Abstract: The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the unique molecular index sequences include variable-length nonrandom sequences. In some implementations, the unique molecular index sequences are associated with the individual polynucleotide fragments based on alignment scores indicating similarity between the unique molecular index sequences and subsequences of sequence reads obtained from the individual polynucleotide fragments. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

Abstract: Provided herein are novel methods, systems and processes for generating and analyzing sequence data for the determination of the presence or absence of one or more genetic variations within a genome of a subject.

Abstract: An apparatus in one embodiment comprises a distributed data processing system in which multiple processing devices communicate with one another over at least one network. The distributed data processing system is configured to obtain reads of biological samples of respective sample sources, with each of the biological samples containing genomic material from a plurality of distinct microorganisms within an environment of a corresponding one of the sample sources, and to perform distributed data analytics to characterize an actual or potential outbreak of at least one of a disease, an infection and a contamination that involves genomic material from multiple ones of the distinct microorganisms in one or more of the sample sources. Performing distributed data analytics illustratively comprises performing local analytics in respective ones of a plurality of data zones, and performing global analytics utilizing results of the local analytics performed in the respective data zones.

Abstract: The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

Abstract: Systems and method for identifying variants associated with a genetic disease can include obtaining calls for a plurality of individuals for a list of variant positions. The calls can be compared to identify variants that are found in affected individuals and absent in non-affected individuals. Such variants can include loss of heterozygosity, trans-phased compound heterozygotes, increased frequency mitochondrial variants, homozygous recessive variants, de novo variants, sex-linked variants, and combinations thereof.

Abstract: An system, and method are disclosed for harmonic modulation of standing wavefields for spatial focusing, manipulation, and patterning of particles, cells, powders, aerosols, colloids, and solids using a multifrequency wave source, a chamber a control module and an analysis module to generate standard wavefields useful for tissue engineering, micro fabrication, therapeutic treatment, and diagnostic tests.

Abstract: Techniques regarding determining thermodynamic observables of a chemical system are provided. For example, one or more embodiments described herein can include a system, which can comprise a memory that can store computer executable components. The system can also include a processor, operably coupled to the memory, and that can execute the computer executable components stored in the memory. The computer executable components can include a potential energy component that can fit a potential energy function to a computed potential energy surface of a molecule. The computer executable components can also include a vibrational mode component that can compute an intramolecular vibrational mode of the molecule based on the potential energy surface fitted with the potential energy function. Also, the computer executable components can include a partition component that can compute a partition function based on the intramolecular vibrational mode.

Abstract: A method of designing a molecule for an environment of interest using a quantum computer includes providing a linear superposition of a plurality of molecular species, the plurality of molecular species being initially weighted by equal initial coefficients; determining a lowest-energy quantum state for the superposition of the plurality of molecular species in a vacuum environment and in the environment of interest using a quantum optimization process; calculating a difference in lowest energy states between the vacuum environment and the environment of interest for each molecular species to provide a cost of the superposition of the plurality of molecular species; performing a quantum optimization process to determine a minimum cost for the superposition of the plurality of molecular species and to determine updated coefficients weighting the plurality of molecular species; and identifying the molecule for the environment of interest based on a comparison of the updated coefficients.

Abstract: Provided is a biological information processing method and a device, a recording medium and a program that are able to predict and control changes in the state of an organism. The expression level of molecules in an organism is measured over a specific time interval; the measured time-series data is divided into a periodic component, an environmental stimulus response component and a baseline component; constant regions of the time-series data are identified from variations in the baseline component or from the amplitude or periodic variations of the periodic component; and causal relation between the identified constant regions is identified. The relation between the external environment and variations in the internal environment is identified and from the identified causal relation between the constant regions, changes in the state of the organism are inferred.

Abstract: Methods, systems and circuits evaluate a subject's risk of developing type 2 diabetes or developing or having prediabetes using at least one defined mathematical model of risk of progression that can stratify risk for patients having the same glucose measurement. The model may include NMR derived measurements of GlycA and a plurality of selected lipoprotein components of at least one biosample of the subject.

Abstract: Embodiments of the invention are directed to methods, systems and computer programs that provide improved risk stratification for people having elevated large HDL-P using at least one defined HDL risk interaction parameter.

Abstract: The present systems and methods introduce deep learning to de novo peptide sequencing from tandem mass spectrometry data, and in particular mass spectrometry data obtained by data-independent acquisition. The systems and methods achieve improvements in sequencing accuracy over existing systems and methods and enables complete assembly of novel protein sequences without assisting databases. To sequence peptides from mass spectrometry data obtained by data-independent acquisition, precursor profiles representing intensities of one or more precursor ion signals associated with a precursor retention time and fragment ion spectra representing signals from fragment ions and fragment retention times are fed into a neural network.

Abstract: An analytic method for improving the efficiency in identifying protein molecular effect information using low resolution x-ray crystallography, by selecting and imaging a protein sample with low resolution x-ray crystallography and assaying the data thus generated as to local ligand strain energy value, followed by calculating a real-space difference density Z for each element and compiling ZDD data therefrom, followed by determining the true protomer/tautomer state of the protein sample by calculating Scorei according to the following equation so that the highest Scorei signifies the molecular effect information: Scorei={((ZDDi??ZDD)/?ZDD)+((SEi??SE)/?SE)}.

Abstract: According to some embodiments of the present disclosure, a device is disclosed. In embodiments, the device stores a computer program comprised of a set of encoded executable instructions; a genomic differentiation object and genomic regulation instructions (GRI) that were used to encode the set of encoded executable instructions. The device further includes a processing system comprising a VDAX and a set of processing cores. The VDAX is configured to: receive encoded instructions to be executed from the set of encoded executable instructions and decode the encoded instructions into decoded executable instruction based on a modified genomic differentiation object and sequences extracted from metadata associated with the encoded instructions. In these embodiments, the modified genomic differentiation object is modified from the genomic differentiation object using the GRI.

Abstract: A device may receive information identifying results of a spectroscopic measurement of an unknown sample. The device may perform a first classification of the unknown sample based on the results of the spectroscopic measurement and a global classification model. The device may generate a local classification model based on the first classification. The device may perform a second classification of the unknown sample based on the results of the spectroscopic measurement and the local classification model. The device may provide information identifying a class associated with the unknown sample based on performing the second classification.

Abstract: Generating a new chemical structure by using a neural network using an expression region that expresses a particular property in a descriptor or an image for a reference chemical structure. The new chemical structure may be generated by changing a partial structure in the reference chemical structure that corresponds to the expression region.

Abstract: Methods and systems are disclosed for encoding and decoding data from genetic traits. In one embodiment, the invention provides a method of encoding data from genetic traits. The method comprises encoding genetic traits information, including using quantum dot wavelengths to identify distinct genetic traits, and using numbers of the quantum dots to represent probabilities associated with the traits. In an embodiment, the invention provides a genetic characteristics decoding system for decoding genetic information encoded using quantum dots in a carrier. The decoding system comprises a light source for charging the quantum dots in the carrier; a scanner for scanning the carrier to retrieve information from the charged quantum dots; and a processing system for processing the retrieved information to determine quantum dot wavelengths to identify distinct genetic traits, and to determine numbers of the quantum dots to identify probabilities associated with the genetic traits.

Abstract: A method for making a modified release composition, comprising: selecting a desired active agent and polymer matrix for formulating into a modified release composition; assessing degradation effect on release of the active agent from the composition including plotting polymer molecular weight (Mwr) at onset of active agent release vs. active agent molecular weight (MwA); predicting performance of multiple potential formulations for the composition based on the degradation assessment and average polymer matrix initial molecular weight (Mwo) to define a library of building blocks; determining the optimal ratio of the building blocks to satisfy a specified release profile; and making a modified release composition based on the optimal ratio determination.

Abstract: A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions.

Abstract: Systems and methods disclosed for recommending beauty products for a subject by using a DNA sequencer to generate genetic information; aggregating genetic information, beauty trend data, and cosmetic product response from a patient population; deep learning with a computer to generate at least one computer implemented classifier that predicts matching beauty products based on the genetic information, beauty trend data, and cosmetic product response from a patient population; and recommending one or more beauty products for the subject.