Abstract: A non-transitory storage medium stores an assembled genetic sequence comprising aligned sequencing reads. An electronic processing device is configured to perform operations including: identifying a possible variant in the assembled genetic sequence; computing value of at least one read property for reads of the assembled genetic sequence; and calling the possible variant conditional upon the computed values of the at least one read property for sequencing reads of the assembled genetic sequence that include the possible variant satisfying an acceptance criterion. The electronic processing device may be further configured to select at least one region of the assembled genetic sequence for validation based on a non random selection criterion.

Abstract: Provided herein are methods for detecting an increased probability or risk of neurodegeneration in a subject. In some embodiments the method comprises assaying a sample from the subject for lysozyme and/or cathepsin S and detecting the lysozyme and/or cathepsin S from the sample, wherein an increased lysozyme and/or cathepsin S compared to levels in a control subject sample indicate an increased probability or risk of neurodegeneration. Methods of treatment and screening assays for determining drug effectiveness are also provided herein.

Abstract: The present invention is directed to a platform (e.g., Web-based) that enables basic and clinical research activities by integrating patient characteristics and clinical outcome data with a variety of high-throughput research data in a unified environment. While several rich data repositories for high dimensional research data exist in the public domain, most focus on a single data type and do not support integration across multiple technologies. The present invention in at least one embodiment includes a broad collection of bioinformatics and systems biology tools for analysis and visualization of four major “omics” types: DNA, mRNA, microRNA, and metabolites, as well as next-generation sequencing. The present invention helps facilitate systems medicine by providing easy identification of trends and patterns in integrated datasets and hence facilitate the use of better targeted therapies for cancer.

Abstract: A method for nucleic acid sequencing includes: disposing a plurality of template polynucleotide strands, sequencing primers, and polymerases in a plurality of defined spaces of a sensor array; exposing template polynucleotide strands to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtaining, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

Abstract: A method and apparatus for determining similarity among gene sequences, for compressing a gene sequence, and for decompressing a gene sequence. The method for determining similarity between a first gene sequence and a second gene sequence includes: moving a sliding window of a predefined length on the first gene sequence and the second gene sequence respectively; extracting a first part String1i of the first gene sequence within the sliding window, and a second part String2i of the second gene sequence within the sliding window during the ith movement of the sliding window; and determining similarity between the first gene sequence and the second gene sequence based on the first part String1i and the second part String2i. Also provided is an apparatus for the above method.

Abstract: A system and method for continuously monitoring as well as identifying and quantifying intracellular components in a cell culture such as microalgal culture of a bioreactor is described. This is done to determine an optimum concentration of intracellular components of interest, such as lipids. The method may be integrated directly with the cultivation chamber to conduct real-time measurements to quickly obtain accurate and continuous information that may be used as feedback to control the cultivation growth conditions. Such characterization may provide highly relevant data to determine if the culture is ready for biofuel processing. If the culture is not ready for biofuel processing, the data allows for the modification of the growth condition in the microalgae culture in order to achieve the desired concentration of the microalgal intracellular component of interest for biofuel processing.

Abstract: In one exemplary embodiment, a method for detecting variants in electropherogram data is provided. The method includes receiving electropherogram data from an instrument and analyzing the electropherogram data to identify mixed bases in the electropherogram data. The method further includes validating the identified mixed bases. Then the method includes determining variants in the electropherogram data based on the validated mixed bases.

Abstract: Disclosed is a human haplotyping method. The method includes: collecting a sequence of a gene to be analyzed; matching and aligning reads of the collected sequence to a reference stored in a database; electing candidate alleles from among alleles of the reference; and selecting a final allele from among the candidate alleles.

Abstract: Embodiments of the present disclosure provide for methods and systems for preparing chromosomal spread for a selected cell so that chromosomal spreads and/or translocations can be correlated with the selected cell.

Abstract: A system includes an interface configured to receive time series data representing information from a plurality of sensors, and a processor configured to construct a behavior model based on the time series data. The processor identifies features in the time series data, divides the time series data of each of the identified features into segments, and extracts feature components from the segments. The processor further constructs a plurality of state graphs, each state graph including components connected by weighted edges, constructs a behavior graph, wherein the state graphs form vertices of the behavior graph, clusters the state graphs in the behavior graph; and selects a representative state graph from each cluster, wherein the behavior model includes the selected state graphs.

Abstract: Novel methods and compositions for identifying one or more factors associated with a nucleic acid sequence (e.g., DNA and/or RNA) of interest are provided.

Abstract: Particles such as blood cells can be categorized and counted by a digital image processor. A digital microscope camera can be directed into a flowcell defining a symmetrically narrowing flowpath in which the sample stream flows in a ribbon flattened by flow and viscosity parameters between layers of sheath fluid. A contrast pattern for autofocusing is provided on the flowcell, for example at an edge of a rear illumination opening. The image processor assesses focus accuracy from pixel data contrast. A positioning motor moves the microscope and/or flowcell along the optical axis for autofocusing on the contrast pattern target. The processor then displaces microscope and flowcell by a known distance between the contrast pattern and the sample stream, thus focusing on the sample stream. Blood cell images are collected from that position until autofocus is reinitiated, periodically, by input signal, or when detecting temperature changes or focus inaccuracy in the image data.

Abstract: The present disclosure describes a method of foreground segmentation and nucleus ranking for scoring dual ISH images. The method has been developed to better identify those nuclei, within a selected field of view, that meet the criteria for dual ISH scoring.

Abstract: The present disclosure provides a method and a system for processing an image. The method includes: an image pre-processing step, including analyzing an image input to be processed so as to obtain a first image; and a spot detecting step, including analyzing the first image so as to compute a spot determining threshold; analyzing the first image so as to acquire a candidate pixel spot, and judging whether the candidate pixel spot is the spot according to the spot determining threshold; computing a sub-pixel center coordinate of the spot and an intensity value of the sub-pixel center coordinate if yes; and discarding the candidate pixel spot if no. According to the method, the image is denoised in the image pre-processing step, such that a calculation in the spot detecting step may be reduced. In addition, the accuracy of determining the image spot may be improved.

Abstract: A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed.

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: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.

Abstract: Analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for solid tumor assessment or cancer screening. However, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. Regarding the size profile of plasma DNA molecules, some studies reported increased integrity of tumor-derived plasma DNA while others reported shorter tumor-derived plasma DNA molecules. We performed an analysis of the size profiles of plasma DNA in patients with cancer using massively parallel sequencing at single base resolution and in a genomewide manner. Tumor-derived plasma DNA molecules were further identified using chromosome arm-level z-score analysis (CAZA). We showed that populations of aberrantly short and long DNA molecules co-existed in the plasma of patients with cancer. The short ones preferentially carried the tumor-associated copy number aberrations. These results show the ability to use plasma DNA as a molecular diagnostic tool.

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: The present disclosure provides a HTP microbial genomic engineering platform that is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. This integrative platform utilizes a suite of HTP molecular tool sets to create HTP genetic design libraries, which are derived from, inter alia, scientific insight and iterative pattern recognition. The HTP genomic engineering platform described herein is microbial strain host agnostic and therefore can be implemented across taxa. Furthermore, the disclosed platform can be implemented to modulate or improve any microbial host parameter of interest.

Abstract: An object is to enable to search genetic information in an encrypted state. An encryption apparatus (200) encrypts a target gene which is genetic information to be stored in a storage apparatus and generates an encrypted gene, as well compares a reference gene which is predefined genetic information with the target gene to generate differential information, and generates an encrypted tag which is encrypted by embedding the generated differential information. A data center (400) stores the encrypted gene with related to the encrypted tag in the storage apparatus. A search apparatus (300) generates a search query which is encrypted by embedding the differential information as a search keyword, and sends the generated search query to a data center (400). The data center (400) specifies the encrypted tag including the differential information specified in the search query, extracts the related encrypted gene, and sends the encrypted gene to the search apparatus (300).

Abstract: Described embodiments enable identification of family networks using combinations of DNA analysis and genealogical information. Genealogical data is provided by users of a genealogical research service or collected from other sources and used to create family trees for each user. DNA samples are also received from the users. By analyzing the DNA samples, potential genetic relationships can be identified between some users. Once these DNA-suggested relationships have been identified, common ancestors can be sought in the respective trees of the potentially related users. Where these common ancestors exist, an inference is drawn that the DNA-suggested relationship accurately represents a familial overlap between the individuals in question. People descended from the same common ancestor are each members of a family network. Members of a family network not in a user's tree may be identified for the user, enabling the user to discover additional ancestors that might otherwise have remained unknown.

Abstract: The present invention is based, in part, on our discovery of compositions and methods that can be used to treat a patient who has a compromised bone (due, for example, to a disease such as osteoporosis or an injury such as a bone fracture). The compositions can also be administered prophylactically. For example, they can be administered to help maintain bone health as a patient ages. More specifically, the compositions include polypeptides that constitute (or that include) a fragment of a calcitonin receptor (CR) and polypeptides that constitute (or include) biologically active variants of those fragments. Sequence-specific formulas are provided herein, and polypeptides conforming to those formulas, as well as nucleic acids encoding them, expression vectors, host cells, pharmaceutical formulations, and methods of their preparation and use are within the scope of the present invention.

Abstract: The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.

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: 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: 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: 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.