Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: Provided in certain embodiments are methods for pairing patient cells and donor cells to prepare cytotoxic T cells. Such cytotoxic T cells could be administered to the patient for treating certain disorders, such as a cancer (for example, brain cancer).

Abstract: Systems, methods, and apparatus for determining at least a portion of fetal genome are provided. DNA fragments from a maternal sample (maternal and fetal DNA) can be analyzed to identify alleles at certain loci. The amounts of DNA fragments of the respective alleles at these loci can be analyzed together to determine relative amounts of the haplotypes for these loci and determine which haplotypes have been inherited from the parental genomes. Loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes common in the population can be used along with the analysis of the DNA fragments of the maternal sample to determine the maternal and paternal genomes. Determination of mutations, a fractional fetal DNA concentration in a maternal sample, and a proportion of coverage of a sequencing of the maternal sample can also be provided.

Abstract: Determining relative relationship includes receiving recombinable deoxyribonucleic acid (DNA) information of a first user and recombinable DNA information of a second user, determining, based at least in part on the recombinable DNA information of the first user and recombinable DNA information of the second user, a predicted degree of relationship between the first user and the second user, and in the event that the expected degree of relationship between the first user and the second user at least meets the threshold, notifying at least the first user about a relative relationship with the second user.

Abstract: The present invention provides methods, systems, and code for accurately classifying whether a sample from an individual is associated with irritable bowel syndrome (IBS). In particular, the present invention is useful for classifying a sample from an individual as an IBS sample using a statistical algorithm and/or empirical data. The present invention is also useful for ruling out one or more diseases or disorders that present with IBS-like symptoms and ruling in IBS using a combination of statistical algorithms and/or empirical data. Thus, the present invention provides an accurate diagnostic prediction of IBS and prognostic information useful for guiding treatment decisions.

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

Abstract: Compositions and methods are provided for the rapid and highly accurate identification of the entire essential genome of any organism under a given selection condition at a resolution of a few base pairs. An engineered transposon bearing an adapter sequence for ultra high throughput adaptor-based sequencing is employed for hyper-saturated transposon mutagenesis. Transposon junctions are subsequently isolated and collectively amplified through a shared parallel PCR strategy such that a second adaptor sequence is further incorporated into template DNA so that the first adaptor sequence and the second adaptor sequence flank the 5? and 3? regions of the sample DNA, respectively. Sample DNA is then sequenced in an ultra high-throughput adaptor-based DNA sequencer using adaptor primers. Transposon insertion sites are mapped onto the organism's genome, allowing for the algorithmic identification of essential genetic elements based on genomic transposition frequency.

Abstract: 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: where X is an N-hydroxy-succinimidyl or similar heterocyclic group. Also provided is a method of mapping protein-protein interactions of protein complexes using various mass spectrometry techniques.

Abstract: 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.

Abstract: Computer processing methods and/or systems for minimizing and/or optimizing data strings in accordance with rules and options. Minimized data strings can represent data sequences important in certain biologic analyses and/or syntheses. In specific embodiments, a request is generated by a user at a client system and received by a server system. The server system accesses initial data indicated or provided by the client system. The server system then performs an analysis to minimize the data needed for further reactions. In specific embodiments, a server can use proprietary methods or data at the server side while protecting those proprietary methods and data from access by the client system.

Abstract: A method for determining a sequence of a biomolecule, the method including binding a plurality of uniform probes to a biomolecule fragment, creating a collection of binding signatures for the fragment with each binding signature representing a series of distances between binding sites within the fragment, and grouping the binding signatures into a plurality of signature clusters based at least in part on distances between the binding sites in each binding signature. For each binding signature in a first cluster, a potential successor binding signature is selected from signature clusters other than the first signature cluster, and one of the potential successor binding signatures is identified as a successor binding signature. The last two steps are repeated until the successor signature represents a terminal signature, resulting in a sequence of signatures representing at least a portion of the biomolecule.

Abstract: The present invention provides a method for identifying siRNA target motifs in a transcript using a position-specific score matrix approach. The invention also provides a method for identifying off-target genes of an siRNA using a position-specific score matrix approach. The invention further provides a method for designing siRNAs with higher silencing efficacy and specificity. The invention also provides a library of siRNAs comprising siRNAs with high silencing efficacy and specificity.

Abstract: 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.

Abstract: A method of processing sequencing data obtained with a polymer sequencing system identifies the most likely monomer sequence of a polymer, regardless of stochastic variations in recorded signals. Polymer sequencing data is recorded and two or more distinct series of pore blocking signals for a section of the polymer are recorded. A value is assigned to each series of pore blocking signals to obtain multiple trial sequences. The probability that each of the trial sequences could have resulting in all of trial sequences is calculated to determine a monomer sequence with the highest probability of resulting in all of the trial sequences, termed the first iteration sequence. The first iteration sequence is systematically altered to maximize the combined probability of the first iteration sequence leading to all the trial sequences in order to obtain a most likely sequence of monomers of the polymer.

Abstract: Method and system providing an automated workflow for installing and/or calibrating laboratory equipment. The workflow empowers an end user to perform installation and calibration thereby reducing the costs associated with such activities. The automated workflow taught herein, can greatly reduce the incidence of calibration error by providing for verification of certain events during the calibration process.

Abstract: 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

Abstract: The invention relates to a method for optimizing a nucleotide sequence for expression of a protein on the basis of the amino acid sequence of the protein, in which for a particular region there is specification of a test sequence with m optimization positions on which the codon occupation is varied, a quality function being used to ascertain the optimal codon occupation on these optimization positions, and one or more codons of this optimal occupation being specified as codons of the optimized nucleotide sequence. These steps are iterated, with the codons of the optimized nucleotide sequence which are specified in the preceding steps remaining unchanged in subsequent iteration steps. The invention additionally relates to a device for carrying out this method.

Abstract: 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.

Abstract: A method and a device are disclosed for monitoring the synthesis of proteins by the ribosome, wherein the ribosome is bound to a first label, for example a donor fluorophore, and a tRNA and/or amino acid are is bound to a second label, for example an acceptor fluorophore, wherein the first and second labels together from a FRET pair. As the ribosome mechanism processes the mRNA and tRNA molecules and synthesizes a polypeptide chain, a light source illuminates the ribosome, exciting the donor fluorophores and thereby the acceptor fluorophores whenever these are in sufficient proximity to a donor. The resulting signals are detected and used as a key for database searching and identification of the protein being synthesized.

Abstract: This invention provides an instrument for obtaining consent for a genetic test that comprises three or more integrated elements including an information element for conveying information to an individual concerning a genetic test, and instruction element for use by a practitioner in instructing individuals on the genetic test and use of the instrument, a collection element for collecting an individual's medical and family history, a assessment element for assessing the individual's retention and understanding of information concerning a genetic test, a certification element for certifying the individual's consent to said tests, as well as housekeeping elements useful for recording a medical record, labeling a sample, and billing. Also provided is a method for obtaining informed consent for a genetic test using an integrated instrument. The instruments and methods disclosed have utility in obtaining informed consent for genetic tests.

Abstract: An apparatus and method for generating a novel sequence in a target genome sequence for generating a novel sequence that does not exist in a reference sequence by using input reads that are not mapped to the reference sequence during genome re-sequencing of a next generation sequencing (NGS) technology. According to the present invention, the novel sequence that is not reflected to the reference sequence of the target genome sequence is generated, and information regarding the novel sequence may be provided.

Abstract: The present invention comprises a method and system for accurate estimation of the ion cyclotron resonance (ICR) parameters in Fourier-transform mass spectrometry (FTMS/FT-ICR MS). The parameters are essential to estimating the mass to charge ratio of an ion from FT-ICR MS data, the intended purpose of the instrument. Achieving greater accuracy in the parameters assists in greater accuracy of the mass to charge ratio of an ion, and obtaining an accurate estimation of the mass to charge ratio of an ion further aides in detecting mass with sub-ppm accuracy. Estimating mass in this manner enhances identification and characterization of large molecules. The inventive method and system thereby enhances the data obtained by conventional FTMS by accurately estimating ICR parameters. Ultimately, accurate estimates of the masses of molecules and detection and characterization of molecules from FT-ICR MS data are obtained.

Abstract: 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.

Abstract: 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 MSn spectrum for a low m/z precursor ion. Such a spectrum contains a rather small amount of information, but this information is highly reliable when used for deducing an amino acid sequence by de novo sequencing. Accordingly, an MSn spectrum for a precursor ion having an m/z value of 500 or less is intentionally obtained, and de novo sequencing is performed on this spectrum to deduce the amino acid sequence covering the range from the m/z of the precursor ion and m/z=0. A highly reliable sequence tag can be generated from the deduced amino acid sequence, the m/z of the precursor ion of the MSn analysis, and the m/z of the precursor ion of the MS2 analysis.

Abstract: Methods for processing hyphenated chromatographic data to delineate components of a sample are disclosed. According to one aspect, the method includes obtaining hyphenated chromatographic data points for a sample, each data point comprising at least three dimensions, one of the dimensions being a continuous dimension, and subjecting at least a portion of the data points to an algorithm that organizes the data points into discrete clusters according to the data points' continuous dimension values by starting at either a smallest or largest value and delineating at a largest gap between adjacent values within a predetermined resolution window, wherein the resulting clusters are of varying width of less than or equal to the width of the resolution window and wherein at least some of the clusters are indicative of components of the sample.

Abstract: 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.

Abstract: The invention provides a high resolution three-dimensional structure of a deacylated transfer RNA protein synthesis modulator in association with a large ribosomal subunit. The protein synthesis modulator binds at least a portion of the E-site of a large ribosomal subunit. The invention provides methods for designing and/or identifying analogs of candidate molecules, for example, analogs or derivatives of the protein synthesis modulator, that bind and/or modulate the protein biosynthetic activity of the ribosome.

Abstract: 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 samp

Abstract: BioMEMS/NEMS appliance biologically monitors an individual, using biosensors to detect cellular components. Data is simulated or analyzed using systems-biology software, which provides diagnostic or therapeutic guidance.

Abstract: The invention provides a method for selecting one or more genes from among a predetermined group of genes whose expression level is significantly different among a first group of individuals in a population in comparison with a second group within the population. The first group of individuals may be, a group of individuals suffering from an illness that responded to a predetermined treatment. The second group of individuals may be a group of individuals suffering from the same illness that did not respond to the treatment.

Abstract: 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 (116) includes a false peak remover (208) that removes any false peaks in an ILS signal and a signal verifier (212) that verifies the ILS signal includes only true peaks based on reference ILS information for the ILS signal.

Abstract: The present invention provides compositions and methods for making and using a transcriptome-wide gene-expression profiling platform that measures the expression levels of only a select subset of the total number of transcripts. Because gene expression is believed to be highly correlated, direct measurement of a small number (for example, 1,000) of appropriately-selected transcripts allows the expression levels of the remainder to be inferred. The present invention, therefore, has the potential to reduce the cost and increase the throughput of full-transcriptome gene-expression profiling relative to the well-known conventional approaches that require all transcripts to be measured.

Abstract: 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.

Abstract: The invention relates to methods and systems (e.g., computer systems and computer program products) for characterizing cellular constituents, particularly genes and gene products. In particular, the invention provides methods for assigning or determining the biological function of uncharacterized genes and gene products by using “response profiles,” i.e., measurements of pluralities of cellular constituents in cells having a modified gene or gene product, as phenotypic markers for the gene or gene product. Methods are provided for clustering such response profiles so that similar or correlated response profiles are organized into the same cluster. The invention also provides databases or “compendiums” of response profiles to which the response profile of an uncharacterized gene or gene product can compared.

Abstract: The present invention is related to a method for determining the sensitizing potential of a chemical (test) compound, comprising the steps of: (a) Providing a suitable cell culture of a specific cell type and providing a test sample and a control sample thereof, said test sample and said control sample being identical, (b) Exposing said test sample to a chemical compound in a solvent and exposing said control sample to said solvent for a predetermined period of time, (c) Determining for the test sample and the control sample gene expressions xi for a subset of i=1 to n genes selected from the group of genes corresponding to SEQ ID NOs 1 to 153, (d) For this subset of n genes looking up in a database the gene expressions xi for a set of control and test samples, the test samples being exposed for said predetermined period of time to a set of chemical sensitizing model compounds comprising both sensitizers and non-sensitizers, (e) Using the gene expressions of the said test sample and the said control sample

Abstract: The present invention relates to methods and systems for the analysis of the dissociation behavior of nucleic acids and the identification of determining whether a genotype is present in a biological sample. This includes methods and systems for determining whether a genotype is present in a biological sample, through generating a dynamic profile an unknown genotype, correlating the dynamic profile to an average profile for a known genotype to generate a correlation value, and determining whether the correlation value falls within an acceptable threshold to determine if the unknown genotype is the known genotype. The present invention also relates to methods and systems for generating a training set to allow a machine to recognize a known genotype from within a class of known genotypes. The training set generated by these methods and systems may be used to assist in identification of unknown genotypes.

Abstract: This invention contemplates an accurate and efficient estimation of gene copy number using oligonucleotide microarrays. The method integrates gene copy number data obtained from perfect match and mismatch probe sequence structure intensities and probe binding affinities. In one embodiment, an accurate determination of single nucleotide polymorphisms (SNPs) sequences is obtained. In another embodiment, an accurate detection and determination of DNA copy number alteration is obtained. In another embodiment, an accurate estimation for RNA gene expression is obtained.

Abstract: 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.

Abstract: 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.

Abstract: Methods and systems of DNA sequencing that compensate for sources of noise in next-generation DNA sequencers are described.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: The methods described herein enable the evaluation of compounds on subjects to assess their therapeutic efficacy or toxic effects. The target of analysis is the underlying biochemical process or processes (i.e., metabolic process) thought to be involved in disease pathogenesis. Molecular flux rates within the one or more biochemical processes serve as biomarkers and are quantitated and compared with the molecular flux rates (i.e., biomarker) from control subjects (i.e., subjects not exposed to the compounds). Any change in the biomarker in the subject relative to the biomarker in the control subject provides information to evaluate therapeutic efficacy of an administered drug or a toxic effect and to develop the compound further if desired. In one aspect of the invention, stable isotope-labeled substrate molecules are administered to a subject and the label is incorporated into targeted molecules in a manner that reveals molecular flux rates through metabolic pathways of interest.

Abstract: Methods for determining a property that affects expression of polynucleotides are provided. A plurality of polynucleotides each encoding a polypeptide sequence is constructed. A frequency that a sequence element is used in a first polynucleotide is different than in a second polynucleotide. Each polynucleotide is expressed in an expression system to obtain an expression property value thereby constructing a dataset that contains, for each respective polynucleotide, sequence element occurrence in the respective polynucleotide and the measured expression property value of the respective polynucleotide. A model is computed that describes variation in the measured expression property values as a function of a plurality of variables and weights.

Abstract: The present invention calculates a sum of the count numbers for each of the marker sites to obtain a maximum value of the sum of the count numbers, enumerates polymorphic identification characters up to the count numbers of the polymorphic nucleotides, permutates the enumerated polymorphic identification characters so as to create any character string that has copy units of which the number equals the maximum value, divides the character string into two by the copy unit to store the divided strings as a combination of the haplotype character strings, calculates the number of identical haplotype character strings in the group, obtains a frequency of the haplotype character string in the group, and estimates the combination of the haplotype character strings (representing haplotypes) of each individual of which frequency satisfying a predetermined condition.

Abstract: Methods for selecting a medication for a patient are described that include determining the patient's genotype for a panel of genes and selecting the medication based on the genotype. Articles of manufacture also are provided that include nucleic acid molecules for detecting alleles of genes encoding drug metabolizing enzymes and genes encoding products involved in neurotransmission.

Abstract: A gene assaying method includes the steps of: acquiring two or more data which should be compared and represents expression levels of a plurality of target genes; converting the expression levels represented by the acquired two or more data into ratios based on the expression level of one of the two or more data; extracting a minimum ratio and a maximum ratio of each target gene; and classifying the plurality of target genes using as a classification border at least one of a first ratio with the peak in a frequency distribution of the minimum ratios and a second ratio with the peak in a frequency distribution of reciprocals of the maximum ratios.