Patents Assigned to Institute for System Biology
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Patent number: 7972791Abstract: The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb).Type: GrantFiled: September 29, 2009Date of Patent: July 5, 2011Assignees: Fred Hutchinson Cancer Research Center, Institute for Systems BiologyInventors: Effie W. Petersdorf, Zhen Guo, Leroy Hood
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Patent number: 7915381Abstract: The invention provides an immunomodulatory flagellin peptide having at least about 10 amino acids of substantially the amino acid sequence GAVQNRFNSAIT (SEQ ID NO:2), or a modification thereof, and having toll-like receptor 5 (TLR5) binding. Methods of inducing an immune response are also provided.Type: GrantFiled: April 17, 2002Date of Patent: March 29, 2011Assignees: Institute for Systems Biology, University of WashingtonInventors: Alan Aderem, Fumitaka Hayashi, Kelly D. Smith, David M. Underhill, Adrian Ozinsky
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Patent number: 7883858Abstract: The present invention relates generally to methods for identifying drug side effects by detecting perturbations in organ-specific molecular blood fingerprints. The invention further relates to methods for identifying drug-specific organ-specific molecular blood fingerprints. As such, the present invention provides compositions comprising organ-specific proteins, detection reagents for detecting such proteins, and panels and arrays for determining organ-specific molecular blood fingerprints.Type: GrantFiled: May 19, 2009Date of Patent: February 8, 2011Assignee: Institute for Systems BiologyInventors: Leroy Hood, Biaoyang Lin
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Patent number: 7879799Abstract: The invention provides methods for generating an antibody specific for the deglycosylated form of a glycopolypeptide using a peptide corresponding to an N-linked glycosylation site of a glycopolypeptide. The invention additionally provides methods for generating an antibody specific for a glycopolypeptide using a peptide corresponding to amino acids adjacent to an authentic N-linked glycosylation site.Type: GrantFiled: August 9, 2007Date of Patent: February 1, 2011Assignee: Institute for Systems BiologyInventors: Dan Martin, Bernd Wollscheid, Rudolf H. Aebersold, Julian Watts
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Publication number: 20110003715Abstract: The invention provides a diverse population of uniquely labeled probes, containing about thirty or more target specific nucleic acid probes each attached to a unique label bound to a nucleic acid. Also provided is a method of producing a population of uniquely labeled nucleic acid probes. The method consists of (a) synthesizing a population of target specific nucleic acid probes each having a different specifier; (b) synthesizing a corresponding population of anti-genedigits each having a unique label, the population having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) hybridizing the populations of target nucleic acid probes to the anti-genedigits, to produce a population in which each of the target specific probes is uniquely labeled. Also provided is a method of detecting a nucleic acid analyte.Type: ApplicationFiled: June 18, 2010Publication date: January 6, 2011Applicant: The Institute for Systems BiologyInventor: Krassen Dimitrov
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Publication number: 20100279382Abstract: The invention provides compositions and methods for identifying and/or quantifying glycopolypeptides from human serum or plasma. The compositions and methods include a plurality of standard peptides containing glycosylation sites determined for human serum/plasma proteins.Type: ApplicationFiled: March 12, 2010Publication date: November 4, 2010Applicant: The Institute for Systems BiologyInventors: Rudolf H. Aebersold, Hui Zhang
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Publication number: 20100267577Abstract: The invention provides methods for identifying and quantifying polypeptides in a sample. The methods include the steps of labeling peptides in a polypeptide sample with an isotope tag; adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag; resolving the labeled sample and standard peptides into a plurality of fractions; analyzing the resolved fractions using mass spectrometry; identifying an isotope-tagged sample peptide in an analyzed fraction; and determining the amount of the identified isotope-tagged sample peptide in the analyzed fraction by comparison to the amount of isotope tagged standard peptide in the same fraction.Type: ApplicationFiled: January 20, 2010Publication date: October 21, 2010Applicant: The Institute for Systems BiologyInventor: Rudolf H. Aebersold
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Patent number: 7807785Abstract: The present invention provides novel androgen regulated nucleic acid molecules. Related polypeptides and diagnostic methods also are provided.Type: GrantFiled: October 26, 2007Date of Patent: October 5, 2010Assignee: Institute for Systems BiologyInventor: Biaoyang Lin
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Patent number: 7794947Abstract: The invention provides methods of detecting polypeptides in a sample. The method can include the steps of cleaving polypeptides in a test sample to generate peptides; adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, wherein the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; washing the array to remove unbound peptides, thereby retaining affinity captured sample peptides and standard peptides; analyzing the affinity captured peptides using mass spectrometry; and determining the presence of bound test peptides and standard peptides. The method can further include the step of quantifying the amount of the test peptides by comparing the ratio of test peptide to corresponding standard peptide.Type: GrantFiled: July 9, 2004Date of Patent: September 14, 2010Assignee: Institute for Systems BiologyInventors: Rudolf H. Aebersold, Hui Zhang
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Publication number: 20100222233Abstract: The invention provides methods of detecting polypeptides in a sample. The method can include the steps of cleaving polypeptides in a test sample to generate peptides; adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, wherein the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; washing the array to remove unbound peptides, thereby retaining affinity captured sample peptides and standard peptides; analyzing the affinity captured peptides using mass spectrometry; and determining the presence of bound test peptides and standard peptides. The method can further include the step of quantifying the amount of the test peptides by comparing the ratio of test peptide to corresponding standard peptide.Type: ApplicationFiled: May 13, 2010Publication date: September 2, 2010Applicant: The Institute for Systems BiologyInventors: Rudolph H. Aebersold, Hui Zhang
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Publication number: 20100216139Abstract: Methods, compositions, and devices are disclosed which use microRNA to detect, predict, treat, and monitor physiological conditions such as disease or injury. microRNA are isolated and their differential expression is measured to provide diagnostic information. This information may then be utilized for evaluation and/or treatment purposes.Type: ApplicationFiled: November 10, 2009Publication date: August 26, 2010Applicants: BATTELLE MEMORIAL INSTITUTE, INSTITUTE FOR SYSTEMS BIOLOGY, THE OHIO STATE UNIVERSITY RESEARCH FOUNDATIONInventors: David Galas, Richard Evan Gelinas, Clay Braden Marsh, Melissa Garnet Piper, Kai Wang, Shile Zhang
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Publication number: 20100216180Abstract: Methods of using halogenated peptides as internal standards for liquid chromatography-mass spectrometry, and novel halogenated peptides useful for the same, are disclosed. In particular, methods of using halogenated peptides as internal standards in proteomic analyses, as well as methods of using halogenated peptides to conduct quality control assessments of and/or to calibrate liquid chromatography-mass spectrometry systems are disclosed.Type: ApplicationFiled: February 17, 2010Publication date: August 26, 2010Applicant: INSTITUTE FOR SYSTEMS BIOLOGYInventors: HAMID MIRZAEI, RUDOLF AEBERSOLD
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Publication number: 20100196883Abstract: The invention provides a method for diagnosing or predicting susceptibility to a prostate neoplastic condition in an individual. The method involves (a) determining a level of RDC1 in a sample from the individual, and (b) comparing the level of RDC1 in the sample to a reference level of RDC1, wherein a level of RDC1 in the sample 2-fold or more higher than the reference level indicates the presence of, or susceptibility to, a prostate neoplastic condition in the individual.Type: ApplicationFiled: February 17, 2009Publication date: August 5, 2010Applicant: The Institute for Systems BiologyInventors: Rudolf H. Aebersold, Michael E. Wright
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Publication number: 20100075866Abstract: The present invention relates generally to methods for identifying drug side effects by detecting perturbations in organ-specific molecular blood fingerprints. The invention further relates to methods for identifying drug-specific organ-specific molecular blood fingerprints. As such, the present invention provides compositions comprising organ-specific proteins, detection reagents for detecting such proteins, and panels and arrays for determining organ-specific molecular blood fingerprints.Type: ApplicationFiled: May 19, 2009Publication date: March 25, 2010Applicant: INSTITUTE FOR SYSTEMS BIOLOGYInventors: Leroy Hood, Biaoyang Lin
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Patent number: 7679039Abstract: The invention provides an apparatus and method for determining the position of a radiation beam. The apparatus includes (a) a first reflective surface and a second reflective surface, the reflective surfaces being placed to form the reflective exterior of a wedge; (b) a first detector placed to detect radiation reflected from the first reflective surface, and (c) a second detector placed to detect radiation reflected from the second reflective surface. The method includes the steps of (a) directing a radiation beam to the reflective exterior of a wedge formed by a first reflective surface and a second reflective surface; (b) selectively detecting radiation reflected from the first reflective surface; (c) selectively detecting radiation reflected from the second reflective surface; and (d) determining the position of the radiation beam based on the difference in the amount of radiation detected from each surface.Type: GrantFiled: April 14, 2008Date of Patent: March 16, 2010Assignee: The Institute for Systems BiologyInventors: Gerrit J. van den Engh, Peter I. Nelson
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Publication number: 20100042329Abstract: The invention provides a method of determining a comparative expression profile in an individual by comparing the expression levels of a sample of molecules in a population of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules, wherein expression levels within the health-associated reference expression region indicate a reference expression profile and wherein expression levels outside the health-associated reference expression region indicate a perturbed expression profile. The invention also provides methods of diagnosing a disease or a health state in an individual by comparing the expression level of a sample of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules.Type: ApplicationFiled: July 1, 2009Publication date: February 18, 2010Applicant: INSTITUTE FOR SYSTEMS BIOLOGYInventors: Leroy Hood, Andrew F. Siegel
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Patent number: 7655433Abstract: The invention provides methods for identifying and quantifying polypeptides in a sample. The methods include the steps of labeling peptides in a polypeptide sample with an isotope tag; adding a plurality of peptide standards to the polypeptide sample, wherein the peptide standards are labeled with an isotopically distinct version of the isotope tag; resolving the labeled sample and standard peptides into a plurality of fractions; analyzing the resolved fractions using mass spectrometry; identifying an isotope-tagged sample peptide in an analyzed fraction; and determining the amount of the identified isotope-tagged sample peptide in the analyzed fraction by comparison to the amount of isotope tagged standard peptide in the same fraction.Type: GrantFiled: June 4, 2003Date of Patent: February 2, 2010Assignee: The Institute for Systems BiologyInventor: Rudolf H. Aebersold
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Publication number: 20100015607Abstract: The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods of making and using such probes are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.Type: ApplicationFiled: December 22, 2006Publication date: January 21, 2010Applicants: NANOSTRING TECHNOLOGIES, INC., INSTITUTE FOR SYSTEMS BIOLOGYInventors: Gary K. Geiss, Sean M. Ferree, Philippa J. Webster, Krassen M. Dimitrov
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Patent number: 7623969Abstract: The invention provides a method for assigning a cellular function to a component of a biochemical system. The method involves (a) determining a multidimensional shape space for one or more components of a biochemical system in a reference state; (b) perturbing a component within said biochemical system; (c) determining a perturbed multidimensional shape space for one or more components of a pathway in said perturbed biochemical system, and (d) identifying a multidimensional coordinate point corresponding to a component of said perturbed pathway altered between reference and perturbed multidimensional shape spaces, said identified component being assigned a cellular function of said perturbed pathway.Type: GrantFiled: January 31, 2002Date of Patent: November 24, 2009Assignee: The Institute for Systems BiologyInventors: Leroy E. Hood, Andrew F. Siegel, Trey E. Ideker
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Patent number: 7615350Abstract: The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e.g., oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb).Type: GrantFiled: October 19, 2007Date of Patent: November 10, 2009Assignees: Fred Hutchinson Cancer Research Center, Institute for Systems BiologyInventors: Effie W. Petersdorf, Zhen Guo, Leroy Hood