Abstract: 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.

Abstract: Systems and methods are provided for performing predictive assignments pertaining to genetic information. One embodiment is a system that includes a genetic prediction server. The genetic prediction server includes an interface that acquires records that each indicate one or more genetic variants determined to exist within an individual, and a controller. The controller selects one or more machine learning models that utilize the genetic variants as input, and loads the machine learning models. For each individual in the records: the controller predictively assigns at least one characteristic to that individual by operating the machine learning models based on at least one genetic variant indicated in the records for that individual. The controller also generates a report indicating at least one predictively assigned characteristic for at least one individual, and transmits a command via the interface for presenting the report at a display.

Abstract: The invention provides methods for analyzing sequence data in which a large amount and variety of reference data are efficiently modeled as a reference graph, such as a directed acyclic graph (DAG). The method includes determining positions of k-mers within a reference graph that represents a genomic sequence and known variation, storing the positions of each k-mer in a table entry indexed by a hash of that k-mer, and identifying a region within the reference graph that includes a threshold number of the k-mers by reading from the table entries indexed by hashes of substrings of a subject sequence. The subject sequence may subsequently be mapped to the candidate region.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Embodiments of the present invention include method, systems and computer program products for algebraic phasing of polyploids. Aspects of the invention include receiving a matrix including a set of two or more single-nucleotide poloymorphisms (SNPs) for two or more sample organisms. Each row of the matrix is set to a ploidy based on a number of ploidies present in the two or more sample organisms. Each allele in the set of two or more SNPs is represented as a binary number. A set of algebraic rules is received, wherein the set of algebraic rules include an algebraic phasing algorithm. And the set of algebraic rules are applied to the matrix to determine a haplotype of a parent of the two or more sample organisms.

Abstract: Modified fungal strains having deleted gene clusters are provided. The modified fungal strains include A. nidulans. The deleted gene clusters are selected from the group of gene clusters responsible for the biosynthesis of sterigmatocystin, emericellamides, asperfuranone, monodictyphenone, terrequinone, F9775A, F9775B, asperthecin, and both portions of the split cluster that makes austinol and dehydroaustinol. Methods for making compounds by culturing the fungus in a growth media and separating the compound from the fungus and/or separating the compound from the growth media are included, as are the compounds and compositions comprising them.

Abstract: Various embodiments perform stable gene analysis of transcriptome sequencing data. In one embodiment, a plurality of datasets each including transcriptome sequencing data are received by a processor. Each of the plurality of datasets includes a plurality of genes and a respective ranking value for each of the plurality of genes. A plurality of rank normalized input datasets is generated based on assigning, for each of the plurality of datasets, a rank to each of the plurality of genes. One or more longest increasing subsequence (LIS) of ranks are identified between each pair of the plurality of rank normalized input datasets. A set of stable genes from the plurality of genes is identified based on each of the one or more LIS of ranks across the plurality of rank normalized input datasets.

Abstract: Compositions and methods for the identification of agents useful for the treatment of neurological disorders, including schizophrenia, are provided.

Abstract: Various embodiments perform stable gene analysis of transcriptome sequencing data. In one embodiment, a plurality of datasets each including transcriptome sequencing data are received by a processor. Each of the plurality of datasets includes a plurality of genes and a respective ranking value for each of the plurality of genes. A plurality of rank normalized input datasets is generated based on assigning, for each of the plurality of datasets, a rank to each of the plurality of genes. One or more longest increasing subsequence (LIS) of ranks are identified between each pair of the plurality of rank normalized input datasets. A set of stable genes from the plurality of genes is identified based on each of the one or more LIS of ranks across the plurality of rank normalized input datasets.

Abstract: The present disclosure is directed to associating computing devices with each other based on computer network activity for selection of content items as part of an online content item placement campaign. A first linking factor is identified based on a connection between a first device and the computer network via a first IP address during a first time period, and based on a connection between a second device and the computer network via the first IP address during the first time period. A number of devices that connect with the computer network via the first IP address is determined. A positive match probability is generated. A second and third linking factors are monitored. A negative match probability is determined based on the second and third linking factors. The first device is linked with the second device based on the positive and negative match probabilities.

Abstract: Provided are conjugates between p97 (melanotransferrin) and polynucleotides such as small interfering RNA (siRNA) molecules, and related compositions and methods of use thereof, for instance, to facilitate delivery of polynucleotides such as siRNA molecules across the blood-brain barrier (BBB) and/or improve their tissue penetration in CNS and/or peripheral tissues, and thereby treat and/or diagnose various diseases, including those having a central nervous system (CNS) component.

Abstract: A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads' positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank. The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.

Abstract: Example implementations are directed to a system to generate keyframes describing the temperature output state of thermal output devices during the synchronous playback of video material. This additional haptic output channel augments the existing audio and video channels. Example implementations provide a manual keyframe authoring interface and an architecture for playing back video with a thermal output channel. Example implementations also involve an automatic keyframe generation method for thermal output accompanying a video, and provide a temperature profile function to enable rapid changing between temperature values for thermal output devices that use open-loop control.

Abstract: Error correction in ancestry classification includes obtaining, from a classifier, initial ancestry classifications associated with portions of two phased haplotypes of a chromosome pair of an individual; performing error correction on an initial ancestry classification, including detecting a phasing error in the initial ancestry classifications; and outputting a corrected ancestry classification in which the phasing error is corrected.

Abstract: The present invention is in the field of molecular diagnostics and relates to a method for classifying samples obtained from patients diagnosed with multiple myeloma into three newly defined clusters. The invention also relates to a method for determining the prognosis of an individual diagnosed with multiple myeloma as well as a method for the prediction of the response to treatment of an individual diagnosed with multiple myeloma. More in particular, the invention provides a method for determining the disease outcome or the prognosis of a patient diagnosed with multiple myeloma by classifying said patient into a high risk or a low risk category, based on a 92 gene classifier.

Abstract: An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM-score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS-score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer.

Abstract: Disclosed are methods for performing aptamer preselection based on unique geometry and the content of stems or loops of the aptamer, which methods are capable of providing suitable binders and also permit selection of aptamers performed essentially entirely on a chip or other device. Also disclosed are kits for aptamer selection.

Abstract: Systems and methods are provided for performing predictive assignments pertaining to genetic information. One embodiment is a system that includes a genetic prediction server. The genetic prediction server includes an interface that acquires records that each indicate one or more genetic variants determined to exist within an individual, and a controller. The controller selects one or more machine learning models that utilize the genetic variants as input, and loads the machine learning models. For each individual in the records: the controller predictively assigns at least one characteristic to that individual by operating the machine learning models based on at least one genetic variant indicated in the records for that individual. The controller also generates a report indicating at least one predictively assigned characteristic for at least one individual, and transmits a command via the interface for presenting the report at a display.

Abstract: Methods, systems, and computer program products for updating annotator collections using run traces are provided herein. A computer-implemented method includes generating one or more alternate versions of one or more document annotators selected from a set of multiple document annotators; executing, on one or more document data sets, (i) one or more document annotators from the set of multiple document annotators and (ii) the one or more alternate versions to generate log information for each document annotator in the set and each alternate version of the one or more alternate versions; and outputting an instruction to modify, based on the generated log information for each document annotator in the set and each alternate version, at least one document annotator from the set with at least one alternate version from the one or more alternate versions.

Abstract: Systems and methods for providing hierarchy scores are described. Generally, influence scores for authors of a crowd may be determined based on emotional scores and echoing of time series data strings. One or more regression lines may be determined based on the influence scores to provide a raw hierarchy score and/or a central hierarchy score. Analysis and/or comparisons of the hierarchy scores may be used to classify the crowd type and output an influential score report.

Abstract: The present disclosure relates to apparatus, systems, compositions, and methods for analyzing a sample containing particles. In some aspects the system comprises an analyzer which may be a visual analyzer. In one aspect, this disclosure relates to a particle imaging system comprising a flowcell through which a sample containing particles is caused to flow, and a high optical resolution imaging device which captures images for image analysis of samples. Other compositions, methods and features of this disclosure are disclosed herein.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: Methods, computer systems, computer-storage media, and graphical user interfaces are provided for visualizing a performance of a machine-learned model. An interactive graphical user interface includes an item representation display area that displays a plurality of item representations corresponding to a plurality of items processed by the machine-learned model. The plurality of item representations are arranged according to scores assigned to the plurality of items by the machine-learned model. Further, each of the plurality of item representations is visually configured to represent a label assigned to a corresponding item.

Abstract: A new method for encoding genomic data that reduces storage footprint by two orders of magnitude while preserving acceptable quality data.

Abstract: A control system (1) for automatically controlling a plurality of devices (2) of a separation and detection process for quantitative sample analysis and according computer program. Such systems and computer programs can be used to operate quantitative sample analysis devices such as for example high performance liquid chromatography (HPLC) devices or the like.

Abstract: A system for modulating a response signal includes aptamer conjugates, e.g., aptamer-particle conjugates, configured to bind with target analytes, a detector configured to detect an analyte response signal transmitted from the body, a modulation source configured to modulate the analyte response signal, and a processor configured to non-invasively detect the one or more target analytes by differentiating the analyte response signal from a background signal, at least in part, based on the modulation. The analyte response signal is related to the binding interaction of the target analytes with the aptamer-particle conjugates. In some examples, the system may also include magnetic particles and a magnetic field source sufficient to distribute the magnetic particles into a spatial arrangement in the body. The analyte response signal may be differentiated from the background signal, at least in part, based on modulation of the signals due, at least in part, to the spatial arrangement of the magnetic particles.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: Methods, computer-accessible medium, and systems for generating a genome wide probe map and/or a genome wide haplotype sequence are provided. In particular, a genome wide probe map can be generated by obtaining a plurality of detectable oligonucleotide probes hybridized to at least one double stranded nucleic acid molecule cleaved with at least one restriction enzyme, and detecting the location of the detectable oligonucleotide probes. For example, genome wide haplotype sequence can be generated by analyzing at least one genome wide restriction map in conjunction with at least one genome wide probe map to determine distances between restriction sites of the genome wide restriction map(s) and locations of detectable oligonucleotide probes of the genome wide probe map(s) and defining a consensus map indicating restriction sites based on the genome wide restriction map(s) and/or locations of detectable oligonucleotide probes based on each of the genome wide probe map(s).

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit that may be connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

Abstract: The present invention provides a system for receiving biological sequence information and activating the synthesis of a biological entity. The system has a receiving unit for receiving a signal encoding biological sequence information transmitted from a transmitting unit. The transmitting unit can be present at a remote location from the receiving unit. The system also has an assembly unit connected to the receiving unit, and the assembly unit assembles the biological entity according to the biological sequence information. Thus, according to the present invention biological sequence information can be digitally transmitted to a remote location and the information converted into a biological entity, for example a protein useful as a vaccine, immediately upon being received by the receiving unit and without further human intervention after preparing the system for receipt of the information.

Abstract: The redundancy in genomic sequence data is exploited by compressing sequence data in such a way as to allow direct computation on the compressed data using methods that are referred to herein as “compressive” algorithms. This approach reduces the task of computing on many similar genomes to only slightly more than that of operating on just one. In this approach, the redundancy among genomes is translated into computational acceleration by storing genomes in a compressed format that respects the structure of similarities and differences important to analysis. Specifically, these differences are the nucleotide substitutions, insertions, deletions, and rearrangements introduced by evolution. Once such a compressed library has been created, analysis is performed on it in time proportional to its compressed size, rather than having to reconstruct the full data set every time one wishes to query it.

Abstract: A method includes identifying, at a processor, a set of communication lines from a plurality of communication lines, the set of communication lines including a first communication line and a second communication line. A first crosstalk characteristic of the first communication line is correlated with a second crosstalk characteristic of the second communication line. The method also includes modifying, at the processor, a first signal corresponding to the first communication line based on a second signal corresponding to the second communication line.

Abstract: Haplotypes of one or more portions of a chromosome of an organism from sequencing information of DNA or RNA fragments can be determined. Heterozygous loci (hets) can be used to determine haplotypes. One allele on a first het can be connected (likely to be on the same haplotype) to an allele on a second het, thereby defining a particular orientation between the hets. Haplotypes can be assembled through these connections. Errors can be identified through redundant connection information, particularly using a confidence value (strength) for a particular connection. The connections among a set of hets can be analyzed to determine likely haplotypes for that set, e.g., an optimal tree of a graph containing the hets. Furthermore, haplotypes of different contiguous sections (contig) of the chromosome can be matched to a particular chromosome copy (e.g., to a particular parental copy). Thus, the phase of an entire chromosome can be determined.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: DNA sequences are analyzed using latent semantic analysis. A set of nucleotide sequences is received in which the set has a first number of sequences. A set of basis vectors is determined, in which the set has a second number of basis vectors, the second number being smaller than the first number. Each basis vector represents a specific combination of predetermined nucleotide segments. For each of the nucleotide sequences, an approximate representation of the nucleotide sequence is determined based on a combination of the basis vectors. For each pair of nucleotide sequences, a distance between the pair of nucleotide sequences is determined according the distance between the approximate representation of the pair of nucleotide sequences. The set of nucleotide sequences are classified based on the distances between the pairs of nucleotide sequences.

Abstract: The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer's, and/or Parkinson's disorder. The methods can also be used to monitor and track changes in a patient's DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient's particular prognosis.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: A differential sequence object is constructed on the basis of alignment of sub-strings via incremental synchronization of sequence strings using known positions of the sub-strings relative to a reference genome sequence. An output file is then generated that comprises only relevant changes with respect to the reference genome.

Abstract: The invention relates to methods of diagnosing susceptibility to cardiovascular disease, including coronary artery disease. MI, abdominal aorta aneurysm, intracranial aneurysm restenosis and peripheral arterial disease, by assessing the presence or absence of alleles of certain polymorphic markers found to be associated with cardiovascular disease. The invention further relates to kits encompassing reagents for assessing such markers, and methods for assessing the probability of response to therapeutic agents and methods using such markers.

Abstract: The present invention provides a highly-safe information processing system that is capable of effectively using nucleotide sequence information differences between individual organisms to offer semantic information useful for each individual organism while properly preventing leakage and illegal use of nucleotide sequence information. Further, the present invention includes steps a and b. Step a is performed to acquire either encrypted nucleotide sequence-related information or cryptographic key that corresponds to positional information indicating a position within a nucleotide sequence.

Abstract: A comprehensive strategy is used to determine valid reference time-concentration curves (TCCs) from image data. The image data corresponds to a series of image scans acquired over time for an area of interest of a patient to which a contrast agent was previously administered. The image scans are initially registered to a common coordinate system. Then, observed potential reference TCCs in the image scans are compared to modeled reference TCCs to determine if the potential reference TCCs are plausible reference TCCs. Thereafter, any plausible reference TCCs are evaluated to determine if they contain residual, isolated motion artifacts. If a plausible reference TCC does not include any motion artifacts, the plausible reference TCC is considered a valid reference TCC. If a plausible reference TCC is determined to include motion artifacts, the plausible reference TCC is modified to a valid reference TCC by removing the motion artifacts, or otherwise the plausible reference TCC is rejected.

Abstract: The present disclosure provides systems and methods for nucleic acid sequence analysis. A system for processing raw nucleic acid sequence data from a genomic sequencer comprises a data processing server having a housing contained therein one or more processing modules. The one or more processing modules can each comprise an electronic control unit programmed to align nucleic acid sequence data from a genomic sequencing device and perform one or more of variant analysis and structural variant analysis on the nucleic acid sequence data. The system can further comprise a computer server in communication with the processing server. The computer server can be programmed or otherwise configured to process and/or analyze the aligned nucleic acid sequence data.

Abstract: Genetic data in row-wise flat files, such as VCF and VCF-like files, comprising a plurality of data elements of different types is analyzed using a parallel framework in an MPP shared-nothing distributed database having a plurality of distributed segments by first parsing the data into groups of data elements of the same types, converting the data into entry-wise genetic data such that the same types of data elements are in a column, and distributing and storing the entry-wise genetic data in the distributed segments. SQL database queries are used to analyze the genetic data, including locating probable significant associations between genotype and phenotype data.

Abstract: Profiling data includes accessing multiple collections of records to store quantitative information for each particular collection including, for at least one selected field of the records in the particular collection, a corresponding list of value count entries, each including a value appearing in the selected field and a count of the number of records in which the value appears. Processing the quantitative information of two or more collections includes: merging the value count entries of corresponding lists for at least one field from each of a first collection and a second collection to generate a combined list of value count entries, and aggregating value count entries of the combined list of value count entries to generate a list of distinct field value entries identifying a distinct value and including information quantifying a number of records in which the distinct value appears for each of the two or more collections.

Abstract: The present invention concerns markers of resistance of HER2 expressing tumors to treatment with HER2 inhibitors, such as HER2 antibodies, including trastuzumab.

Abstract: A method and apparatus for determining hemoglobin concentration is provided. A method aspect includes the steps of: a) depositing an unlyzed, substantially undiluted blood sample into an analysis chamber adapted to quiescently hold the sample for analysis; b) imaging the sample in a region of the analysis chamber where the height of the chamber is no more than about twenty microns (20?) or no less than about two microns (2?), to produce image signals representative of the optical density of the imaged region; c) determining a sample representative optical density value using the image signals representative of the optical density of the imaged region; and d) determining the hemoglobin concentration of the sample using the sample representative optical density value.

Abstract: A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the integrated circuit connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.