In Silico Screening Patents (Class 506/8)
  • Publication number: 20140243220
    Abstract: Described herein are methods for analyzing complex host-microbial mixtures. The disclosed methods may be used to diagnosis or prognose in a subject an inflammatory disease, which is caused by or contributed to by microbes.
    Type: Application
    Filed: February 25, 2014
    Publication date: August 28, 2014
    Applicant: J. Craig Venter Institute
    Inventor: Rembert Pieper
  • Publication number: 20140243221
    Abstract: Methods for identifying and/or distinguishing a homogeneous population of cells based on their replication domain timing profile using high resolution genomic arrays or sequencing procedures are provided. These methods may be used to compare the replication timing profile for a population of cells to another replication timing profile(s), a replication timing fingerprint, and/or one or more informative segments of a replication timing fingerprint, which may be simultaneously or previously determined and/or contained in a database, to determine whether there is a match between them. Based on such information, the identity of the population of cells may be determined, or the identity of the population of cells may be distinguished from other populations of cells or cell types. Methods for determining a replication timing fingerprint for particular cell types are also provided.
    Type: Application
    Filed: May 2, 2014
    Publication date: August 28, 2014
    Applicant: FLORIDA STATE UNIVERSITY RESEARCH FOUNDATION
    Inventors: David M. GILBERT, Tyrone RYBA, Ichiro HIRATANI
  • Publication number: 20140220576
    Abstract: DNA taggants in which the nucleotide sequences are defined according to combinatorial mathematical principles. Methods of defining nucleotide sequences of the combinatorial DNA taggants, and using such taggants for authentication and tracking and tracing an object or process are also disclosed.
    Type: Application
    Filed: April 14, 2014
    Publication date: August 7, 2014
    Applicant: JEANSEE LLC
    Inventor: Anthony J. MACULA
  • Publication number: 20140221221
    Abstract: Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
    Type: Application
    Filed: February 7, 2014
    Publication date: August 7, 2014
    Applicant: Caris MPI, Inc.
    Inventors: Daniel D. Von Hoff, David M. Loesch, Arlet Alarcon, Robert J. Penny, Alan Wright, Matthew J. McGinniss, Ryan P. Bender, Traci Pawlowski
  • Publication number: 20140221222
    Abstract: Provided herein are methods and systems of molecular profiling of diseases, such as cancer. In some embodiments, the molecular profiling can be used to identify treatments for a disease, such as treatments that were not initially identified as a treatment for the disease or not expected to be a treatment for a particular disease.
    Type: Application
    Filed: April 9, 2014
    Publication date: August 7, 2014
    Applicant: Caris MPI, Inc.
    Inventors: Daniel D. Von Hoff, David M. Loesch, Arlet Alarcon, Robert J. Penny, Alan Wright, Matthew J. McGinniss, Ryan P. Bender, Traci Pawlowski
  • Publication number: 20140213770
    Abstract: The present invention relates to improved methods for antibody engineering, e.g., humanization. In particular, the disclosure provides a high-throughput antibody humanization process that can be automated by computer-implementation.
    Type: Application
    Filed: December 20, 2013
    Publication date: July 31, 2014
    Applicant: AbbVie, Inc.
    Inventors: Feng DONG, Jijie GU, Chung-Ming HSIEH
  • Publication number: 20140200148
    Abstract: An apparatus for glycan analysis is disclosed. The apparatus includes a plurality of loading wells adapted to receive a plurality of samples; a plurality of capillaries arranged in correspondence with the loading wells, each of the capillaries including a first portion including a stacking gel and a second portion including a resolving gel; and a plurality of eluting wells arranged in correspondence with the capillaries and adapted to receive a portion of the samples having traversed the capillaries.
    Type: Application
    Filed: August 10, 2012
    Publication date: July 17, 2014
    Applicant: LIFE TECHNOLOGIES CORPORATION
    Inventor: Peter Slade
  • Publication number: 20140194299
    Abstract: Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X)10YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.
    Type: Application
    Filed: January 30, 2014
    Publication date: July 10, 2014
    Applicant: New England Biolabs, Inc.
    Inventors: YU ZHENG, RICHARD J. ROBERTS
  • Publication number: 20140179807
    Abstract: The present invention includes an apparatus, system and method for the development and use of transcriptional modules by obtaining individual gene expression levels from cells obtained from one or more patients with a disease or condition; recording the expression value for each gene in a table that is divided into clusters; iteratively selecting gene expression values for one or more transcriptional modules by: selecting for the module the genes from each cluster that match in every disease or condition; removing the selected genes from the analysis; and repeating the process of gene expression value selection for genes that cluster in a sub-fraction of the diseases or conditions; and iteratively repeating the generation of modules.
    Type: Application
    Filed: October 17, 2013
    Publication date: June 26, 2014
    Applicant: Baylor Research Institute
    Inventors: Damien Chaussabel, Jacques Banchereau
  • Publication number: 20140179537
    Abstract: The present invention relates to methods and compositions for diagnosing, monitoring, prognosticating, analyzing, etc., polymicrobial diseases. The present invention also relates to the microbial community present in the digestive tract and lumen in normal subjects, and subjects with digestive tract diseases, especially diseases of the colon, such as inflammatory bowel disease, including ulcerative colitis, Crohn's syndrome, and pouchitis. The present invention especially relates to compositions and methods for diagnosing and prognosticating the mentioned diseases and conditions, e.g., to determine the presence of the disease in a subject, to determine a therapeutic regimen, to determine a therapeutic regimen, to determine the onset of active disease, to determine the predisposition to the disease, etc.
    Type: Application
    Filed: November 25, 2013
    Publication date: June 26, 2014
    Applicants: Rush University, George Mason Intellectual Properties, Inc.
    Inventor: Patrick M. Gillevet
  • Publication number: 20140171332
    Abstract: The invention provides for carrying out 3-dimensional similarity searching by comparing a probe molecule to each member of a 3-dimensional database. The probe molecule is overlapped with each member of a database of molecules and then the database molecule is rotated and translates until its similarity with the probe molecule is maximized. The system can contain ten different scoring functions to rate the similarity between the two molecules. Each function employs different molecular features when scoring a particular comparison. Some methods are based on the relative shape of the two molecules, and some are based on the overlap of key atoms such as oxygen, nitrogen, sulfur, and/or halogens.
    Type: Application
    Filed: December 5, 2013
    Publication date: June 19, 2014
    Applicant: Hudson Robotics, Inc.
    Inventors: Alan H. Katz, Philip J. Farrelly
  • Publication number: 20140162887
    Abstract: Methods and compositions for determining and/or predicting a response to a therapy, prognosis of a cancer subject or survival of a cancer and kits for performing the same are described herein.
    Type: Application
    Filed: February 6, 2012
    Publication date: June 12, 2014
    Applicant: BIOARRAY THERAPEUTICS, INC.
    Inventors: Katherine J. Martin, Marcia V. Fournier
  • Publication number: 20140161721
    Abstract: This document provides methods and materials related to genetic variations of developmental disorders. For example, this document provides methods for using such genetic variations to assess susceptibility of developing Autism Spectrum Disorder.
    Type: Application
    Filed: February 8, 2013
    Publication date: June 12, 2014
    Inventors: Eli Hatchwell, Peggy S. Eis, Stephen Scherer, Aparna Prasad
  • Patent number: 8741811
    Abstract: Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment).
    Type: Grant
    Filed: November 30, 2011
    Date of Patent: June 3, 2014
    Assignee: The Chinese University of Hong Kong
    Inventors: Yuk Ming Dennis Lo, Kwan Chee Chan, Wai Kwun Rossa Chiu, Peiyong Jiang
  • Publication number: 20140141981
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Application
    Filed: February 3, 2014
    Publication date: May 22, 2014
    Applicant: Natera, Inc.
    Inventors: Bernhard Zimmermann, Matthew Hill, Philippe Lacroute, Michael Dodd
  • Publication number: 20140121120
    Abstract: Methods for identifying disease-related pathways that can used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.
    Type: Application
    Filed: June 10, 2013
    Publication date: May 1, 2014
    Applicant: Ingenuity Systems, Inc.
    Inventors: Richard O. Chen, Raymond J. Cho, Ramon M. Felciano, Bret Holley, Viresh Patel, Daniel R. Richards, Sushma Selvarajan, Keith Steward, Sara Schneider
  • Publication number: 20140121121
    Abstract: A system and method for determining individualized medical intervention for a particular disease state, and especially for cancers, that includes the molecular profiling of a biological sample from the patient, determining whether any molecular findings including one or more genes, one or more gene expressed proteins, one or more molecular mechanisms, and/or combinations of such exhibit a change in expression compared to a reference, and identifying a non-specific disease therapy or agent capable of interacting with the genes, gene expressed proteins, molecular mechanisms, or combinations of such molecular findings that exhibited a change in expression.
    Type: Application
    Filed: January 8, 2014
    Publication date: May 1, 2014
    Applicant: Caris MPI, Inc.
    Inventors: Daniel D. Von Hoff, Robert J. Penny
  • Publication number: 20140113829
    Abstract: Systems and methods of selecting combinatorial coordinately dysregulated biomarker subnetworks are provided. In one embodiment, a method comprises comparing the normalized gene expression data to a predetermined threshold to provide binary gene expression data associated with phenotype samples and control samples, analyzing subnetwork states of the binary gene expression data associated with phenotype samples and control samples to identify gene expression patterns that occur in phenotype samples and do not occur in control samples and identifying a subnetwork that provides gene expression patterns indicative of a sample being a phenotype sample.
    Type: Application
    Filed: April 22, 2011
    Publication date: April 24, 2014
    Applicant: CASE WESTERN RESERVE UNIVERSITY
    Inventors: Mehmet Koyuturk, Mark Chance, Rod Nibbe, Salim Akhter Chowdhury
  • Publication number: 20140066321
    Abstract: Provided are histidyl-tRNA synthetase variant polypeptides, X-ray crystallographic and NMR spectroscopy structures of HRS polypeptides, and related compositions and methods for therapy and drug discovery.
    Type: Application
    Filed: July 23, 2013
    Publication date: March 6, 2014
    Applicants: aTyr Pharma, Inc.
    Inventors: Zhiwen Xu, Zhiyi Wei, Xiang-Lei Yang, Mingjie Zhang, Paul Schimmel
  • Publication number: 20140066320
    Abstract: Described herein are technologies pertaining to computationally-efficiently performing genome-wide association studies. Feature selection methods are used to identify genetic markers for addressing potential confounding in the data. Then, single SNPs, or groups of genetic markers are analyzed to ascertain whether such groups are causal or tagging of causal as to a specified phenotype, after taking in to account the feature-selected SNPs. Group and univariate analysis is accomplished by way of analyzing a group of genetic markers conditioned upon other genetic markers that are found to be predictive of the specified phenotype.
    Type: Application
    Filed: September 4, 2012
    Publication date: March 6, 2014
    Applicant: MICROSOFT CORPORATION
    Inventors: David Earl Heckerman, Jennifer Listgarten, Christoph Anthony Lippert, Jing Xiang, Nicolo Fusi, Carl M. Kadie, Robert I. Davidson
  • Publication number: 20140051137
    Abstract: A group of bacterial dihydroxy-acid dehydratases having a [2Fe-2S] cluster was discovered. Bacterial [2Fe-2S] DHADs were expressed as heterologous proteins in bacteria and yeast cells, providing DHAD activity for conversion of 2,3-dihydroxyisovalerate to ?-ketoisovalerate or 2,3-dihydroxymethylvalerate to ?-ketomethylvalerate. Isobutanol and other compounds may be synthesized in pathways that include bacterial [2Fe-2S] DHAD activity.
    Type: Application
    Filed: March 15, 2013
    Publication date: February 20, 2014
    Applicant: Butamax(TM) Advanced Biofuels LLC
    Inventor: Butamax(TM) Advanced Biofuels LLC
  • Publication number: 20140038294
    Abstract: Systems and methods are provided for defining a nucleic acid construct for integration at locus L of an organism. Nucleic acid requests are received, each such request specifying a genetic change to L. The request are expanded into component polynucleotides which are then arranged into {AR1, . . . , ARm} different arrangements, each ARi in {AR1, . . . , ARm} defining a different arrangement of the component polynucleotides. A score Si for each ARi in {AR1, . . . , ARm} is determined based on whether source constructs encoding a portion of ARi are physically present. An ARf in {AR1, . . . , ARm} is selected based on the score for ARf. Primer pairs are calculated to amplify the portions of ARf not represented in the source constructs. The portions of ARf amplified by the primer pairs and the portions of ARf in the source constructs, ordered by ARf, define the nucleic acid construct.
    Type: Application
    Filed: October 11, 2012
    Publication date: February 6, 2014
    Applicant: Amyris Biotechnologies, Inc.
    Inventors: Darren M. Platt, Michael W. Bissell, Sunil S. Chandran, Brian L. Hawthorne, Erik Jedediah Dean, Christopher Dolan
  • Publication number: 20140038833
    Abstract: Disclosed are data processing and analysis methods for gene expression data for identifying endogenous reference genes and a composition for the quantitative analysis of gene expression, comprising a pair of primers and/or probes useful in amplifying the identified endogenous reference genes. Introduced with the concepts of “Zero's proportion” and CV, the method allows different datasets to be integrally analyzed, thereby searching for novel reference genes. By the method, 2,087 genes are first found as housekeeping genes which are expressed in most tissues, and the usefulness thereof in the relative quantification of different target genes is determined by analyzing their expression stability. Of the 2,087 genes, 13 genes show higher expression stability with lower expression levels across a wide range of samples than traditional reference genes such as GAPDH and ACTS, and therefore are suitable for the normalization of universal genes having relatively low expression levels.
    Type: Application
    Filed: September 28, 2012
    Publication date: February 6, 2014
    Applicant: SNU R&DB FOUNDATION
    Inventors: Young Kee Shin, Mi Jeong Kwon, En Sel Oh, Yong Ho In, Sang Seok Koh
  • Publication number: 20140030776
    Abstract: A group of bacterial dihydroxy-acid dehydratases having a [2Fe-2S] cluster was discovered. Bacterial [2Fe-2S] DHADs were expressed as heterologous proteins in bacteria and yeast cells, providing DHAD activity for conversion of 2,3-dihydroxyisovalerate to ?-ketoisovalerate or 2,3-dihydroxymethylvalerate to ?-ketomethylvalerate. Isobutanol and other compounds may be synthesized in pathways that include bacterial [2Fe-2S] DHAD activity.
    Type: Application
    Filed: March 15, 2013
    Publication date: January 30, 2014
    Applicant: Butamax(TM) Advanced Biofuels LLC
    Inventor: Butamax(TM) Advanced Biofuels LLC
  • Publication number: 20140018247
    Abstract: Embodiments of the inventions provide crystals of AmiS/Urel superfamily, urea-channel protein, methods of crystallizing such protein, and crystalline structures of such protein obtained by x-ray diffraction. Embodiments of the invention provide methods of identifying or designing antagonists and/or agonists of AmiS/Urel-superfamily, urea-channel protein based on crystalline structures thereof. In certain embodiments of the invention, the AmiS/Urel-superfamily, urea-channel protein is the Helicobacter pylori protein, HpUreI.
    Type: Application
    Filed: April 23, 2013
    Publication date: January 16, 2014
    Inventors: Hartmut Leucke, Reginald McNulty, George Sachs
  • Publication number: 20130345267
    Abstract: The present invention relates to a method for identifying compounds that modulate the activity of p300/CBP. Compounds of the invention are identified by designing or screening for a compound which binds to at least one amino acid residue of the newly identified lysine-CoA inhibitor binding site, L1 loop, electronegative pocket, or electronegative groove of the HAT domain of p300/CBP and testing the compound for its ability to modulate the activity of p300/CBP. Compositions and methods for preventing or treating diseases or disorders associated with p300/CBP are also provided as is a method for producing a semi-synthetic HAT domain.
    Type: Application
    Filed: May 30, 2013
    Publication date: December 26, 2013
    Inventors: Ronen Marmorstein, Xin Liu, Philip A. Cole, Ling Wang, Erin M. Bowers, David J. Meyers, Chandrani Mukherjee
  • Publication number: 20130338015
    Abstract: An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.
    Type: Application
    Filed: March 13, 2013
    Publication date: December 19, 2013
    Applicant: Emerald Therapeutics, Inc.
    Inventor: Emerald Therapeutics, Inc.
  • Publication number: 20130340110
    Abstract: This disclosure concerns marker-assisted plant selection and breeding. In specific embodiments, methods of identifying optimized marker panels for predicting the presence of a plant trait of interest, and/or marker panels thereby identified, are provided.
    Type: Application
    Filed: June 13, 2013
    Publication date: December 19, 2013
    Inventors: KELLY R. ROBBINS, JAN ERIK BACKLUND
  • Publication number: 20130338016
    Abstract: A method of tissue analysis integrates a pathology diagnostic step (subjective human inspection of a stained tissue section or image of it) with one or more gene/biomarker tests to enable perform of both procedures side-by-side on the same instrument.
    Type: Application
    Filed: April 17, 2013
    Publication date: December 19, 2013
    Applicant: Vala Sciences, Inc.
    Inventor: Vala Sciences, Inc
  • Publication number: 20130324425
    Abstract: The present invention relates to a method for identifying target regions existing in the interface of monomers constituting the PiIT protein with the view to design molecules potentially applicable in impairing the activity of this protein, thus controlling infectious processes. The method is characterized in (i) selecting at least one amino acid sequence constituting the PiIT monomer; (ii) developing a three-dimensional computational model of the PiIT homo-hexameric structure; (iii) analyzing and determining, with computer aid, the interface-forming residues (IFR) and their physicochemical and structural characteristics for all the chains of the models of hexameric complexes generated; (iv) selecting the regions to be used as therapeutic targets (and preferred therapeutic targets) in the interface between the monomers based on the intensity of determined parameters; (v) computer-aided design of molecules potentially capable of effecting bindings and/or interactions between target regions of the monomers.
    Type: Application
    Filed: September 8, 2011
    Publication date: December 5, 2013
    Applicant: EMPRESA BRASILEIRA DE PESQUISA AGROPECUARIA- EMBRAPA
    Inventors: Goran Neshich, Izabella Agostinho Pena Neshich, Jose Gilberto Jardine, Leticia Nishimura, Ivan Mazoni, Jose Salim
  • Publication number: 20130324426
    Abstract: Method to create in silico protein mutants with improved expression level in an expression host compared to an original protein. The mutants retain unaltered or minimally altered function and specific activity that is at the same or higher level compared to the original protein. The method also allows predicting one or more optimal expression host(s) for the given protein and mutants for maximum production level in the predicted optimal host(s). The method is based on optimizing protein sequence parameters that are important for protein expression, such as amino acid composition, guanine-cytosine (GC) content, RNA secondary structure, amount of charged amino acids on the surface, and length of the protein, among other parameters.
    Type: Application
    Filed: May 30, 2013
    Publication date: December 5, 2013
    Inventor: Elena E. Brevnova
  • Publication number: 20130303387
    Abstract: The present invention relates to a method for predicting three-dimensional structure of a protein from its sequence. Three-dimensional structure may be determined by: (a) generating a multiple sequence alignment for a candidate protein having a known sequence; (b) identifying a covariance matrix between all pairs of sequence positions in the multiple sequence alignment; (c) inverting the covariance matrix and identifying predicted evolutionary constraints using a statistical model of the candidate protein; and (d) simulating folding of an extended chain structure of the candidate protein using the predicted constraints.
    Type: Application
    Filed: May 9, 2013
    Publication date: November 14, 2013
    Inventors: Chris Sander, Debora S. Marks
  • Publication number: 20130303386
    Abstract: The present invention provides a method for identifying differential activation of a bisubstrate protein modifying enzyme between samples, comprising: (i) incubating a first sample with x different concentrations of the non-protein substrate of said enzyme, wherein x is 2 or greater than 2; (ii) quantifying modification of a polypeptide in said sample at each of the x different concentrations of the non-protein substrate; (iii) determining the affinity of said enzyme for said non-protein substrate; (iv) repeating steps (i) to (iii) for a second or subsequent sample; and (v) comparing the affinity of said enzyme for said non-protein substrate between said samples; wherein a difference in affinity of said enzyme for said non-protein substrate between samples is indicative of differential activation of said enzyme between samples. The present invention also provides a method for identifying an in vivo substrate of a bisubstrate protein modifying enzyme.
    Type: Application
    Filed: October 18, 2011
    Publication date: November 14, 2013
    Inventors: Pedro Rodriguez Cutillas, Bart Vanhaesebroeck, Luisa Marie Beltran
  • Publication number: 20130274286
    Abstract: The present invention relates to identification of a compound which inhibits the enzyme NMPRTase and glioma cancer cell growth and further used for glioma therapy. Pre-B-cell colony enhancing factor 1 gene (PBEF1) encodes nicotinamide phosphoribosyltransferase (NMPRTase), which catalyses the rate limiting step in the salvage pathway of NAD metabolism in mammalian cells. PBEF1 transcript and protein levels have been shown to be elevated in glioblastoma and a chemical inhibitor of NMPRTase has been shown to specifically inhibit cancer cells. Here a structure based drug discovery approach has been reported with an aim to develop novel inhibitors for glioblastoma therapy. Present invention relates to virtual screening using docking of ligands from a large library of 13,000 compounds against NMPRTase as the macromolecular target resulting in short listing of 34 possible ligands, of which six were tested experimentally, using the NMPRTase enzyme inhibition assay and further with the glioma cell viability assays.
    Type: Application
    Filed: March 31, 2011
    Publication date: October 17, 2013
    Applicant: COUNCIL OF SCIENTIFIC AND INDUSTRIAL RESEARCH
    Inventors: Somasundaram Kumaravel, Nagasuma Chandra
  • Publication number: 20130267429
    Abstract: Biological sample target classification, detection and selection methods are described, together with related arrays and oligonucleotide probes.
    Type: Application
    Filed: May 2, 2013
    Publication date: October 10, 2013
    Inventors: Shea GARDNER, Crystal J. JAING, Kevin MCLOUGHLIN, Thomas SLEZAK, James B. THISSEN, Marisa Wailam TORRES
  • Publication number: 20130261007
    Abstract: A method of constructing a data architecture for use in identifying connections between perturbagens and genes associated with skin tone. The method includes providing a gene expression profile for a control cell, generating a gene expression profile for a cell exposed to a perturbagen, identifying genes differentially expressed in response to the perturbagen, creating an ordered list of identifiers, storing the ordered list as an instance on a computer readable medium, and constructing a data architecture of stored instances.
    Type: Application
    Filed: March 27, 2013
    Publication date: October 3, 2013
    Applicant: The Procter & Gamble Company
    Inventors: Tomohiro HAKOZAKI, Wenzhu ZHAO, Robert Lloyd BINDER, Jun XU
  • Publication number: 20130259847
    Abstract: Described herein is a discovery Platform Technology for analyzing a biological system or process (e.g.
    Type: Application
    Filed: September 7, 2012
    Publication date: October 3, 2013
    Applicant: BERG PHARMA LLC
    Inventors: Vivek K. Vishnudas, Rangaprasad Sarangarajan, Niven Rajin Narain, Min Du, Tony Walshe
  • Publication number: 20130252831
    Abstract: A “malignancy-risk” (MR) gene signature score was developed with abundant proliferative genes using principal component analysis. This MR gene signature was shown to be a predictive and prognostic factor of overall survival in early-stage NSCLC. The malignancy-risk signature showed a significant association with OS, with poor survival seen in patients having a higher MR score and better survival seen in patients having a low MR score. As a prognostic factor, the MR gene signature showed a positive correlation with TNM stage, histologic grade, and smoking status. Combination of the MR signature with each clinical parameter often showed the best survival in the low MR group with good clinical outcome. The MR gene profile, tested with a PCA scoring method, discriminated overall survival in lung cancer patients was a predictor independent of pathological staging and other clinical parameters.
    Type: Application
    Filed: May 10, 2013
    Publication date: September 26, 2013
    Applicant: H. Lee Moffitt Cancer Center and Research Institute, Inc.
    Inventor: Dung-Tsa Chen
  • Publication number: 20130251720
    Abstract: The present invention relates to compositions and methods of using those compositions for the diagnosis and treatment of immune related diseases.
    Type: Application
    Filed: October 9, 2012
    Publication date: September 26, 2013
    Applicant: GENENTECH, INC.
    Inventors: HILARY CLARK, DAN EATON, LINO GONZALEZ, JR., JANE GROGAN, JASON A. HACKNEY, KRISTIN HARDEN, XIN YU
  • Publication number: 20130237435
    Abstract: The present invention provides a method for searching for or identifying a useful gene logically, systematically, and efficiently in an extremely short time without largely relying on searcher's knowledge, experience, or the like and even without sequentially conducting gene disruption experiments as in conventional techniques of searching for a useful gene. The present invention also provides an apparatus for the method. Virtual gene clusters each comprising two or more genes are individually scored by summing the respective pieces of differential expression information (obtained using, for example, microarrays) of genomic genes on a per-cluster basis. On the basis of the obtained scores of the virtual gene clusters, a gene cluster containing a useful gene and the useful gene contained in the cluster are searched for.
    Type: Application
    Filed: September 22, 2011
    Publication date: September 12, 2013
    Applicant: National Institute of Advanced Industrial Science and Technology
    Inventors: Masayuki Machida, Hideaki Koike, Maiko Umemura, Kiyoshi Asai, Katsuhisa Horimoto, Totai Mitsuyama
  • Publication number: 20130225425
    Abstract: The application provides methods of modulating NR2F6 in a cell or animal in need thereof by administering an effective amount of a NR2F6 modulator.
    Type: Application
    Filed: October 15, 2012
    Publication date: August 29, 2013
    Inventors: Christine Victoria Ichim, Richard Alexander Wells
  • Publication number: 20130210648
    Abstract: Compositions, methods and kits are described for identifying biomolecules (e.g., proteins and nucleic acids) expressed in a biological sample that are associated with the presence, development, or progression of a disease (such as cancer), or more generally determination of the etiology or risk factors associated with a disease. Sample types analyzed by the disclosed methods include but are not limited to archival tissue blocks that have been preserved in a fixative, tissue biopsy samples, tissue microarrays, and so forth. The methods disclosed herein correlate expression profiles of biomolecules with various disease types, and allow for the determination of relative survival rates; in some embodiments, the methods permit determination of survival rates for a subject with cancer. In other embodiments, the disclosure relates to methods for evaluating therapeutic regimes for the treatment, such as treatment of cancer.
    Type: Application
    Filed: March 15, 2013
    Publication date: August 15, 2013
    Inventor: The United States of America, as represented by the Secretary, Department of Health and Human Services
  • Publication number: 20130195916
    Abstract: A method and system are disclosed for identifying and/or locating complex patterns in an amino acid sequence stored in a computer file or database. According to an aspect of the present invention, techniques are provided to facilitate queries of protein databases. For protein descriptions received in response to the queries, embodiments of the present invention may scan the received protein descriptions to identify and locate Replikin patterns. A Replikin pattern is defined to be a sequence of 7 to about 50 amino acids that include the following three (3) characteristics, each of which may be recognized by an embodiment of the present invention: (1) the sequence has at least one lysine residue located six to ten amino acid residues from a second lysine residue; (2) the sequence has at least one histidine residue; and (3) at least 6% of the amino acids in the sequence are lysine residues.
    Type: Application
    Filed: March 6, 2013
    Publication date: August 1, 2013
    Inventors: Samuel Bogoch, Elenore S. Bogoch, Anne-Elenore Bogoch Borsanyi, Samuel Winston Bogoch
  • Publication number: 20130196864
    Abstract: Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.
    Type: Application
    Filed: February 8, 2013
    Publication date: August 1, 2013
    Applicant: DNA TWOPOINTO, INC.
    Inventors: Sridhar Govindarajan, Jeremy S. Minshull, Jon E. Ness
  • Publication number: 20130178377
    Abstract: Described herein are highly accurate metaproteomic based methods for diagnosing urogenital and kidney infections, which are easy to perform and that also provide information regarding the extent of the infection, the causative agent(s) and the nature of the host response.
    Type: Application
    Filed: December 27, 2012
    Publication date: July 11, 2013
    Applicant: J. Craig Venter Institute
    Inventor: J. Craig Venter Institute
  • Publication number: 20130123281
    Abstract: Compositions and methods which modulate diseases and disorders related to transducin ?-like protein 1 (TBL1) activity, including but not limited to cancer, inflammation, and bone related diseases.
    Type: Application
    Filed: November 12, 2012
    Publication date: May 16, 2013
    Applicant: BETA CAT PHARMACEUTICALS, LLC
    Inventors: Hariprasad M. Vankayalapati, Stephen Horrigan
  • Publication number: 20130123120
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Application
    Filed: November 21, 2012
    Publication date: May 16, 2013
    Applicant: NATERA, INC.
    Inventor: Natera, Inc.
  • Publication number: 20130116125
    Abstract: The present invention is relevant to proteins and novel methods of protein evolution. The present invention further relates to methods of identifying and mapping mutant polypeptides formed from, or based upon, a template polypeptide.
    Type: Application
    Filed: March 4, 2011
    Publication date: May 9, 2013
    Applicant: BIOATLA, LLC
    Inventor: Jay M. Short
  • Publication number: 20130102480
    Abstract: The present invention provides a prediction device, a prediction method, a program, and a recording medium, with which whether or not desired aptamer sequences are enriched can be predicted easily. The prediction device of the present invention 10 includes an input unit 11, a calculation unit 12, and a prediction unit 13. The input unit 11 is a unit through which sequence information on a target aptamer sequence group including selected aptamers in a target pool and a reference aptamer sequence group including reference aptamer sequences are inputted. The calculation unit 12 calculates the free energy of the target aptamer sequence group and the free energy of the reference aptamer sequence group. The prediction unit 13 compares the free energy of these sequence groups, and predicts that the target pool is an enriched pool when the free energy of the target aptamer sequence group is lower than the free energy of the reference aptamer sequence group.
    Type: Application
    Filed: July 2, 2011
    Publication date: April 25, 2013
    Applicants: KANAGAWA PREFECTURAL HOSPITAL ORGANIZATION, NEC SOFT, LTD.
    Inventors: Jou Akitomi, Shintarou Katou, Shotaro Tsuji, Takashi Ohtsu, Iwao Waga
  • Publication number: 20130096017
    Abstract: Motility contrast imaging (MCI) is a depth-resolved holographic technique to extract cellular and subcellular motion inside tissue. The holographic basis of the measurement technique makes it highly susceptible to mechanical motion. The motility contrast application, in particular, preferably includes increased mechanical stability because the signal is based on time-varying changes caused by cellular motion, not to be confused with mechanical motion of the system. The use of the resulting spectrogram response signatures, or “fingerprint” data, of known compounds is disclosed to screen new compounds for leads as to those having potentially beneficial mechanisms of action. The “fingerprint” data of known toxic compounds can be used to screen new compounds for toxicity.
    Type: Application
    Filed: June 17, 2011
    Publication date: April 18, 2013
    Applicant: PURDUE RESEARCH FOUNDATION
    Inventors: David D. Nolte, Kwan Jeong