Gene Sequence Determination Patents (Class 702/20)
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Patent number: 10949516Abstract: An information processing apparatus includes: a memory, and a processor configured to extract feature points from a biometric image of a living body, generate groups each including a certain number of feature points, obtain a first feature value of each of the groups, compares the first feature value with a second feature value which is a feature value of each of groups each including the certain number of feature points included in enrolled biometric information, specify, as a pair, two groups similar to each other, obtain a first degree of similarity between a first feature point included in a first group of the pair and a second feature point included in a second group of the pair in accordance with a number of groups similar to the first group of the pair, and authenticate the living body based on the degree of similarity.Type: GrantFiled: December 19, 2018Date of Patent: March 16, 2021Assignee: FUJITSU LIMITEDInventor: Kazuya Uno
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Patent number: 10936746Abstract: Methods and systems are disclosed for genetic manipulation and for securing communication of genetic sequences. In one example, a sequence security system comprises a security device communicatively coupled to a separator module, the separator module comprising a first separator device and a second separator device. The security device may store instructions in non-transitory memory that are executable by a processor to receive a source sequence from the first separator device at a receiving module, receive manipulation instructions from the second separator device at the receiving module, and apply the manipulation instructions to the source sequence to form a target sequence via a transforming module. Thus, the source sequence and the manipulation instructions may be maintained separate from one another until the source sequence and the manipulation instructions are received at the receiving module, for example.Type: GrantFiled: December 11, 2017Date of Patent: March 2, 2021Assignee: SEROTINY, INC.Inventors: Justin Farlow, Colin Farlow
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Patent number: 10938415Abstract: Method for encoding of quality values of a data structure, whereby said data structure comprises a set of genomic reads, wherein the method comprises the following steps executable by a data processing system: ascertain the quality values of each read covering a certain index locus, —determine a codebook identifier identifying a specific codebook from a plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each code-book provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, —quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and —encode all determined codebook identifiers using a first entropy encoder and encode all quType: GrantFiled: July 16, 2018Date of Patent: March 2, 2021Assignee: GOTTFRIED WILHELM LEIBNIZ UNIVERSITÄT HANNOVERInventors: Jan Voges, Jörn Ostermann
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Patent number: 10918014Abstract: A fertilization precision control method for water and fertilizer integrated equipment and a control system thereof includes the following steps: step S1, establishing a fertilization precision control model of the water and fertilizer integrated equipment; and step S2, solving an optimal solution of the fertilization precision control model by adopting estimation of distribution algorithms.Type: GrantFiled: April 7, 2018Date of Patent: February 16, 2021Assignee: CAMCE WHU DESIGN & RESEARCH CO., LTD.Inventors: Lin Yang, Guangxing Wu, Zhengguang Wu, Tailai Li, Chonghua Mao
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Patent number: 10909687Abstract: 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.Type: GrantFiled: September 26, 2019Date of Patent: February 2, 2021Assignee: Ventana Medical Systems, Inc.Inventors: Anindya Sarkar, Jim Martin
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Patent number: 10902936Abstract: The present invention provides for a method to identify a hospital acquired infection. The method includes computing the number of changes over time between an infection sample and at least a subset of the plurality of infection samples and determining if the number of changes over time is within an interval of an expected number of changes. If so, marking the infection sample as a hospital acquired infection.Type: GrantFiled: July 11, 2016Date of Patent: January 26, 2021Assignee: Koninklijke Philips N.V.Inventors: Henry Lin, Sitharthan Kamalakaran
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Patent number: 10896742Abstract: Disclosed are techniques for predicting a trait of an individual and identifying a set of enriched record collections of a genetic community. To predict a trait of an individual, DNA features and non-DNA features of the individual are accessed to generate a feature vector that is inputted into a machine learning model. The machine learning model generates a prediction of the trait. The prediction may be based on an inheritance prediction and/or a community prediction. To identify a set of enriched record collections, individuals belonging to a genetic community are identified and a set of candidate record collections are accessed. A community count and a background count is determined for each candidate record collection. The set of enriched record collections are identified based on a comparison of the community count and the background count. The genetic community may be annotated using the set of enriched record collections.Type: GrantFiled: October 31, 2019Date of Patent: January 19, 2021Assignee: Ancestry.com DNA, LLCInventors: Ahna R. Girshick, Natalie Telis, Julie M. Granka, Asher Keith Haug Baltzell, Shiya Song
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Patent number: 10867693Abstract: The invention generally relates to genomic studies and specifically to improved methods for read mapping using identified nucleotides at known locations. The invention provides methods of using identified nucleotides at known places in a genome to guide the analysis of sequence reads from that genome by excluding potential mappings or assemblies that are not congruent with the identified nucleotides. Information about a plurality of SNPs in the subject's genome is used to identify candidate paths through a genomic directed acyclic graph (DAG). Sequence reads are mapped to the candidate paths.Type: GrantFiled: January 8, 2015Date of Patent: December 15, 2020Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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Patent number: 10861203Abstract: Systems and methods for creating filtered data using graphical methodology. Stored data relationally-linked by an ontology are representable in rows and columns format. The system receives a first input selecting a first data source, displays a portion of the first data source in a first chart, receives a second input identifying a portion of the first chart, generates a first filter based on the identified portion, receives a third input selecting a linked object set, displays an indicator of the linked object set in a second sidebar, displays a portion of the linked object set in a second chart depicting information of the linked object set filtered by the first filter, receives a fourth input identifying a portion of the second chart, generates a second filter based on the identified portion, and displays fields of the linked object set, filtered by the first and second filter, in a third chart.Type: GrantFiled: February 12, 2019Date of Patent: December 8, 2020Assignee: PALANTIR TECHNOLOGIES INC.Inventors: Daniel Cervelli, Timothy Slatcher, Adam Storr
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Patent number: 10861585Abstract: An information processing apparatus includes a memory and a processor coupled to the memory and configured to extract data having x times y bits from genome data in which a mutation pattern at each gene mutation position is represented as x bits, such that the extracted data is constituted by y data pieces each having x bits at y respective mutation positions, x and y being integers greater than or equal to 1, respectively, to refer to an addend table that stores a plurality of addend data associated with respective x-times-y-bit data to identify addend data corresponding to the extracted data, and to use an SIMD instruction to add the identified addend data to count data at positions corresponding to the y mutation positions in the genome data, the count data indicating counts of occurrences of mutation patterns in the genome data.Type: GrantFiled: September 11, 2017Date of Patent: December 8, 2020Assignee: FUJITSU LIMITEDInventors: Yoshifumi Ujibashi, Minoru Nakamura
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Patent number: 10854317Abstract: A method to align a next generation sequencing read to a reference sequence includes: (a) receiving a sequencing read; (b) performing a first alignment of the sequencing read to a reference sequence so as to identify a target sequence within the reference sequence whereto the sequencing read maps; (c) selecting a first and a second anchor sequence; (d) attaching the first anchor sequence to the upstream region of the sequencing read and the second anchor sequence to the downstream region of the sequencing read so as to generate an extended sequencing read; (e) attaching the first anchor sequence to the upstream region of the target sequence and the second anchor sequence to the downstream region of the target sequence, so as to generate an extended target sequence; (f) performing a second alignment of the extended sequencing read to the extended target sequence, so that the second alignment is more correctly mapped to the target sequence than the first alignment; (g) identifying a position where one or more bType: GrantFiled: December 28, 2018Date of Patent: December 1, 2020Inventors: Ko-Wen Wu, Kun-Lin Li
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Patent number: 10847250Abstract: This invention relates to a binomial calculation of copy number of data obtained from a mixed sample having a first source and a second source.Type: GrantFiled: February 10, 2014Date of Patent: November 24, 2020Assignee: Ariosa Diagnostics, Inc.Inventors: Craig Struble, John Stuelpnagel
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Patent number: 10839940Abstract: Exemplary embodiments of the present disclosure relate generally to methods, computer-accessible medium and systems for assembling haplotype and/or genotype sequences of at least one genome, which can be based upon, e.g., consistent layouts of short sequence reads and long-range genome related data. For example, a processing arrangement can be configured to perform a procedure including, e.g., obtaining randomly located short sequence reads, using at least one score function in combination with constraints based on, e.g., the long range data, generating a layout of randomly located short sequence reads such that the layout is globally optimal with respect to the score function, obtained through searching coupled with score and constraint dependent pruning to determine the globally optimal layout substantially satisfying the constraints, generating a whole and/or a part of a genome wide haplotype sequence and/or genotype sequence, and converting a globally optimal layout into one or more consensus sequences.Type: GrantFiled: December 23, 2009Date of Patent: November 17, 2020Assignee: NEW YORK UNIVERSITYInventors: Bhubaneswar Mishra, Giuseppe Narzisi
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Patent number: 10832797Abstract: The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The invention also includes methods and systems for evaluating the quality of the alignment between the reads and the reference sequence construct. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.Type: GrantFiled: October 17, 2014Date of Patent: November 10, 2020Assignee: Seven Bridges Genomics Inc.Inventor: Deniz Kural
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Patent number: 10816537Abstract: Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.Type: GrantFiled: April 15, 2019Date of Patent: October 27, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Patent number: 10803381Abstract: Techniques related to implementing neural networks for speech recognition systems are discussed. Such techniques may include processing a node of the neural network by determining a score for the node as a product of weights and inputs such that the weights are fixed point integer values, applying a correction to the score based on a correction value associated with at least one of the weights, and generating an output from the node based on the corrected score.Type: GrantFiled: September 9, 2014Date of Patent: October 13, 2020Assignee: Intel CorporationInventors: Piotr Rozen, Georg Stemmer
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Patent number: 10777304Abstract: 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.Type: GrantFiled: July 24, 2017Date of Patent: September 15, 2020Inventors: Michael H. Baym, Bonnie Berger Leighton, Po-Ru Loh
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Patent number: 10748663Abstract: Techniques are disclosed for discovering, biological elements, functions and pathways, and environmental and nutritional factors related to diseases and medical syndromes. The techniques preprocess database query results and harmonize data using natural language processing before transforming them into the frequency space. The transformed results are analyzed with various categories of machine learning algorithms whose results are normalized, ranked and selectively combined, weighted or un-weighted, to produce a single result ranking the most important elements affecting a target disease or medical syndrome. The invention also uses alternative algorithms producing hypotheses on associations between medical topics, which are used as suggestions for exploratory medical research.Type: GrantFiled: April 30, 2018Date of Patent: August 18, 2020Inventor: Efthymios Kalafatis
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Patent number: 10734105Abstract: A system for informed selection of prescriptive therapies. The system includes a computing device configured to receive compositional training data containing a plurality of unclassified data entries. The system is configured to retrieve a user biological profile and generate an unsupervised machine-learning model that utilizes a biological profile as an input and outputs a therapy response label. The system selects a therapy response model and receives from a remote device a proposed prescriptive therapy. The system creates a therapy response model and identifies a prescriptive therapy label for a proposed prescriptive therapy.Type: GrantFiled: November 30, 2019Date of Patent: August 4, 2020Inventor: Kenneth Neumann
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Patent number: 10733701Abstract: Systems and methods for dynamic visualization of genomic data are provided in which a genomic visualization system adapts presentation of information content according to scale-relevant annotations within a sequence object.Type: GrantFiled: October 24, 2018Date of Patent: August 4, 2020Assignee: Five3 Genomics, LLCInventors: Charles Joseph Vaske, John Zachary Sanborn, Stephen Charles Benz
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Patent number: 10726946Abstract: A method for computing free energy difference between a reference molecule and a target molecule. The target molecule has the common set of atoms PAB and a set of atoms PB. The method includes applying a potential to restrain an interaction of the additional atomic component from the set of atoms PB with the common set of atoms PAB in the initial state. The method includes determining one or more transition states along a transformation path between the initial state and target state. The method includes scaling the restrain potential correspondingly along the transformation path until the potential becomes zero when a corresponding end state is reached, and calculating the free energy difference between the reference molecule and the target molecule using a value obtained along the transformation path from the initial state to the target state.Type: GrantFiled: August 22, 2017Date of Patent: July 28, 2020Assignee: Schrödinger, Inc.Inventors: Lingle Wang, Yuqing Deng, Yujie Wu, Byungchan Kim, Robert L. Abel
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Patent number: 10726359Abstract: Embodiments in the present disclosure relate generally to computer network architectures for machine learning, artificial intelligence, and automated improvement and regularization of forecasting models, providing rapid improvement of the models. Embodiments may generate such rapid improvement of the models either occasionally on demand, or periodically, or as triggered by events such as an update of available data for such forecasts. Embodiments may indicate, after the improvement of the models, that various web applications using the models may be rerun to seek improved results for the web applications. Embodiments may include a combination of third-party databases to drive the forecasting models, including social media data, financial data, socio-economic data, medical data, search engine data, e-commerce site data, and other databases.Type: GrantFiled: August 6, 2019Date of Patent: July 28, 2020Assignee: Clarify Health Solutions, Inc.Inventors: Jean P. Drouin, Samuel H. Bauknight, Todd Gottula, Yale Wang, Adam F. Rogow, Jeffrey D. Larson, Justin Warner
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Patent number: 10724110Abstract: The invention provides systems and methods for analyzing viruses by representing viral genetic diversity with a directed acyclic graph (DAG), which allows genetic sequencing technology to detect rare variations and represent otherwise difficult-to-document diversity within a sample. Additionally, a host-specific sequence DAG can be used to effectively segregate viral nucleic acid sequence reads from host sequence reads when a sample from a host is subject to sequencing. Known viral genomes can be represented using a viral reference DAG and the viral sequence reads from the sample can be compared to viral DAG to identify viral species or strains from which the reads were derived. Where the viral sequence reads indicate great genetic diversity in the virus that was infecting the host, those reads can be assembled into a DAG that itself properly represents that diversity.Type: GrantFiled: February 3, 2016Date of Patent: July 28, 2020Assignee: Seven Bridges Genomics Inc.Inventors: Devin Locke, Piotr Szamel
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Patent number: 10705008Abstract: 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.Type: GrantFiled: March 17, 2014Date of Patent: July 7, 2020Assignee: Iris International, Inc.Inventors: Bart J. Wanders, Brett Jordan, Gregory A. Farrell, Thomas H. Adams, Warren Groner
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Patent number: 10685740Abstract: Methods and systems for monitoring and determining antimicrobial resistance and antimicrobial treatment using genomic subtype information. Various embodiments utilize molecular epidemiology and next-generation sequencing technologies (NGS) to monitor multi-drug resistant pathogens and provide early insight into emergent microbial threats.Type: GrantFiled: March 10, 2016Date of Patent: June 16, 2020Assignee: Koninklijke Philips N.V.Inventors: Sitharthan Kamalakaran, Pramod Mayigowda, Henry Lin, Sonia Chothani
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Patent number: 10622096Abstract: 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.Type: GrantFiled: September 8, 2017Date of Patent: April 14, 2020Assignee: Edico Genome CorporationInventors: Pieter van Rooyen, Michael Ruehle, Rami Mehio
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Patent number: 10607719Abstract: 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.Type: GrantFiled: December 3, 2012Date of Patent: March 31, 2020Assignee: Koninklijke Philips N.V.Inventors: Sunil Kumar, Randeep Singh, Biswaroop Chakrabarti, Subodh Kumar
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Patent number: 10597696Abstract: 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.Type: GrantFiled: September 18, 2014Date of Patent: March 24, 2020Assignee: University of Notre Dame du LacInventors: Kasturi Haldar, Md. Suhail Alam
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Patent number: 10600503Abstract: 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.Type: GrantFiled: August 3, 2012Date of Patent: March 24, 2020Assignee: GEORGETOWN UNIVERSITYInventors: Subha Madhavan, Michael A. Harris, Yuriy Gusev, Andrew Shinohara, David M. Tanenbaum, Kevin Rosso
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Patent number: 10597711Abstract: 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.Type: GrantFiled: April 9, 2013Date of Patent: March 24, 2020Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: Earl Hubbell, Jonathan Schultz
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Patent number: 10586609Abstract: 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.Type: GrantFiled: October 29, 2015Date of Patent: March 10, 2020Assignee: International Business Machines CorporationInventors: Jian Dong Ding, Sheng Huang, Junchi Yan, Ya Nan Zhang, Jun Zhu
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Patent number: 10564123Abstract: 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.Type: GrantFiled: May 11, 2018Date of Patent: February 18, 2020Assignee: UNITED ARAB EMIRATES UNIVERSITYInventors: Mahmoud F. Y. Al Ahmad, Hina Laghari
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Patent number: 10557821Abstract: 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.Type: GrantFiled: February 1, 2019Date of Patent: February 11, 2020Assignee: LIFE TECHNOLOGIES CORPORATIONInventors: David Denny, David Woo, Manjula Aliminati, Siva Kumar Samsani, Stephanie Schneider, Yoke Peng Lim, Sylvia Chang
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Patent number: 10540324Abstract: 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.Type: GrantFiled: January 9, 2019Date of Patent: January 21, 2020Assignee: SYNTEKABIO CO., LTD.Inventors: Jongsun Jung, Sunho Lee, Sojeong Ka, Jonghui Hong, Yangrae Cho
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Patent number: 10515450Abstract: 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.Type: GrantFiled: October 20, 2017Date of Patent: December 24, 2019Assignee: University of Florida Research Foundation, Inc.Inventors: Tanmay P. Lele, Wallace Gregory Sawyer
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Patent number: 10503967Abstract: 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.Type: GrantFiled: November 23, 2015Date of Patent: December 10, 2019Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIAInventors: Majid Sarrafzadeh, Foad Dabiri, Hyduke Noshadi
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Patent number: 10501779Abstract: 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.Type: GrantFiled: May 11, 2012Date of Patent: December 10, 2019Assignee: President and Fellows of Harvard CollegeInventors: Chao-ting Wu, Brian Beliveau
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Patent number: 10495561Abstract: 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.Type: GrantFiled: March 17, 2014Date of Patent: December 3, 2019Assignee: Iris International, Inc.Inventors: Bart J. Wanders, Brett Jordan, Gregory A. Farrell, Thomas H. Adams, Warren Groner
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Patent number: 10475190Abstract: 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.Type: GrantFiled: July 25, 2017Date of Patent: November 12, 2019Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Anindya Sarkar, Jim Martin
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Patent number: 10467749Abstract: 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.Type: GrantFiled: October 5, 2017Date of Patent: November 5, 2019Assignee: GENEMIND BIOSCIENCES COMPANY LIMITEDInventors: Weibin Xu, Huan Jin, Qin Yan, Zefei Jiang, Zhiliang Zhou
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Patent number: 10428367Abstract: 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.Type: GrantFiled: July 13, 2016Date of Patent: October 1, 2019Assignee: ILLUMINA, INC.Inventors: Robert C. Kain, Min-Jui Richard Shen, John A. Moon, Helmy A. Eltoukhy
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Patent number: 10373707Abstract: 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.Type: GrantFiled: December 31, 2018Date of Patent: August 6, 2019Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATIONInventors: Laxmi P. Parida, Filippo Utro
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Patent number: 10364467Abstract: 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.Type: GrantFiled: January 12, 2016Date of Patent: July 30, 2019Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang
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Patent number: 10364465Abstract: 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.Type: GrantFiled: August 15, 2014Date of Patent: July 30, 2019Assignee: Life Technologies CorporationInventors: Mona Shahbazian, Kara Norman, Aron Lau, Nakul Nataraj
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Patent number: 10345217Abstract: 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.Type: GrantFiled: January 25, 2018Date of Patent: July 9, 2019Assignee: Iris International, Inc.Inventors: Bart J. Wanders, Thomas H. Adams, Gregory A. Farrell, Warren Groner, Xiaodong Zhao
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Patent number: 10336998Abstract: 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.Type: GrantFiled: March 16, 2018Date of Patent: July 2, 2019Assignee: Zymergen Inc.Inventors: Zach Serber, Erik Jedediah Dean, Shawn Manchester, Katherine Gora, Michael Flashman, Erin Shellman, Aaron Kimball, Shawn Szyjka, Barbara Frewen, Thomas Treynor, Kenneth S. Bruno
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Patent number: 10311239Abstract: 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).Type: GrantFiled: February 21, 2014Date of Patent: June 4, 2019Assignee: Mitsubishi Space Software Co., Ltd.Inventors: Shigeki Tanishima, Nori Matsuda
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Patent number: 10296710Abstract: 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.Type: GrantFiled: June 15, 2016Date of Patent: May 21, 2019Assignee: Ancestry.com DNA, LLCInventors: Mathew J. Barber, Ross E. Curtis, Catherine Ann Ball, Kenneth Gregory Chahine
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Patent number: 10294290Abstract: 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.Type: GrantFiled: November 10, 2016Date of Patent: May 21, 2019Assignee: The Research Foundation for The State University of New YorkInventor: Srinivas Pentyala
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Patent number: 10289800Abstract: 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.Type: GrantFiled: May 20, 2013Date of Patent: May 14, 2019Inventors: John Stuelpnagel, Craig Struble, Eric Wang