Rosetta Inpharmatics LLC Patent applications |
Patent application number | Title | Published |
20100113287 | METHODS FOR ASSESSING THE REPRESENTATION OF NUCLEIC ACID MOLECULES IN A NUCLEIC ACID LIBRARY - The invention provides methods for evaluating the representation of expected nucleic acid molecules in a test population of nucleic acid molecules. The methods each comprise the steps of: (a) hybridizing a population of sample nucleic acid molecules obtained from a test population of nucleic acid molecules to a substrate comprising a population of target nucleic acid molecules, wherein (i) each target nucleic acid molecule comprises a predetermined sequence corresponding to an expected nucleic acid molecule, and (ii) each target nucleic acid molecule is localized to a defined area of the substrate; and (b) evaluating the representation of expected nucleic acid molecules in the test population of nucleic acid molecules by analyzing the pattern of hybridization of the sample population of nucleic acid molecules to the target nucleic acid molecules. | 05-06-2010 |
20100106460 | NON-CONTIGUOUS REGIONS PROCESSING - Non-contiguous regions of interest as well as contiguous regions of interest are similarly processed. After an isotope peak detector has identified isotope peaks on LC/MS images, a microaligner microaligns bounding areas of identified isotope peaks and redefines the bounding areas to help subsequent scoring process. Forms of isotope peaks influence formation of a peak association matrix and a mass/charge association map which creates association in the mass/charge dimension. A correlation scorer produces reproducibility scores as well as quality scores to help aid scientists to discover biological features of interest. | 04-29-2010 |
20100040552 | METHODS TO EVALUATE GLUCOCORTICOID RECEPTOR AGONISTS AND ANTAGONISTS FOR EFFECTS ON NEURON-LIKE CELLS - The present invention provides methods for identifying a modulator of glucocorticoid receptor activity. In one embodiment, the methods include the steps of (a) contacting neuron-like cells, in vitro, with a chemical agent; (b) measuring the expression of a member, or group of members, of a group of genes (as defined herein) in the neuron-like cells contacted with the chemical agent; and (c) determining whether the chemical agent significantly alters the expression of the member, or group of members, of the group of genes, thereby determining whether the chemical agent is likely to be a modulator of glucocorticoid receptor activity. In another embodiment, an in vivo method for identifying a modulator of glucocorticoid receptor activity is provided. | 02-18-2010 |
20100035966 | METHODS AND COMPOSITIONS FOR REGULATING CELL CYCLE PROGRESSION - In one aspect, a method is provided of inhibiting proliferation of a mammalian cell comprising introducing into said cell an effective amount of at least one at least one small interfering RNA agent (iRNA), wherein said iRNA comprises a nucleotide sequence of at least 15 nucleotides, wherein the nucleotide sequence comprises a seed region consisting of nucleotide positions 1 to 12, wherein position 1 represents the 5′ end of the iRNA nucleotide sequence and wherein said seed region comprises a nucleotide sequence of at least six contiguous nucleotides that is complementary to six contiguous nucleotides within positions 1 to 12 of a nucleotide sequence, wherein position 1 represents the 5″end of the nucleotide sequence, wherein the nucleotide sequence is selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7 and SEQ ID NO:8. In some embodiments, the method comprises introducing at least one iRNA that inhibits the expression of at least one miR-16 responsive gene selected from TABLE 5 into the mammalian cell. | 02-11-2010 |
20100029511 | CDNA SYNTHESIS USING NON-RANDOM PRIMERS - The present invention provides methods for selectively amplifying a target population of nucleic acid molecules in a population of RNA template molecules (e.g., all mRNA molecules expressed in a cell type except for the most highly expressed mRNA species). The invention also provides a method of generating a population of oligonucleotide primers for transcriptome profiling of total RNA from a subject of interest. | 02-04-2010 |
20090280470 | EXTRACTION AND DIAGNOSTIC FLUID DEVICES, SYSTEMS AND METHODS OF USE - The present invention provides devices, systems and methods for RNA isolation from biological samples containing white blood cells, such as whole blood. The devices have a device body that includes a first chamber having a first membrane that selectively binds white blood cells, a second chamber having a second membrane that reversibly binds RNA and a plurality of ports that are removably attached to a reagent pack and waste receptacle via a valving system controlled by a control unit. | 11-12-2009 |
20090192135 | Human Niemann Pick C1-Like 1 Gene (NPC1L1) Polymorphisms and Methods of Use Thereof - The present invention relates to the identification and use of single nucleotide polymorphisms and haplotypes in the Niemann Pick C1-Like 1 (NPC1L1) gene. In particular, methods are provided for correlating NPC1L1 polymorphisms and haplo-types with the responsiveness of a pharmaceutically active compound administered to a human subject. The invention further relates to a method for estimating the responsiveness of a pharmaceutically active compound administered to a human subject which method comprises determining at least one polymorphism in the NPC1L1 gene. The methods are based on determining polymorphisms in the NPC1L1 gene and correlating the responsiveness of a pharmaceutically active compound in the human by reference to one or more polymorphism in NPC1L1. The invention further relates to isolated nucleic acids comprising within their sequence the polymorphisms as defined herein, to nucleic acid primers and oligonucleotide probes capable of hybridizing to such nucleic acids and to a diagnostic kit comprising one or more of such primers and probes for detecting a polymorphism in the NPC1L1 gene. | 07-30-2009 |
20090157326 | Diagnosis and prognosis of breast cancer patients - The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein. | 06-18-2009 |
20090141954 | Peak Reassembly - In differential and non-differential analyses, composite images derived from replicates of liquid-chromatography/mass-spectrometry processes can provide scientists with a better signal-to-noise ratio in discovering biological features of interest. Certain distinct peaks in composite images point to distinct biological features but some distinct peaks in composite images may also point to biological features that have common chemical species ancestry. A peak reassembly process is used to indicate whether two adjacent peaks should point to a biological feature using complementation analysis and collision analysis. | 06-04-2009 |
20090123912 | Methods for quantitating small RNA molecules - In one aspect, the present invention provides methods for amplifying a microRNA molecule to produce DNA molecules. The methods each include the steps of: (a) using primer extension to make a DNA molecule that is complementary to a target microRNA molecule; and (b) using a universal forward primer and a reverse primer to amplify the DNA molecule to produce amplified DNA molecules. In some embodiments of the method, at least one of the forward primer and the reverse primer comprise at least one locked nucleic acid molecule. | 05-14-2009 |
20090011488 | METHODS FOR STORING COMPOSITIONS USEFUL FOR SYNTHESIZING NUCLEIC ACID MOLECULES - In one aspect, the present invention provides methods for storing a composition useful for synthesizing nucleic acid molecules. The methods of this aspect of the invention include the steps of: (a) freezing multiple aliquots of a liquid composition comprising from 1000 units/mL to 5000 units/mL of a reverse transcriptase, or from 10,000 units/mL to 50,000 units/mL of an RNA polymerase, wherein the multiple aliquots of the liquid composition are disposed within multiple receptacles defined by a container body; and (b) a step selected from the group consisting of (1) storing the frozen aliquots at a temperature below −15° C., and (2) drying the frozen aliquots to produce dried aliquots of the composition, wherein each dried aliquot of the composition comprises an amount of water that is less than 0.1% by weight of the dried aliquot, and storing the dried aliquots at a temperature below −15° C. | 01-08-2009 |
20090004645 | Methods for Identifying Genes that Mediate a Response of a Living Cell to an Agent - In one aspect, the present invention provides methods for determining whether a gene mediates the response of a living cell to an agent. In another aspect, the present invention provides methods to identify a mammalian subject responsive to a KSP inhibitor. | 01-01-2009 |