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Seven Bridges Genomics Inc patents


Recent patent applications related to Seven Bridges Genomics Inc. Seven Bridges Genomics Inc is listed as an Agent/Assignee. Note: Seven Bridges Genomics Inc may have other listings under different names/spellings. We're not affiliated with Seven Bridges Genomics Inc, we're just tracking patents.

ARCHIVE: New 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 | Company Directory "S" | Seven Bridges Genomics Inc-related inventors


Data security in bioinformatic sequence analysis

Systems and methods for protecting information stored in private references that are available to be queried—e.g., graph-based sequence references that users query through an interface, providing short reads to obtain the results of an alignment against the reference sequence—analyze the query and/or alignment results to determine whether the query represents an attack. The analysis may be performed before returning results to a user, and in some cases before performing the alignment.. ... Seven Bridges Genomics Inc

Watermarking for data security in bioinformatic sequence analysis

Embodiments of the invention protect information stored in graph-based sequence references by “watermarking” the graph with uniquely identifiable information. The watermark identifies the graph or version thereof in a detectable but nonintrusive manner. ... Seven Bridges Genomics Inc

Systems and methods for analyzing sequence data

The invention provides methods for comparing one set of genetic sequences to another without discarding any information within either set. A set of genetic sequences is represented using a directed acyclic graph (dag) avoiding any unwarranted reduction to a linear data structure. ... Seven Bridges Genomics Inc

Generation and use of simulated genomic data

Embodiments of the invention utilize a graph-based approach for simulating genomic datasets from large scale populations. Genomic data may be represented as a directed acyclic graph (dag) that incorporates individual sample data including variant type, position, and zygosity. ... Seven Bridges Genomics Inc

Systems and methods for aligning sequences to personalized references

Techniques for generating a personalized reference sequence construct for an individual to align sequence reads obtained for the individual. The techniques include: obtaining a plurality of sequence reads for an individual; obtaining information identifying a plurality of locations; genotyping the plurality of sequence reads for the plurality of locations to obtain a first set of variants for the individual for at least some of the plurality of locations; identifying a second set of variants associated with the first set of variants; generating a personalized reference sequence construct using the second set of variants; and aligning the plurality of sequence reads to the personalized reference sequence construct.. ... Seven Bridges Genomics Inc

Systems and methods for aligning sequences to graph references

Various embodiments of the disclosure relate to systems and methods for aligning a sequence read to a graph reference. In one embodiment, the method comprises selecting a first node from a graph reference, the graph reference comprising a plurality of nodes connected by a plurality of directed edges, at least one node of the plurality of nodes having a nucleotide sequence. ... Seven Bridges Genomics Inc

Systems and methods for sequence encoding, storage, and compression

Genomic data is written to disk in a compact format by dividing the data into segments and encoding each segment with the smallest number of bits per character necessary for whatever alphabet of characters appears in that segment. A computer system dynamically chooses the segment boundaries for maximum space savings. ... Seven Bridges Genomics Inc

Hashing data-processing steps in workflow environments

Various approaches for data storage and retrieval for a computer memory include processing a computational workflow having multiple data-processing steps, generating and storing a first hash value associated with a first step of the data-processing steps based on an input to the first step, generating and storing a second hash value associated with a second step of the data-processing steps based on the generated first hash value, and reconstructing a computational state of the workflow based on the second hash value, and thereby avoid re-execution of a portion of the workflow corresponding to the second hash value.. . ... Seven Bridges Genomics Inc

Systems and methods for detecting recombination

A method for screening for disease in a genomic sample is includes receiving a representation of a reference genome comprising a sequence of symbols. The presence of a predicted mutational event is identified in a location of the reference genome. ... Seven Bridges Genomics Inc

Systems and methods for processing computational workflows

In one embodiment, a method of processing a computational workflow comprises receiving a description of a computational workflow. The description comprises a plurality of steps, in which each step has at least one input and at least one output, and further wherein an input from a second step depends on an output from a first step. ... Seven Bridges Genomics Inc

Computer method and system of identifying genomic mutations using graph-based local assembly

Computer-implemented methods and systems for performing a local assembly of a genomic region of interest include the de novo or assisted creation of a directed graph, such as a directed acyclic graph (dag), from a plurality of obtained nucleotide sequence reads. First and second sequence reads are aligned to each other to define at least one node of the dag. ... Seven Bridges Genomics Inc

Systems and methods for reconciling variants in sequence data relative to reference sequence data

Techniques for identifying variations in sequence data relative to reference sequence data. The techniques include accessing information specifying multiple sets of variants in the sequence data relative to reference sequence data, each of the multiple sets of variants being generated by using a respective variant identification technique; and determining, using the information specifying the multiple sets of variants in the sequence data, a reconciled set of variants in the sequence data relative to the reference sequence data, the determining comprising: determining whether a first variant is present at a first position in the sequence data based, at least in part, on one or more variants at one or more other positions in the sequence data.. ... Seven Bridges Genomics Inc

Method and apparatus for identifying tandem repeats in a nucleotide sequence

A method and corresponding apparatus for identifying tandem repeats in a nucleotide sequence is described. Tandem repeats can be identified by identifying one or more lines present in a self-alignment plot of the nucleotide sequence. ... Seven Bridges Genomics Inc

Systems and methods for genotyping with graph reference

Genomic references are structured as a reference graph that represents diploid genotypes in organisms. A path through a series of connected nodes and edges represents a genetic sequence. ... Seven Bridges Genomics Inc

07/27/17 / #20170211205

Systems and methods for encoding genetic variation for a population

In one embodiment, a method of encoding variation data for a population comprises receiving, by a variant encoding engine executing on a processor, information describing genetic variation of a population of individuals. The information comprises a plurality of variable sites within the reference genome of the population and the genotypes of a plurality of individuals in the population with respect to those variable sites. ... Seven Bridges Genomics Inc

07/20/17 / #20170206242

Methods and systems for generating, by a visual query builder, a query of a genomic data store

A method for generating a query of a genomic data store includes receiving, by a query generator executing on a computing device, from a graphical user interface, an identification of a first entity of a first entity class for inclusion in a resource description framework (rdf) query. The method includes receiving from the graphical user interface, an identification of a second entity of the first entity class, the second entity having a bi-directional relationship with the first entity. ... Seven Bridges Genomics Inc

07/13/17 / #20170199960

Systems and methods for adaptive local alignment for graph genomes

Systems and methods for analyzing genomic information can include obtaining a sequence read including genetic information; identifying, within a graph representing a reference genome, a plurality of candidate mapping positions that relate to the genetic information, the graph comprising nodes representing genetic sequences and edges connecting pairs of nodes; determining, by means of a computer system, whether an alignment with the graph surrounding each of the plurality of candidate mapping positions is advanced or basic; and performing for each candidate mapping position, by means of the computer system, a local alignment based on whether the local alignment is advanced or basic. The advanced local alignment can include a first-local-alignment algorithm, and the basic local alignment includes a second-local-alignment algorithm. ... Seven Bridges Genomics Inc

07/13/17 / #20170199959

Genetic analysis systems and methods

Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing. The graph branches into plural paths, each defined by pointers to other fixed locations in the memory, where the genomes diverge due to either divergent homology or non-homologous portions. ... Seven Bridges Genomics Inc

07/13/17 / #20170199764

Systems and methods for smart tools in sequence pipelines

The invention relates to bioinformatics pipelines and wrapper scripts that call executables in those pipelines and that also identify beneficial changes to the pipelines. A tool in a pipeline has a smart wrapper that can cause the tool to analyze the sequence data it receives but that can also select a change to the pipeline when circumstances warrant. ... Seven Bridges Genomics Inc

07/13/17 / #20170198351

Systems and methods for analyzing circulating tumor dna

The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor dna. A patient-specific reference directed acyclic graph (dag) represents known human genomic sequences and non-tumor dna from the patient as well as known tumor-associated mutations. ... Seven Bridges Genomics Inc

04/20/17 / #20170109383

Biological graph or sequence serialization

Methods of the invention include representing biological data in a memory subsystem within a computer system with a data structure that is particular to a location in the memory subsystem and serializing the data structure into a stream of bytes that can be deserialized into a clone of the data structure. In a preferred genomic embodiment, the biological data comprises genomic sequences and the data structure comprises a genomic directed acyclic graph (dag) in which objects have adjacency lists of pointers that indicate the location of any object adjacent to that object. ... Seven Bridges Genomics Inc

03/02/17 / #20170058365

Systems and methods for analyzing viral nucleic acids

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. ... Seven Bridges Genomics Inc

03/02/17 / #20170058341

Systems and methods for mitochondrial analysis

The invention provides methods of analyzing an individual's mtdna by transforming available reference sequences into a directed graph that compactly represents all the information without duplication and comparing sequence reads from the mtdna to the graph to identify the individual or describe their mtdna. A directed graph can represent all of the genetic variation found among the mitochondrial genomes across all of a number of reference organisms while providing a single article to which sequence reads can be aligned or compared. ... Seven Bridges Genomics Inc

03/02/17 / #20170058320

Systems and methods for epigenetic analysis

The invention provides systems and methods for determining patterns of modification to a genome of a subject by representing the genome using a graph, such as a directed acyclic graph (dag) with divergent paths for regions that are potentially subject to modification, profiling segments of the genome for evidence of epigenetic modification, and aligning the profiled segments to the dag to determine locations and patterns of the epigenetic modification within the genome.. . ... Seven Bridges Genomics Inc








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