Abstract: Methods are provided for conducting a dual-probe assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments; hybridizing each of the set of released recognition element fragments to a coded oligonucleotide probe and using resulting hybridized released recognition elements as primers for copying the coded oligonucleotide probe to produce a sect of target-associated codes, wherein each of the coded oligonucleotide probes comprises a code from a set of codes, each code comprises at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides; and performing a detection event to identify a set of detected codes of the target-associated codes.

Abstract: Methods are provided for conducting an assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments comprising the recognition element sequence; combining the released recognition element fragments with an additional nucleic acid sequence from a set of additional nucleic acid sequences to create a circular nucleic acid, wherein the circular nucleic acid comprises a target-associated code and additional sequence elements; and performing a detection event to identify a set of detected codes of the target-associated codes.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: Methods are provided for conducting an assay for a set of targets. The methods include (a) performing a methylation sensitive transformation process on a sample comprising a set of target nucleic acid sequences; (b) performing a hybridization and ligation reaction with an encoded detection probe from a set of encoded detection probes unique for each of the targets, the probes comprising a nucleotide sequence code from a set of nucleotide sequence codes to generate an amplifiable probe, wherein the probes unique for unmethylated targets are not amplifiable; and (c) performing an amplification and detection process on the sample, wherein the methylated targets are detected by decoding the amplified codes associated with the methylated targets.

Abstract: Methods for assaying polypeptide targets are provided that include: (a) binding each target in a sample potentially comprising a set of polypeptide targets to a capture agent to yield a set of capture agent-target complexes; (b) performing a recognition event on the capture agent-target complexes to yield capture agent-target complexes comprising an encoded probe, the encoded probe comprising a code from a set of codes, each code comprising at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides; (c) performing a molecular transformation event to produce modified encoded probes in the presence of the target and unmodified encoded probes in the absence of the target, in which the modified probes can be amplified and the unmodified probes cannot be amplified in an amplification event; and (d) performing the amplification event and detecting the targets by decoding the codes that are amplified.

Abstract: A method of conducting an assay for a set of targets, comprising: subjecting each target of a set of targets to a recognition event, in which each target is uniquely recognized by and bound to a recognition element associated with a code from a set of codes, thereby yielding a set of coded targets comprising the target and the recognition element; subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element produces a modified recognition element, thereby yielding a set of modified recognition elements comprising the code; subjecting each code of the set of modified recognition elements to an amplifying event, in which each code is amplified, thereby yielding a set of amplified codes; subjecting each amplified code of the set of amplified codes to a detection event, thereby decoding the code.

Abstract: A method of conducting an assay for a set of targets, the method comprising: providing a set of targets; subjecting each target of the set of targets to a recognition event, in which each target is uniquely recognized by and bound to a recognition element associated with a code from a set of codes, thereby yielding a set of coded targets comprising the target and the recognition element; subjecting each recognition element of the set of coded targets to a transformation event, in which a molecular transformation of each recognition element produces a modified recognition element, thereby yielding a set of modified recognition elements comprising the code; subjecting each code of the set of modified recognition elements to an amplifying event, in which each code is amplified, thereby yielding a set of amplified codes; subjecting each amplified code of the set of amplified codes to a detection event, thereby determining the nucleic acid sequence of the code.

Abstract: Methods are provided for conducting an assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments comprising the recognition element sequence; combining the released recognition element fragments with an additional nucleic acid sequence from a set of additional nucleic acid sequences to create a circular nucleic acid, wherein the circular nucleic acid comprises a target-associated code and additional sequence elements; and performing a detection event to identify a set of detected codes of the target-associated codes.

Abstract: Methods are provided for conducting a dual-probe assay on a set of nucleic acid targets, including: combining a set of dual probes with a sample composition potentially comprising a set of nucleic acid targets to form a set of cleavable ternary nucleic acid complexes; releasing from the cleavable ternary nucleic acid complex a set of recognition element fragments; hybridizing each of the set of released recognition element fragments to a coded oligonucleotide probe and using resulting hybridized released recognition elements as primers for copying the coded oligonucleotide probe to produce a sect of target-associated codes, wherein each of the coded oligonucleotide probes comprises a code from a set of codes, each code comprises at least one segment encoding one or more symbols that correspond to a sequence of one or more nucleotides; and performing a detection event to identify a set of detected codes of the target-associated codes.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.

Abstract: A method and system for correlating genome data with EMR/MR data is disclosed herein. The method includes identifying a plurality of sources of genome data. The method also includes generating an index file for each of the plurality of genome files. The method also includes transmitting each index file to a central depository. The method also includes identifying electronic medical record (EMR) and/or personal health record (PHR) data at each source of the plurality of sources of genome data. The method also includes correlating each genome file of the plurality of genome files with a corresponding EMR/MR data.

Abstract: A method and system for correlating genome data with EMR/PHR data is disclosed herein. The method includes identifying a plurality of sources of genome data. The method also includes generating an index file for each of the plurality of genome files. The method also includes transmitting each index file to a central depository. The method also includes identifying electronic medical record (EMR) and/or personal health record (PHR) data at each source of the plurality of sources of genome data. The method also includes correlating each genome file of the plurality of genome files with a corresponding EMR/PHR data.

Abstract: A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit (CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline.