Abstract: Novel systems methods and kits are disclosed for determining effects of Nucleic Acid (NA) editing procedures. The technique (methods systems and kits) of the present invention are adapted for receiving sequencing data indicative of pluralities of reads, RTx={riTx} and RMc={rjMc}, of the multiplexed amplifications of each of the edit and control NA collections, originating from a similar source of NAs whereby a certain NA editing procedure was applied to the edit NA collection; and processing the sequencing data, per each particular type of adverse effect of interest to determine a statistical model for classifying whether that type of adverse effect actually occurred due to the NA editing procedure. The technique is suitable for determining occurrences of INDEL types and/or TRANSLOCATION types/species of adverse effect.

Abstract: A molecular data storage system is presented for encoding data-block(s). The system includes one or more populations of molecular sequences, each population encoding a respective one of the data-blocks. Each molecular sequence comprises a data encoding section comprising a sequence of similar predetermined length N of short k-mers, whereby in each population the data encoding sections of all molecular sequences have the similar predetermined length N. The short k-mers serve as data encoding building blocks of the data encoding sections, whereby valid short k-mers serving as data encoding building blocks form a subset of a building-block-set consisting of a number Z of different preselected short k-mers each presenting a unique combination of a number k of bases of a preselected set of bases, characterized in that all the Z types of short k-mers in said building-block-set have a similar predetermined size k?2 (plurality) of bases.

Abstract: Methods and devices obtain cellular-component, e.g., proteins, RNA, DNA, metabolites, and combinations of these, from a solid tissue in-vivo using electroporation, and subsequently profile such tissue either inside or outside the subject's body. A method for determining if a solid tissue of a subject includes a benign or malignant tumor, or if a space occupying lesion (SOL) within the solid tissue is malignant or benign, includes placing at least one electroporation-electrode within the solid tissue, or within the SOL or in proximity thereto; applying pulsed electric field (PEF) via the at least one electroporation-electrode to thereby induce permeabilization of cells of the solid tissue or the SOL, and consequently release of at least one cellular-component therefrom to an extracellular matrix between and surrounding the cells; extracting the at least one cellular-component from the extracellular matrix.

Abstract: A data storage system and method are provided, as well as systems and methods for fabrication, and writing and reading of data therein. The data storage system includes at least one population of molecular sequences including chains of basic molecular building-blocks, and defining at least one respective data-block encoding data in the data storage system. The data of the data-block is encoded in a sequence S=(?1, ?2, . . . , ?k . . . , ?K-1, ?K) of encoded letters {?k} associated with an alphabet ??{?m}|m=1 to M, which are encoded according to the types of basic molecular building-blocks appearing at k respective location along storage segments of the molecular sequences of the population. The molecular sequences include a number Z of different types of basic molecular building-blocks {En}|n=1 to Z, while the alphabet ? has a size M strictly greater than the number Z of types of building-blocks.

Abstract: Systems and methods for displaying gene- and/or protein-related data with respect to chromosome maps at locations identifying relevant positioning of the genes with which the gene- and/or protein related data are associated. Multiple experiments may be plotted onto the display adjacent one or more chromosome maps. Automatic extraction of genomic location, based on accession numbers or other unique identifiers and cross connection with expression data is provided. Statistical assessments of correlations between expression and genome localization may be performed. Zooming capabilities, thumbnail/fullview toggling, browsability and linked data may be included as features of the visualization systems described.

Abstract: Embodiments of the disclosure relate to apparatus for recommending items from a catalog of items to users in a population of users, configured to determine values for a measure of association between transactions of users with items in a first catalog and transactions of users with items in a second catalog and provide recommendations to users for transacting with items in the catalogs based on the determined values of association.

Abstract: A method of genome analysis is provided. In certain embodiments, the method of comprises: a) contacting a genomic sample comprising a double-stranded DNA with a site-specific nicking endonuclease to provide a nicked double-stranded DNA comprising a plurality of nick sites, in which the nicking endonuclease nicks a site adjacent to a variable nucleotide; b) contacting the nicked double-stranded DNA with a polymerase in the presence of a nucleotide composition comprising a first labeled nucleotide comprising a first label, thereby producing a labeled double-stranded DNA that is not labeled at every nick site; c) stretching out the labeled double-stranded DNA to provide a stretched, labeled double-stranded DNA; and d) imaging the stretched, labeled double-stranded DNA to identify a labeling pattern on the stretched labeled double-stranded DNA.

Abstract: A method of sample analysis is provided. In certain embodiments, the method comprises: a) site-specifically labeling a test genome with at least two different labels to produce a labeled genome labeled at a plurality of discrete sites across the genome; b) stretching a nucleic acid of the labeled genome to produce a linear pattern of the different labels along a region of a stretched nucleic acid; c) reading the labels along the region to provide a test pattern comprising a sequence of colors emitted by the labels; d) comparing the test pattern to a plurality of reference patterns obtained from a reference genome, in which the reference patterns are mapped to corresponding genomic locations in the reference genome; and e) identifying one or more reference patterns that match the test pattern, thereby mapping a location for the region in the test genome.

Abstract: Various embodiments of the present invention determine various quality metrics that reflect the quality of two or more identically-executed or similar array-based comparative-genomic-hybridization (“aCGH”) experiments. In certain embodiments of the present invention, a pairwise quality metric is generated for each possible pair of aCGH experimental results within a set of aCGH experimental results. The pairwise quality metrics may be summed and optionally normalized to produce an overall quality metric for the set of aCGH experimental results. Various pairwise quality metrics can be used in different embodiments of the present invention, including pairwise quality metrics based on measures of aberration overlap.

Abstract: Embodiments of the present invention include methods and systems for analysis of comparative genomic hybridization (“CGH”) data, including CGH data obtained from microarray experiments.

Abstract: Methods and compositions for detecting copy number variations between nucleic acid samples are provided. Also provided are kits for practicing methods in accordance with the invention.

Abstract: A polymerase chain reaction (PCR) mixture containing at least one unstructured nucleic acid primer pair is provided. In certain embodiments, the mixture may also contain: nucleotides, a DNA polymerase, and PCR reaction reagents, as well as a nucleic acid sample. The reaction mixture may be employed in, for example, a PCR reaction.

Abstract: The invention provides genes (DEA genes) that are differentially expressed in atherosclerotic lesions and polypeptides encoded by these genes. The invention provides compositions comprising a targeting agent conjugated to a functional moiety, wherein the targeting agent selectively binds to a polypeptide encoded by one a DEA gene. The functional moiety can be an imaging agent, therapeutic agent, etc. The invention further provides methods for providing diagnostic or prognostic information related to atherosclerosis involving detecting expression or activity of an expression product of one or more of the DEA genes. The invention further provides therapeutic methods comprising administering to a subject a composition comprising a targeting agent conjugated to a functional moiety that binds selectively binds to a polypeptide encoded by a DEA gene.

Abstract: Various embodiments of the present invention are directed to methods and systems for automatic, statistically meaningful detection of aberrations common to multiple samples within a sample set. Many various aberration-calling techniques are used to identify aberrant intervals within each of the samples of the sample set. A set of candidate intervals is constructed to include the aberrant intervals identified by the aberration-calling technique, as well as two-way intersections of the identified aberrant intervals. A score indicating the statistical relevance of each candidate interval with respect to each sample is next assigned to each candidate interval. Then, a total significance score is assigned to each candidate interval based on the individual scores for the candidate interval with respect to each sample. The most statistically significant candidate intervals may be selected based on the total significance scores assigned to the candidate intervals.

Abstract: Various embodiments of the present invention determine a zero point, or centralization constant ?, for an array-based comparative genomic hybridization (“aCGH”) data set by identifying a zero-point value, or centralization constant ?, that, when used in an aberration-calling analysis of the aCGH data, results in the fewest number of array-probe-complementary genomic sequences identified as having abnormal copy numbers with respect to a control genome, or, in other words, results in the greatest number of array-probe-complementary genomic sequences identified as having normal copy numbers. In one embodiment, interval-based analysis of an aCGH data set may be carried out using a range of putative zero-point values, and the zero-point value for which the maximum number of genomic sequences are determined to have normal copy numbers may then be selected.

Abstract: The overexpression of certain marker genes including Wnt5a has been found useful in the identification of more aggressive forms of malignant melanoma. Therefore, the overexpression of these genes in tumor samples of malignant melanoma may be useful in the diagnosis, profiling, and treatment of patients suffering from this disease. Inhibitors of Wnt5a activity may be useful in the treatment of aggressive forms of malignant melanoma. Inhibition of Wnt5a activity may be effected by any method including anti-sense therapy, gene therapy, and pharmaceutical intervention.

Abstract: Various embodiments of the present invention are directed to methods and systems for sequencing a target molecule. In one embodiment of the present invention, a spectrum of the target molecule is determined. A decoration pattern of the target molecule is determined using physical methods. One or more candidate molecule sequences are determined based on having nucleic acid sequences that are consistent with the spectrum and the decoration pattern of the target molecule.

Abstract: In various embodiments of the present invention, initial gene-expression data is initially partitioned into classes by patient, subject, or other identifier of a source of samples, expression-level-differences are computed for each gene with respect to each initial partition, and a rank consistency score or fold-change consistency score is computed for each gene from the expression-level difference metrics computed for each initial partition. In other words, rather than partitioning gene-expression-level data directly into two or more classes relative to an event of interest, the gene-expression-level data is first partitioned according to sample source, and then each sample-source partition is partitioned into two or more classes relative to an event of interest. Levels of significance, or p-values, can be straightforwardly computed for both rank consistency scores and fold-change consistency scores.

Abstract: Methods, tools, systems and computer readable media for analyzing CGH data, together with data from an independent source. Independent data is compared with the CGH data, wherein the CGH data is characterized by sets of defined regions differentiated by at least one property. Enrichment is assessed for at least one subset of the data from an independent source with regard to at least one of the sets of defined regions in the CGH data. Methods, tools, systems and computer readable media for visualizing CGH data as it is impacted by data from an independent source are also provided. A relationship between at least one defined set of the CGH data and at least one set of sequence elements defined in the data from an independent source may be visualized.

Abstract: Embodiments of the present invention are directed to increasing the reliability, precision, and resolution of identification, by analysis of comparative genomic hybridization (“CGH”) data and array-based comparative genomic hybridization (“aCGH”) data, of intervals along one or more chromosomes in which the copy number of the DNA subsequence within the interval in a sample genome is difference from the copy number of the DNA subsequence within a standard, or normal, genome. In various embodiments of the present invention, statistical data-quality measures are incorporated into comprehensive, quality-based interval-scores.