In Silico Screening Patents (Class 506/8)
  • Publication number: 20110059853
    Abstract: For assessing classification annotations assigned to DNA sequences stored in a reference database, the DNA sequences are grouped by species using established classification schemes. Subsequently, a measure of distance between pairs of DNA sequences is determined by aligning the respective sequences and determining the measure of distance based on a score of similarity between the aligned DNA sequences. Determined are one or more centroid sequences which have the shortest aggregate measure of distance to the other DNA sequences in the respective group (species). Assigned to the DNA sequences as a quantitative confidence level for their classification annotations is in each case the measure of distance between the respective DNA sequence and the centroid sequence. The assessment and rating of the classification annotations with these confidence levels make it possible to provide to a user a quantitative indication of the degree of representativeness of a DNA sequence for a particular species.
    Type: Application
    Filed: November 29, 2007
    Publication date: March 10, 2011
    Applicant: SMARTGENE GMBH
    Inventors: Stefan Emler, Pierre-André Michel
  • Publication number: 20110053787
    Abstract: The present invention relates to novel methods and products for assessing the physiological status of a subject. More particularly, the invention relates to methods of assessing the presence, risk or stage of a cancer in a subject by identifying or measuring the levels of proteins that exhibits post-stop peptides in a sample from the subject. The invention is also suitable to assess the responsiveness of a subject to a treatment, as well as to screen candidate drugs and design novel therapies. The invention may be used in any mammalian subject, particularly in human subjects.
    Type: Application
    Filed: January 16, 2009
    Publication date: March 3, 2011
    Inventors: Marie Brulliard, Bernard Bihain
  • Publication number: 20110045996
    Abstract: An analysis technique for genetic data to detect alternative spliced exons. Exon expression of similar data is analyzed using a robust regression technique to find outliers to the main regression. False outliers are detected and removed. The remaining outliers are identified as potential alternative splicing events.
    Type: Application
    Filed: August 21, 2008
    Publication date: February 24, 2011
    Inventors: Gene Yeo, Fred H. Gage
  • Patent number: 7893007
    Abstract: In order to obtain a novel binding protein against a chosen target, DNA molecules, each encoding a protein comprising one of a family of similar potential binding domains and a structural signal calling for the display of the protein on the outer surface of a chosen bacterial cell, bacterial spore or phage (genetic package) are introduced into a genetic package. The protein is expressed and the potential binding domain is displayed on the outer surface of the package. The cells or viruses bearing the binding domains which recognize the target molecule are isolated and amplified. The successful binding domains are then characterized. One or more of these successful binding domains is used as a model for the design of a new family of potential binding domains, and the process is repeated until a novel binding domain having a desired affinity for the target molecule is obtained.
    Type: Grant
    Filed: October 22, 2008
    Date of Patent: February 22, 2011
    Assignee: Dyax Corp.
    Inventors: Robert Charles Ladner, Sonia Kosow Guterman, Bruce Lindsay Roberts, William Markland, Arthur Charles Ley, Rachel Baribault Kent
  • Publication number: 20110039713
    Abstract: The invention relates to the FCGR2B gene and its promoter. In particular, the invention relates to FCGR2B promoters with specific nucleotides at polymorphic sites. Characterization of the nucleotides at polymorphic sites is useful for characterizing the gene and the protein and is useful for determining predisposition or susceptibility to certain diseases and infections in a subject or a population of subjects. Such characterization of the gene or protein is also useful for determining immunoresponsiveness or responsiveness to therapeutic agents in a subject or population of subjects. Thus, disclosed herein are a variety of related nucleic acids, methods and tools.
    Type: Application
    Filed: August 9, 2010
    Publication date: February 17, 2011
    Inventors: ROBERT P. KIMBERLY, JEFFREY EDBERG, KAIHONG SU, JIANMING WU
  • Publication number: 20110039714
    Abstract: Aspects of the present invention include probes, methods, systems that have stand alone utility and may comprise features of a drug discovery system or method. The present invention also includes pharmaceutical compositions. In more detail, the present invention provides molecular probes and methods for producing molecular probes. The present invention provides also provides systems and methods for new drug discovery. An embodiment of the present invention utilizes sets of probes of the present invention and a new approach to computational chemistry in a drug discovery method having increased focus in comparison to heretofore utilized combinatorial chemistry. The present invention also provides computer software and hardware tools useful in drug discovery systems.
    Type: Application
    Filed: October 8, 2010
    Publication date: February 17, 2011
    Inventors: Adnan M. M. Mjalli, Chris Wysong, Jerome Baudry, Thomas Scott Yokum, Rob Andrews, William K. Banner
  • Publication number: 20110033377
    Abstract: The present invention relates generally to the field of diagnostic and prognostic assays for a gynecological condition. More particularly, the present invention provides an assay for diagnosing the presence of or a risk of having a gynecological cancer or a sub-type thereof or a stage of the cancer or complications arising therefrom or other gynecological condition including an inflammatory disorder.
    Type: Application
    Filed: April 21, 2009
    Publication date: February 10, 2011
    Applicant: Healthlinx Limited
    Inventors: Dominic J. Autelitano, Tracey A. Edgell, Nick Gatsios, Leodevico L. Ilag
  • Publication number: 20110030090
    Abstract: The invention provides isolated peptide-methionine sulfoxide reductase nucleic acids and their encoded proteins. The present invention provides methods and compositions relating to altering peptide-methionine sulfoxide reductase levels in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.
    Type: Application
    Filed: April 1, 2010
    Publication date: February 3, 2011
    Applicant: E. I. du Pont de Nemours and Company
    Inventors: Saverio Carl Falco, Omolayo O. Famodu, Blake C. Meyers, Guo-Hua Miao, Joan T. Odell, J. Antoni Rafalski, Catherine J. Thorpe, Hajime Sakai, Zude Weng
  • Publication number: 20110028334
    Abstract: The present invention provides systems, methods, and compositions for performing molecular tests. In particular, the present invention provides methods, compositions and systems for generating target sequence-linked solid supports (e.g., beads) using a solid support linked to a plurality of capture sequences and capture primers composed of a 3? target-specific portion and a 5? capture sequence portion. In certain embodiments, the target sequence linked solid support is used in sequencing methods (e.g., pyrosequencing, zero-mode waveguide type sequencing, nanopore sequencing, etc.) to determine the sequence of the target sequence (e.g., in order to detect the identity of a target nucleic acid in sample).
    Type: Application
    Filed: July 30, 2010
    Publication date: February 3, 2011
    Applicant: IBIS BIOSCIENCES, INC.
    Inventor: Mark A. Hayden
  • Publication number: 20110028333
    Abstract: A method of employing DNA methylation analysis for the diagnosis, prognosis, and prediction of cancer.
    Type: Application
    Filed: April 30, 2010
    Publication date: February 3, 2011
    Applicant: BROWN UNIVERSITY
    Inventors: Brock C. Christensen, Karl T. Kelsey
  • Publication number: 20110028335
    Abstract: Disclosed is the three-dimensional (3-D) structure of the GLP-1 receptor (GLP-1R) and methods by which the structure may be used to develop compounds that bind to, and/or modulate the GLP-1R. The technology described herein may be applied to the development of compounds that target the GLP-1R, or may be used to develop target compound that may bind to, and/or modulate the activity of the GLP-1R.
    Type: Application
    Filed: April 8, 2009
    Publication date: February 3, 2011
    Applicant: TRANSTECH PHARMA, INC.
    Inventor: Mohan Rao
  • Publication number: 20110021364
    Abstract: The invention provides a method of predicting the size of a dog that will be attained in adulthood, comprising typing the nucleotide(s) present for a single nucleotide polymorphic (SNP) marker present in the genome of the dog at a position equivalent to position 201 in one or more of the sequences identified in Table 1, and/or at one or more positions which are in linkage disequilibrium with any one of these positions, and thereby predicting the size of the dog that will be attained in adulthood.
    Type: Application
    Filed: November 7, 2008
    Publication date: January 27, 2011
    Applicant: MARS, INCORPORATED
    Inventors: Paul Glyn Jones, Stephen Harris, Alan James Martin
  • Publication number: 20100317537
    Abstract: The invention relates to apparatus and methods for studying intracellular rheology. The invention further relates to use of such apparatus and methods to screen for potentially therapeutic molecules that give rise to rheological effects within a cell. As one example, the disclosed ballistic intracellular nanorheology (BIN) apparatus and methods may be employed in a high-throughput screen to identify mediators or inhibitors of the cytoskeletal modifications involved in cancer metastasis.
    Type: Application
    Filed: February 13, 2009
    Publication date: December 16, 2010
    Applicant: University of Florida Research Foundation, Inc.
    Inventors: Yiider Tseng, Jerry S.H. Lee, Pei-Hsun Wu
  • Publication number: 20100317536
    Abstract: A crystal comprising the collagen binding domain of human GPVI is provided and defined by structural atomic coordinates. Employing computer modeling based on the crystal structure, including methods for identifying inhibitors of GPVI collagen binding activity, methods for screening libraries of compounds for potential to bind to the GPVI collagen binding domain, and methods of identifying a compound useful for the treatment of a GPVI-mediated disorder, are also provided.
    Type: Application
    Filed: March 28, 2007
    Publication date: December 16, 2010
    Applicant: University of Cincinnati
    Inventors: Andrew B. Herr, Katsunori Horii
  • Publication number: 20100312072
    Abstract: A method of estimating a grade of a prostate cancer from zinc data associated with the prostate, the zinc data being arranged gridwise in a plurality of picture-elements representing a zinc map of the prostate. The method comprises, clustering the zinc map according to zinc levels associated with the picture-elements, and estimating a cancer grade of at least one tissue region, based, at least in part, on zinc levels associated with a cluster of picture-elements representing the tissue region.
    Type: Application
    Filed: January 1, 2009
    Publication date: December 9, 2010
    Applicant: Yeda Research And Development Co. Ltd.
    Inventors: Amos Breskin, Rachel Chechik, Sana Shilstein, Marco Cortesi
  • Publication number: 20100311601
    Abstract: The present invention provides the identification and combination of genes that are expressed in tumors that are responsive to a given therapeutic agent and whose combined expression can be used as an index that correlates with responsiveness to that therapeutic agent. One or more of the genes of the present invention may be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by that agent or class of agents such as hormonal or endocrine therapy or chemotherapy.
    Type: Application
    Filed: May 3, 2010
    Publication date: December 9, 2010
    Applicants: Nuvera Biosciences, Inc., The Board of Regents of the University of Texas System
    Inventors: W. Fraser Symmans, Christos Hatzis, Lajos Pusztai
  • Publication number: 20100311600
    Abstract: A method for the parallel identification of one or more metabolite species within a biological sample is provided. The method comprises producing a first spectrum by subjecting the sample to a nuclear magnetic resonance analysis, the first spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; producing a second spectrum by subjecting the sample to a mass spectrometry analysis, the spectrum containing individual spectral peaks representative of the one or more metabolite species contained within the sample; subjecting each of the individual spectral peaks to a statistical pattern recognition analysis to identify the one or more metabolite species contained within the sample; and identifying the one or more metabolite species contained within the sample by analyzing the individual spectral peaks of the mass and nuclear magnetic resonance spectra.
    Type: Application
    Filed: October 3, 2008
    Publication date: December 9, 2010
    Inventors: Daniel M. Raftery, Zhengzheng Pan, Haiwei Gu
  • Publication number: 20100304984
    Abstract: The invention provides materials and methods for detecting the expression of genes encoding cytochrome p450, nuclear X receptors, phase H transferases, and solute carrier family uptake pumps. The materials include sets of primers, PCR amplicons and arrays. The methods of the invention include hybridization assays. Kits and assays for the detection of the expression of the genes are also provided by the invention. In addition, the invention provides the use of the materials and methods of the invention in drug screening assays.
    Type: Application
    Filed: November 8, 2007
    Publication date: December 2, 2010
    Applicant: NOAB BIODISCOVERIES INC.
    Inventors: Robert Shipman, Jodi A Morrison, Ines De Lannoy
  • Publication number: 20100304983
    Abstract: An efficient computational method and system for predicting the folding regions and associated secondary and tertiary structures of a protein is disclosed. Methods and systems for sorting amino acid sequences based on predicted structures, as well as methods and systems for determining the presence or absence of genes in nucleic acid sequences or structural mutations in amino acid sequences are also disclosed. A method and system for the design of a protein is also disclosed.
    Type: Application
    Filed: April 18, 2008
    Publication date: December 2, 2010
    Applicant: The Research Foundation of State University of New York
    Inventors: Charles Michael Fortmann, Yeona Kang, David H. Coleman
  • Publication number: 20100298308
    Abstract: The mechanism by which the high bone mass (HBM) mutation (G171V) of the Wnt coreceptor LRP5 regulates the canonical Wnt signaling was investigated. The mutation was previously shown to reduce Dkk protein-1-mediated antagonism, suggesting that the first YWTD repeat domain where G171 is located may be responsible for Dkk protein-mediated antagonism. However, we found that the third YWTD repeat, but not the first repeat domain, is required for DKK1-mediated antagonism. Instead, we found that the G171V mutation disrupted the interaction of LRP5 with Mesd, a chaperon protein for LRP5/6 that is required for the coreceptors' transport to cell surfaces, resulting in less LRP5 molecules on the cell surface. Although the reduction in the level of cell surface LRP5 molecules led to a reduction in Wnt signaling in a paracrine paradigm, the mutation did not appear to affect the activity of coexpressed Wnt in an autocrine paradigm.
    Type: Application
    Filed: November 14, 2006
    Publication date: November 25, 2010
    Inventors: Dianqing (Dan) Wu, Dakai Liu, James J. Donegan
  • Publication number: 20100298200
    Abstract: The present invention relates to the field of therapeutic methods to screen for compounds on the basis of their ability to influence Wnt activity. The screening process is applied to both a physical library of a series of compounds and a virtual library of compounds that affect Wnt activity. In one aspect, the virtual screening process could be carried out where a permutational library of small peptides is substituted for the small organic molecules. The inventive methods may be used to empirically test for effects on Wnt activity and may also be applied to any pair of proteins involved in protein-protein interactions.
    Type: Application
    Filed: May 22, 2009
    Publication date: November 25, 2010
    Inventors: Dakai Liu, Xiaofeng Li, Richard Jin, Yuaxin Liang, Wei Cheng, Riddhi Bhattacharyya, Guangrong Zhang
  • Publication number: 20100296963
    Abstract: The present invention relates to a crystal structure of a plasma membrane proton pump type ATPase. The invention further describes method for identification of modulators of ATPases as well as uses of such modulators. Based on the provided three dimensional structure of the ATPase, various method, such as computer implemented methods may be used for identification of modulators, such putative modulators may be further analysed using in vitro and in vivo experiments to confirm there functionality. Several modulator interaction regions are described as target of regulation by ATPase modulators.
    Type: Application
    Filed: December 12, 2008
    Publication date: November 25, 2010
    Applicants: Aarhus Universitet, Kobenhavns Universitet
    Inventors: Michael G. Palmgren, Morten Buch-Pedersen, Bjørn Pañella Pedersen, Poul Nissen
  • Publication number: 20100292088
    Abstract: The present invention provides methods and compositions for detecting mutations in a DNAH11 gene of a subject to diagnose primary ciliary dyskinesia (PCD) in the subject and/or to identify a subject as having an increased risk of having PCD and/or to identify a carrier of a PCD mutation.
    Type: Application
    Filed: May 14, 2010
    Publication date: November 18, 2010
    Inventors: Maimoona Banoo Abdul Hamid Zariwala, Michael R. Knowles
  • Publication number: 20100292087
    Abstract: Disclosed is a method of predicting clinical tumor outcome by providing gene expression from a tumor sample. The method utilizes a novel genetic screen to identify genes that contribute to chemotherapeutic responsiveness, using formalin fixed paraffin embedded clinical samples of epithelial cancer, specifically serous ovarian cancer. The method is useful in predicting tumor responsiveness to chemotherapeutics, including alkylating agents, cisplatin, antimetabolites, plant alkaloids, and antitumor antibiotics. A microarray screen showed formalin fixed paraffin embedded samples can identify genes related to chemotherapeutic response with 86% efficiency.
    Type: Application
    Filed: April 23, 2010
    Publication date: November 18, 2010
    Applicant: UNIVERSITY OF SOUTH FLORIDA
    Inventor: Johnathan M. Lancaster
  • Patent number: 7833942
    Abstract: A method for simplification of a microbial genome or microbial nucleic acid comprising treating microbial genome or nucleic acid with an agent that modifies cytosine to form derivative microbial nucleic acid and amplifying the derivative microbial nucleic acid to produce a simplified form of the microbial genome or nucleic acid.
    Type: Grant
    Filed: December 5, 2005
    Date of Patent: November 16, 2010
    Assignee: Human Genetic Signatures Pty. Ltd.
    Inventors: Douglas Spencer Millar, George L. Gabor Miklos
  • Publication number: 20100285980
    Abstract: Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer and/or the likelihood of a beneficial response to chemotherapy for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene expression-tumor region ratios, tumor-associated stromal surface area, and gene cliques, i.e. genes that co-express with a validated biomarker and thus may be substituted for that biomarker in an assay, are also provided.
    Type: Application
    Filed: April 30, 2010
    Publication date: November 11, 2010
    Inventors: Steven Shak, Drew Watson, Xitong Li, Lawrence Lee, Kim Langone
  • Publication number: 20100285979
    Abstract: The present invention relates to the use of genes differentially expressed in benign thyroid lesions and malignant thyroid lesions for the diagnosis and staging of thyroid cancer.
    Type: Application
    Filed: August 27, 2008
    Publication date: November 11, 2010
    Inventors: Martha Allen Zeiger, Nijaguna B. Prasad, Steven K. Libutti, Christopher B. Umbricht
  • Publication number: 20100279881
    Abstract: There are many clinical instances in which, during the course of a disease, a patient may produce an antibody directed to unknown protein target(s). The targeted antigen(s) may be autoantigens (e.g., autoimmune diseases), microbial antigens (e.g., infectious diseases), allergens or, as in the case of B lymphoproliferative disorders and monoclonal gammopathies, antigens of unknown identity. When the antigen source is known or suspected, it may be feasible to construct a cDNA expression library and identify it. However, with no clues as to the antigen's origin, expression screening is impossible. We describe a new search strategy to overcome this limitation. We term the approach Epitope-Mediated Antigen Prediction (E-MAP). The technology enables one to link antibodies of unknown specificity to their cognate/target antigens in the protein database without requiring prior knowledge of their cellular source. We also describe a clinical application of the E-MAP technology to the study of multiple myeloma.
    Type: Application
    Filed: January 31, 2008
    Publication date: November 4, 2010
    Inventors: Seshi R. Sompuram, Steven A. Bogen
  • Publication number: 20100279883
    Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.
    Type: Application
    Filed: June 9, 2010
    Publication date: November 4, 2010
    Inventors: Nicholas M. Sampas, Bo Curry, Peter Tsang, Doron Lipson, Zohar H. Yakhini
  • Publication number: 20100279882
    Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.
    Type: Application
    Filed: April 30, 2010
    Publication date: November 4, 2010
    Inventors: Mostafa Ronaghi, Dirk Evers, Jason Richard Betley
  • Publication number: 20100273665
    Abstract: The present invention provides a sensor apparatus based on 2D films or 3D assemblies of cubic nanoparticles capped with an organic coating. The apparatus is used to determine the composition and preferably measure the concentration of volatile and non-volatile compounds in a sample, with very high sensitivity. Methods for use of the apparatus in applications such as diagnosis of disease, food quality and environmental control are disclosed.
    Type: Application
    Filed: November 20, 2008
    Publication date: October 28, 2010
    Applicant: TECHNION RESEARCH AND DEVELOPMENT FOUNDATION LTD.
    Inventors: Hossam Haick, Ekaterina Dovgolevsky
  • Publication number: 20100273666
    Abstract: A method of analyzing wound samples is provided. The analysis typically involves the use of mass spectrometry.
    Type: Application
    Filed: December 10, 2008
    Publication date: October 28, 2010
    Inventors: Stephanie F. Bernatchez, Katri M. Huikko
  • Publication number: 20100273664
    Abstract: The present invention relates to the determination of intra- or intermolecular interaction between molecules in aqueous solution, said method comprising the steps of: (a) determining the dehydration (?Gdehydration) of all atoms in the intermolecular interface, (b) adding the vacuum hydrogen bond energy (?H-bond), and (c) further adding the change in the free enthalpy of the interacting partners upon their interaction. The obtained results can be used for the prediction if and to what extent two molecules of various origin fit to each other.
    Type: Application
    Filed: October 20, 2007
    Publication date: October 28, 2010
    Applicants: BAYER CROPSCIENCE AG, UNIVERSITAET HAMBURG
    Inventors: Gudrun Lange, Robert Klein, Juergen Albrecht, Matthias Rarey, Ingo Reulecke
  • Publication number: 20100261614
    Abstract: The present invention relates to nucleic acid sequences from Bacillus thuringiensis and, in particular, to genomic DNA sequences. The invention encompasses nucleic acid molecules present in non-coding regions as well as nucleic acid molecules that encode proteins, fragments of proteins, tRNA's, fragments of tRNA's, rRNA's and fragments of rRNA's. In addition, proteins and fragments of proteins so encoded and antibodies capable of binding the proteins are encompassed by the present invention. The invention also relates to methods of using the disclosed nucleic acid molecules, proteins, fragments of proteins, RNA's, and antibodies, for example, for gene identification and analysis, and preparation of constructs.
    Type: Application
    Filed: April 19, 2010
    Publication date: October 14, 2010
    Inventors: David R. Corbin, Thomas M. Malvar, Hridayabhiranjan Shukla
  • Publication number: 20100261613
    Abstract: Quantitative expression datasets are created and used in the identification, monitoring and treatment of disease states and characterization of biological conditions. Quantitative datasets are derived from subject samples and enable evaluation of a biological condition. Such quantitative datasets may be used to provide an output score indicative of the biological state of a subject through analysis against a profile dataset.
    Type: Application
    Filed: July 28, 2008
    Publication date: October 14, 2010
    Inventors: Michael Centola, Philip Alex, Nicholas Knowlton, Mark Barton Frank
  • Publication number: 20100248974
    Abstract: A crystal, a preparation method and 3D structure of CD147 extracellular region are provided. Such 3D structure is useful in the determination of the active site of CD147 extracellular region by computer modeling or molecular docking method. The crystal and/or 3D structure are useful in a structure-based drug design and the selection of an antibody, a ligand or an interacting molecule of CD 147 extracellular region.
    Type: Application
    Filed: October 24, 2007
    Publication date: September 30, 2010
    Inventors: Zhinan Chen, Ping Zhu, Xiaoling Yu, Bin Yang, Xiangmin Yang, Zheng Zhang
  • Publication number: 20100242137
    Abstract: The invention provides isolated pyruvate dehydrogenase kinase nucleic acids and their encoded polypeptides. The present invention provides methods and compositions relating to altering pyruvate dehydrogenase kinase levels in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.
    Type: Application
    Filed: June 7, 2010
    Publication date: September 23, 2010
    Applicant: EI DU PONT DE NEMOURS AND COMPANY; AND PIONEER HI-BRED INTERNATIONAL INC
    Inventors: Quinn Qun Zhu, Sabine S. Hantke, Xiping Niu, Zheng Peizhong, Michele Morgante, Joan T. Odell, Saverio Carl Falco, Yiwen Fang, J. Antoni Rafalski, Hajime Sakai, Edgar B. Cahoon, Rebecca E. Cahoon, Jian-Ming Lee, Guo-Hua Miao, Zhongsen Li, Anthony J. Kinney
  • Publication number: 20100240542
    Abstract: As disclosed herein, the present invention provides for kits and a composition for diagnosis, prognosis, drug discovery, drug development, and patient stratification. The kits can comprise a plurality of binding elements for cell surface markers, and a plurality of binding elements for state-specific intracellular markers. The kits can further comprise a plurality of modulators directed for the particular cell function or signaling pathways. The kits can further include fixatives, permeabilizing agent, buffers, containers, instructions, and software for data analysis/compilation.
    Type: Application
    Filed: March 23, 2010
    Publication date: September 23, 2010
    Applicant: Nodality, Inc.
    Inventors: David Soper, David Rosen, Todd Covey, Ying-Wen Huang, Wendy Fantl, Ralph Lin
  • Publication number: 20100234236
    Abstract: The present invention relates to methods for drug repositioning. More particularly, this invention relates to methods for selecting approved drugs or combinations of approved drugs for use in new therapeutic indications. This approach is situated in a cross section between drug repositioning and disease treatment by combinations of drugs with additive or synergistic action. The invention also allows to define drugs or drug combinations for treating the unmet medical need in diseases neglected by majority of Pharma companies, such as orphan diseases.
    Type: Application
    Filed: November 28, 2008
    Publication date: September 16, 2010
    Applicant: PHARNEXT
    Inventors: Daniel Cohen, Ilya Chumakov
  • Publication number: 20100227768
    Abstract: The present invention provides methods and compositions related to genomic profiling, and in particular, to assigning probabilistic measure of clinical outcome for a patient having a disease or a tumor using segmented genomic profiles such as those produced by representational oligonucleotide microarray analysis (ROMA).
    Type: Application
    Filed: December 14, 2006
    Publication date: September 9, 2010
    Inventors: Michael H. Wigler, James B. Hicks, Alexander Krasnitz, Anders P. Zettenberg
  • Publication number: 20100222224
    Abstract: The present invention is directed to a method and apparatus that satisfies the need for a bioelectronic tongue for food allergy detection. The method of detecting concentration of food allergen incorporates antibodies into an electronic tongue to create a bioelectronic tongue. Additionally the method uses impedance, capacitance, and/or other related electrochemical methods for detecting analyte in complex media. Furthermore the method additionally includes methods to subtract out non-specific interactions. The method also subtracts non-specific interactions. The device/apparatus is a Bioelectronic Tongue for detecting allergen in diluted food samples. The device includes: a sensor array; an impedance or capacitance analyzer; a preprocessor; a feature extractor; a pattern recognizer; and an output device indicating an allergen concentration.
    Type: Application
    Filed: September 3, 2009
    Publication date: September 2, 2010
    Inventors: Ian Ivar Suni, Yin Huang, Stephanie Ann Caswell Schuckers
  • Publication number: 20100222225
    Abstract: This invention contemplates an accurate and efficient estimation of gene copy number using oligonucleotide microarrays. The method integrates gene copy number data obtained from perfect match and mismatch probe sequence structure intensities and probe binding affinities. In one embodiment, an accurate determination of single nucleotide polymorphisms (SNPs) sequences is obtained. In another embodiment, an accurate detection and determination of DNA copy number alteration is obtained. In another embodiment, an accurate estimation for RNA gene expression is obtained.
    Type: Application
    Filed: April 7, 2010
    Publication date: September 2, 2010
    Inventors: Wenjiang Fu, Yalu Wen, Ming Li
  • Publication number: 20100216654
    Abstract: The present invention includes biomolecules and use of these biomolecules for differential diagnosis of prostate cancer and/or non-malignant disease of the prostate. In an embodiment, the present invention provides methods for detecting biomolecules within a biological sample as well as a database comprising of mass profiles of biomolecules specific for healthy subjects, subjects having a non-malignant disease of the prostate and subjects having prostate cancer. The invention further includes kits for differential diagnosis of prostate cancer and/or non-malignant disease of the prostate in a biological sample.
    Type: Application
    Filed: March 12, 2008
    Publication date: August 26, 2010
    Applicant: MIRACULINS, INC.
    Inventors: Katrin Stedronsky, Douglas Barker, Yilan Zhang
  • Publication number: 20100216655
    Abstract: The present invention discloses variants that are predictive of human pigmentation patterns. The invention furthermore relates to variants that are useful for determining risk of skin cancer, including melanoma and basal cell carcinoma. The disclosed variants can be utilized for the determination of the natural pigmentation patterns of a human individual, and for determining a susceptibility to melanoma and basal cell carcinoma, from a sample of genetic material. Methods and kits including the variants described are useful in e.g. forensic testing and diagnostic applications.
    Type: Application
    Filed: October 13, 2008
    Publication date: August 26, 2010
    Inventor: Patrick SULEM
  • Publication number: 20100197514
    Abstract: The present invention relates to a protein crystal of at least one binding site of a human aromatase. The present invention also relates to a fully processed human cytochrome P450 aromatase and a protein crystal thereof. The present invention further relates to methods of making and using the aromatase and the protein crystal thereof.
    Type: Application
    Filed: March 29, 2010
    Publication date: August 5, 2010
    Applicant: HAUPTMAN-WOODWARD MEDICAL RESEARCH INSTITUTE, INC.
    Inventor: Debashis GHOSH
  • Publication number: 20100197598
    Abstract: The present invention discloses novel macromolecule transduction domain (MTD) peptides which facilitate the traverse of a biologically active molecule across the cell membrane. Also disclosed are polynucleotides encoding the MTD peptides, methods of identifying the MTD peptides; methods of genetically engineering a biologically active molecule to have cell permeability by using the MTD peptides, methods of importing a biologically active molecule into a cell by using the MTD peptides, and uses thereof.
    Type: Application
    Filed: January 29, 2008
    Publication date: August 5, 2010
    Applicant: PROCELL THERAPEUTICS INC
    Inventors: Dae Woong Jo, Jae Sun Ko, Jin Sook Kim, Kyung Mi Park, Jin Kyung Song, Jung Hee Lim, Thi Thuy Nga Do, Thi Lan Phuong Do, Minh Tam Duong
  • Publication number: 20100197513
    Abstract: A system, a method and a computer-readable medium are provided for associating a nucleic acid profile or proteomic profile with a patient state, to utilize a healthcare protocol or guideline for decision support, in which the patient state provides a description of a current status and a history of a patient, and the nucleic acid profile or proteomic profile is an analysis of characteristics including genetic constitution, gene expression, or modification of the protein content of the tissue or cell, all of which aid in diagnosis of the disease state of a patient. The nucleic acid profile or proteomic profile shows a molecular indicator of the patient state. The invention also provides a method for associating a stage in the healthcare protocol or guideline with the nucleic acid profile or proteomic profile.
    Type: Application
    Filed: August 2, 2007
    Publication date: August 5, 2010
    Applicant: KONINKLIJKE PHILIPS ELECTRONICS N.V.
    Inventor: Yasser Alsafadi
  • Publication number: 20100191735
    Abstract: Systems and methods collect and screen a biological material to facilitate its selection and use for therapeutic and/or research purposes. The systems and methods take into account both objective and semi-objective attributes manifest in a biological material, such as genetic, phenotypic, clinical, and genealogic attributes. The diverse array of the objective and semi-objective attributes enhances the level of confidence that the biological material can be best matched with a particular research or therapeutic purpose.
    Type: Application
    Filed: December 18, 2009
    Publication date: July 29, 2010
    Inventors: George Reiss, Linda Kelley
  • Publication number: 20100184609
    Abstract: It is proposed by the present invention the use of ternary matrices as an adapter of molecular biological information for integration of the said biological information. Another exclusive aspect of the present invention consists in a method of search and visualization of molecular biological information stored in at least one database, wherein a preferred implementation of the method is made using a computer program and wherein the same may be accessed using a computer network such as the Internet.
    Type: Application
    Filed: May 14, 2008
    Publication date: July 22, 2010
    Applicants: FUNDAÇÃO DE AMPARO Á PESQUISA DO ESTADO DE SÃO PÃO PAULO- FAPESP, FUNDAÇÃO ARY FRAUZINO PARA PESQUISA E CONTROLE DO CÂNCER, FUNDAÇÃO ZERBINI, Fabio PASSETTI, Paulo Sergio Lopes DE OLIVEIRA
    Inventors: Fabio Passetti, Paulo Sergio Lopes De Oliveira, Jeryes Farah, Victor Senos Dobroff, Marcelo Garcia, Carlos Alberto de Braganca Pereira, Francisco Elói Soares De Araújo, Carlos Gil Moreira Ferreira
  • Publication number: 20100179067
    Abstract: Methods and kits are provided for determining the probability of lung cancer, for managing treatment of subjects with potential lung cancer and for molecular staging of lung tumors. The methods include determining an amount of each member of a panel of biomarkers in a sample from the subject, wherein the panel of biomarkers comprises at least two of the proteins alpha-1-antitrypsin, carcinoembryonic antigen, squamous cell carcinoma antigen, retinol binding protein, transferrin, and haptoglobin; and assigning the subject to a group having a higher or lower probability of lung cancer based on the determined amount of each biomarker the panel.
    Type: Application
    Filed: May 19, 2008
    Publication date: July 15, 2010
    Inventors: Edward F. Patz, JR., Michael J. Campa