Abstract: Method and system for predicting a complete tandem mass spectrum of a molecule are disclosed. For example, the method includes training a prediction model using a dataset with features that incorporate at least one physiochemical feature derived from one or more peptide sequences and predicting complete tandem mass spectra of a molecule using the prediction model, the complete tandem mass spectra including backbone fragment ions and non-backbone fragment ions.

Abstract: The system disclosed implements a secure method for facilitating secure exchange of health information among various stakeholders, including data owners or contributors, data requestors or miners, and medical providers, including hospitals, clinics, and research laboratories. Additional aspects of the system provide means for conducting secure research on health data collected from data contributors. Health information is exchanged using a decentralized system that incentivizes data contributors to provide health data to data miners. The data miners, which may be pharmaceutical companies, medical laboratories, or hospitals, use various methods in order to perform research on aggregated contributor data, while maintaining contributor privacy.

Abstract: Technologies for identifying one or more neoepitope peptides include generating a database that includes peptide sequences within a predefined range of length of residues, assigning a prior probability to each of the peptide sequences in the database, obtaining mass spectra of a plurality of fragments of a target molecule produced by mass spectrometry, determining, for each mass spectrum, matching scores of peptide-spectrum matches between the mass spectra and the peptide sequences in the database as a function of prior probabilities of the peptide sequences and matching probabilities, and determining a subset of the peptide-spectrum matches that has a corresponding matching score higher than a threshold.

Abstract: The system disclosed implements a secure method for facilitating secure exchange of health information among various stakeholders, including data owners or contributors, data requestors or miners, and medical providers, including hospitals, clinics, and research laboratories. Additional aspects of the system provide means for conducting secure research on health data collected from data contributors. Health information is exchanged using a decentralized system that incentivizes data contributors to provide health data to data miners. The data miners, which may be pharmaceutical companies, medical laboratories, or hospitals, use various methods in order to perform research on aggregated contributor data, while maintaining contributor privacy.

Abstract: System and methods are provided for performing privacy-preserving, high-performance, and scalable DNA read mapping on hybrid clouds including a public cloud and a private cloud. The systems and methods offer strong privacy protection and have the capacity to process millions of reads and allocate most of the workload to the public cloud at a small overall cost. The systems and methods perform seeding on the public cloud using keyed hash values of individual sequencing reads' seeds and then extend matched seeds on the private cloud. The systems and methods are designed to move the workload of read mapping from the extension stage to the seeding stage, thereby ensuring that the dominant portion of the overhead is shouldered by the public cloud.

Abstract: Method including securely calculating, by a processor in electrical communication with a genome registry, an edit-distance between a query private genome and a second private genome, and securely calculating, by the processor, a set difference size between the query genome and the second private genome are disclosed. Systems capable of performing similar patient queries while preserving privacy are also disclosed.

Abstract: Illustrative embodiments of methods and apparatus for identifying one or more intact glycopeptides in a sample are disclosed. According to one illustrative embodiment, a method may comprise receiving data representing a plurality of mass spectra obtained from mass spectrometry of the sample, scoring data representing each of the plurality of mass spectra against data associated with target glycopeptides, and identifying one or more intact glycopeptides in the sample based at least in part on the scoring of the data representing each of the plurality of mass spectra.

Abstract: System and methods are provided for performing privacy-preserving, high-performance, and scalable DNA read mapping on hybrid clouds including a public cloud and a private cloud. The systems and methods offer strong privacy protection and have the capacity to process millions of reads and allocate most of the workload to the public cloud at a small overall cost. The systems and methods perform seeding on the public cloud using keyed hash values of individual sequencing reads' seeds and then extend matched seeds on the private cloud. The systems and methods are designed to move the workload of read mapping from the extension stage to the seeding stage, thereby ensuring that the dominant portion of the overhead is shouldered by the public cloud.

Abstract: System and methods are provided for performing privacy-preserving, high-performance, and scalable DNA read mapping on hybrid clouds including a public cloud and a private cloud. The systems and methods offer strong privacy protection and have the capacity to process millions of reads and allocate most of the workload to the public cloud at a small overall cost. The systems and methods perform seeding on the public cloud using keyed hash values of individual sequencing reads' seeds and then extend matched seeds on the private cloud. The systems and methods are designed to move the workload of read mapping from the extension stage to the seeding stage, thereby ensuring that the dominant portion of the overhead is shouldered by the public cloud.

Abstract: Illustrative embodiments of methods and apparatus for identifying one or more intact glycopeptides in a sample are disclosed. According to one illustrative embodiment, a method may comprise receiving data representing a plurality of mass spectra obtained from mass spectrometry of the sample, scoring data representing each of the plurality of mass spectra against data associated with target glycopeptides, and identifying one or more intact glycopeptides in the sample based at least in part on the scoring of the data representing each of the plurality of mass spectra.

Abstract: System and methods are provided for performing privacy-preserving, high-performance, and scalable DNA read mapping on hybrid clouds including a public cloud and a private cloud. The systems and methods offer strong privacy protection and have the capacity to process millions of reads and allocate most of the workload to the public cloud at a small overall cost. The systems and methods perform seeding on the public cloud using keyed hash values of individual sequencing reads' seeds and then extend matched seeds on the private cloud. The systems and methods are designed to move the workload of read mapping from the extension stage to the seeding stage, thereby ensuring that the dominant portion of the overhead is shouldered by the public cloud.

Abstract: A method of inferring presence of at least one protein in a sample includes entering a peptide training data set into a statistical inference model. The method further includes training the statistical inference model with the peptide training data set. The method further includes determining predicted detectability of at least one peptide present in the sample with the trained statistical inference model. The method further includes inferring the presence of the at least one protein in the sample based upon the determined predicted detectability. Methods for quantifying proteins present in a sample are also disclosed.

Abstract: A new Eulerian Superpath approach to fragment assembly in DNA sequencing that resolves the problem of repeats in fragment assembly is disclosed. The invention provides for the reduction of the fragment assembly to a variation of the classical Eulerian path problem. This reduction opens new possibilities for repeat resolution and allows one to generate provably optimal error-free solutions of the large-scale fragment assembly problems.