Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: The present invention relates to proteomics, and techniques for predicting of mass spectrometry data of chains of amino acids, such as peptides, proteins, or combinations thereof. Particularly, aspects of the present invention are directed to a computer implemented method that includes obtaining a digital representation of a peptide sequence, the digital representation including a plurality of container elements, each container element of the plurality of container elements representing an amino acid residue; encoding, using a bidirectional recurrent neural network of long short term memory cells, each container element as an encoded vector; and decoding, using a fully-connected network, each of the encoded vectors into a theoretical output spectrum. The theoretical output spectra are represented as a one-dimensional data set or a multi-dimensional data set including intensity values for each fragment ion including one or more of the amino acid residues in the theoretical output spectra.

Abstract: CNA biomarkers can include nucleic acid sequences that are present in circulating nucleic acids obtained from circulatory systems of a population known to have cancer, but that are rarely present, if at all, in circulating nucleic acids obtained from circulatory systems of a control population. Information is received describing one or more sequences obtained from circulating nucleic acids in a population known to have cancer. Information is also received describing one or more sequences obtained from circulating nucleic acids in a control population. A cluster analysis within a predetermined portion of a genome uses the one or more sequences in the circulating nucleic acids obtained from the population known to have cancer and the one or more sequences in the circulating nucleic acids obtained from the control population. Information is generated identifying one or more biomarkers for the cancer based on a cluster search within results of the cluster analysis.

Abstract: A method for designing a multi-objective primer pair is disclosed. The method includes inputting a DNA template fragment, a length of a forward primer, a length of a reverse primer, at least two objectives and optimal values for each of the at least two objectives to a computer system; generating, by the computer system, a plurality of primer pairs according to the DNA template fragment, the length of the forward primer and the length of the reverse primer; and calculating, by the computer system, numerical values of the at least two objectives of each of the plurality of primer pairs and inputting the numerical values of the at least two objectives of each of the plurality of primer pairs to a Pareto Chart tool to obtain at least one primer pair, and taking the primer pair as an optimal solution of the DNA template fragment.

Abstract: A feature identifying method and an electronic device are provided. The method includes: obtaining a plurality of physiological information obtained by measuring a subject at a plurality of time points in one day; converting the plurality of physiological information into a plurality of correlation features respectively; establishing a plurality of first risk prediction models according to the plurality of correlation features, and identifying at least one first correlation feature from the plurality of correlation features according to the plurality of first risk prediction models; establishing a plurality of second risk prediction models according to the at least one first correlation feature, and identifying, according to the plurality of second risk prediction models, at least one second correlation feature capable of predicting a specific disease from the at least one first correlation feature; and outputting the at least one second correlation feature.

Abstract: Methods and systems for CRISPR positive selection are described. CRISPR positive selection uses DNA sequencing to identify genes that their perturbation by CRISPR guide RNAs is correlated to the phenotype. In some aspects, disclosed are genome-wide CRISPR/Cas9 screening methods to identify genetic modifiers. Also disclosed are the apparatuses used for performing the methods.

Abstract: A method for linking a natural product and gene cluster is disclosed. In some embodiments, monomers of natural products are predicted from a gene sequence. In other embodiments, monomers of natural products are predicted from a chemical structure of a natural product. In another embodiment, monomers predicted from gene sequences are aligned with monomers predicted from chemical structures.

Abstract: Techniques for determining therapy scores for at least two of an anti-PD1 therapy, an anti-CTLA4 therapy, an IL-2 therapy, an IFN alpha therapy, an anti-cancer vaccine therapy, an anti-angiogenic therapy, and an anti-CD20 therapy. The techniques include determining, using sequencing data for the subject and information indicating distribution of biomarker values across one or more reference populations, a first set of normalized biomarker scores for a first set of biomarkers associated with a first therapy; and a second set of normalized biomarker scores for a second set of biomarkers associated with a second therapy; providing the first set of normalized biomarker scores as input to a statistical model to obtain a first therapy score for the first therapy; and providing the second set of normalized biomarker scores as input to the statistical model to obtain a second therapy score for the second therapy.

Abstract: A genomic data analyzer maybe configured to detect and characterize biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events. The variant analysis module maybe used in next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays.

Abstract: Methods and systems for extracellular vesicle characterization are provided herein. Embodiments of the methods include inputting measured physical, biological, or chemical aspects of extracted extracellular vesicles. Next, an information architecture that characterizes relationships between biological entities and diseases in humans or other vertebrates is generated. Then, relationships between the measured physical, biological, or chemical aspects of the isolated extracellular vesicles with the information architecture are automatically inferred, thereby characterizing extracellular vesicles.

Abstract: Methods and apparatus for compressing and decompressing genetic information from an individual. In one arrangement, a data compression method generates a compressed representation of at least a portion of an individual's genome by receiving an input file having a representation of the genome as a sequence of variants defined relative to a reference genome. A reference database having a plurality of reference lists of genetic variants from other individuals is accessed. Each reference list has a sequence of genetic variants from a single, phased haplotype. Two mosaics of segments from the reference lists are identified which match the genome to within a threshold accuracy. Each mosaic represents a single one of the two haplotypes of the individual's genome and includes a portion of the sequence of genetic variants from one of the reference lists. The compressed representation is generated by encoding the two mosaics and deviations from the two mosaics.

Abstract: Nucleic acid sequence mapping/assembly methods are disclosed. The methods initially map only a contiguous portion of each read to a reference sequence and then extends the mapping of the read at both ends of the mapped contiguous portion until the entire read is mapped (aligned). In various embodiments, a mapping score can be calculated for the read alignment using a scoring function, score (i, j)=M+mx, where M can be the number of matches in the extended alignment, x can be the number of mismatches in the alignment, and m can be a negative penalty for each mismatch. The mapping score can be utilized to rank or choose the best alignment for each read.

Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for reconstructing and simulating neocortical microcircuitry. In one aspect, a method includes providing a model of neural tissue, the model including different types of neural cells and dynamic synaptic interconnections between the neural cells, changing a parameter in the model; and identifying a change in a computational state of the model of the neural tissue responsive to the change in the parameter. The change in the parameter can, e.g., change behavior of neural cells of at least one type, change interconnectivity between neural cells, or target a location within a volume in the model that interacts with multiple types of neural cells.

Abstract: The systems and methods provided herein relate to the performance of inverse reconstruction algorithms from ultrasound radiofrequency data and stress-strain data. These systems and methods can be applied to any soft tissue mechanical measurements, providing information about both mechanical properties and fiber orientation, and the relationships between them.

Abstract: A computer implemented system and method facilitates a cycle of generation, sharing, and refinement of volumes related to stimulation of anatomical tissue, such as brain or spinal cord stimulation. Such volumes can include target stimulation volumes, side effect volumes, and volumes of estimated activation. A computer system and method also facilitates analysis of groups of volumes, including analysis of differences and/or commonalities between different groups of volumes.

Abstract: A method of managing sequencing progress includes obtaining a plurality of samples and controlling a gene sequencing computing device to execute gene sequencing on the plurality of samples. Once a sequencing result is obtained by sending a query instruction to the gene sequencing computing device, sequencing information of the plurality of samples is displayed when a sequencing progress of the plurality of samples is determined to be meeting the preset condition according to the sequencing result.

Abstract: Techniques for simulating networks using dynamics-based constraints are disclosed.

Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or more match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.

Abstract: This disclosure provides for a highly-efficient and scalable compression tool that compresses quality scores, preferably by capitalizing on sequence redundancy. In one embodiment, compression is achieved by smoothing a large fraction of quality score values based on k-mer neighborhood of their corresponding positions in read sequences. The approach exploits the intuition that any divergent base in a k-mer likely corresponds to either a single-nucleotide polymorphism (SNP) or sequencing error; thus, a preferred approach is to only preserve quality scores for probable variant locations and compress quality scores of concordant bases, preferably by resetting them to a default value. By viewing individual read datasets through the lens of k-mer frequencies in a corpus of reads, the approach herein ensures that compression “lossiness” does not affect accuracy in a deleterious way.

Abstract: Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.