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Gene sequence determination

Subclass of:

702 - Data processing: measuring, calibrating, or testing

702001000 - MEASUREMENT SYSTEM IN A SPECIFIC ENVIRONMENT

702019000 - Biological or biochemical

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DocumentTitleDate
20130030714METHODS FOR THE SURVEY AND GENETIC ANALYSIS OF POPULATIONS - The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.01-31-2013
20100057374Genotype calling - Determining a genetic sequence for a particular site on an individual's genome is disclosed, including: receiving a measurement associated with a particular sequence for the particular site on the individual's genome, receiving contextual information associated with a context of the individual within a larger collection of genetic information, and using the measurement associated with the particular sequence and the contextual information to compute an improved determination of the genetic sequence at the particular site on the individual's genome.03-04-2010
20090287420Method and system to characterize transcriptionally active regions and quantify sequence abundance for large scale sequencing data - This invention provides a quantitative method to determine transcriptionally active regions and quantify sequence abundance from large scale sequencing data. The invention also provides a system based on reference sequences to design and implement the method. The system processes large scale sequence data from high throughput sequencing, generates transcriptionally active region sequences as necessary, and quantifies the sequence abundance of the gene or transcriptionally active region. The method and system are useful for many analyses based on RNA expression profiling.11-19-2009
20100057372RAPID IDENTIFICATION OF PROTEINS AND THEIR CORRESPONDING SOURCE ORGANISMS BY GAS PHASE FRAGMENTATION AND IDENTIFICATION OF PROTEIN BIOMARKERS - Embodiments of the present invention relate to the identification of proteins using laser desorption ionization mass spectrometry, the identification of source organisms comprising the identified proteins and a computer readable storage medium storing instructions that, when executed by a computer cause the computer to perform a method for the identification of proteins using mass spectra generated through the application of laser desorption ionization mass spectrometry of the proteins.03-04-2010
20130138358ALGORITHMS FOR SEQUENCE DETERMINATION - The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.05-30-2013
20130041593Method for fast and accurate alignment of sequences - Genomic sequence matching and alignment techniques are disclosed. In one embodiment of the invention, computerized methods are provided for analyzing sequence similarity data obtained by means of a table of all local hits recorded between query sequence and reference index. The table of local hits represents all occurrences of query subsequences in reference index that stored all transitions between single l-mer prefix to multiple m-mer suffixes. The index data structure may take a variety of forms, including an array or a tree. The base position of each transition from l-prefix to m-suffix is recorded in k-bit masked form. The positions data structure may take a variety of forms as well, including an array or a tree. The table of local hits derived from l-prefix, m-suffix and k-position reference index is used by a series of low time and space complexity algorithms for optimizing alignment between query and reference.02-14-2013
20130041594AUTOMATED DECISION SUPPORT FOR ASSOCIATING AN UNKOWN BIOLOGICAL SPECIMEN WITH A FAMILY - Three methods of predicting whether an unknown biological specimen of a missing person originates from a member of a particular family comprise an initial automated decision support (ADS) algorithm for determining a list of relatives of the missing person for DNA typing and which typing technologies of available technologies to use for a listed relative. The ADS algorithm may be implemented on computer apparatus including a processor and an associated memory. The ADS method comprises determining a set of relatives of available family member relatives for DNA typing via a processor from a stored list of family member relatives according to one of a rule base, a table of hierarchically stored relatives developed based on discriminatory power or by calculating the discriminatory power for available family relatives to type. The ADS method may further comprise comparing at least one set of DNA typing data for the unknown biological specimen to DNA typing data from biological specimens from the determined set of relatives; calculating by the processor a likelihood function that the person is related to the family; and outputting a decision whether or not the person is related to the family.02-14-2013
20090240441SYSTEM AND METHOD FOR ANALYSIS AND PRESENTATION OF GENOMIC DATA - A method for analyzing genomic data that includes obtaining genomic sequence information from an anonymous individual, processing the information via a secure computerized algorithm, and presenting phenotypic information to the individual based upon the genomic sequence information.09-24-2009
20120185178Methods and Computer Software for Detecting Splice Variants - Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.07-19-2012
20120185177HARNESSING HIGH THROUGHPUT SEQUENCING FOR MULTIPLEXED SPECIMEN ANALYSIS - A method of associating a DNA sequence with a specimen pooled among a plurality of specimens, where the specimens may be pooled according to any number of pooling schemes, including the Chinese Remainder Theorem, random pool selection, shifted transversal design, and Chinese Remainder Sieve. A unique identifier is associated with each specimen according to the pooling scheme such that a decoder may associate a DNA sequence with each specimen after next-generation sequencing according to the unique identifier and the chosen pooling scheme.07-19-2012
20090125248System, Method and computer program product for integrated analysis and visualization of genomic data - Described is a system for analysis and visualization of genomic data. The system allows a user to select at least one individual sample. The sample has chromosomal data representing a genome with a chromosome and also includes chromosomal measurements of at least one event at a particular location on the chromosome. A frequency of event is generated based on the selected sample. The frequency of event is a frequency of occurrence of the event in the selected sample. At least one annotation can be selected that includes chromosomal region specific information as related to the chromosome. Finally, the chromosomal data, the annotation, and the frequency of event on a display can all be simultaneously displayed, thereby allowing a user to view chromosomal region specific information with respect to a particular chromosomal event.05-14-2009
20100138165Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.06-03-2010
20120191366Methods and Apparatus for Assigning a Meaningful Numeric Value to Genomic Variants, and Searching and Assessing Same - The present invention relates to methods, apparatus and computer systems for assigning a numerical value to a genotype at a single- or multi-base segment in an individual's genome to denote the presence of a match or a mismatch of a nucleic acid base sequence of one or more chromosomal copies of the segment, as compared to the nucleic acid base sequence at a reference genome segment that corresponds to the segment of the individual's genome. The methods involve assigning a single digit numerical value to the match or the mismatch of each chromosomal copy of the segment in the genome, so that the numerical value assigned to a mismatch is greater than the numerical value of the match. A null symbol is assigned to a no call determination. The assigned numerical values are summed and a total numerical value which is a single digit or a fixed number of digits is obtained. The steps are repeated to create a vector of total numerical values for the segment among the set of genomes, to thereby obtain a segment-specific pattern of genotype match/mismatch between a set of genomes and the nucleic acid base sequence at the reference genome segment. The segment-specific pattern, also referred to as a “diff pattern” can be used to filter or uncover specific trends or sub-patterns across a set of genomes, and more quickly identify genotypic/phenotypic relationships by identifying sites where the distribution of genotypes in the set of genomes relates in a distinctive, causal way to the distribution of a given phenotype among the individuals whose genomes are under study.07-26-2012
20130073217Phased Whole Genome Genetic Risk In A Family Quartet - In an embodiment of the present invention, three novel human reference genome sequences were developed based on the most common population-specific DNA sequence (“major allele”). Methods were developed for their integration into interpretation pipelines for highthroughput whole genome sequencing.03-21-2013
20130073216METHOD, SYSTEM AND APPARATUS TO PREDICT AND/OR RECOGNIZE AND/OR CLASSIFY BIOLOGICAL SEQUENCES - A method, a system and an apparatus for predicting and/or recognizing and/or classifying biological sequences, specially sequence families with binding site recognition motifs poorly conserved, comprising, advantageously, the use of neural networks rules; providing enhanced and more accurate results; and is preferably used when the biological sequence is a promoter.03-21-2013
20110015870Information Processing System Using Nucleotide Sequence-Related Information - 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.01-20-2011
20130060481Systems and Methods for Identifying Structurally or Functionally Significant Nucleotide Sequences - Provided are methods, systems, and computer readable media for comparing word statistics between a significant amino acid sequence and a significant nucleotide sequence wherein the comparison instructs further research.03-07-2013
20130060483DETERMINATION OF COPY NUMBER VARIATIONS USING BINOMIAL PROBABILITY CALCULATIONS - This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.03-07-2013
20130060482METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING - A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.03-07-2013
20120116688METHOD, COMPUTER-ACCESSIBLE MEDIUM AND SYSTEM FOR BASE-CALLING AND ALIGNMENT - Exemplary methods, procedures, computer-accessible medium, and systems for base-calling, aligning and polymorphism detection and analysis using raw output from a sequencing platform can be provided. A set of raw outputs can be used to detect polymorphisms in an individual by obtaining a plurality of sequence read data from one or more technologies (e.g., using sequencing-by-synthesis, sequencing-by-ligation, sequencing-by-hybridization, Sanger sequencing, etc.). For example, provided herein are exemplary methods, procedures, computer-accessible medium and systems, which can include and/or be configured for obtaining raw output from a sequencing platform configured to be used for reading fragment(s) of genomes, obtaining reference sequences for the genomes obtained independently from the raw output, and generating a base-call interpretation and/or alignment using the raw output and the reference sequences. For example, a score function can be determined based on information associated with the sequencing platform that can be used to analyze polymorphisms based on the base-call interpretation and/or alignment.05-10-2012
20120116687SYSTEM AND METHOD FOR GENOTYPE ANALYSIS AND ENHANCED MONTE CARLO SIMULATION METHOD TO ESTIMATE MISCLASSIFICATION RATE IN AUTOMATED GENOTYPING - The present invention relates to methods and systems for the analysis of the dissociation behavior of nucleic acids. The present invention includes methods and systems for analyzing dynamic profiles of genotypes of nucleic acids, including the steps of using a computer, including a processor and a memory, to convert dynamic profiles of known genotypes of a nucleic acid to multi-dimensional data points, wherein the dynamic profiles each comprise measurements of a signal representing a physical change of a nucleic acid containing the known genotype relative to an independent variable; using the computer to reduce the multi-dimensional data points into reduced-dimensional data points; and generating a plot of the reduced-dimensional data points for each genotype. The present invention also relates to methods and systems for calculating error statistics for an assay for identifying a genotype in a biological sample using an enhanced Monte Carlo simulation method to generate a set of N random data points for each known genotype within a class of known genotypes, where each set of N random data points has the same mean data point and covariance matrix as a data set for each of the known genotypes.05-10-2012
20100121582METHODS FOR ACCURATE SEQUENCE DATA AND MODIFIED BASE POSITION DETERMINATION - Disclosed herein are methods of determining the sequence and/or positions of modified bases in a nucleic acid sample present in a circular molecule with a nucleic acid insert of known sequence comprising obtaining sequence data of at least two insert-sample units. In some embodiments, the methods comprise obtaining sequence data using circular pair-locked molecules. In some embodiments, the methods comprise calculating scores of sequences of the nucleic acid inserts by comparing the sequences to the known sequence of the nucleic acid insert, and accepting or rejecting repeats of the sequence of the nucleic acid sample according to the scores of one or both of the sequences of the inserts immediately upstream or downstream of the repeats of the sequence of the nucleic acid sample.05-13-2010
20120232805Computerized Amino Acid Composition Enumeration - A computerized method and apparatus for enumerating one or more amino acid compositions is disclosed that provides one or more processors, a data storage communicably coupled to the one or more processors and a user interface communicably coupled to the one or more processors. The three or more user-specified characteristics are received from the data storage or the user interface. The one or more amino acid compositions are enumerated for all the peptides having a length less than or equal to the maximum length and a mass less than or equal to the mass limit using the one or more processors. The enumerated amino acid compositions are filtered based on the one or more other user-specified characteristics using the one or more processors. The filtered amino acid compositions and the mass of the filtered amino acid compositions are stored in the data storage.09-13-2012
20130166221METHOD AND SYSTEM FOR SEQUENCE CORRELATION - A method and system are provided for evaluating the correlation between sequences by entering segments of one sequence in a database and comparing segments of the other sequence with the index values to find correlated segments. The correlated segments are analysed to determine whether the spacing is within a defined range indicating that a correlation threshold has been met. A processing methodology may be employed whereby a coarse potential alignment algorithm is first applied to determine potential alignment at a plurality of potential alignment positions, which are filtered based on alignment scores, and a fine alignment algorithm is then applied.06-27-2013
20110125411Uniquemer Algorithm for Identification of Conserved and Unique Subsequences - A first protein sequence associated with the organism is identified, wherein the first protein sequence comprises a plurality of ordered residues. A plurality of sub-sequences is generated based on the first protein sequence, wherein each sub-sequence comprises a plurality of contiguous residues and a starting residue number of each sub-sequence differs from a starting residue number of another sub-sequence by one position in the first protein sequence. A first unique sub-sequence comprising a first set of contiguous residues based on the plurality of sub-sequences is identified, wherein the first unique sub-sequence is specific to the organism and is identified based on a dataset of protein sequences and stored.05-26-2011
20110301862System for array-based DNA copy number and loss of heterozygosity analyses and reporting - 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.12-08-2011
20110301863PREDICTION METHOD FOR THE SCREENING, PROGNOSIS, DIAGNOSIS OR THERAPEUTIC RESPONSE OF PROSTATE CANCER, AND DEVICE FOR IMPLEMENTING SAID METHOD - 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.12-08-2011
20110288785COMPRESSION OF GENOMIC BASE AND ANNOTATION DATA - 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.11-24-2011
20110295519IDENTIFICATION OF RIBOSOMAL DNA SEQUENCES - 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.12-01-2011
20090125247GENE EXPRESSION MARKERS OF RECURRENCE RISK IN CANCER PATIENTS AFTER CHEMOTHERAPY - The present invention relates to genes, the expression levels of which are correlated with likelihood of breast cancer recurrence in patients after tumor resection and chemotherapy.05-14-2009
20090125244BROAD-BASED NEUROTOXIN-RELATED GENE MUTATION ASSOCIATION FROM A GENE TRANSCRIPT TEST - 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.05-14-2009
20090125245Methods For Rapid Forensic Analysis Of Mitochondrial DNA - The present invention provides methods for rapid forensic analysis of mitochondrial DNA by amplification of a segment of mitochondrial DNA containing restriction sites, digesting the mitochondrial DNA segments with restriction enzymes, determining the molecular masses of the restriction fragments and comparing the molecular masses with the molecular masses of theoretical restriction digests of known mitochondrial DNA sequences stored in a database.05-14-2009
20090222216System and Method to Improve Accuracy of a Polymer - The sequencing of individual monomers (e.g., a single nucleotide) of a polymer (e.g., DNA, RNA) is improved by reducing the motion of the polymer due to thermally-driven diffusion to reduce the spatial error in the position of the polymer within a measurement device. A major system parameter, such as average translocation velocity or measurement time, is selected based on the characteristics of the sensing system utilized, and an algorithm jointly optimizes the sequencing order error rate and the monomer identification error rate of the system.09-03-2009
20110172930DISCOVERY OF t-HOMOLOGY IN A SET OF SEQUENCES AND PRODUCTION OF LISTS OF t-HOMOLOGOUS SEQUENCES WITH PREDEFINED PROPERTIES - System(s) and method(s) for analysis and design of genome sequences are provided. A graph representation of a genome sequence facilitates generation of a thermodynamic based quantity, e.g., an entropy-based and enthalpy-based thermodynamic tolerance [τ], which in turn affords estimation of a gene sequence potential function that depends at least upon structural and functional properties of the gene sequence. The gene sequence potential (Φ) is determined, at least in part, via a generalized Schrödinger equation for the thermodynamic tolerance. Gene sequence potential and thermodynamic tolerance [τ], and derived quantities, like thermodynamic tolerance profile and generalized homology, provide an analytic instrument for characterization of natural and synthetic gene sequences, and in conjunction with graph-based algorithms embodies a tool for design of genome sequences with predetermined properties.07-14-2011
20120035860GC Wave Correction for Array-Based Comparative Genomic Hybridization - 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.02-09-2012
20080270041SYSTEM AND METHOD FOR BROAD-BASED MULTIPLE SCLEROSIS ASSOCIATION GENE TRANSCRIPT TEST - Broad-based gene association transcript test for multiple sclerosis and data structure. Multiple sclerosis considerations for this unique test include a custom set of genetic sequences associated in peer-reviewed literature with various known multiple sclerosis related to exposure to toxic substances. Such multiple sclerosis symptoms include specific genetic expressions linked to symptoms of the disease. 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.10-30-2008
20100125421System and method for determining a dosage for a treatment - An system and method for allowing the real-time diagnostics of various genotype-related treatments while allowing for the changing of demographic data such as a person's age, weight, etc. Various embodiments and methods of new processes include the assembly and association of genetic material samples, the preparation of microarrays with representative genetic material samples in a pattern best suited for analysis as well as manipulation, and delivery of assimilated and compiled data in the form of an electronic document for determining a dosage for a treatment.05-20-2010
20090292482Methods and Systems for Generating Cell Lineage Tree of Multiple Cell Samples - A method of generating a cell lineage tree of a plurality of cells of an individual is provided. The method comprising: (a) determining at least one genotypic marker for each cell of the plurality of cells; and (b) computationally clustering data representing the at least one genotypic marker to thereby generate the cell lineage tree of the plurality of cells of the individual.11-26-2009
20110172929SYSTEM AND METHOD FOR PREDICTION OF PHENOTYPICALLY RELEVANT GENES AND PERTURBATION TARGETS - Disclosed herein is a systems biology approach to prediction of phenotypically relevant genes such as oncogenes and perturbation targets. Interactions from a comprehensive cellular network such as the B Cell Interactome (BCI) can be used to identify those that become affected, or dysregulated, by a phenotype (e.g, disease, tumor and cancer) or perturbation (e.g., drug treatment) based on correlation changes between expression profiles of gene pairs in the interactions upon removal or addition of samples showing the phenotype or perturbation. Genes can be ranked based on the affected interactions involving the genes to predict phenotypically relevant genes and/or perturbation targets.07-14-2011
20100292933Methods, systems, and compositions for classification, prognosis, and diagnosis of cancers - 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.11-18-2010
20080281530GENOMIC DATA PROCESSING UTILIZING CORRELATION ANALYSIS OF NUCLEOTIDE LOCI - Processing of genomic data is provided utilizing correlation analysis of first and second nucleotide loci employing a selected comparison type and value. The comparison type is either intersection or proximity type, and the comparison value is either a number (n) of nucleotide positions, wherein n≧1, or a percent number (pn) of nucleotide positions, wherein pn≧0, to be employed in comparing the loci. When intersection type is selected, correlation is defined by the loci overlapping with at least the number (n) of nucleotide positions in common, or by the loci overlapping with at least the percent number (pn) of nucleotide positions in common relative to a smaller one of the first and second loci, or when proximity type is selected, correlation is defined by the first and second loci being within at least the number (n) of nucleotide positions.11-13-2008
20080228410Genetic attribute analysis - A bioinformatics method, software, database and system for genetic attribute analysis are presented in which non-identical sets of genetic attributes comprising nucleotide sequences are compared to determine whether proteins encoded by those nucleotide sequences are functionally equivalent and, therefore, whether genetic information contained in the sets of genetic attributes can be considered equivalent. Sets of genetic attributes are determined to be equivalent based on whether they are able to satisfy one or more predetermined equivalence rules for comparing non-identical protein-encoding nucleotide sequences. A determination of equivalence between sets of genetic attributes can enable the compression of thousands of individual DNA nucleotide attributes into a single categorical attribute, as well as enable determinations of co-association of attributes, predisposition prediction and predisposition modification of individuals.09-18-2008
20080288177PHARACOGENETIC METHOD FOR PREDICTION OF THE EFFICACY OF METHOTREXATE MONOTHERAPY IN RECENT-ONSET ARTHRITIS - 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.11-20-2008
20080288178Sequencing system with memory - The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, pcr, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.11-20-2008
20090150084GENOME IDENTIFICATION SYSTEM - The present invention belongs to the field of genomics and nucleic acid sequencing. It involves a novel method of sequencing biological material and real-time probabilistic matching of short strings of sequencing information to identify all species present in said biological material. It is related to real-time probabilistic matching of sequence information, and more particular to comparing short strings of a plurality of sequences of single molecule nucleic acids, whether amplified or unamplied, whether chemically synthesized or physically interrogated, as fast as the sequence information is generated and in parallel with continuous sequence information generation or collection.06-11-2009
20080208482Display Producing System - A system for producing a display of the DNA identity of an individual comprises means for inputting a plurality of numbers and/or letters obtained through an individual's DNA analysis which are representative of a plurality of DNA loci; means for correlating inputted numbers and/or letters with predetermined colours; and means for producing a display with an array of coloured regions representative of each DNA locus and positioning said coloured regions in the same location of the display for each individual for which a display is produced.08-28-2008
20080275652GENE-BASED ALGORITHMIC CANCER PROGNOSIS - Gene-Based Algorithmic Cancer Prognosis relates to methods and systems for prognosis determination in tumor samples. The methods and systems measure gene expression in a tumor sample and applying a gene-expression grade index (GGI) or a relapse score (RS) to yield a number c risk score.11-06-2008
20090119022Emericella Nidulans Genome Sequence On Computer Readable Medium and Uses Thereof - The present invention relates to nucleic acid sequences from the filamentous fungus, 05-07-2009
20120197540MARKERS TO PREDICT SURVIVAL OF BREAST CANCER PATIENTS AND USES THEREOF - The present invention relates to a method to predict the mortality risk of a subject (p) affected of breast cancer comprising measuring the expression level of 105 specific genes in a biological sample, obtaining the prognostic score, S(p), that indicates the expression levels of said genes in said subject (p) affected of cancer, and predicting the mortality risk of said subject (p) affected of cancer.08-02-2012
20090138209PROGNOSTIC APPARATUS, AND PROGNOSTIC METHOD - A computer-readable storage medium storing a program causing a computer to execute, (a) extracting prediction factors from gene expression data, (b) predicting based on gene expression data of a patient to be prognosticated, whether expression levels of the prediction factors of the patient are similar to the expression levels of a good prognosis group or the expression levels of a poor prognosis group, and (c) extracting prediction factors indicating a poor prognosis from the prediction factors of the patient as poor prognosis determining factors. Poor prognosis determining factors are extracted in which increase and decrease trends of the expression levels coincide with increase and decrease trends of expression levels supposed when abnormal phenomena related to predetermined diseases occur, and the poor prognosis determining factors extracted for the respective abnormal phenomena are outputted.05-28-2009
20110224916Fitness determination for DNA codeword searching - An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two embodiments are implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes. Experimental results demonstrate that the GA embodiment can find ˜99% of the words in locally optimum libraries, and that the hybrid architecture embodiment provides more than 1000 times speed-up compared to a software only implementation.09-15-2011
20090006002COMPARATIVE SEQUENCE ANALYSIS PROCESSES AND SYSTEMS - Provided herein are processes for rapidly identifying or determining sequence information in a sample nucleic acid by comparing sample nucleic acid sequence information to reference nucleic acid sequence information or information obtained from reference samples. Also provided are automated systems for conducting comparative sequence analyses.01-01-2009
20090326832GRAPHICAL MODELS FOR THE ANALYSIS OF GENOME-WIDE ASSOCIATIONS - Systems and methods are provided for the identification of genotype-phenotype associations in genome-wide association (GWA) studies. In an illustrative implementation, a data correlation environment comprises a population structure engine and at least one instruction set to instruct the population structure engine to process pedigree or population genetic data to generate a population structure sub-model according to a selected graphical model-based data correlation paradigm. Illustratively, the parameter of the resulting generalized linear mixed model can be learned using a variational approximation.12-31-2009
20090012719SYSTEM AND METHOD FOR IDENTIFICATION OF SYNERGISTIC INTERACTIONS FROM CONTINUOUS DATA - 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.01-08-2009
20090024333Methods and systems relating to mitochondrial DNA phenotypes - In one aspect, a system includes, but is not limited to, at least one computer program for use with at least one computer system and wherein the computer program includes a plurality of instructions, including but not limited to, one or more instructions for determining at least one correlation between at least one mitochondrial DNA-influencing event and at least one aspect of mitochondrial DNA phenotype information regarding at least one individual.01-22-2009
20090082975METHOD OF SELECTING AN ACTIVE OLIGONUCLEOTIDE PREDICTIVE MODEL - The present invention provides a method of identifying a predictor of antisense oligonucleotide activity by identifying properties of oligonucleotides, evaluating oligonucleotide activity of the oligonucleotides, and correlating oligonucleotide activity with the properties. A high correlation between oligonucleotide activity and a property indicates that the property is a predictor of oligonucleotide activity.03-26-2009
20090099789Methods and Systems for Genomic Analysis Using Ancestral Data - The present disclosure provides methods and systems for assessing an individual's genotype correlations to a phenotype by analyzing the individual's genomic profile and using ancestral data to determine the correlations between genotypes and phenotypes.04-16-2009
20080262747NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected.10-23-2008
20090012720System and Method for Identification of MicroRNA Target Sites and Corresponding Targeting MicroRNA Sequences - A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.01-08-2009
20090037118METHODS FOR PREDICTING THREE-DIMENSIONAL STRUCTURES FOR ALPHA HELICAL MEMBRANE PROTEINS AND THEIR USE IN DESIGN OF SELECTIVE LIGANDS - A method for practical prediction of the three-dimensional structure of α-helical membrane proteins (HMPs) is described. The method allows one to predict the binding site and structure for strongly bound ligands. The method combines a protocol of computational methods enabling a complete ensemble of packings to be sampled and systematically reducing this ensemble to progressively more accurate structures until at the end there remain a few that might be functionally relevant and likely to play a role in all binding and activation processes. This method is well suited to automatic operation making it practical to obtain, for example, the ensemble of important structures for all human GPCRs. With this ensemble of all active GPCR structures in the human body, an infimum method is presented to maximize efficacy toward the selected target while minimizing binding to all other GPCRs to eliminate toxicity arising from cross-reacting with other GPCRs (a most common source of drug failure). This infimum method is broadly applicable to any set of proteins where a ligand is desired to be able to modulate the function of one protein while not affecting the function of other proteins.02-05-2009
20120173159METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR NUCLEIC ACID SEQUENCING - A method for nucleic acid sequencing includes receiving a plurality of signals indicative of a parameter measured for a plurality of defined spaces, at least some of the defined spaces including one or more sample nucleic acids, the signals being responsive to a plurality of nucleotide flows introducing nucleotides to the defined spaces; determining, for at least some of the defined spaces, whether the defined space includes a sample nucleic acid; processing, for at least some of the defined spaces determined to include a sample nucleic acid, the received signals to improve a quality of the received signals; and predicting a plurality of nucleotide sequences corresponding to respective sample nucleic acids for the defined spaces based on the processed signals and the nucleotide flows.07-05-2012
20090076734Gene Signature for the Prediction of Radiation Therapy Response - Described are mathematical models and method, e.g., computer-implemented methods, for predicting tumor sensitivity to radiation therapy, which can be used, e.g., for selecting a treatment for a subject who has a tumor.03-19-2009
20090105961METHODS OF NUCLEIC ACID IDENTIFICATION IN LARGE-SCALE SEQUENCING - The present invention provides methods for determining a base probability in a target nucleic acid within an experimental data set. The methods of the invention provide specific methods of improving accuracy of base calling for experimental sequencing data compared to conventional methods. The experimental base values used in the methods of the present invention provide relative base probabilities within an experimental data set that are robust and uniformly optimal regardless of the experimental conditions.04-23-2009
20090105962METHODS AND SYSTEMS FOR IDENTIFYING MOLECULAR PATHWAY ELEMENTS - The present invention provides methods and systems useful in determining molecular pathways and elements of molecular pathways. In particular, the present invention provides for the discovery of new molecular pathway elements using Bayesian networks and gene expression information.04-23-2009
20090037117Differential Dissociation and Melting Curve Peak Detection - Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.02-05-2009
20110246084METHODS AND SYSTEMS FOR ANALYSIS OF SEQUENCING DATA - The present technology relates to the methods and systems for analysis of sequencing data. In particular, methods and systems for characterizing a target nucleic acid while determining the nucleotide sequence of the target nucleic acid are described. Certain embodiments include methods and systems for identifying the source of a target nucleic acid by comparing the accumulating nucleotide sequence of a target nucleic acid to a population of reference nucleotide sequences.10-06-2011
20110246083Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.10-06-2011
20110246081Metabolomics-Based Identification of Disease-Causing Agents - A method, computer-readable medium, and system for identifying one or more metabolites associated with a disease, comprising: comparing gene expression data from diseased cells to gene expression data from control cells in order to deduce genes that are differentially-regulated in the diseased cells relative to the control cells; based on enzyme function and pathway data for all human metabolites that utilize the genes that are differentially-regulated in the disease cells, identifying one or more metabolites whose intracellular levels are higher or lower in diseased cells than in control cells, and thereby associating the one or more metabolites with the disease.10-06-2011
20110246082METHOD FOR SPECTRAL DNA ANALYSIS - The present invention relates a method for analyzing a DNA sequence. The DNA sequence by converting the DNA sequence into a plurality of binary indicator sequences (BIS), and applying short term Fourier transform (STFT) on the binary indicator sequences. A binning function (BF) is applied to the Fourier coefficients (Usk_X(k)) and thereby modifying the corresponding Fourier coefficients (Usk_X(k)). Finally, substantially equal modified Fourier coefficients (Usk_X(k)) is found. The invention provides the user with a much improved ability to see unique strong patterns in vast amount of DNA sequence data.10-06-2011
20110246085System, method, and computer software for the presentation and storage of analysis results - 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.10-06-2011
20100057373Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs - 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. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.03-04-2010
20110071767Hepatotoxicity Molecular Models - The present invention includes methods of predicting hepatotoxicity of test agents and methods of generating hepatotoxicity prediction models using algorithms for analyzing quantitative gene expression information. The invention also includes microarrays, computer systems comprising the toxicity prediction models, as well as methods of using the computer systems by remote users for determining the toxicity of test agents.03-24-2011
20120303287METHODS AND SYSTEMS FOR CONSERVATIVE EXTRACTION OF OVER-REPRESENTED EXTENSIBLE MOTIFS - Methods and systems of extracting extensible motifs from a sequence include assigning a significance to extensible motifs within the sequence based upon a syntactic and statistical analysis, and identifying extensible motifs having a significance that exceeds a predetermined threshold.11-29-2012
20120303286SYSTEM FOR ANIMAL HEALTH DIAGNOSIS - A diagnosis of the health of an animal is obtained through a combination of computerized data and human interpretation. Data relates to the physical characteristics of the animal, and includes data obtained from a physical inspection of the animal. A blood or other fluid sample is used to obtain a computer generated laboratory analysis. This is reported through an internet network to the clinical pathologist. The clinical pathologist has the data relating to the physical characteristics, and thereby makes a diagnosis of the animal health. A drop-down menu on a computer screen provides supplemental reports to support the diagnosis. This can be enhanced by further input from the pathologist through keyboard entry into the computer to obtain an integrated computer report having the laboratory analysis, supplemental report, and selectively an enhanced report. The integrated report is electronically communicated to a client.11-29-2012
20110257896Differential Filtering of Genetic Data - Computer software products, methods, and systems are described which provide functionality to a user conducting experiments designed to detect and/or identify genetic sequences and other characteristics of a genetic sample, such as, for instance, gene copy number and aberrations thereof. The presently described software allows the user to interact with a graphical user interface which depicts the genetic information obtained from the experiment. The presently disclosed methods and software are related to bioinformatics and biological data analysis. Specifically, provided are methods, computer software products and systems for analyzing and visually depicting genotyping data on a screen or other visual projection. The presently disclosed methods and software allow the user conducting the experiment to differentially filter complex genetic data and information by varying genetic parameters and removing or highlighting visually various regions of genetic data of interest (CytoRegions). These differential filters may be applied by the user to the entire set of genetic data and/or only to the specific CytoRegions of interest.10-20-2011
20080243397SOFTWARE FOR DESIGN AND VERIFICATION OF SYNTHETIC GENETIC CONSTRUCTS - The present invention provides methods for designing and verifying nucleic acid molecules having one or more desired properties. The methods are typically encoded into software, and typically include use of databases and algorithms to determine if nucleic acid molecules designed to have various elements in functional relationships have the intended properties. The result is achieved by determining if the various elements of the designed nucleic acid are in the correct order and physical relationship to other elements, and that the proper elements are selected. Computer systems for implementing the method, as well as business methods for reaping monetary gain from use of the methods, are also disclosed.10-02-2008
20100262379Sequencing System With Memory - The present teachings provide a device including a memory. According to various embodiments, the memory is readable, writable, and rewritable. The present teachings further provide processing stations, e.g., for carrying out electrophoresis, per, genetic analysis, sample preparation, and/or sample cleanup, etc., that are capable of reading from and/or writing/rewriting to such memory.10-14-2010
20110213563SYSTEM AND METHOD TO CORRECT OUT OF PHASE ERRORS IN DNA SEQUENCING DATA BY USE OF A RECURSIVE ALGORITHM - An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values09-01-2011
20130158885GENOME SEQUENCE MAPPING DEVICE AND GENOME SEQUENCE MAPPING METHOD THEREOF - Provided are a genome sequence mapping device and a genome sequence mapping method. The genome sequence mapping device may include a controller and a genome sequence analyzer configured to map target sequence data to reference sequence data. The genome sequence analyzer transforms the reference sequence data and the target sequence data into frequency domains to determine a position of the target sequence data to be mapped among the reference sequence data. The genome sequence mapping device calculates a correlation between reference sequence data and target sequence data in a frequency domain to immediately determine whether the reference sequence data and the target sequence data match each other.06-20-2013
20080255768METHODS OF DETERMINING RELATIVE GENETIC LIKELIHOODS OF AN INDIVIDUAL MATCHING A POPULATION - Provided are methods of determining an individual's relative likelihood of having a genetic match with one or more local populations as compared to a generic index population. Also provided are systems, apparatuses, kits, and machine-readable medium relating to such methods. The methods may be used for example, to identify an individual's or individual's ancestor's most likely geographic origin, or to identify the breed, species, kingdom, etc. of an organism.10-16-2008
20080255767Method and Device For Detection of Splice Form and Alternative Splice Forms in Dna or Rna Sequences - The invention relates to a method and a device for detection of splice sites in DNA or RNA sequences comprising three steps: a) examining a training set of sequences comprising DNA or RNA sequences with known splice sites by an automated, discriminative training device for detecting splicing patterns, especially in a predetermined window around the known splice sites; b) scanning a sequence comprising DNA or RNA sequences containing unknown splice sites for the occurrence of the splicing patterns detected in step a); and c) calculation of a cumulative splice score in dependence of a maximization of the margin between the true splice forms and all wrong splice forms in the sequence. The invention also relates to a method and a device for detection of splice forms and alternative splice forms in DNA or RNA sequences.10-16-2008
20090048785Methods And Systems For Analyzing Biological Samples - Methods, computer readable storage media and systems which can be used for analyzing labeled biological samples, identifying chromosomal aberrations, identifying genetically abnormal cells and/or computationally scanning the samples using randomly or randomized scanning methods are provided. Specifically, the present invention can be used to analyze FISH-stained samples and automatically identify chromosomal aberrations associated with abnormal intensity ratio of stained occurrences in the sample.02-19-2009
20120310544SYSTEMS AND METHODS FOR IDENTIFYING STRUCTURALLY OR FUNCTIONALLY SIGNIFICANT AMINO ACID SEQUENCES - Methods and computer readable storage mediums for identifying structurally or functionally significant amino acid sequences encoded by a genome are disclosed. At least one structurally or functionally significant amino acid sequence encoded by a genome may be identified by compiling an observed frequency for each of a plurality of amino acid words encoded by the genome, calculating with a computer an expected frequency for each of the plurality of amino acid words encoded by the genome, and identifying at least one structurally or functionally significant amino acid sequence encoded by the genome based at least in part on the observed and expected frequencies for each of the plurality of amino acid words encoded by the genome.12-06-2012
20120310543System and Method to Improve Sequencing Accuracy of a Polymer - The sequencing of individual monomers (e.g., a single nucleotide) of a polymer (e.g., DNA, RNA) is improved by reducing the motion of the polymer due to thermally-driven diffusion to reduce the spatial error in the position of the polymer within a measurement device. A major system parameter, such as average translocation velocity or measurement time, is selected based on the characteristics of the sensing system utilized, and an algorithm jointly optimizes the sequencing order error rate and the monomer identification error rate of the system.12-06-2012
20090299650SYSTEMS AND METHODS FOR FILTERING TARGET PROBE SETS - Systems and methods for using the same to filter target probes sets are provided. In certain embodiments, the system and methods are implemented on a web-based platform. Also provided are computer program products for executing the subject methods.12-03-2009
20110264379INVESTIGATIONS - 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.10-27-2011
20090024334Database for analyzing gene function and method of analyzing gene function by DSPA - A method of constructing a gene function database comprising measuring the cell viabilities, against a plural number of drugs at various concentrations, of transformed eukaryotic cells overexpressing a plural number of function-known genes and parental cell line thereof, calculating the ratios of IC01-22-2009
20080281531Method for Diagnosing Depression - This invention relates to a method for diagnosing whether or not a subject suffers from depression in a simple manner with high accuracy using the peripheral whole blood sample of the subject. Specifically, the present invention relates to a method for diagnosing depression comprising the steps of: measuring expression levels of 18 genes selected from the group consisting of FASLG; CX3CR1, TBX21, ID2, SLAMF7, PRSS23, YWHAQ, TARDBP, ADRB2, PPP1R8, MMAA, SQLE, PDHA1, HAVCR2, RACGAP1, AHNAK, EDG8, and DUSP5, in peripheral blood isolated from a subject; and determining whether or not the subject suffers from depression based on the expression levels of the 18 genes.11-13-2008
20120078530METHOD FOR DETERMINING RECEPTOR-LIGAND PAIRS - The present invention provides a method of determining related proteins, the method comprising obtaining sequences of interest, wherein the sequences are amino acid sequences for proteins or nucleotide sequences encoding proteins; comparing segments of each sequence of interest with a database of amino acid or nucleotide sequences; generating a profile for each sequence of interest comprising a list of all sequences from the database of sequences that have segments corresponding to the segments of each sequence of interest; and comparing the database sequences appearing in the profile of each sequence of interest to the database sequences appearing in the profile of every other sequence of interest, wherein similar profiles indicate that the sequences of interest correspond to related proteins while dissimilar profiles indicate that the sequences of interest do not correspond to related proteins, wherein profiles are similar if there is at least a 30% overlap between the database sequences appearing in the profiles of the sequences of interest.03-29-2012
20120041686DIAGNOSTIC FOR LUNG DISORDERS USING CLASS PREDICTION - 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.02-16-2012
20120046877SYSTEMS AND METHODS TO DETECT COPY NUMBER VARIATION - 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.02-23-2012
20080215251Computational method for choosing nucleotide sequences to specifically silence genes - A method for identifying subsequences in a polynucleotide sequence for specifically silencing a target gene is provided. The method is described for identifying sequences effective in silencing a target gene or a series of genes, but not others. Subsequences can be identified and scored using comparisons based on percent sequence identity with respect to a target reference sequence and siRNA algorithm analysis. The resulting subsequences may be ranked based on score, percent sequence identity. The identification of subsequences may be performed using a sliding window to identify all subsequences of a set length within the sequence. A user interface may be provided for displaying the results to a user.09-04-2008
20110106454METHOD AND SYSTEM FOR COMPARATIVE GENOMICS - A method and system for representing a similarity between at least two genomes that includes detecting gene clusters which are common to the at least two genomes and representing the common gene clusters in a PQ tree. The PQ tree includes a first internal node (P node), that allows permutation of the children thereof, and a second internal node (Q node), that maintains unidirectional order of the children thereof.05-05-2011
20120123695METHODS FOR ASSESSING RESPONSIVENESS OF B-CELL LYMPHOMA TO TREATMENT WITH ANTI-CD40 ANTIBODIES - The invention provides methods and kits useful for predicting or assessing responsiveness of a patient having B-cell lymphoma to treatment with anti-CD40 antibodies.05-17-2012
20120215463Rapid Genomic Sequence Homology Assessment Scheme Based on Combinatorial-Analytic Concepts - The present invention relates to methods and apparatus for rapid assessment of genomic sequences using the difference set model. The invention provides methods to determine the presence and identity of similarities and differences in genomic sequences. In particular, the invention provides methods and apparatus to assess homology, the presence and identity of insertion and deletion segments and the presence and identity of single nucleotide polymorphisms in genomic sequences.08-23-2012
20120173158TIME-WARPED BACKGROUND SIGNAL FOR SEQUENCING-BY-SYNTHESIS OPERATIONS - Methods for analyzing signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the method comprises formulating a function that models the output signal of a representative empty well of a reactor array. A time transformation is applied to the empty well function to obtain a time-warped empty well function. The time-warped empty well function is fitted to an output signal from the loaded well representative of a flow that results in a non-incorporation event in the loaded well. The fitted time-warped empty well function can then be used to analyze output signals from the loaded well for other flows.07-05-2012
20120173157METHOD AND APPARATUS FOR RECOVERING GENE SEQUENCE USING PROBE MAP - A method of recovering a nucleic acid sequence using a probe map includes: aligning a probe onto a target sequence based on a result in which the probe is hybridized to the target sequence; determining a representative value representing each aligned position of the probe; and recovering a base sequence of the target sequence by using a probe map to which the determined representative values and base sequence information of the probe are mapped.07-05-2012
20120221255System, Method, and Computer Software Product for Genotype Determination Using Probe Array Data - An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.08-30-2012
20130173177NUCLEIC ACID SEQUENCE ANALYSIS - This document provides materials and methods involved in nucleic acid sequence analysis. For example, methods and materials for distinguishing sequencing errors (e.g., sequencing and/or PCR artifacts) from true polymorphic sequence variations (e.g., single-nucleotide polymorphisms, sequence insertions, sequence deletions, or combinations thereof) are provided. In addition, methods and materials for determining homozygosity or heterozygosity are provided.07-04-2013
20100049449Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs - 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. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.02-25-2010
20100010749SEQUENCING - The invention relates to improvements in sequencing of polymers. In particular, the invention relates to a method of sequencing a polymer, the method comprising providing a plurality of data sets, each set comprising data representing the concentration of synthesised polymers from a plurality of chain termination reactions, wherein the data sets include termination artefacts; aligning two or more of the data sets based on at least one termination artefact present in said two or more data sets; and determining the polymer sequence based on the aligned data.01-14-2010
20100268478Sequencing Nucleic Acid Polymers with Electron Microscopy - This invention relates to using an electron microscope to sequence by direct inspection of labeled, stretched DNA. This method will have higher accuracy, lower cost, and longer read length than current DNA sequencing methods.10-21-2010
20120253689AB INITIO GENERATION OF SINGLE COPY GENOMIC PROBES - Single copy sequences suitable for use as DNA probes can be defined by computational analysis of genomic sequences. The present invention provides an ab initio method for identification of single copy sequences for use as probes which obviates the need to compare genomic sequences with existing catalogs of repetitive sequences. By dividing a target reference sequence into a series of shorter contiguous sequence windows and comparing these sequences with the reference genome sequence, one can identify single copy sequences in a genome. Probes can then be designed and produced from these single copy intervals.10-04-2012
20080288179NORMALIZATION OF DATA - Methods for normalizing output from an instrument employing a reference standard or non-fluorescing substance disposed within at least one of a plurality of reaction chambers. The method comprises collecting and analyzing a signal associated with the reference standard or non-fluorescing substance to determine a normalizing bias. The normalizing bias is then applied to the data signal collected from a remainder of the plurality of reaction chambers.11-20-2008
20120330567METHODS AND SYSTEMS FOR DATA ANALYSIS - The present disclosure provides computer implemented methods and systems for analyzing datasets, such as large data sets output from nucleic acid sequenceing technologies. In particular, the present disclosure provides for data analysis comprising computing the BWT of a collection of strings in an incremental, character by character, manner. The present disclosure also provides compression boosting strategies resulting in a BWT of a reordered collection of data that is more compressible by second stage compression methods compared to non-reordered computational analysis.12-27-2012
20120330566SEQUENCE ASSEMBLY AND CONSENSUS SEQUENCE DETERMINATION - Computer implemented methods, and systems performing such methods for processing signal data from analytical operations and systems, and particularly in processing signal data from sequence-by-incorporation processes to identify nucleotide sequences of template nucleic acids and larger nucleic acid molecules, e.g., genomes or fragments thereof. In particularly preferred embodiments, nucleic acid sequences generated by such methods are subjected to de novo assembly and/or consensus sequence determination.12-27-2012
20080319679SYSTEMS AND METHODS FOR ANALYZING MICROARRAYS - The present invention discloses methods and systems for analyzing microarray data. The method includes the general steps of providing microarray data, normalizing the data using a least trimmed squares regression, and then analyzing the normalized microarray data to obtain a desired result such as an expression profile. There is also disclosed a method of subdividing an array into subarrays before normalization. This approach provides a method for improving measurement accuracy and salvaging array data from arrays containing minor defects. Also disclosed is a Probe-Treatment-Reference (PTR) model for streamlining normalization and summarization of microarray data by allowing multiple references. Other aspects of the present invention include computer systems and computer readable media encoding methods of the present invention.12-25-2008
20120323498MIRFILTER: EFFICIENT NOISE REDUCTION METHOD TO IDENTIFY MIRNA AND TARGET GENE NETWORKS FROM GENOME-WIDE EXPRESSION DATA - A computer implemented method of identifying potential micoRNA targets and biomarkers comprises receiving data identifying a first set of mRNA sequences into computer accessible memory. Each mRNA sequence in the first set has a region that is upstream of a translation start site, a region that is downstream of a translation stop site, and an open reading frame. The method further comprises receiving data identifying a second set of microRNA (miRNA) sequences into the computer accessible memory. Each microRNA sequence has a 5′ miRNA section and a 3′ miRNA section. Each mRNA sequence is characterized by an expression pattern in the first set as being up-regulated, down-regulated, or uncharged as compared to a control sample and each miRNA sequence in the second set as being up-regulated, down-regulated, or uncharged as compared to the control sample. It is then determined which mRNA sequences from the first set are susceptible to being regulated by microRNA from the second set. A set of consistent relationships is identified between the miRNA and the mRNA determined from the mRNAs that have been characterized.12-20-2012
20110276277SIZE-BASED GENOMIC ANALYSIS - 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.11-10-2011
20120101738Compositions and methods for biological remodeling with frozen particle compositions - Certain embodiments disclosed herein relate to compositions, methods, devices, systems, and products regarding frozen particles. In certain embodiments, the frozen particles include materials at low temperatures. In certain embodiments, the frozen particles provide vehicles for delivery of particular agents. In certain embodiments, the frozen particles are administered to at least one biological tissue.04-26-2012
20100094563System and Method for Consensus-Calling with Per-Base Quality Values for Sample Assemblies - The present teachings disclose a method for evaluation of a polynucleotide sequence using a consensus-based analysis approach. The sequence analysis method utilizes quality values for a plurality of aligned sequence fragments to identify consensus basecalls and calculate associated consensus quality values. The disclosed method is applicable to resolution of single nucleotide polymorphisms, mixed-based sequences, heterozygous allelic variants, and heterogeneous polynucleotide samples.04-15-2010
20100169026Algorithms for sequence determination - The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.07-01-2010
20130013220METHOD AND APPARATUS FOR ANALYZING DNA - The distribution and/or ratio of Thymine, Cytosine, Adenine and Guanine of a DNA sequence from a target organism are organized and analyzed. The result is then used to determine the possible impacts the target organism may have in a host such as a human body. The corresponding treatment and prevention strategies may also be determined. The goal is to provide an effective way to diagnose, treat and prevent diseases such as infectious diseases, to test the safety of food and drugs, and therefore to create natural and effective solutions for health care and food supply. For example, a DNA analysis method configured according to the invention receives a DNA sequence input and converts it into a reassembled sequence. A result based on the reassembled sequence may then be output. Determination of the analysis result, treatment and prevention strategies may also be output.01-10-2013
20090125246Method and Apparatus for the Determination of Genetic Associations - Procedure and tool to determine genetic associations. The method allows to identify, without the need for predictive hypothesis, genes that influence, either individually or preferably collectively, the appearance of any phenotypic trait shared by several groups of individuals; groups in each of which the characteristic appears in a different context as they can be different diseases, a different reaction to the same treatment or different manifestations of the same disease. For each phenotypic context, a study is carried out of cases and controls, giving rise to associations of genes or combinations of genes with statistical significance. These associations are filtered, eliminating those that also appear when comparing controls versus controls. Of the remaining associations, those that have appeared in all the cases and controls are selected, preferably rationalized, and are validated by analysing their presence in larger groups.05-14-2009
20080243398System and method for cleaning noisy genetic data and determining chromosome copy number - Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Genetic material from the target individual is acquired, amplified and the genetic data is measured using known methods. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment of the invention, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment of the invention, the chromosome copy number can be determined from the measured genetic data of a single or small number of cells, with or without genetic information from one or both parents. In another embodiment of the invention, these determinations are made for the purpose of embryo selection in the context of in-vitro fertilization. In another embodiment of the invention, the genetic data can be reconstructed for the purposes of making phenotypic predictions.10-02-2008
20080243396Systems and methods for sub-genomic region specific comparative genome hybridization probe selection - Systems and methods for using the same to select one or more comparative genome hybridization (CGH) probes specific for a sub-genomic region of interest are provided. Also provided are computer program products for executing the subject methods.10-02-2008
20130144540CONSTRAINED DE NOVO SEQUENCING OF PEPTIDES - A peptide sequencing system derives a peptide sequence from a mass spectrum. The system can receive a description for a peptide sequence constraint, such that the constraint indicates a symbol pattern that is to be present in a peptide sequence derived from the mass spectrum. Then, the system generates a peptide sequence based on the mass spectrum and the constraint, such that the peptide sequence matches the constraint and has a mass that matches the total mass of the peptide as determined from the mass spectrum.06-06-2013
20090076735Method, system and software arrangement for comparative analysis and phylogeny with whole-genome optical maps - The present invention provides a method for organizing genomic information from multiple organisms. In one embodiment of the invention, phylogenetic trees can be constructed for the organisms. The method of the present invention is termed CAPO, Comparative Analysis and Phylogeny with Optical-Maps. Optical maps of organisms are obtained and phylogeny between the organisms is determined by optical map comparison and bipartite graph matching between the organisms, as, for example, computed by a stable marriage algorithm.03-19-2009
20080215252Method of Determining Base Sequence of Nucleic Acid and Apparatus Therefor - In a preferred embodiment, an exploring needle of a probe 09-04-2008
20080215250Molecular toxicology modeling - The present invention is based on the elucidation of the global changes in gene expression and the identification of toxicity markers in tissues or cells exposed to a known toxin. The genes may be used as toxicity markers in drug screening and toxicity assays. The invention includes a database of genes characterized by toxin-induced differential expression that is designed for use with microarrays and other solid-phase probes.09-04-2008
20110270533SYSTEMS AND METHODS FOR ANALYZING NUCLEIC ACID SEQUENCES - 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.11-03-2011
20110270532Systems And Methods For Identifying Exon Junctions From Single Reads - 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.11-03-2011
20130090861INTERNAL SIZING/LANE STANDARD SIGNAL VERIFICATION - A method for verifying an ILS signal for DNA processing includes obtaining the ILS signal, determining acquisition times between peaks of the ILS signal, obtaining acquisition times between peaks in reference ILS information for the ILS signal, and verifying the ILS signal based on the ILS acquisition times and the reference ILS acquisitions times. An ILS signal processor (04-11-2013
20130090860METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING - A method for nucleic acid sequencing includes: receiving a signal comprising measurements of a parameter measured in response to a plurality of nucleotide flows flowed in a space comprising a sample nucleic acid; normalizing the signal to obtain a normalized signal; adaptively normalizing the normalized signal to obtain an adaptively normalized signal; and predicting a sequence of base calls corresponding to the sample nucleic acid using the adaptively normalized signal.04-11-2013
20130096845CUMULATIVE DIFFERENTIAL CHEMICAL ASSAY IDENTIFICATION - An apparatus comprising: a value receiver, configured to receive fluorescence values measured during a chemical reaction involving a test sample, each value pertaining to a respective physical parameter value, a difference calculator, configured to calculate differences, each difference being between respective one of the measured fluorescence values and one of reference fluorescence values of a reference sample, each reference fluorescence value pertaining to a respective physical parameter value, a cumulative index calculator, configured to calculate a cumulative index, by selecting a first difference among the calculated differences, and selecting and adding to the first difference differences, each one of the added differences being selected according to a proximity standard applied on each two differences selected in a sequence, the proximity standard being based on proximity of physical parameter values and difference size, and a similarity determiner, configured to determine similarity between the samples, using the calculated cumulative index.04-18-2013
20130103322Method and System for Analyzing Mass Spectrometry Data - Provided is a technique for accurately identifying a peptide even if the peptide cannot be identified by MS/MS ion search or de novo sequencing. The technique uses an MS04-25-2013
20130124100Processing and Analysis of Complex Nucleic Acid Sequence Data - The present invention is directed to logic for analysis of nucleic acid sequence data that employs algorithms that lead to a substantial improvement in sequence accuracy and that can be used to phase sequence variations, e.g., in connection with the use of the long fragment read (LFR) process.05-16-2013
20130131995System And Method to Correct Out of Phase Errors In DNA Sequencing Data by Use of a Recursive Algorithm - An embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of template molecules is described that comprises the steps of detecting signals generated in response to nucleotide species introduced during a sequencing reaction; generating an observed value for the signal detected from each of the nucleotide species; defining positive incorporation values and negative incorporation values from the observed values using a carry forward value and an incomplete extension value; revising the carry forward value and the incomplete extension value using a noise value that is derived from observed values associated with the negative incorporation values; re-defining the positive incorporation values and the negative incorporation values using the revised carry forward value and the revised incomplete extension value; and repeating the steps of revising and re-defining until convergence of the positive incorporation values and the negative incorporation values05-23-2013
20130144541MASS SPECTROMETRY-CLEAVABLE CROSS-LINKING AGENTS TO FACILITATE STRUCTURAL ANALYSIS OF PROTEINS AND PROTEIN COMPLEXES, AND METHOD OF USING SAME - Novel cross-linking compounds that can be used in mass spectrometry, tandem mass spectrometry, and multi-stage tandem mass spectrometry to facilitate structural analysis of proteins and protein complexes are provided and have the formula:06-06-2013
20110251798Methods for high throughput genotyping - Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.10-13-2011
20120259556SYSTEM AND METHODS FOR INDEL IDENTIFICATION USING SHORT READ SEQUENCING - 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.10-11-2012
20120283958GENERALIZED NETWORK THREADING APPROACH FOR PREDICTING A SUBJECT'S RESPONSE TO HEPATITIS C VIRUS THERAPY - Methods for predicting a response of a virus to an antiviral therapy are provided.11-08-2012
20130158884METHOD FOR IDENTIFYING NUCLEOTIDE SEQUENCE, METHOD FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE, APPARATUS FOR IDENTIFYING NUCLEOTIDE SEQUENCE, APPARATUS FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE, PROGRAM FOR IDENTIFYING NUCLEOTIDE SEQUENCE, AND PROGRAM FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE - The object of the present invention is to provide a method for identifying a nucleotide sequence necessary for expressing affinity for a target substance with respect to a nucleotide sequence of a nucleic acid molecule such as an aptamer having such affinity for the target substance, based on similarity between nucleotide sequences and an evaluated value of the affinity of the nucleotide sequence, and a method for predicting a secondary structure of the nucleic acid molecule including the identified nucleotide sequence. The method of present invention includes the steps of extracting a single-stranded region by excluding based capable of forming a stem structure from the nucleotide sequence of the nucleic acid molecule; and searching a motif sequence from the single-stranded region, based on an evaluated value of the affinity.06-20-2013
20120010823System for the quantification of system-wide dynamics in complex networks - 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 C01-12-2012
20120046878METHODS FOR ANALYZING HIGH DIMENSIONAL DATA FOR CLASSIFYING, DIAGNOSING, PROGNOSTICATING, AND/OR PREDICTING DISEASES AND OTHER BIOLOGICAL STATES - 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.02-23-2012
20130204537Amino Acid Sequence Analyzing Method and Amino Acid Sequence Analyzing Apparatus - The amino acid sequence is deduced by using de novo sequencing, to prevent the correct amino acid sequence from not being ranked high as candidates. Amino acid sequence candidates are computed by finding the longest path by a branch and using a bound method based on the spectrum data on the target peptide and the known amino acid sequence. A tree-structured directed graph is used where amino acid sequences are set as nodes and the peak intensities corresponding to the amino acids are set as branches. In a sequence put at a node in the highest layer, an amino acid is placed at a terminal, and as the layer goes deeper, amino acids are sequentially placed from both terminals toward the center of the sequence. The final score is estimated based on the remaining amino acids, and if the score is small, the search is halted.08-08-2013
20120072124GENES ASSOCIATED WITH PROGRESSION AND RESPONSE IN CHRONIC MYELOID LEUKEMIA AND USES THEREOF - The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.03-22-2012
20120095697METHODS FOR ESTIMATING GENOME-WIDE COPY NUMBER VARIATIONS - Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.04-19-2012
20120095696METHODS AND APPARATUS FOR GENETIC EVALUATION - Rapid and definitive bioagent detection and identification can be carried out without nucleic acid sequencing. Analysis of a variety of bioagents and samples, such as air, fluid, and body samples, can be carried out to provide information useful for industrial, medical, and environmental purposes. Nucleic acid samples of unknown or suspected bioagents may be collected, optimal primer pairs may be selected, and the nucleic acid may be amplified. Expected mass spectra signal models may be generated and selected, the actual mass spectra of the amplicons may be obtained. The expected mass spectra most closely correlating with the actual mass spectra may be determined using a joint maximum likelihood analysis, and base counts for the actual mass spectra and the expected mass spectra may be obtained. The most likely candidate bioagents may then be determined.04-19-2012

Patent applications in class Gene sequence determination