Abstract: This invention relates to DNA microarray technology, and more specifically to methods and kits for identifying autism and autism spectrum disorders in humans.

Abstract: A device, method and system are provided for diagnosing a disease using a gene expression reader to analyze biological samples and output gene expression values to calculate a scaling factor using a computer by counting a number of link counts Cn for groups of an individual genes' expression values at different times at a threshold value C or for groups of genes' expression values at a single time at the threshold value C, calculating an average number Cave of the link counts Cn, calculating a largest number M of the Cn, iteratively applying a relation Cave=M/log(M) for different threshold values C, comparing data of the Cave values versus M/log(M), and calculating a fitting to the compared data to output the scaling factor a. The scaling factor a is compared with other scaling factors a? in a database to output a report of estimates for a degree of health.

Abstract: The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, i.e., the heterozygote or either of the two homozygotes. The method allows for rapid, automatable analysis of genetic linkage to even complex polygenic traits.

Abstract: A method for testing the linearity or non-linearity of an actual analyte concentration and a test result, where the actual concentration of the analyte and a test result are determined so that a computation based upon an algorithm may be performed, which allows computation of various variables so that regression may be performed and the linear significance may be determined.

Abstract: Efficient sequence specific gene silencing is possible through the use of siRNA technology. By selecting particular siRNAs by rationale design, one can maximize the generation of an effective gene silencing reagent, as well as methods for silencing genes.

Abstract: The present invention provides methods and systems for an automated method of identifying allele values from data files derived from processed fluorophore emissions detected during the observation of fluorophore labeled nucleotide probes used in analyzing polymorphic DNA are provided. These methods are used in the rapid and efficient distinguishing of targeted polymorphic DNA sites without control samples.

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: A corrective method is described for processing results of transcriptome experiments obtained by differential analysis includes the following steps: obtaining the results of the level of expression of genes under a reference condition, and calculating the mean level of expression of each of such genes; obtaining the results of the level of expression of such genes under a treatment condition, and calculating the mean level of expression for each of such genes; calculating the modulation coefficient for the level of expression for each of such genes; calculating a p-value associated with each modulation coefficient; and calculating isobar curves of p-value as a function of the mean level of expression of each of such genes under the reference condition; calculating and associating a median modulation coefficient on the isobar curve of each p-value observed. The processing of results of experiments carried out on DNA chips is also described.

Abstract: A method for detecting DNA variation. First, by aligning trace data of a sample DNA sequence to trace data of a reference DNA sequence to produce an aligned sample DNA sequence. Then, inputting the trace data of the bases of both the reference DNA sequence and the aligned sample DNA sequence for a particular frame number into a non-linear mathematical function of an anti-correlation calculation scheme for all the frame numbers. Minimal values will be produced at the particular frame number for DNA base trace data of the aligned sample DNA sequence which are not a variation as compared to the reference DNA sequence. Values above the minimal values will be produced at the particular frame number for DNA base trace data of the aligned sample DNA sequence which are a variation as compared to the reference DNA sequence.

Abstract: An information processing system includes a processor configured for: defining a simulation space comprising a plurality of fragments and a plurality of processing nodes; determining a weight corresponding to the computational cost for a given pairwise fragment interaction; assigning the weight to the simulation space at a point between the two interacting fragments; performing a spatial partitioning of a volume of the simulation space such that all partitions have substantially the same weight; and assigning a computation of the pairwise fragment interaction to any node that has the positions of both groups of fragments.

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: The invention includes a prediction method for the screening or diagnosis or therapeutic management or prognosis of prostate cancer, including collecting individual input data and providing predictive information on the risk linked to a type of disease. The input data includes at least one variable or a combination of variables of the genetic type such as the identification of markers of genetic polymorphisms considered as being linked to the development of the disease. The invention also provides an individual prediction device for the screening or diagnosis or therapeutic management or prognosis of prostate cancer including first means for acquiring individual information data by a user, and at least a first software interface on which the said first means operate. The invention additionally includes a computer program product having the method and providing predictive information on risk linked to a disease.

Abstract: The problem of analyzing, visualizing an interpreting data of DNA arrays (array CGH and SNP arrays) in a clinical setting becomes very important as DNA arrays take over clinical diagnostics. Reporting of detected chromosomal aberrations are complicated with data noise and presence of “normal” chromosomal variants that may occur even in healthy patients. Clinicians are facing interpretation of array data and detected chromosomal anomalies in patient samples every day. The disclosed system provides means for automated detection of chromosomal anomalies in individual samples. It also enables its users to interpret detected aberrations in an efficient manner so that clinically relevant anomalies get reported and aberrations that can occur in healthy patients get ignored. It also allows its users to accumulate and mine data from multiple human samples and re-use it in daily diagnostic operations to improve clinical interpretation of newly acquired samples.

Abstract: Pharmacogenetic methods for determining a predicting responsiveness to antifolate therapy for subjects that present with recent-onset undifferentiated arthritis. The methods are based on the determination of a set of clinical parameter values and determining a predicted responsiveness to antifolate therapy by correlating the parameter values with predefined responsiveness values associated with ranges of parameter values. Parameters values that are decisive for responsiveness to antifolate therapy may include polymorphisms in the methylenetetrahydrofolate dehydrogenase (MTHFD1) gene as well as in three genes involved in the adenosine release pathway, the presence or absence of Rheumatoid factors, gender, pre- or postmenopausal status and/or smoking status.

Abstract: Method(s) for identifying rDNA sequences from a sample containing plurality of unknown DNA sequences are described herein. The method includes selecting one or more target clusters, from a plurality of reference clusters, corresponding to the query sequence. The target clusters are selected based on a composition based analysis. A proportion of probable rDNA clusters from the target clusters is identified. Based on the proportion of the probable rDNA clusters, the query sequence is identified as an rDNA.

Abstract: The present disclosure relates to methods and systems that may be used for detection of one or more pathogens and determining one or more agents in response to pathogen detection.

Abstract: Significance of biological pathway in disease state is predicted by (a) providing expression level data for a plurality of biomolecules differentially expressed in a disease state, compared with same biomolecules expressed in a non-diseased state: (b) determining presence probability of the biomolecules in disease state; (c) determining effect of each biomolecule from the plurality of biomolecules on the expression of different downstream biomolecules within pathway to provide perturbation factor for each biomolecule in the pathway; (d) combining statistical significance of differentially expressed biomolecules present in the disease state, with a sum of perturbation factors for all of the biomolecules, generating an impact factor; (e) calculating statistical significance of impact factor based upon determined probability of having statistical significant presence of differentially expressed biomolecules in step (b) and the sum of perturbation factors in step (c); and (f) outputting statistical significance o

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: An electronic hybridization assay implements a hybridization reaction, or a sequence analysis, on sequences representative of the sequences of the molecules under examination to provide an output representative of a chemical hybridization reaction. An electronic hybridization machine implements a correlation algorithm where the correlation output provides information regarding the relationship between the molecules under examination. In one aspect, the degree of similarity between the molecules is indicated by the correlation output value. In another aspect, a locus of similarity between the molecules is indicated by a maximum value in the correlation output sequence. In a particular aspect, the sequences are encoded in an optimized format to optimize the operation of the operation of the electronic hybridization machine.

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: A genomic data computer system receives a data set comprising sequenced genomic bases and associated annotations that form sequenced base-annotation pairs. The computer system determines a frequency distribution for the base-annotation pairs in the data set. The computer system determines variable-length identification codes for the base-annotation pairs based on the frequency distribution. The computer system converts the sequenced base-annotation pairs into a corresponding series of the variable-length identification codes that require a smaller amount of storage than the original data.

Abstract: Techniques for linking non-coding and gene coding regions of a genome are provided. In one aspect, a method of determining associations between non-coding sequences and gene coding sequences in a genome of an organism comprises the following steps. At least one conserved region is identified from one or more non-coding sequences. Additional instances of the conserved region are located in the untranslated or amino acid coding regions of one or more genes in the organism under consideration, and the conserved region is associated with the one or more biological processes in which these one or more genes participate.

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: The present invention provides methods, systems and compositions for predicting disease susceptibility in a patient. In some embodiments, methods for the classification, prognosis, and diagnosis of cancers are provided. In other embodiments, the present invention provides statistical methods for building a gene-expression-based classifier that may be employed for predicting disease susceptibility in a patient, for classifying carcinomas, and for the prognosis of clinical outcomes.

Abstract: Generally, computer implemented remote monitoring system which generates a viewable reduced byte data representation for each one of a plurality of analyzed instrument signals. Specifically, a flow cytometer remote monitoring system which generates a viewable reduced byte data representation for each one of a plurality analyzed flow cytometer signals.

Abstract: Systems, methods, and apparatuses for performing a prenatal diagnosis of a sequence imbalance are provided. A shift (e.g. to a smaller size distribution) can signify an imbalance in certain circumstances. For example, a size distribution of fragments of nucleic acids from an at-risk chromosome can be used to determine a fetal chromosomal aneuploidy. A size ranking of different chromosomes can be used to determine changes of a rank of an at-risk chromosome from an expected ranking. Also, a difference between a statistical size value for one chromosome can be compared to a statistical size value of another chromosome to identify a significant shift in size. A genotype and haplotype of the fetus may also be determined using a size distribution to determine whether a sequence imbalance occurs in a maternal sample relative to a genotypes or haplotype of the mother, thereby providing a genotype or haplotype of the fetus.

Abstract: A method provides an index that is indicative of the state of a subject, as to a biological condition, based on a sample from the subject. An embodiment of this method includes: deriving from the sample a profile data set, the profile data set including a plurality of members, each member being a quantitative measure of the amount of a distinct RNA or protein constituent in a panel of constituents selected so that measurement of the constituents enables evaluation of the biological condition; and in deriving the profile data set, achieving such measure for each constituent under measurement conditions that are substantially repeatable; and applying values from the profile data set to an index function that provides a mapping from an instance of a profile data set into a single-valued measure of biological condition, so as to produce an index pertinent to the biological condition of the subject.

Abstract: The invention relates to methods and systems for predicting or estimating the melting temperature of duplex nucleic acids, in the presence of divalent cations, particularly duplexes of oligonucleotides which may be used as, for example, but not limited to primers or probes in PCR and/or hybridization assays. The methods and algorithms use novel formulas, having terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of divalent cation salt conditions on the melting temperature.

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract: Statistical models for identifying associations are described herein. By way of example, a system for identifying associations between variables can include a model builder and an association identifier. The model builder can receive observations about the variables and generate a null model and a non-null model. The association identifier can assess the strength of the association between the variables by determining how much the non-null model better explains the observed data than the null model. Additionally or alternatively, the structure of the observed data can be inferred simultaneously with the statistical model.

Abstract: An exemplary embodiment of system, computer-accessible medium and method for comparing a first genome to a second genome. For example, a first genome may be compared to a second genome by building a first library for the first genome and a second library for the second genome, providing a plurality of matches between elements in the first library common to elements in the second library, ranking each match to determine a likelihood of similarity between the common elements in the first and second libraries; and associating matches having a predetermined likelihood. The association may be performed efficiently by a stable marriage procedure.

Abstract: A method of investigation a sample is provided, the sample being a mixture of DNA arising from more than one source. The method includes analysing the sample to obtain a genotype for the DNA present in the sample and assigning a prior probability distribution to the genotype. The likelihood function is considered and a posterior probability distribution for the genotype is established. In this way a probabilistic assessment of the genotype of the major or minor contributor to the sample can be obtained. This is beneficial over prior methods which use a deterministic method, and so involve the use of rule based methods.