Patents Assigned to Institute for System Biology
  • Publication number: 20190156919
    Abstract: The present disclosure describes systems and methods to elucidate unknown relationships and interactions between and among complex biological systems and components thereof. The systems and methods can inform clinical interventions in individuals before phenotypes of an adverse condition emerge.
    Type: Application
    Filed: December 11, 2018
    Publication date: May 23, 2019
    Applicants: ARIVALE, INC., INSTITUTE FOR SYSTEMS BIOLOGY
    Inventors: Andrew Tyler Magis, John Carl Earls, Nathan Price
  • Publication number: 20190084929
    Abstract: Crosslinking molecules that permit efficient identification of specifically associated proteins and the sites of crosslinking in biological or other samples include two cleavable bonds that are cleavable under the same conditions as peptide bonds in mass spectrometric determinations. Sets of the invention crosslinkers may be provided with isobaric labels containing reporter ions of differing molecular weights to permit relative quantitation of crosslinked protein pairs.
    Type: Application
    Filed: March 10, 2017
    Publication date: March 21, 2019
    Applicant: Institute for Systems Biology
    Inventors: Jie LUO, Jeff RANISH
  • Publication number: 20190032157
    Abstract: Practical assays to identify compounds that overcome the resistance of M. tuberculosis to bedaquiline are based on transcription factors Rv0324 and Rv0880 shown to mediate this resistance.
    Type: Application
    Filed: January 6, 2017
    Publication date: January 31, 2019
    Applicants: Institute for Systems Biology, Center for Infectious Disease Research
    Inventors: Eliza PETERSON, Nitin S. BALIGA
  • Patent number: 10030053
    Abstract: Embodiments of the disclosure encompass compositions and methods for generating immune responses in an animal or human host. Embodiments of the compositions encompass proteins derived from the surface proteins of bacteria and protozoa, and in particular the flagellum component flagellin, and which have adjunctival properties when administered in conjunction with an immunogen. Embodiments of the compositions of the disclosure are modified to incorporate a heterologous transmembrane-cytoplasmic domain allowing the peptides to be incorporated into virus-like particles. Embodiments of the methods of generating an immunological response in an animal or human comprise exposing the immune system of an animal or human host to an immunogen and a virus-like particle comprising an adjuvant polypeptide including a host cell Toll-like receptor ligand polypeptide having a transmembrane-cytoplasmic tail polypeptide, and a heterologous signal peptide.
    Type: Grant
    Filed: February 13, 2015
    Date of Patent: July 24, 2018
    Assignees: Emory University, Institute for Systems Biology
    Inventors: Richard L. Compans, Baozhong Wang, Jadranmka Boza, Ioanna Skountzou, Alan A. Aderem
  • Patent number: 10006071
    Abstract: Methods are provided to control the harvesting of desired metabolic byproducts from hypersaline photosynthetic algae. Methods are presented to control secretion of said metabolic products in monocultures and co-cultures after accumulation of byproducts. The metabolic byproduct secretion is controlled by controlling caspase activity.
    Type: Grant
    Filed: December 16, 2014
    Date of Patent: June 26, 2018
    Assignee: Institute for System Biology
    Inventors: Nitin S. Baliga, Monica V. Orellana, Kenia Whitehead, W. Lee Pang
  • Patent number: 9920380
    Abstract: 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. Also provided is a method of detecting a nucleic acid analyte. The method consists of (a) contacting a mixture of nucleic acid analytes under conditions sufficient for hybridization with a plurality of target specific nucleic acid probes each having a different specifier; (b) contacting the mixture under conditions sufficient for hybridization with a corresponding plurality of anti-genedigits each having a unique label, the plurality of anti-genedigits having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) uniquely detecting a hybridized complex between one or more analytes in the mixture, a target specific probe, and an anti-genedigit.
    Type: Grant
    Filed: March 11, 2013
    Date of Patent: March 20, 2018
    Assignee: The Institute for Systems Biology
    Inventors: Krassen M. Dimitrov, Dwayne L. Dunaway
  • Patent number: 9890419
    Abstract: 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: Grant
    Filed: May 20, 2016
    Date of Patent: February 13, 2018
    Assignees: NanoString Technologies, Inc., The Institute for Systems Biology
    Inventors: Gary K. Geiss, Sean M. Ferree, Philippa Jane Webster, Krassen M. Dimitrov
  • Patent number: 9856532
    Abstract: Concentrations of certain miRNA, mRNA and/or protein markers in the biological fluids and/or tissues of a subject are used to determine the probability that the subject does or does not have Posttraumatic Stress Disorder (PTSD). The concentrations of these markers in fluids and/or tissues are different in subjects with PTSD as compared to subjects who do not suffer from this disorder.
    Type: Grant
    Filed: March 14, 2013
    Date of Patent: January 2, 2018
    Assignee: INSTITUTE FOR SYSTEMS BIOLOGY
    Inventors: Leroy Hood, Kai Wang, Inyoul Lee, Yong Zhou, Ji Hoon Cho, Dhimankrishna Ghosh
  • Patent number: 9726667
    Abstract: Point of care methods to detect the probability or status of tuberculosis infection in individuals by determining presence or absence of one or more peptide of SEQ ID NOS:1-22 in a biological fluid of a subject are described. These methods may be assays based on affinity reagents specifically reactive with these peptides.
    Type: Grant
    Filed: March 6, 2015
    Date of Patent: August 8, 2017
    Assignee: INSTITUTE FOR SYSTEMS BIOLOGY
    Inventors: Robert L. Moritz, Mark Sartain, Zdenek Spacil, Ulrike Kusebauch, David Campbell
  • Publication number: 20170176439
    Abstract: A signature of proteins occurring in glioblastoma multiforme (GBM) tissue comprised of 33 cell surface proteins (GBMSig) that distinguish subjects with GBM from healthy controls with more than 98% accuracy is described. In addition, four of the members of this signature are particularly useful as blood-borne markers of GBM. Certain other members of the signature are indicators of the possible efficacy of the use of TGF-?1 inhibitors in the treatment of this condition. Methods to treat and to stratify GBM based on GBMSig proteins are also disclosed.
    Type: Application
    Filed: December 23, 2016
    Publication date: June 22, 2017
    Applicant: Institute for Systems Biology
    Inventors: Dhimankrishna GHOSH, Charles S. COBBS, Nathan D. PRICE, Leroy HOOD
  • Patent number: 9677130
    Abstract: Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5? end and polyA sequences coupled to a tag at the 3? end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3? ends of these molecules.
    Type: Grant
    Filed: February 15, 2012
    Date of Patent: June 13, 2017
    Assignee: Institute For Systems Biology
    Inventors: Kai Wang, Shile Zhang, David Galas
  • Publication number: 20170010229
    Abstract: The invention provides an unbiased method to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells by applying the unbiased determination technique of SWATH-MS or the biased technique of SRM-MS to a thermal shift assay to evaluate drug target interactions. In addition, the results created by SWATH-MS can be analyzed by SRM-MS in a biased manner to assess the binding of a test compound to a multiplicity of proteins in the same sample, including samples from living cells.
    Type: Application
    Filed: July 5, 2016
    Publication date: January 12, 2017
    Applicant: Institute for Systems Biology
    Inventors: Robert L. MORITZ, Samuel BADER, Ulrike KUSEBAUCH
  • Publication number: 20160370354
    Abstract: The invention provides a method to detect an abnormal condition or disease state by assessing a characteristic response pattern of responder cells to indicators contained in a biological fluid of a subject. A characteristic disease-associated pattern can be obtained by determining the response pattern of responder cells to that of bodily fluids or fractions thereof from subjects known to exhibit a particular abnormal condition optionally comparing said pattern to such pattern elicited by fluids or fractions from normal subjects and identifying elements that differ. The identified elements constitute a characteristic or differential pattern which can then be used to identify the presence or stage of a disease in a test subject.
    Type: Application
    Filed: August 30, 2016
    Publication date: December 22, 2016
    Applicant: Institute for Systems Biology
    Inventors: Jennifer Joy SMITH, John David AITCHISON, Leslie Rae MILLER
  • Publication number: 20160265057
    Abstract: Methods to detect amyotrophic lateral sclerosis (ALS) or presymptomatic Alzheimer's disease (PSAD) using an indicator cell assay platform (iCAP) in a test subject are described. Specifically, the disclosure provides a method comprising contacting a biological fluid of said test subject with indicator cells and assessing said indicator cells for the level of expression of an exon of CKIgamma2 that encodes the C-terminal palmitoylated region of said CKIgamma2, to determine the probability that a test subject is afflicted with amyotrophic lateral sclerosis (ALS). Further disclosed are methods of using indicator cells that are pan neuronal populations of glutamatergic (and/or GABAergic) neurons to determine the probability of the presence of presymptomatic or symptomatic Alzheimer's disease (PSAD) in a test subject.
    Type: Application
    Filed: September 25, 2014
    Publication date: September 15, 2016
    Applicant: Institute for Systems Biology
    Inventors: Jennifer Joy SMITH, Samuel Anthony DANZIGER, John David AITCHISON, Leslie Rae MILLER
  • Patent number: 9371563
    Abstract: 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: Grant
    Filed: March 11, 2013
    Date of Patent: June 21, 2016
    Assignees: NanoString Technologies, Inc., The Institute for Systems Biology
    Inventors: Gary K. Geiss, Sean M. Ferree, Philippa Jane Webster, Krassen M. Dimitrov
  • Patent number: 9334315
    Abstract: The present invention relates to a purified molecules, including antibodies, that bind specifically to murine ?-catenin phosphorylated at amino acid position Serine552 and to orthologs thereof, such as mammalian orthologs, including human orthologs. Methods of making and using such purified molecules are also provided. Kits containing such purified molecules are further provided.
    Type: Grant
    Filed: December 15, 2011
    Date of Patent: May 10, 2016
    Assignees: Stowers Institute for Medical Research, Institute For Systems Biology
    Inventors: Xi He, Tong Yin, Qiang Tian, Weiguo Tao, Leroy Hood, Linheng Li
  • Patent number: 9234895
    Abstract: The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.
    Type: Grant
    Filed: August 8, 2012
    Date of Patent: January 12, 2016
    Assignee: Institute for Systems Biology
    Inventors: Leroy Hood, Biaoyang Lin
  • Patent number: 9103834
    Abstract: 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: Grant
    Filed: December 9, 2013
    Date of Patent: August 11, 2015
    Assignee: Institute for Systems Biology
    Inventors: Leroy Hood, Biaoyang Lin
  • Patent number: 9002652
    Abstract: The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.
    Type: Grant
    Filed: January 27, 2006
    Date of Patent: April 7, 2015
    Assignee: Institute for Systems Biology
    Inventors: Leroy Hood, Biaoyang Lin
  • Patent number: 8911965
    Abstract: Enhanced yields of photosynthetically fixed carbon produced by hypersaline photosynthetic algae are provided by co-culturing with a halophilic archaea. Further, methods are provided to control harvesting of desired metabolic products from hypersaline photosynthetic algae by controlling caspase activity.
    Type: Grant
    Filed: April 22, 2011
    Date of Patent: December 16, 2014
    Assignee: Institute for Systems Biology
    Inventors: Nitin S. Baliga, Monica V. Orellana, Kenia Whitehead, W. Lee Pang