In Silico Screening Patents (Class 506/8)
  • Patent number: 9499593
    Abstract: The disclosure provides modified biotin-binding proteins which can be expressed in soluble form in high yield in bacteria. Also provided are fusion proteins comprising the modified biotin-binding protein and an antigen. The disclosure further provides non-hemolytic variants of alpha-hemolysin from S. aureus and fusion protein comprising non-hemolytic variant of alpha-hemolysin and a biotin-binding domains. Immunogenic compositions comprising the proteins are also disclosed and use of such immunogenic compositions for inducing an immune response or for vaccinating a subject are also disclosed.
    Type: Grant
    Filed: May 11, 2012
    Date of Patent: November 22, 2016
    Assignee: Children's Medical Center Corporation
    Inventors: Richard Malley, Yingjie Lu, Fan Zhang
  • Patent number: 9494478
    Abstract: The present invention, in one embodiment, provides a method of measuring pressure or temperature using a sensor including a sensor element composed of a plurality of carbon nanotubes. In one example, the resistance of the plurality of carbon nanotubes is measured in response to the application of temperature or pressure. The changes in resistance are then recorded and correlated to temperature or pressure. In one embodiment, the present invention provides for independent measurement of pressure or temperature using the sensors disclosed herein.
    Type: Grant
    Filed: September 24, 2013
    Date of Patent: November 15, 2016
    Assignee: UT-BATTELLE, LLC
    Inventors: Ilia N. Ivanov, David B. Geohegan
  • Patent number: 9447456
    Abstract: Methods and systems of quantifying a target material in solution include detection of a size change of a hybridized nucleic acid complex, without the use of nanobeads. In particular, the examples include providing a plurality of nucleic acid fragments and a species-specific oligonucleotide tags, measuring the size of the nucleic acid fragments and/or oligonucleotides to predetermine a standard distribution of the solution(s), introducing the oligonucleotides in a solution containing nucleic acid target materials and/or non-target materials, and hybridizing the oligonucleotides with the species-specific target material if present in the solution. The size of the nucleic acid complexes in solution are then measured after hybridization, and the presence or non-presence of the species-specific target material is detected and/or quantified by comparing the measured size of the nucleic acid complexes after hybridization to the standard distribution.
    Type: Grant
    Filed: September 12, 2012
    Date of Patent: September 20, 2016
    Assignee: University of Notre Dame du Lac
    Inventors: Carol Tanner, Steven Ruggiero
  • Patent number: 9236236
    Abstract: A sample preparation and analysis system. The system includes a housing with a sample preparation station and a sample analysis station positioned within the housing. The sample analysis station is spaced away from the sample preparation station. A transport assembly is configured to move at least one sample within the housing and between the sample preparation station and the sample analysis station.
    Type: Grant
    Filed: July 17, 2014
    Date of Patent: January 12, 2016
    Assignee: Thermo Fisher Scientific Oy
    Inventors: Robert DeWitte, Juhani Siidorov, Vesa Nuotio, Jukka Saukkonen, John Edward Brann, III, Terry N. Olney
  • Patent number: 9234025
    Abstract: The present invention relates to an extracellular binding domain for an allosteric inhibitor, whereby said binding domain is derived from a single membrane span tyrosine kinase receptor. More specifically, the invention relates to an extracellular domain derived from a Fibroblast Growth Factor Receptor (FGFR). It further relates to the use of this domain for the identification of similar domains in the extracellular part of other tyrosine kinase receptors, and to a screening method for identification of a small compound allosteric inhibitor.
    Type: Grant
    Filed: July 2, 2010
    Date of Patent: January 12, 2016
    Assignees: SANOFI, VIB VZW, LIFE SCIENCES RESEARCH PARTNERS VZW, VRIJE UNIVERSITEIT BRUSSEL
    Inventors: Peter Carmeliet, Frederik De Smet, Joost Schymkowitz, Frédéric Rousseau, Corentin Herbert
  • Publication number: 20150148242
    Abstract: The present application is directed to methods and systems for identifying small molecule compounds in mixtures using a library comprising calculated structures and corresponding calculated mass spectral fragmentation patterns of known and/or hypothetical small molecule compounds that may be in the mixture and screening of a mass spectrum of the mixture using the library to identify matching fragmentation patterns. If a mass spectral fragmentation pattern present in the mass spectrum of the mixture matches a calculated fragmentation pattern of one of the known or hypothetical compounds this confirms the identity of a compound in the mixture as the known or hypothetical compound. The method represents a platform method that can be used for a multitude of purposes related to the screening and identification of compounds in mixtures.
    Type: Application
    Filed: June 5, 2013
    Publication date: May 28, 2015
    Applicant: McMaster University
    Inventors: Nathan Magarvey, Aubrey Bailey Morgan Wyatt, Chad William Johnston, Ashraf Ibrahim, Bin Ma, Lian Yang
  • Publication number: 20150133362
    Abstract: Aspects of the invention provide methods for selecting a candidate oligonucleotide for activating expression of a target gene. Further aspects of the invention provide methods of selecting a set of oligonucleotides that is enriched in oligonucleotides that activate expression of a target gene. Further aspects provide single stranded oligonucleotides that modulate gene expression and compositions and kits comprising the same. Methods for modulating gene expression using the single stranded oligonucleotides are also provided.
    Type: Application
    Filed: May 16, 2013
    Publication date: May 14, 2015
    Applicants: RaNA Therapeutics, Inc., The General Hospital Corporation d/b/a Massachusetts General Hospital
    Inventors: Arthur M. Krieg, Romesh Subramanian, James McSwiggen, Jeannie T. Lee
  • Patent number: 9026413
    Abstract: A method of modeling phase characteristics of thermodynamic systems utilizing pseudo-properties strategy and a reduced number of variables is disclosed herein. The method describes a means of determining the probability of phase splitting of mixtures of materials at a given temperature, pressure, and composition by characterizing the functions that describe the system via pseudo-properties, and also by describing the system in n?1 or fewer variables, where n represents the number of components in the system of interest. In an embodiment, a multi-component system is characterized in one variable, thereby providing simplified thermodynamic models in a time-efficient manner. In addition, the information generated by this reduced-variable calculation can further be used as a starting point for calculations of equations of state.
    Type: Grant
    Filed: September 20, 2012
    Date of Patent: May 5, 2015
    Assignee: Invensys Systems, Inc.
    Inventors: Gang Xu, David Bluck
  • Publication number: 20150119262
    Abstract: This disclosure relates generally to the prediction of a gene target of an enhancer based on genomic proximity and a comparison to a set of known enhancer-gene pairs. A gene can be selected a gene from a given cell type. A domain can be established bi-directionally around the gene, and enhancers located within the domain can be identified. The enhancers located within the domain can be considered to be in close genomic proximity to the gene. For each enhancer, a test pair of the enhancer and the gene can be established and compared to a set of known enhancer-gene pairs. The prediction can be established based on the comparison and the genomic proximity.
    Type: Application
    Filed: October 27, 2014
    Publication date: April 30, 2015
    Inventor: Peter C/ Scacheri
  • Publication number: 20150105274
    Abstract: The present invention relates to improved and integrated methods for the characterisation of an interaction site on a target protein that modulates the phenotype of a mammalian cell, such as a phenotype other than death and/or reduced growth. Such methods of the present invention include those to identify a target protein modulates such a phenotype of a mammalian cell, and optionally to characterise an interaction site on said target protein. Such identification and characterisation methods are useful in the development of research tools and/or therapeutics, such protein/peptide or small molecule therapeutics. Accordingly, the present invention also relates to methods of: identification of a ligand, such as a small molecule ligand, that binds to such a target protein; and identification a compound being a candidate modulator of said phenotype of a mammalian cell.
    Type: Application
    Filed: February 7, 2013
    Publication date: April 16, 2015
    Applicants: Phylogica Limited, Cambridge Enterprise Limited
    Inventors: Paul Watt, Bryn Hardwick, Grahame McKenzie, Ashok Venkitaraman
  • Publication number: 20150105450
    Abstract: The present invention relates to novel short interfering RNA (siRNA) molecules that are multi-targeted. More specifically, the present invention relates to siRNA molecules that target two or more sequences. In one embodiment, multi-targeting siRNA molecules are designed to incorporate features of siRNA molecules and features of micro-RNA (miRNA) molecules. In another embodiment, multi-targeting siRNA molecules are designed so that each strand is directed to separate targets.
    Type: Application
    Filed: December 22, 2014
    Publication date: April 16, 2015
    Applicant: CITY OF HOPE
    Inventors: John J. ROSSI, Ola SNOVE, JR., Ali EHSANI, Pal SAETROM, JR., Britta HOEHN, Jane ZHANG, Lars AAGAARD
  • Publication number: 20150105272
    Abstract: The present invention is directed to compositions and methods for the independent and unconstrained identification of attractor metagenes as surrogates of pure biomolecular events as well as the use of such attractor metagenes in performing medical diagnosis, prognosis, and developing appropriate therapeutic regimes.
    Type: Application
    Filed: October 21, 2014
    Publication date: April 16, 2015
    Applicant: The Trustees of Columbia University in the City of New York
    Inventors: Dimitris Anastassiou, Wei Yi Cheng
  • Publication number: 20150099694
    Abstract: Devices, systems, and methods for strain-specific identification and assessment of susceptibility of microorganisms based on the response of sensors in a colorimetric sensor array to metabolic products of the microorganism.
    Type: Application
    Filed: April 26, 2013
    Publication date: April 9, 2015
    Applicant: Specific Technologies LLC
    Inventors: Sung Hyun Lim, Raymond Anthony Martino, Paul A. Rhodes
  • Publication number: 20150089684
    Abstract: This invention provides transgenic plant cells with recombinant DNA for expression of proteins that are useful for imparting enhanced agronomic trait(s) to transgenic crop plants. This invention also provides transgenic plants and progeny seed comprising the transgenic plant cells where the plants are selected for having an enhanced trait selected from the group of traits consisting of enhanced water use efficiency, enhanced cold tolerance, increased yield, enhanced nitrogen use efficiency, enhanced seed protein and enhanced seed oil. Also disclosed are methods for manufacturing transgenic seed and plants with enhanced traits.
    Type: Application
    Filed: September 8, 2014
    Publication date: March 26, 2015
    Inventors: Mark Scott Abad, Adrian Lund, Terry Bradshaw
  • Publication number: 20150080238
    Abstract: The presently disclosed subject matter provides methods for improving the efficacy of a plant breeding program aimed at altering phenotypic traits for which associations with genetic markers can be established. Genome-wide genetic values of individuals are computed based on the individuals' marker genotypes and the associations established between genetic markers and phenotypic traits. Individuals and breeding schemes are then selected based both on the individuals' genome-wide genetic value and on the distributions of these genetic values for the potential progenies derived through the breeding schemes under evaluation. The presently disclosed subject matter also provides systems and computer program products for performing the disclosed methods as well as plants selected, provided, or produced by any of the methods herein and transgenic plants created by any of the methods herein.
    Type: Application
    Filed: November 20, 2014
    Publication date: March 19, 2015
    Applicant: SYNGENTA PARTICIPATIONS AG
    Inventors: Michel Francois RAGOT, Gilles GAY, Roland FISCH, David WILLÉ, Denis LESPINASSE, Michel LHERMINE, Orgerus ARGILLIER
  • Publication number: 20150079066
    Abstract: The disclosure provides a general method for the production of protein variants with a reduced aggregation propensity without affecting the thermodynamic stability of the variant with respect to the wild-type protein.
    Type: Application
    Filed: April 18, 2013
    Publication date: March 19, 2015
    Inventors: Frederic Rousseau, Joost Schymkowitz, Ashok Ganesan, Aleksandra Siekierska, Frederik De Smet, Joost Van Durme
  • Publication number: 20150080237
    Abstract: A new pipeline for the rational design and interpretation of biomarker panels is provided. The pipeline includes: generating the maximally informative marker set from biomarker databases; selecting an optimal biomarker panel based on the desired accuracy, economic, and experimental constraints; and interpreting the assay results by a statistically robust matching to reference data. The pipeline can also be used to identify biological samples, including cell types and progenitor cells.
    Type: Application
    Filed: April 19, 2013
    Publication date: March 19, 2015
    Inventors: Craig E. Nelson, Ion Mandoiu, Hector Leonardo Aguila
  • Publication number: 20150072876
    Abstract: Gene expression analysis is generally performed on heterogeneous tissue samples consisting of multiple cell types. Current methods developed to separate heterogeneous gene expression rely on prior knowledge of the cell-type composition and/or signatures—these are not available in most public datasets. We present a novel method to identify the cell-type composition, signatures and proportions per sample without need for a priori information. The method was successfully tested on controlled and semi-controlled datasets and performed as accurately as current methods that do require additional information. As such, this method enables the analysis of cell-type specific gene expression using existing large pools of publically available microarray datasets.
    Type: Application
    Filed: July 21, 2014
    Publication date: March 12, 2015
    Applicant: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Neta Zuckerman, Yair Noam, Andrea Goldsmith, Peter P. Lee
  • Publication number: 20150065362
    Abstract: Disclosed herein are computer-based systems, media and methods of generating dynamic classifiers and uses thereof. The dynamic classifiers may be generated from a subset of cases and/or a subset of genes that have a molecular similarity to a subject suffering from a cancer. Thus, the dynamic classifiers may be subject-specific. The dynamic classifiers may be used in the diagnosis, prognosis and/or monitoring of a status or outcome of a cancer in a subject in need thereof.
    Type: Application
    Filed: August 28, 2014
    Publication date: March 5, 2015
    Inventors: Balázs Gyorffy, Steven C. Quay, Shu-Chih Chen
  • Publication number: 20150065357
    Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.
    Type: Application
    Filed: November 7, 2014
    Publication date: March 5, 2015
    Inventor: Richard John Fox
  • Publication number: 20150065361
    Abstract: Various embodiments provide lossless compression of an enumeration space for genetic founder lines. In one embodiment, an input comprising a set of genetic founder lines and a maximum number of generations G is obtained. A set of genetic crossing templates of a height h is generated. A determination is made if at least a first genetic crossing template in the set of genetic crossing templates is redundant with respect to a second genetic crossing template in the set of genetic crossing templates. Based on the at least first genetic crossing template being redundant is redundant with respect to the second genetic crossing template, the at least first genetic crossing template is removed from the set of genetic crossing templates. This process of removing the at least first genetic crossing template from the set of genetic crossing templates the redundant creates an updated set of genetic crossing templates.
    Type: Application
    Filed: October 9, 2013
    Publication date: March 5, 2015
    Applicant: International Business Machines Corporation
    Inventors: David C. HAWS, Laxmi P. PARIDA
  • Publication number: 20150056620
    Abstract: The present invention provides methods of: identifying pathogens in biological samples from humans and animals, resolving a plurality of etiologic agents present in samples obtained from humans and animals, determining detailed genetic information about such pathogens or etiologic agents, and rapid detection and identification of bioagents from environmental, clinical or other samples.
    Type: Application
    Filed: August 29, 2014
    Publication date: February 26, 2015
    Inventors: David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke, Lawrence B. Blyn, Raymond Ranken, Thomas A. Hall
  • Publication number: 20150057166
    Abstract: Certain embodiments provide a method for crystallizing a GPCR. The method may employ a fusion protein comprising, from N-terminus to C-terminus: a) a first portion of a family C G-protein coupled receptor (GPCR), wherein the first portion comprises the TM1, TM2 and TM3, regions of the GPCR; b) a stable, folded protein insertion; and c) a second portion of the GPCR, wherein the second portion comprises the TM4, TM5 TM6 and TM7 regions of the GPCR.
    Type: Application
    Filed: October 17, 2014
    Publication date: February 26, 2015
    Inventor: BRIAN KOBILKA
  • Publication number: 20150051090
    Abstract: In one aspect, the invention relates to a method for identifying a small molecule which binds an evolved three dimensional topological feature on a target protein. In certain embodiments, the three dimensional topological feature evolves on the target protein as a result of binding by a biomolecule to the target protein. In certain embodiments, the small molecule modulates an activity of the target protein. In certain embodiments, the evolved three dimensional topological features are identified using molecular dynamics simulation.
    Type: Application
    Filed: August 19, 2014
    Publication date: February 19, 2015
    Inventor: Yibing SHAN
  • Publication number: 20150023949
    Abstract: Methods for treatment and diagnosis of pervasive developmental disorders in humans are described.
    Type: Application
    Filed: March 5, 2013
    Publication date: January 22, 2015
    Inventors: Niven Rajin Narain, Paula Patricia Narain
  • Publication number: 20150023974
    Abstract: The present invention relates to the identification of a TLR2 binding epitope wherein binding of a binding member to the epitope serves to inhibit TLR2 activation and/or signalling. Polypeptide fragments of TLR2 and three-dimensional structures comprising one or more amino acid residues His318, Pro320, Gln321 or Arg321, Tyr323, Lys347, Phe349, Leu371, Glu375, Tyr376 and His398 of TLR2 which define the identified epitope are provided for use in generating binding members. Also provided are binding members which bind to the identified epitope and methods of using same for the treatment and/or prevention of conditions associated with TLR2 activation and/or signalling.
    Type: Application
    Filed: March 29, 2013
    Publication date: January 22, 2015
    Inventors: Nils Kuklik, Wolf-Dieter Schubert
  • Publication number: 20150024951
    Abstract: Methods for identifying disease-related pathways that can be 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: July 28, 2014
    Publication date: January 22, 2015
    Inventors: Richard O. CHEN, Raymond J. CHO, Ramon M. FELCIANO, Bret HOLLEY, Viresh PATEL, Daniel R. RICHARDS, Sushma SELVARAJAN, Keith STEWARD, Sara Tanenbaum SCHNEIDER
  • Publication number: 20150011620
    Abstract: The present invention relates to the field of anti-invasive compounds and methods for predicting the anti-invasive activity of said compounds, as well as their use in the prevention and/or treatment of diseases associated with undesired cell invasion; in particular, this invention relates to the field of anti-invasive chalcone-like compounds.
    Type: Application
    Filed: January 30, 2013
    Publication date: January 8, 2015
    Inventors: Marc Bracke, Christian Stevens, Tine De Ryck, Bart Roman, Barbara Vanhoecke
  • Publication number: 20140371079
    Abstract: Cancer-targeting peptides having a PX1LX2 motif, in which X1 is His or an amino acid residue with a hydrophobic side chain and X2 is Pro, Phe, or Trp. Also disclosed herein are conjugates containing the cancer-targeting peptides and uses thereof in cancer treatment and diagnosis.
    Type: Application
    Filed: August 13, 2014
    Publication date: December 18, 2014
    Inventors: John Yu, Alice L. Yu, H.C. Wu, I-Ju Chen, Sheng-hung Wang
  • Publication number: 20140364434
    Abstract: Methods and systems for identifying a cancer patient suitable for treatment with a PARP inhibitor. A 6-gene, 7-gene and 8-gene predictor panels of genes that are predictive of patient resistance or sensitivity to PARP inhibitors such as Olaparib.
    Type: Application
    Filed: June 6, 2014
    Publication date: December 11, 2014
    Applicant: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Anneleen Daeman, Denise M. Wolf, Laura J. Van 't Veer, Paul T. Spellman, Joe W. Gray
  • Publication number: 20140351962
    Abstract: The present invention provides a method of testing a dog to determine the susceptibility of the dog to liver copper accumulation, comprising detecting in a sample the presence or absence in the genome of the dog of one or more polymorphisms selected from: (a) Chr22_3167534 (SEQ ID NO: 144), Chr22_3135144 (SEQ ID NO: 145), Chr20_55461150 (SEQ ID NO: 146), ChrX_120879711 (SEQ ID NO: 147), Chr19_6078084 (SEQ ID NO: 148), Chr15_62625262 (SEQ ID NO: 149), Chr14_39437543 (SEQ ID NO: 150), Chr15_62625024 (SEQ ID NO: 151), Chr3_86838677 (SEQ ID NO: 152), Chr24_4011833 (SEQ ID NO: 153), Chr18_60812198 (SEQ ID NO: 154), Chr10_65209946 (SEQ ID NO: 155), and the CGCCCC repeat at chromosome location 22:3135287; (b) one or more polymorphisms in linkage disequilibrium with a said polymorphism (a); and/or (c) Chr32_38904515 (SEQ ID NO: 156), Chr8_4892743 (SEQ ID NO: 157) and Chr8_4880518 (SEQ ID NO: 158).
    Type: Application
    Filed: December 6, 2012
    Publication date: November 27, 2014
    Applicant: MARS, INC.
    Inventors: Alan James Martin, Paul Glyn Jones, Adrian Watson, Jan Rothuizen, Hille Fieten, Pieter Antonius Jozef Leegwater
  • Publication number: 20140328838
    Abstract: A method of producing a non-immunogenic immunoglobulin for administration to a target species is provided wherein the method comprises substituting amino acid residues in framework regions of a donor immunoglobulin with amino acid residues present at a corresponding position in framework regions of at least one immunoglobulin derived from the target species. Also provided are antibodies produced by the method of the invention, including novel humanised and caninised anti-NGF antibodies. The invention extends to nucleic acids encoding same and to methods of treating pain and arthritis in a human or dog using said antibodies and/or nucleic acids.
    Type: Application
    Filed: September 5, 2012
    Publication date: November 6, 2014
    Inventor: David Gearing
  • Publication number: 20140315731
    Abstract: Methods and systems for evaluating biological dataset profiles relating to toxic agents including candidate pharmaceuticals, environmental agents, biowarfare and chemical warfare agents are provided, where datasets comprising information for multiple cellular parameters are compared and identified, and used in the evaluation of candidate agents.
    Type: Application
    Filed: April 21, 2014
    Publication date: October 23, 2014
    Applicant: DISCOVERX CORPORATION
    Inventor: Ellen L. Berg
  • Publication number: 20140315742
    Abstract: The present invention relates to methods and kits to assess an absorbed dose of ionizing radiation and/or the severity of tissue injury from radiation in a patient. The invention also relates to algorithms used to calculate an absorbed dose of radiation based on biomarker measurements of a plurality of biomarkers that are altered relative to a normal control in the event of radiation exposure.
    Type: Application
    Filed: September 28, 2012
    Publication date: October 23, 2014
    Applicants: MESO SCALE TECHNOLOGIES, LLC, THE HENRY M. JACKSON FOUNDATION FOR THE ADVANCEMENT OF MILITARY MEDICINE, INC.
    Inventors: William F Blakely, Eli N. Glezer, John Kenten, Sudeep Kumar, Anu Mathew, Natalia I. Ossetrova, George Sigal
  • Publication number: 20140309121
    Abstract: A method of categorising a human according to pre-determined categories using Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI-MS) is disclosed. A method is provided to discriminate humans based on gender, for example, by comparing MALDI-MS sample spectral data in the m/z range 2,000 to 30,000 and comparing these sample spectral data with reference spectral data obtained from pre-categorised humans.
    Type: Application
    Filed: July 24, 2012
    Publication date: October 16, 2014
    Inventors: Simona Francese, Leesa Susanne Ferguson, Rosalind Wolstenholme, Florian Wulfert, Judith Marlou Fonville
  • Publication number: 20140309122
    Abstract: Systems and methods are disclosed for Knowledge-Driven Sparse Learning to Identify Interpretable High-Order Feature Interactions. This is done by generating one or more functional groups from gene features and gene and protein interaction grouping; selecting informative genes and functional interactions that exhibit differential patterns for the target disease and to generate a reduced feature space; and searching exhaustively on the reduced feature space by examining all possible pairs of interacting features (and possibly higher-order feature interactions) to identify combination of markers and complex patterns of feature interactions that are informative about the phenotypes in a sparse learning framework to select informative interactions and genes.
    Type: Application
    Filed: April 3, 2014
    Publication date: October 16, 2014
    Applicant: NEC Laboratories America, Inc.
    Inventors: Renqiang Min, Yanjun Qi, Salim Akhter Chowdhury
  • Publication number: 20140303228
    Abstract: The disclosure provides biomarkers of amyotrophic lateral sclerosis (ALS). The disclosure also provides various methods of using the biomarkers, including methods for diagnosis of ALS, methods of determining predisposition to ALS, methods of monitoring progression/regression of ALS, methods of assessing efficacy of compositions for treating ALS, methods of screening compositions for activity in modulating biomarkers of ALS, methods of treating ALS, as well as other methods based on biomarkers of ALS.
    Type: Application
    Filed: October 17, 2012
    Publication date: October 9, 2014
    Inventors: Kay A. Lawton, Meredith V. Brown, Bruce Neri, Rebecca Caffrey, Michael V. Milburn
  • Publication number: 20140303069
    Abstract: Anti-microbial peptides and methods of use are provided.
    Type: Application
    Filed: November 20, 2012
    Publication date: October 9, 2014
    Inventors: Guangshun Wang, Biswajit Mishra
  • Publication number: 20140303011
    Abstract: The invention provides for a method for distinguishing spore preparation procedures using spore molecular signatures, the method comprising harvesting spores from a sample; extracting molecules from the spores, fractionating the extracted molecules for analysis; generating molecular signatures from the fractionated molecules, and comparing the molecular signatures to a library of molecular signatures.
    Type: Application
    Filed: March 22, 2012
    Publication date: October 9, 2014
    Applicant: UCHICAGO ARGONNE, LLC
    Inventors: Daniel Shabacker, Adam Driks
  • Publication number: 20140296085
    Abstract: The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient, The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.
    Type: Application
    Filed: November 2, 2012
    Publication date: October 2, 2014
    Applicant: GENOMIC HEALTH, INC.
    Inventors: Joffre B. Baker, Dominick S. Sinicropi, Robert J. Pelham, Michael R. Crager, Francois Collin, James C. Stephans, Mei-Lan Liu, John D. Morlan, Kunbin Qu
  • Publication number: 20140296081
    Abstract: Methods for creating a library of recurrently mutated genomic regions and for using the library to analyze cancer-specific and patient-specific genetic alterations in a patient are provided. The methods can be used to measure tumor-derived nucleic acids in patient blood and thus to monitor the progression of disease. The methods can also be used for cancer screening.
    Type: Application
    Filed: March 13, 2014
    Publication date: October 2, 2014
    Inventors: Maximilian Diehn, Arash Ash Alizadeh, Aaron M. Newman, Scott V. Bratman
  • Publication number: 20140286964
    Abstract: The present invention provides methods for designing agents such as ligands capable of binding to a Janus kinase (Jak), particularly a Jak2 JH2, and especially a JH2 V617F, screening methods for identifying agents such as ligands and small molecules capable of binding to the same, and computer assisted methods for designing and identifying such agents. Further, the present invention provides methods for treating myeloproliferative neoplasias (MPNs) along with agents such as ligands and small molecules identified or designed using the methods described.
    Type: Application
    Filed: October 24, 2012
    Publication date: September 25, 2014
    Inventors: Stevan R. Hubbard, Rajintha M. Bandarayanake, Olli Silvennoinen, Daniela Ungureanu
  • Publication number: 20140274752
    Abstract: Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.
    Type: Application
    Filed: October 18, 2012
    Publication date: September 18, 2014
    Inventors: Erich D. Blume, John P. Burke, Hui Huang
  • Publication number: 20140274749
    Abstract: Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.
    Type: Application
    Filed: March 15, 2013
    Publication date: September 18, 2014
    Inventor: Affymetrix, Inc.
  • Publication number: 20140275088
    Abstract: In one aspect, the present invention relates to a method of identifying compounds useful in modifying the activity of Aldolase.
    Type: Application
    Filed: October 25, 2012
    Publication date: September 18, 2014
    Inventors: Timothy J. Cardozo, Jürgen Bosch, Sondra Maureen Nemetski
  • Publication number: 20140274750
    Abstract: The invention generally relates to sequence assembly and particularly to ordering the alignment of contigs to reference maps. The invention provides systems and methods for assembling contigs by aligning those contigs to a reference map in descending order of placement confidence. Each placement decreases the number of possible placements for the remaining contigs, which otherwise would have been likely to match in numerous places. Contigs are thereby placed along the reference genome with confidence and thus can be assembled into a genome-scale sequence assembly.
    Type: Application
    Filed: March 14, 2014
    Publication date: September 18, 2014
    Applicant: OpGEN, INC.
    Inventor: Deacon John Sweeney
  • Publication number: 20140274751
    Abstract: Provided herein is technology relating to identifying unknown compounds and particularly, but not exclusively, to methods and systems for identifying unknown compounds by gas chromatography-mass spectrometry by use of retention index as a second dimension for identification.
    Type: Application
    Filed: August 3, 2012
    Publication date: September 18, 2014
    Applicant: SMITHS DETECTION INC.
    Inventors: Charles Sadowski, Greger Andersson, Kevin Judge
  • Publication number: 20140250546
    Abstract: The invention relates to efficient, high-throughput methods, systems, and DNA constructs for identification and isolation of terminator sequences causing enhanced transcription. The invention further relates to terminator sequences isolated with such methods and their use for enhancing gene expression.
    Type: Application
    Filed: July 20, 2012
    Publication date: September 4, 2014
    Applicant: BASF PLANT SCIENCE COMPANY GMBH
    Inventors: Julia Verena Hartig, Alrun Nora Burgmeier, Josef Martin Kuhn, Linda Patricia Loyall, Elke Duwenig
  • Publication number: 20140249035
    Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.
    Type: Application
    Filed: April 18, 2014
    Publication date: September 4, 2014
    Applicant: Codexis Mayflower Holdings, LLC
    Inventor: Richard John Fox
  • 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