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In silico screening

Subclass of:

506 - Combinatorial chemistry technology: method, library, apparatus

506007000 - METHOD OF SCREENING A LIBRARY

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DocumentTitleDate
20110177959Methods and Devices for Detecting Kidney Transplant Rejection - Methods and devices for diagnosing, monitoring, or determining kidney transplant rejection or an associated disorder in a mammal are described. In particular, methods and devices for diagnosing, monitoring, or determining kidney transplant rejection or an associated disorder using measured concentrations of a combination of three or more analytes in a test sample taken from the mammal are described.07-21-2011
20100130371SYSTEM, METHOD, DEVICE, AND COMPUTER PROGRAM PRODUCT FOR EXTRACTION, GATHERING, MANIPULATION, AND ANALYSIS OF PEAK DATA FROM AN AUTOMATED SEQUENCER - A system, method, device, and computer program product to extract and gather peak information from an automated sequencer of bioinformatics into a peak database, and to manipulate and analyze the peak information within the database.05-27-2010
20110195851SYSTEMS AND METHODS FOR DETERMINING THERAPEUTIC POTENTIAL - Systems and methods for determining therapeutic potential. In at least one embodiment of a system of the present disclosure, the system comprises a detection platform, a computer processor and a database. The processor, in at least one embodiment of a method of the present disclosure, has and executes a software program operational to determine a binding characteristic of the detection agent and a stabilized diagnostic marker in each of the plurality of detection sites on the platform, compare the binding characteristic, and determining the stabilizing agent with the greatest effect on the binding characteristic between the detection agent and the diagnostic marker. Further, at least one embodiment of a system for determining the therapeutic potential of a therapeutic compound of the present disclosure is able to generate a binding record using the compared binding characteristics, and deliver the binding record to a recipient.08-11-2011
20100113295Associations Using Genotypes and Phenotypes - The present invention discloses methods for combining data on genetic variations and phenotypes of individuals to predict a phenotype-of-interest. The present invention also discloses kits that can be used to determine if an individual has or does not have a phenotype-of-interest. The kit can include at least one diagnostic tool and written instructions.05-06-2010
20100113292METHODS OF OBTAINING ACTIVE ANTISENSE COMPOUNDS - Methods for obtaining antisense oligonucleotides with activity against a desired target are provided. Methods of identifying oligonucleotide sequence motifs which are predictive of antisense oligonucleotide activity are provided, as are motifs identified according to this method. Methods of selecting effective antisense oligonucleotide sequences and effective antisense target sequences are provided, as are sequences selected according to these methods. In other methods of the invention, oligonucleotides are designed to hybridize to target sequences containing one or more activity-enhancing motifs. Antisense oligonucleotides designed according to these methods are also provided.05-06-2010
20130079233Methods and Systems for Predicting HIV-1 Coreceptor Tropism - Methods and systems for predicting coreceptor tropism are provided. In certain embodiments, the methods may include obtaining the amino acid and/or nucleic acid sequence of at least a portion of the envelope or envelope coding region from a biological sample obtained from a subject; analyzing the amino acid sequence, nucleic acid sequence, or both of the portion of the envelope or envelope coding region using a case based reasoning analysis; and determining the coreceptor tropism. Also provided are systems and computer readable media for utilizing the systems or performing the methods are disclosed.03-28-2013
20130035244Method for Characterising a Molecule - The invention relates to a method for characterising three-dimensional objects, including steps comprising: i) generating a three-dimensional reconstruction of a three-dimensional object; ii) generating a mesh of the object, said mesh being made up of points connected two-by-two by a ridge; iii) characterising the points and/or faces of the mesh of the object according to the statuses of remarkable properties at said points; iv) splitting the object into contiguous three-dimensional regions based on the mesh and the characterisation of the points thereof; v) creating a database of regions that represent objects of an environment; and/or vi) screening a region on a database in order to find objects that contain similar and/or complementary regions; and/or vii) inferring functions of the objects according to similarities in the regions thereof; and/or viii) inferring interactions between objects by complementarity of the regions thereof; and/or ix) specifying the frequency of a region in an environment.02-07-2013
20100113291COMPLEXES OF NADP WITH THE PROTEIN MABA OF MYCOBACTERIUM TUBERCULOSIS OR WITH MUTANTS THEREOF, AND THEIR USES FOR DESIGNING AND SCREENING ANTIBIOTICS - The main subject of the present invention is the use of complexes of NADP with the protein MabA, or with a derived protein, and more particularly the crystallographic coordinates of these proteins in the frame of said complexes, within the framework of the implementation of methods for designing and screening ligands of these proteins, and advantageously ligands inhibiting the enzymatic activity of these proteins, namely antibiotics capable of being used within the framework of the treatment of mycobacteriosis.05-06-2010
20090156414Genetic Analysis in Racing Animals - The invention relates to products and processes for determining or predicting sporting performance, ability or aptitude of horses and other performance animals through the study of nucleotide sequence variants, genetic types or profiles, in particular the study of mitochondrial sequence variants. The invention is useful in the horseracing industry.06-18-2009
20090124508Computational diagnostic methods for identifying organisms and applications thereof - Methods for identifying organisms within a mixture using a minimal set of reagents are provided. The methods also allow for identifying the presence of not yet sequenced organisms, as well as for classification based on evolutionary lineage.05-14-2009
20090124507SYSTEM AND METHOD FOR RAPID SEARCHING OF HIGHLY SIMILAR PROTEIN-CODING SEQUENCES USING BIPARTITE GRAPH MATCHING - An exemplary embodiment of system, computer-accessible medium and method for comparing a first genome to a second genome. For example, a first genome may be compared to a second genome by building a first library for the first genome and a second library for the second genome, providing a plurality of matches between elements in the first library common to elements in the second library, ranking each match to determine a likelihood of similarity between the common elements in the first and second libraries; and associating matches having a predetermined likelihood. The association may be performed efficiently by a stable marriage procedure.05-14-2009
20130045878PROCESS FOR IDENTIFICATION OF PATHOGENS - Processes are described that include computational tools for identification of unknown pathogenic organisms and other threat agents (e.g., rare variants) in samples. The processes can be conducted without specific a priori knowledge of the unknown. Identification may include fragmenting a genome from one or more candidate organisms and READs and/or CONTIGs segments for the unknown organism in silico to form fragments, and determining the statistical relevance of exact fragment matches between the sample fragments and the candidate fragments.02-21-2013
20090042732METHODS FOR SIMPLIFYING MICROBIAL NUCLEIC ACIDS BY CHEMICAL MODIFICATION OF CYTOSINES - 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.02-12-2009
20130053259SEQUENCE BASED ENGINEERING AND OPTIMIZATION OF SINGLE CHAIN ANTIBODIES - The invention provides methods of using sequence based analysis and rational strategies to modify and improve the structural and biophysical properties of single chain antibodies (scFvs), including stability, solubility, and antigen binding affinity. These methods and strategies can be used individually or in combination. The methods of the present invention also include the use of a database comprising scFv sequences from an experimentally screened scFv library of antibodies that have been selected to have superior solubility and stability. The invention also provides methods of using the properties found for these selected antibodies in a general approach for reshaping scFv antibodies to improve stability and solubility properties of a single chain antibody fragment.02-28-2013
20110160071Novel Proteins and Methods for Designing the Same - Aspects of the invention relate to variant proteins and methods for designing and using the same. In some embodiments, the invention relates to methods for determining a functional variant of a protein that is restricted by one or more known legal rights, such as patent rights. Functional variants according to this invention are free of such restrictions.06-30-2011
20100197514PROTEIN CRYSTAL OF HUMAN CYTOCHROME P450 AROMATASE AND USES THEREOF - 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.08-05-2010
20100222225Microarray-Based Gene Copy Number Analyses - 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.09-02-2010
20100137149DATA PROCESSING, ANALYSIS METHOD OF GENE EXPRESSION DATA TO IDENTIFY ENDOGENOUS REFERENCE GENES - Disclosed are a data processing and analysis method of 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 the amplification of the identified endogenous reference genes. Introduced with the concepts of “Zero's proportion’ and CV, the me 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. Out of the 2,087 genes, 13 genes are found to show higher expression stability with lower expression levels across a wide range of samples than traditional reference genes such as GAPDH and ACTB, and therefore are suitable for the normalization of universal genes having relatively low expression levels.06-03-2010
20110143952CHROMATOGRAPHIC DEVICE AND METHOD OF FABRICATION AND CHROMATOGRAPHIC METHODS - A chromatographic device for use in multi-dimensional GC is described having a gas flow channel means having an inlet and an outlet, and including a first length of tube defining a first stage and a second length of tube defining a second stage; wherein each of the first length of tube defining a first stage and second length of tube defining a second stage is microfabricated in the plane of a planar substrate layer such that each length of tube comprises a bore defining a closed curve in cross section. A GC assembly further comprising modulator, injector and detector and a method of fabrication of device and assembly are described. A method of analysing multi-dimensional GC data is described.06-16-2011
20100137151Protein Expression Profile Database - This invention describes the use of peptide profiling to identify, characterize, and classify biological samples. In complex samples, many thousands of different peptides will be present at varying concentrations. The invention uses liquid chromatography and similar methods to separate peptides, which are then identified and quantified using mass spectrometry. By identification it is meant that the correct sequence of the peptide is established through comparisons with genome sequence databases, since the majority of peptides and proteins are unannotated and have no ascribed name or function. Quantification means an estimate of the absolute or relative abundance of the peptide species using mass spectrometry and related techniques including, but not limited to, pre- or post-experimental stable or unstable isotope incorporation, molecular mass tagging, is differential mass tagging, and amino acid analysis.06-03-2010
20110301048DIAGNOSIS AND PROGNOSIS OF BREAST CANCER PATIENTS - The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the statistical methods disclosed herein.12-08-2011
20100216655SEQUENCE VARIANTS FOR INFERRING HUMAN PIGMENTATION PATTERNS - 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.08-26-2010
20110287953METHOD FOR DISCOVERING POTENTIAL DRUGS - The preset invention relates to a process for discovering potential treatment strategy for a given disease, providing a niche for PPI network construction, target prioritization, and potential drug identification for a given disease, particular a cancer, based on the interaction between prioritized NPC targets (e.g. cliques and bottleneck genes) and drugs.11-24-2011
20110028333DIAGNOSING, PROGNOSING, AND EARLY DETECTION OF CANCERS BY DNA METHYLATION PROFILING - A method of employing DNA methylation analysis for the diagnosis, prognosis, and prediction of cancer.02-03-2011
20090054247POLYNUCLEOTIDES ENCODING PROTEINS INVOLVED IN PLANT METABOLISM - 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.02-26-2009
20090163369Detection of Pathogenic Microorganisms Using Fused Sensor Data - A system and method to search spectral databases to identify unknown materials, specifically pathogenic microorganisms. A library is provided, having sublibraries containing reference data sets of known materials and test data sets, both generated by at least one spectroscopic data generating instrument. For each test data set, each sublibrary associated with the instrument used is searched. A set of scores for each searched sublibrary is produced, representing the likelihood of a match between the reference data set and test data set. Relative probability values are calculated for each searched sublibrary. All relative probability values are fused producing a set of final probability values, used in determining whether the unknown material is represented through a known material in the library. The known material represented in the libraries having the highest final probability value is reported, if the highest final probability value is greater than or equal to the minimum confidence value.06-25-2009
20090203532PROCESS FOR GENERATION OF PROTEIN AND USES THEROF - A method of generating a protein with an improved functional property, the method comprising: 08-13-2009
20090170715Prognostic and diagnostic method for cancer therapy - The present invention provides novel methods and kits for diagnosing the presence of cancer within a patient, and for determining whether a subject who has cancer is susceptible to different types of treatment regimens. The cancers to be tested include, but are not limited to, prostate, breast, lung, gastric, ovarian, bladder, lymphoma, mesothelioma, medulloblastoma, glioma, and AML. Identification of therapy-resistant patients early in their treatment regimen can lead to a change in therapy in order to achieve a more successful outcome. One embodiment of the present invention is directed to a method for diagnosing cancer or predicting cancer-therapy outcome by detecting the expression levels of multiple markers in the same cell at the same time, and scoring their expression as being above a certain threshold, wherein the markers are from a particular pathway related to cancer, with the score being indicative or a cancer diagnosis or a prognosis for cancer-therapy failure. This method can be used to diagnose cancer or predict cancer-therapy outcomes for a variety of cancers. The markers can come from any pathway involved in the regulation of cancer, including specifically the PcG pathway and the “stemness” pathway. The markers can be mRNA, microRNA, DNA, or protein.07-02-2009
20100035759IN SILICO GENERATION OF ASPARAGINE-LINKED GLYCAN STRUCTURE DATABASES AND USE OF SUCH - The present invention discloses a method for easy and quick in silico generation of a very large asparagine-linked glycan structure (N-glycan) database and the use of the database and mass spectrometric data for the determination of N-glycan structures. A two dimensional array of single characters is used to represent all distinct outer branch structures of N-glycan structures. We use a computer program and the array to generate a very large number of unique N-glycan structures. For the determination of N-glycan structures based on mass spectrometric data, a search engine is used to search the N-glycan structure database to find N-glycan structure candidates and correlate a predicted mass spectrum of each of the N-glycan structure candidates with an experimental mass spectrum. With the present invention, intact N-glycan structures and their fragments can be displayed graphically.02-11-2010
20100113294DEFINED GLYCOPROTEIN PRODUCTS AND RELATED METHODS - The invention provides methods, databases and systems for making glycoprotein products having defined properties.05-06-2010
20100113293SYSTEMIC LUPUS ERYTHEMATOSUS DIAGNOSTIC ASSAY - The present invention provides compositions and methods for aiding in the diagnosis, monitoring and prognosis of SLE in a subject and for identifying potential therapeutic agents to treat and/or ameliorate the symptoms associated with SLE. Accordingly, embodiments of the invention are directed to methods of identifying the gene expression profile of a suitable sample by screening for the presence of a differentially expressed SLE-associated gene isolated from a sample containing or suspected of containing a cell that can differentially express an SLE-associated gene.05-06-2010
20110201510Method and System for Detecting Materials - Disclosed is a method for detecting one or both of the native material in an object and any foreign material in the object by parallel-mode spectroscopy, comprising parallel-mode data acquisition, signal processing and data reduction and providing results. Parallel-mode data acquisition comprises producing an interrogating signal simultaneously containing electromagnetic radiation of sufficient bandwidth in the range of approximately 10 GHz to approximately 25 THz to allow simultaneous detection of a plurality of signals at a plurality of frequencies, each signal being at some amplitude, which collectively provide a unique spectral signature of a material whose detection is desired. The signal processing and data reduction comprises processing a signal resulting from exposing the object to the interrogating radiation to produce a three-dimensional data matrix representative of at least any foreign or native material associated with the object. Correlation technique is used to compare the data matrix to a reference library.08-18-2011
20080214405MOLECULARLY IMPRINTED POLYMER - A computer aided rational molecular design method that includes establishing a virtual library of functional monomers each having a portion that is capable of polymerizing and a functional group that is capable of interacting with a template molecule with the aid of a computer, designing a molecular model of a biological template molecule by a computer facilitated molecular mechanical method and screening said virtual library of functional monomers and selecting those monomers which have the highest binding score to the template molecule by their functional group.09-04-2008
20110269634Methods and Compositions for Risk Stratification - The present invention provides an approach for the simultaneous determination of the activation states of a plurality of proteins in single cells. This approach permits the rapid detection of heterogeneity in a complex cell population based on activation states, and the identification of cellular subsets that exhibit correlated changes in activation within the cell population. Moreover, this approach allows the correlation of cellular activities or properties. In addition, the use of potentiators of cellular activation allows for characterization of such pathways and cell populations.11-03-2011
20090275480UNIVERSAL READOUT FOR TARGET IDENTIFICATION USING BIOLOGICAL MICROARRAYS - A method and apparatus for implementing the method is provided. The method involves performing an indirect competitive binding assay on a microarray to identify biological or chemical targets and screen for compounds of interest. The microarray comprises a common ligand located among membrane-, lipid- or protein-associated active binding sites. The method takes advantage of known or well-characterized binding kinetics, and steric interference between biological or chemicals targets of interest and universal readout units for different binding sites within the limited confines of a microspot. The biological targets, chemicals or organisms can specifically bind to target-binding sites, while the universal readout unit binds to the ligands in the microspot.11-05-2009
20100248974CRYSTAL STRUCTURE OF CD147 EXTRACELLULAR REGION AND USE THEREOF - 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.09-30-2010
20110269633INFLAMMATORY BIOMARKERS FOR MONITORING DEPRESSIVE DISORDERS - Materials and Methods related to developing a unipolar depression (MDD) disease score in a subject using a multi-parameter system to measure a plurality of parameters, and an algorithm to calculate a score.11-03-2011
20120295796System and Method of Predicting Chemical Interaction and Functionality of Molecules - A system and method of identifying a target molecule that bind to the bioactive site of a protein or protein complex is described. The system and method includes the steps of calculating the information signature of a first molecule that is known to bind to the bioactive site of a protein or protein complex, wherein the information signature is a string of numerical values based on the average distance and physico-chemical properties of each atom of a plurality of atoms in the first molecule, calculating the information signature of each target molecule in a library of target molecules, comparing the information signature of the first molecule to the information signatures of the target molecules, and selecting the target molecules having an information signature that is similar to the information signature of the first molecule.11-22-2012
20110207618CLASS LABEL PREDICTING APPARATUS AND METHOD - According to an embodiment of the present invention, it is possible to rapidly and accurately predict a class label of a predetermined test sample by extracting a disease-specific gene pair from gene pairs on a microarray data set representing an expression level for each of genes of a genome and for each of a plurality of samples by considering the correlation in a normal class and the correlation in a disease class, selecting a highest specific gene pair with the highest correlation among the extracted disease-specific genes, and predicting the class label of the predetermined test sample by using the selected highest specific gene pair.08-25-2011
20100279883Probe Design Methods and Microarrays for Comparative Genomic Hybridization and Location Analysis - 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.11-04-2010
20090036320Rational Design of Binding Proteins That Recognize Desired Specific Sequences - Methods and compositions are provided for creating a binding protein that recognizes a rationally chosen recognition sequence in which a first amino acid has been substituted for a second amino acid using site-directed mutagenesis of a member protein of a set of proteins at an identified position or positions correlated with recognition of a chosen specified target module in the recognition sequence. A system is provided for automating the storage and manipulation of the correlations between positions and types of amino acid residues in the binding protein with specific modules at specified positions in the target recognition sequence and for designing and creating proteins with novel specificities.02-05-2009
20090036319Methods and systems for pairwise filtering candidate probe nucleic acid sequences - Aspects of the invention include methods of systems of pairwise filtering candidate probe nucleic acid sequences. Aspects of the invention further include methods and systems of selecting candidate probe nucleic acid sequences from plurality thereof, which methods and systems employ a pairwise elimination ranked record of a plurality of candidate probe nucleic acids for a genomic region of interest.02-05-2009
20080274908DIAGNOSIS OF MELANOMA BY NUCLEIC ACID ANALYSIS - The present invention provides methods for diagnosing melanoma in a subject by analyzing nucleic acid molecules obtained from the subject. The present invention also provides methods for distinguishing melanoma from dysplastic nevi and/or normal pigmented skin. The methods include analyzing expression or mutations in epidermal samples, of one or more skin markers. The methods can include the use of a microarray to analyze gene or protein profiles from a sample.11-06-2008
20080293579Crystal structure of polo-like kinase 3 (PLK3) and binding pockets thereof - The invention relates to molecules or molecular complexes, which comprise binding pockets of PLK3 or its structural homologues. The invention relates to crystallizable compositions and crystals comprising PLK3. The present invention also relates to a data storage medium encoded with the structural coordinates of molecules and molecular complexes which comprise the PLK3 or PLK3-like ATP-binding pockets. The present invention also relates to a computer comprising such data storage material. The computer may generate a three-dimensional structure or graphical three-dimensional representation of such molecules or molecular complexes. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for, identify and design compounds, including inhibitory compounds that bind to PLK3 or homologues thereof.11-27-2008
20090264302METHODS, SYSTEMS AND COMPUTER PROGRAM PRODUCTS FOR DETERMINING TREATMENT RESPONSE BIOMARKERS - The invention relates to methods for the identification of biomarkers suitable for determining patient treatment response as well as systems and computer program products of use in such methods.10-22-2009
20100137150Sequence Based Engineering and Optimization of Single Chain Antibodies - The invention provides methods of using sequence based analysis and rational strategies to modify and improve the structural and biophysical properties of single chain antibodies (scFvs), including stability, solubility, and antigen binding affinity. These methods and strategies can be used individually or in combination. The methods of the present invention also include the use of a database comprising scFv sequences from an experimentally screened scFv library of antibodies that have been selected to have superior solubility and stability. The invention also provides methods of using the properties found for these selected antibodies in a general approach for reshaping scFv antibodies to improve stability and solubility properties of a single chain antibody fragment.06-03-2010
20100137148System and Method for Radioisotope Identification - A system and method are providing for analyzing radiation signature data (i.e., spectral data) produced by a detector device against stored data representing the computed interaction of known radioisotopic spectra with a representative cross section for each of a small number of material groups. Each material group comprises materials expected to be in a detection path of the detector and which exhibit similar cross sections. Comparative analysis is made of the spectral data received from the detector for threat materials to determine whether the spectral data indicates presence of a threat material in the interrogated space. The system and method is not limited to any particular detector type, and may be used with any detector that produces spectral data.06-03-2010
20090137410METHOD FOR COMPUTER-BASED PROCESSING OF BIOLOGICAL DATA - A method for computer-based processing of biological data, comprising the steps of: selecting a gene as lead gene to be patented; searching homologues for the selected lead gene; creating a patent pool on the basis of the selected lead gene; generating and outputting a pool report for the planned patent application.05-28-2009
20090137409COMPUTATIONAL METHODS FOR SYNTHETIC GENE DESIGN - The present invention is drawn to methods for designing synthetic nucleotide sequences encoding polypeptides of interest. The methods involve organizing a database of sequences as a set of N-length oligomer sequences and compiling a list of probability scores for each N-length sequence. The probability scores are used to substitute one or more higher-scoring sequences into the parent nucleotide sequence to generate an optimized sequence. The nucleotide sequence of interest may be further optimized by removing either or both of unintended open reading frames or undesired short DNA elements, and/or substituting oligomer sequences to achieve a specific G:C content. These methods may be used for optimizing expression of heterologous genes in any organism, particularly in plants. The method generates synthetic sequences with a composition similar to that of a target database. These synthetic sequences may be used, for example, for regulating pesticidal activity or herbicide resistance in organisms, particularly plants or plant cells.05-28-2009
20090062136IDENTIFYING COMPONENTS OF A NETWORK HAVING HIGH IMPORTANCE FOR NETWORK INTEGRITY - A computer system (03-05-2009
20090325812Nanoparticles having oligonucleotides attached thereto and uses therefor - The invention provides methods of detecting a nucleic acid. The methods comprise contacting the nucleic acid with one or more types of particles having oligonucleotides attached thereto. In one embodiment of the method, the oligonucleotides are attached to nanoparticles and have sequences complementary to portions of the sequence of the nucleic acid. A detectable change (preferably a color change) is brought about as a result of the hybridization of the oligonucleotides on the nanoparticles to the nucleic acid. The invention also provides compositions and kits comprising particles. The invention further provides methods of synthesizing unique nanoparticle-oligonucleotide conjugates, the conjugates produced by the methods, and methods of using the conjugates. In addition, the invention provides nanomaterials and nanostructures comprising nanoparticles and methods of nanofabrication utilizing nanoparticles. Finally, the invention provides a method of separating a selected nucleic acid from other nucleic acids.12-31-2009
20100004136Methods, Systems, and Software for Identifying Functional Bio-Molecules - 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.01-07-2010
20100004135Methods, Systems, and Software for Identifying Functional Bio-Molecules - 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.01-07-2010
20090298702NUCLEIC ACID SEQUENCING USING A COMPACTED CODING TECHNIQUE - Methods and apparatuses for nucleic aced sequencing using a compacted code technique are disclosed. In one embodiment, a method includes providing a nucleic acid to be sequenced, determining the identity of each base in a subsequence of bases in the nucleic acid, encoding the identity of the subsequence in a format having a number of bytes that is less than the number of bases, and storing the encoded identity.12-03-2009
20090291854Identification of Pathogens - Disclosed is a method for identification of microbial pathogens in a body fluid sample comprising the following steps: a) providing a body fluid sample; b) lysing the microbial pathogens and performing a nucleic acid amplification reaction on the microbial DNA encoding 16S or 18S rRNA wherein or whereafter the amplified nucleic acids are labelled; c) contacting the labelled amplified nucleic acids of step b) with a microarray comprising on defined areas on the microarray's surface immobilised probes for microbial DNA encoding 16S or 18S rRNA from microbial pathogens; d) detecting the binding of one or more species of the labelled amplified nucleic acids to a probe by detecting a labelled amplified nucleic acid being specifically bound to the microarray; and e) identifying a microbial pathogen in the body fluid sample by correlating the detected binding of the labelled amplified nucleic acids with the defined areas of the immobilised probes for microbial DNA encoding 16S or 18S rRNA from microbial pathogens.11-26-2009
20090118132Classification of Acute Myeloid Leukemia - The present invention relates to rapid and reliable approaches to leukemia prognostication. In addition to methods, the invention also provides related kits and systems.05-07-2009
20090082213CONSTRUCTION OF DIVERSE SYNTHETIC PEPTIDE AND POLYPEPTIDE LIBRARIES - The present invention concerns the design and construction of diverse peptide and polypeptide libraries. In particular, the invention concerns methods of analytical database design for creating datasets using multiple relevant parameters as filters, and methods for generating sequence diversity by directed multisyntheses oligonucleotide synthesis. The present methods enable the reduction of large complex annotated databases to simpler datasets of related sequences, based upon relevant single or multiple key parameters that can be individually directly defined. The methods further enable the creation of diverse libraries based on this approach, using multisynthetic collections of discrete and degenerate oligonucleotides to capture the diverse collection of sequences, or portions thereof.03-26-2009
20090192046Chemo-selective identification of therapeutics - Disclosed is the use of a therapeutic filter for simultaneous screening against multiple targets coupled with subsequent in silico drug discovery utilizing biologically active compounds for the identification and selection of gene sets having characteristic expression profiles for formation of an active compound database with subsequent identification of therapeutically effective agents by scanning and matching in said active compound database.07-30-2009
20110230362COMPARATIVE GENOMIC HYBRIDIZATION ARRAY METHOD FOR PREIMPLANTATION GENETIC SCREENING - A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.09-22-2011
20090247417METHOD AND SYSTEM FOR DRUG SCREENING - The invention provides a system and method for screening drugs from candidate compounds selected from a library. The system includes multiple hardware components and a computer software system for scheduling and coordinating the operations of the hardware components. A user of the system requests a series of assays to be performed on the candidate compounds. Each assay is associated with a test acceptance criteria. Interdependencies of these assays may be specified. The software system schedules the hardware components to run each assay with minimum hardware idle time possible based on the assays requested and the interdependencies of these assays specified. The software system coordinates and directs the flow of samples and data through the system. A decision whether a sample can proceed to the next assay as scheduled may be made automatically based on test acceptance criteria, or manually modified by the user. All assays can be performed in an automated fashion once the samples are provided to the system.10-01-2009
20100160172METHODS AND SYSTEMS OF DNA SEQUENCING - Methods and systems of DNA sequencing that compensate for sources of noise in next-generation DNA sequencers are described.06-24-2010
20100167942Compositions, Methods and Related Uses for Cleaving Modified DNA - 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)07-01-2010
20100261614Bacillus thuringiensis Chromosomal Genome Sequences and Uses Thereof - The present invention relates to nucleic acid sequences from 10-14-2010
20100261613METHODS FOR INFLAMMATORY DISEASE MANAGEMENT - 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.10-14-2010
20110059853Method And Computer System For Assessing Classification Annotations Assigned To DNA Sequences - 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.03-10-2011
20100216654BIOMARKERS OF PROSTATE CANCER AND USES THEREOF - 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.08-26-2010
20100227768Method for designing a therapeutic regimen based on probabilistic diagnosis for genetic diseases by analysis of copy number variations - 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).09-09-2010
20100234236Novel Disease Treatment by Predicting Drug Association - 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.09-16-2010
20100144542METHODS FOR HIGH THROUGHPUT GENOTYPING - Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.06-10-2010
20100167941Particle based assay system - The invention provides a particle comprising a surface, wherein a portion of the surface is capable of emitting electromagnetic radiation and another portion of the surface is capable of emitting a differential electromagnetic radiation (either different intensity, different frequency or no radiation), and wherein the arrangement of said portions of the surface defines a spatially distributed code for identifying the particle. The invention also provides method of manufacturing a particle having an identifying code comprising providing a particle with a functionalized surface which comprises functional binding moieties and selectively removing a plurality of the functional binding moieties from the surface to create a pattern of functionalized and differentially-functionalized zones on the surface. Various liquid-based assay methods employing the particle of the invention and a kit comprising the particle of the invention are also disclosed.07-01-2010
20090075830SYSTEM FOR IDENTIFYING AND ANALYZING EXPRESSION OF ARE-CONTAINING GENES - The present invention relates to a gene discovery system and gene expression systems specific for genes encoding ARE-containing mRNAs. In one aspect, the present invention relates to computational methods of selecting coding sequences of ARE-genes from databases using a one or more ARE search sequences. The ARE search sequences are from 10 to 80 nucleotides in length and comprise a sequence which is encompassed by one of the following two sequences: (a) WU/T(AU/TU/TU/TA)TWWW, SEQ ID NO. 1, wherein none or one of the nucleotides outside of the parenthesis is replaced by a different nucleotide, and wherein W represents A, U, or T; and (b) U/T(AU/TU/T/U/T)n, SEQ ID NO. 2 wherein n indicates that the search sequence comprises from 3 to 12 of the tetrameric sequences contained within the parenthesis. The method comprises extracting from the databases, those nucleic acids whose protein coding sequences are upstream and contiguous with a 3′ untranslated region (UTR) that comprises one of the ARE search sequences. The present invention also relates to methods of selectively amplifying RNA and cDNA molecules using primers derived from and complementary to the consensus 5′ sequence motifs and primers derived from and complementary to the ARE search sequence. The present invention also relates to methods of selectively amplifying ARE genes which employ a 3′ primer which is from 15 to 50 nucleotides and length and comprises from 2 to 10 pentamers having the sequence TAAAT. The pentameric sequences in the primers are either overlapping or non-overlapping. The 3′ primers are used in the reverse transcription step of the methods, the polymerase chain reaction (PCR) amplification step of the methods, or in both the reverse transcription step and the PCR amplification step of the methods. The present invention also relates to methods of making libraries which comprise portions of the ARE genes that are selectively amplified by the present methods and to methods of making microarrays which comprise probes that hybridize under stringent conditions to portions of the protein coding sequences of the ARE genes that are selectively amplified by the present methods. The present invention also relates to libraries and the microarrays that are made by such methods.03-19-2009
20090137408Methods, systems, and apparatus for facilitating the design of molecular constructs - A system and method for aiding in the design of molecular constructs is provided. A feature set associated with a molecular building block in a construct may be determined, wherein the feature set may comprise data indicative of third party rights that restrict use of the molecular segment or the lack of such rights. The method may include steps of defining a molecular structure for use in the construct; searching a database including a plurality of molecular structures and a plurality of rights, each right of the plurality of rights associated with each of the plurality of molecular structures; and displaying rights associated with the defined molecular structures in response to the search of said database. The system may include a library aggregating a plurality of intellectual property rights relating to fabricating biological constructs; a licensing module licensing the intellectual property rights required to make the specific construct for a fee; an accounts receivable module receiving the fee from a potential maker of the specific construct; and an accounts payable module distributing remuneration to the holders of the intellectual property rights required to make the specific construct.05-28-2009
20080287308SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA - An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.11-20-2008
20110245092DIAGNOSING AND MONITORING DEPRESSION DISORDERS BASED ON MULTIPLE SERUM BIOMARKER PANELS - Materials and Methods related to developing a unipolar depression (MDD) disease score in a subject using a multi-parameter system to measure a plurality of parameters, and an algorithm to calculate a score.10-06-2011
20110028334CAPTURE PRIMERS AND CAPTURE SEQUENCE LINKED SOLID SUPPORTS FOR MOLECULAR DIAGNOSTIC TESTS - 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).02-03-2011
20110045996ROBUST REGRESSION BASED EXON ARRAY PROTOCOL SYSTEM AND APPLICATIONS - 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.02-24-2011
20110086767MUTANTS OF GLYCOSIDE HYDROLASES AND USES THEREOF FOR SYNTHESIZING COMPLEX OLIGOSACCHARIDES AND DISACCHARIDE INTERMEDIATES - Method for preparing the disaccharide α-D-glucopyranosyl-(1→4)-2-N-acetyl-2-deoxy-α-D-glucopyranoside, comprising the step of using a mutant of a wild type glycoside hydrolase.04-14-2011
20090312190Methods and Proteins for the Prophylactic and/or Therapeutic Treatment of Four Serotypes of Dengue Virus and Other Flaviviruses - The present invention is related to the field of the pharmaceutical industry, and describes a conserved area on the surface of the E protein that can be used for the development of wide-spectrum antiviral molecules to be employed in the prophylaxis and/or treatment of infections due to Dengue Virus serotypes 1-4 and other flaviviruses. The invention also covers chimeric proteins to be used as vaccines or as a prophylactic or therapeutic treatment against the four serotypes of Dengue Virus and other flaviviruses.12-17-2009
20090312191METHOD AND SYSTEM FOR THE DETECTION OF ATYPICAL SEQUENCES VIA GENERALIZED COMPOSITIONAL METHODS - A method and system for determining whether a sequence fragment g is atypical with respect to a reference sequence G using compositional methods and including constructing a template from G and g respectively containing a sequence of characters for a comparison with one another, wherein a number of characters contained in the template exceeds two. For the case where the sequences at hand are genetic, the atypicality detection can be used to determine whether a given sequence fragment g is the result of a horizontal transfer event.12-17-2009
20100197513SYSTEMS AND METHODS FOR ASSOCIATING NUCLEIC ACID PROFILES AND PROTEOMIC PROFILES WITH HEALTHCARE PROTOCOLS AND GUIDELINES IN A DECISION SUPPORT SYSTEM - 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.08-05-2010
20100056385METHODS FOR IDENTIFYING SETS OF OLIGONUCLEOTIDES FOR USE IN AN IN VITRO RECOMBINATION PROCEDURE - In silico nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.03-04-2010
20110098186PHYSIOGENOMIC METHOD FOR PREDICTING DRUG METABOLISM RESERVE FOR ANTIDEPRESSANTS AND STIMULANTS - Disclosed herein are compositions and methods relevant to a novel Drug Metabolism Reserve Physiotype to determine the metabolic capacity of a human individual. The Drug Metabolism Reserve Physiotype allows the determination of the innate metabolic capacity of the patient relevant to antidepressant and stimulant treatment and can be predicted and diagnosed simply from a blood sample. In the disclosed method, an individual is genotyped for a plurality of polymorphisms in a gene encoding CYP2C9, a gene encoding CYP2C19 and a gene encoding CYP2D6, and the genotypes are used to produce four novel indices, which relate to the metabolic capacity of the human individual.04-28-2011
20110152109BIOLOGICAL SAMPLE TARGET CLASSIFICATION, DETECTION AND SELECTION METHODS, AND RELATED ARRAYS AND OLIGONUCLEOTIDE PROBES - Biological sample target classification, detection and selection methods are described, together with related arrays and oligonucleotide probes.06-23-2011
20110039713POLYMORPHISMS IN THE FCGR2B PROMOTER AND USES THEREOF - 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.02-17-2011
20110039714Probes, Systems, and Methods for Drug Discovery - 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.02-17-2011
20100062947CIRCULAR CHROMOSOME CONFORMATION CAPTURE (4C) - The present invention relates in one aspect to a method for analysing the frequency of interaction of a target nucleotide sequence with one or more nucleotide sequences of interest (eg. one or more genomic loci) comprising the steps of: (a) providing a sample of cross-linked DNA; (b) digesting the cross-linked DNA with a primary restriction enzyme; (c) ligating the cross-linked nucleotide sequences; (d) reversing the cross linking; (e) optionally digesting the nucleotide sequences with a secondary restriction enzyme; (f) optionally ligating one or more DNA sequences of known nucleotide composition to the available secondary restriction enzyme digestion site(s) that flank the one or more nucleotide sequences of interest; (g) amplifying the one or more nucleotide sequences of interest using at least two oligonucleotide primers, wherein each primer hybridises to the DNA sequences that flank the nucleotide sequences of interest; (h) hybridising the amplified sequence(s) to an array; and (i) determining the frequency of interaction between the DNA sequences.03-11-2010
20090298703Method for Automated Tissue Analysis - The invention provides an improved method for identifying and interpreting tissue specimens and/or cells derived from tissue specimens. A panel of cell-based reagents provides a number of readouts of cellular states or biomarkers that together define a profile of a diversity of cellular states or biomarkers in a tissue specimen representing the “systems” nature of biology. This cellular profile is interpreted using informatics tools, to identify similarities between specimens, in vivo medical conditions, and suggest options for treating medical conditions.12-03-2009
20090118133BIOLOGICAL DATASET PROFILING OF CARDIOVASCULAR DISEASE AND CARDIOVASCULAR INFLAMMATION - Methods and systems for evaluating biological dataset profiles relating to inflammatory cardiovascular conditions are provided, where datasets comprising information for multiple cellular parameters are compared and identified, and used in the evaluation of candidate pharmacologic agents for suitability as therapeutic agents.05-07-2009
20120202699Method For The Determination Of Intra- And Intermolecular Interactions In Aqueous Solution - The present invention relates to the determination of intra- or intermolecular interaction between molecules in aqueous solution, the method comprising the steps of: (a) determining the dehydration of all atoms in the intermolecular interface, (b) adding the vacuum hydrogen bond energy, 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.08-09-2012
20110166032Design and Use of Sortilin Specific Molecular Imaging Ligands - The present invention provides methods for design and identification of Vps10p domain receptor specific molecular imaging ligands based on the atomic coordinates of said Vps10p-domain. The present invention also relates to the preparation and use of such ligands for the preparation of a target specific imaging reagent or molecular imaging probe useful in detection of said Vps10p-domain receptor involved in disease.07-07-2011
20110021364PREDICTIVE TEST FOR ADULT DOG BODY SIZE - 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.01-27-2011
20110053787Compositions and Methods of Detecting Post-Stop Peptides - 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.03-03-2011
20110028335Ligands For The GLP-1 Receptor And Methods For Discovery Thereof - 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.02-03-2011
20100285980GENE EXPRESSION PROFILE ALGORITHM AND TEST FOR LIKELIHOOD OF RECURRENCE OF COLORECTAL CANCER AND RESPONSE TO CHEMOTHERAPY - 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.11-11-2010
20100285979DIAGNOSTIC TOOL FOR DIAGNOSING BENIGN VERSUS MALIGNANT THYROID LESIONS - 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.11-11-2010
20110263444METHOD FOR EXAMINING PROGNOSIS OF BREAST CANCER - Disclosed is a method for examining prognosis of breast cancer including the steps of: (A) extracting RNA from a specimen collected from a subject, (B) preparing a determination sample using the extracted RNA, (C) determining the expression level of each gene in the specific gene groups using the obtained determination sample, (D) analyzing the expression level of the determined each gene, and (E) examining prognosis of breast cancer, based on the obtained analysis result are performed.10-27-2011
20100304984PREDICTION OF POTENTIAL DRUG-DRUG INTERACTIONS USING GENE EXPRESSION PROFILING OF DRUG TRANSPORTERS, CYTOCHROME P450S AND NUCLEAR X RECEPTORS - 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.12-02-2010
20110257023METHODS, SYSTEMS, AND SOFTWARE FOR IDENTIFYING FUNCTIONAL BIOMOLECULES - 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.10-20-2011
20100184609USE OF A TERNARY MATRIX AS AN ADAPTER FOR MOLECULAR BIOLOGICAL INFORMATION, AND A METHOD TO SEARCH AND TO VISUALIZE MOLECULAR BIOLOGICAL INFORMATION STORED IN AT LEAST ONE DATABASE - 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.07-22-2010
20100029493DESIGN OF SYNTHETIC NUCLEIC ACIDS FOR EXPRESSION OF ENCODED PROTEINS - A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.02-04-2010
20100022401Avidin-like proteins from symbiotic bacteria - An isolated protein which is structurally and functionally similar to avidin but with improved properties, such as better affinity towards biotin conjugate, useful immunological properties or faster biotin dissociation rate, compared to avidin and streptavidin.01-28-2010
20100130372ALGORITHMS FOR CLASSIFICATION OF DISEASE SUBTYPES AND FOR PROGNOSIS WITH GENE EXPRESSION PROFILING - Methods for generating a normalized expression signal for microarray data based on a theoretical distribution at the unit level to produce a normalized expression signal for the single microarray that is independent of other microarrays. The method typically includes receiving microarray data representing a plurality of probe pairs for a single microarray, determining, for each probe pair, differences between intensities of perfect match (PM) probes and intensities of mismatched (MM) probes, determining a difference signal, D, based on the determined differences, and scaling the difference signal, D, to produce an expression signal, DS. The method also typically includes normalizing the expression signal based on a theoretical distribution at the unit level to produce a normalized expression signal for the single microarray that is independent of other microarrays.05-27-2010
20100240542KITS FOR MULTIPARAMETRIC PHOSPHO ANALYSIS - 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.09-23-2010
20090062135METHODS FOR THE IDENTIFICATION OF MICRORNA AND THEIR APPLICATIONS IN RESEARCH AND HUMAN HEALTH - The present invention concerns a method for prediction and identification of microRNA precursors (pre-microRNA) and microRNA molecules using data processing programs and databases. The invention also pertains to the isolated form of these pre-microRNAs, microRNA molecules and derived nucleic acids there of. The invention also relates to recombinant vector, host cell, support, pharmaceutical composition or kit comprising such microRNA molecules or there of derivated molecules. The invention also applies to the use of such microRNA molecules and/or their identified targets in research, prognostic, diagnostic tools/methods as well as for therapeutic applications.03-05-2009
20100222224Bioelectronic tongue for food allergy detection - 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. In order to implement the method of detecting food allergens on a bioelectronic tongue a computer readable medium containing an executable program is used for performing the analysis of a food sample. The executable program performs the acts of: preprocessing data from an impedance analyzer; extracting a feature pattern; recognizing a pattern of features of data representing a concentration of food allergen contained is the food sample; and outputs allergen concentration data.09-02-2010
20100279882SEQUENCING METHODS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.11-04-2010
20100179067SERUM BIOMARKERS FOR THE EARLY DETECTION OF LUNG CANCER - 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.07-15-2010
20110136686SEQUENCE MATCHING ALLOWING FOR ERRORS - Systems, methods, and other embodiments associated with sequence matching with no more than a number E errors are disclosed. A test fragment to be located within a target sequence with at most a number E errors is received. The test fragment is broken into E+1 test sub-fragments. If one test sub-fragment is located within the target sequence with no errors; a determination is made as to whether the other test sub-fragments are located within the target sequence adjacent to the one test sub-fragment with a total of at most E errors. If the other test sub-fragments are located within the target sequence adjacent the one test sub-fragment with at most E errors, a location of the test fragment within the target sequence is returned.06-09-2011
20120040847Personal Diabetic Carbohydrate Counting Procedure System and Method - A program interface for diabetic users to streamline the process of carbohydrate counting of meals. The present invention helps diabetic patients keep track of their blood glucose levels and help the users to calculate their require insulin intake for each meal. The invention comprises of a database of foods which users can select from for the calculation of nutrition and carbohydrates. The users are able to select their assigned carbohydrate to insulin ratio for the calculation of the amount of insulin that is required for the meal. Essential data is then stored and accessible for future corrective analysis.02-16-2012
20110105345Methods for the Analysis of High Resolution Melt Curve Data - The present application provides for various embodiments of methods for the analysis of high resolution melt (HRM) curve data; where statistical assay variations in melt curve data may result from system noise in an analysis system. Such system noise may arise from various sources, such as the thermal non-uniformity of a thermocycler block in a thermal cycler apparatus, a detection system, etc. Additionally, various methods for the analysis of HRM curve data may provide an identification of a sample without the need for a user inputted information.05-05-2011
20120058905DNA Sequences Encoding Caryophyllaceae and Caryophyllaceae-Like Cyclopeptide Precursors and Methods of Use - Naturally-occurring and modified recombinant nucleic acid molecules have been isolated that encode linear pre-cursors of cyclopeptides of the Caryophyllaceae (Ccps) and Caryophyllaceae-like (Clcps) type V1 class of cyclopeptides. Such nucleic acid molecules are useful for producing cyclopeptides and their linear precursors by recombinant methods.03-08-2012
20120252684METHODS OF POPULATING DATA STRUCTURES FOR USE IN EVOLUTIONARY SIMULATIONS - In particular, this invention provides novel methods of populating data structures for use in evolutionary modeling. In particular, this invention provides methods of populating a data structure with a plurality of character strings. The methods involve encoding two or more biological molecules into character strings to provide a collection of two or more different initial character strings; selecting at least two substrings from the pool of character strings; concatenating the substrings to form one or more product strings about the same length as one or more of the initial character strings; adding the product strings to a collection of strings; and optionally repeating this process using one or more of the product strings as an initial string in the collection of initial character strings.10-04-2012
20120108449CRYSTAL STRUCTURE OF ISOGLUTAMINYL CYCLASE - A crystal comprising human isoglutaminyl cyclase having a characterised space group of P1211 and unit cell dimensions of +/−5% of a=126.51 Å, b=109.68 Å, c=159.53 Å, α=90.0°, β=104.9° and γ=90.0°.05-03-2012
20120108448SYSTEM AND METHOD FOR CURATING MASS SPECTRAL LIBRARIES - Systems and method for curation of mass spectral libraries. In general, the systems and methods provided herein (a) obtain an experimentally derived mass spectrum of a compound of interest; (b) identify a peak in the mass spectrum that represent an experimental m/z value for an ion fragment of the compound of interest; (c) remove from the mass spectrum any peak that does not correspond to the compound of interest; and (d) replace the experimental m/z value for the peak identified in step (b) with a calculated theoretical m/z value for the ion fragment.05-03-2012
20120015834METHODS FOR ARTIFICIAL COMBINATORIAL CONTROL OF BIOLOGICAL SYSTEMS - Methods and systems for determining a set of control molecules for use in a combinatorial approach for the treatment of medical conditions, including providing one or more sets of control molecules, where each control molecule within the set acts on a set of targets and the number of control molecules within the one or more sets of control molecules is fewer than the number of targets within the sets of targets; and searching within the sets of control molecules to identify a subset of control molecules that together with a subset of targets form an artificial system to produce a biological effect through the modulation of the subset of targets.01-19-2012
20100125042PERIPHERAL GENE EXPRESSION BIOMARKERS FOR AUTISM - The disclosed invention comprises methods and materials for screening cells for genetic profiles associated with autism spectrum disorders. The methods typically involve isolating a cell from an individual and then observing the expression profile of one or more genes in the cell, wherein certain expression patterns of the genes observed are associated with autism spectrum disorders.05-20-2010
20110092379GENOTYPING METHOD AND MEANS THEREOF FOR USE IN TRACEABILITY SCHEMES - The invention discloses means and methods for genotyping an individual head of cattle. Individual's DNA is genotyped utilising the herein defined PCR SNaP-shot protocol. The protocol comprises two PCR steps where the first step (PCR1) includes adding primers (SEQ ID No. 1-30) and/or primers extended at their 5′ end with a common 10 base motif (ACGTTGGATG) to the PCR1 reaction. The second step (PCR2) includes adding extension primers (SEQ ID No. 31-45), and/or primers adjacent to corresponding specific SNPs. Further steps include producing amplicons from a PCR1 mixture comprising template DNA and the first primer set to yield PCR1 products, using PCR1 products as templates to a set of extension primers to yield PCR2 products. Size and colour separation is achieved by adding tails of different lengths to the PCR2 primers. PCR2 products are separated and the results compared with SNP profiles from the databank to obtain matching.04-21-2011
20120071333USES OF SYSTEMS WITH DEGREES OF FREEDOM POISED BETWEEN FULLY QUANTUM AND FULLY CLASSICAL STATES - Disclosed herein are systems and uses of systems operating between fully quantum coherent and fully classical states. Such systems operate in what is termed the “Poised realm” and exhibit unique behaviors that can be applied to a number of useful applications. Non-limiting examples include drug discovery, computers, and artificial intelligence03-22-2012
20110065593Computer Methods and Devices for Detecting Kidney Damage - Methods and devices for diagnosing, monitoring, or determining a renal disorder in a mammal are described. In particular, methods and devices for diagnosing, monitoring, or determining a renal disorder using measured concentrations of a combination of three or more analytes in a test sample taken from the mammal are described.03-17-2011
20120122712Methods for Sequencing a Biomolecule by Detecting Relative Positions of Hybridized Probes - A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.05-17-2012
20090131265BIOMARKERS FOR NEURODEGENERATIVE DISORDERS - The present invention provides methods for diagnosing neurodegenerative disease, such as Alzheimer's Disease, Parkinson's Disease, and dementia with Lewy body disease by detecting a pattern of gene product expression in a cerebrospinal fluid sample and comparing the pattern of gene product expression from the sample to a library of gene product expression pattern known to be indicative of the presence or absence of a neurodegenerative disease. The methods also provide for monitoring neurodegenerative disease progression and assessing the effects of therapeutic treatment. Also provided are kits, systems and devices for practicing the subject methods.05-21-2009
20100311601INDEX OF GENOMIC EXPRESSION OF ESTROGEN RECEPTOR (ER) AND ER-RELATED GENES - 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.12-09-2010
20100173791PROCESS DESIGN USING MASS SPECTROMETRY - The present invention provides a facile and efficient method for determining a chromatographic protocol for separating a target protein from one or more second protein impurity. Also provided is a database facilitating the determination of an appropriate separation protocol.07-08-2010
20100292088METHODS AND COMPOSITIONS FOR DETECTING GENETIC MARKERS ASSOCIATED WITH PRIMARY CILIARY DYSKINESIA - 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.11-18-2010
20080261820Methods to Analyze Biological Networks - The present invention relates to a family of graph-theory based methods for the analysis of intracellular signaling networks created from biomedical literature using data-mining processes or acquired through high-content experiments. The methods of the present invention can be used to identify functional dynamic modules within biological networks that can be analyzed quantitatively for input/output relationships. In particular, the present invention relates to a computer-aided method for the in-silico analysis of signaling and other cellular interaction pathways to rank drug targets, identify biomarkers, predict side effects, and classify/diagnose patients.10-23-2008
20100273666METHODS OF ANALYZING WOUND SAMPLES - A method of analyzing wound samples is provided. The analysis typically involves the use of mass spectrometry.10-28-2010
20100273665CHEMICAL SENSORS BASED ON CUBIC NANOPARTICLES CAPPED WITH AN ORGANIC COATING - 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.10-28-2010
20100273664Method For The Determination Of Intra- And Intermolecular Interactions In Aqueous Solution - 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 (ΔG10-28-2010
20100009859RATIONALLY DESIGNED SELECTIVE BINDING POLYMERS - A polymer able to bind a target compound selectively is designed by producing a virtual library of polymerisable monomers, and molecular models of the target compound and one or more potential interferents. The library is screened to identify monomers with substantial differences in strengths of binding to (a) target and (b) interferent. Monomers favouring the target may be used to produce polymers for selectively binding the target, for use in separation or analytical processes.01-14-2010
20100292087METHOD OF PREDICTING CHEMOTHERAPEUTIC RESPONSIVENESS OF CANCER - 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.11-18-2010
20120220472METHOD FOR INTEGRATING LARGE SCALE BIOLOGICAL DATA WITH IMAGING - There is disclosed a method of extracting large scale biological, biochemical or molecular information about an index disease, biological state, or systems from imaging by correlating the imaging features associated with said disease, state or system with corresponding large scale biological data.08-30-2012
20120083418METHOD FOR DESIGNING PRIMERS FOR SELEX METHOD, METHOD FOR PRODUCING THE PRIMERS, METHOD FOR PRODUCING APTAMERS, SYSTEM FOR DESIGNING THE PRIMERS, AND COMPUTER PROGRAM AND RECORDING MEDIUM FOR DESIGNING THE PRIMERS - A method for designing primers, being capable of efficiently designing primers for a SELEX method is provided. The method for designing primers of the present invention includes the steps of: (S04-05-2012
20110124515Methods and Systems for Pre-Conceptual Prediction of Progeny Attributes - Methods and systems for assessing the probabilities of the expression of one or more traits in progeny are described.05-26-2011
20110124514Protein Signature Evaluation Platform - A set of known protein sequences associated with an organism is identified, wherein each known protein sequence comprises a plurality of ordered residues. A set of scores associated with a set of residues of the plurality of ordered residues is identified, wherein each score indicates a frequency of a residue in sequence context. A set of unique sub-sequences of the set of known protein sequences is identified. A plurality of protein signature residues is determined based on the set of scores associated with the set of residues and the set of unique sub-sequences.05-26-2011
20120258875METHODS AND APPARATUS FOR CHARACTERIZING POLYMERIC MIXTURES - The invention provides methods and apparatus for characterizing complex polymeric mixture of interest. Candidate solutions are eliminated from a solution space using one or more experimental measurements of a polymeric mixture of interest. The elimination step can be repeated one or more times using different experimental measurements produced by various chemical and physical protocols, so that the remaining candidate solutions converge to describe the actual polymeric mixture under investigation. Once the composition of the complex polymeric mixture has been characterized, the information thus generated can be used to facilitate, for example, the manufacture of a bio-equivalent of the complex polymeric mixture.10-11-2012
20120258874INTERROGATORY CELL-BASED ASSAYS AND USES THEREOF - Described herein is a discovery Platform Technology for analyzing a biological system or process (e.g., a disease condition, such as cancer) via model building.10-11-2012
20120322671METHODS AND SYSTEMS FOR PRE-CONCEPTUAL PREDICTION OF PROGENY ATTRIBUTES - Methods and systems for assessing the probabilities of the expression of one or more traits in progeny are described.12-20-2012
20110237446Detection of Pathogenic Microorganisms Using Fused Raman, SWIR and LIBS Sensor Data - A system and method to search spectral databases to identify unknown materials, specifically pathogenic microorganisms. A library is provided, having sublibraries containing reference data sets of known materials and test data sets, both generated by at least one spectroscopic data generating instrument. For each test data set, each sublibrary associated with the instrument used is searched. A set of scores for each searched sublibrary is produced, representing the likelihood of a match between the reference data set and test data set. Relative probability values are calculated for each searched sublibrary. All relative probability values are fused producing a set of final probability values, used in determining whether the unknown material is represented through a known material in the library. The known material represented in the libraries having the highest final probability value is reported, if the highest final probability value is greater than or equal to the minimum confidence value.09-29-2011
20120289417T Cell Epitope Databases - The invention relates to databases of T cell epitopes, especially helper T cell epitopes, for rapid interrogation of protein sequences for the presence of T cell epitopes. The invention includes full or partial databases and data structures of T cell epitopes including epitopes identified especially by ex vivo T cell assays with test peptides and includes T cell epitopes identified by extrapolation of data from test peptides. The present invention also includes high throughput methods for determining the T cell epitope activity of peptides for subsequent inclusion in databases and data structures including methods where subsets of T cell especially regulatory T cells are removed or inhibited from T cell assays in order to maximize the sensitivity of detection of T cell epitope activity.11-15-2012
20110160070COPD BIOMARKER SIGNATURES - The present invention relates to methods of detecting differentially expressed protein expression indicative of COPD in a test sample. The detection of circulating levels of proteins within an identified COPD biomarker signature can aid in COPD diagnosis and disease monitoring, as well as in the prediction of responses to therapeutics. Evaluation of the biomarker signatures disclosed, or a subset of biomarkers thereof, provides a level of discrimination not found with individual markers.06-30-2011
20130178377METAPROTEOMIC METHOD FOR DIAGNOSIS OF BACTERIURIA, UROGENITAL TRACT AND KIDNEY INFECTIONS FROM URINARY PELLET SAMPLES - 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.07-11-2013
20120252683Binding Affinity Scoring Function Penalizing Compounds Which Make Unfavorable Hydrophobic Contacts With Localized Water Molecules In The Receptor Active Site - A method of scoring binding affinity of a proposed ligand molecule for a receptor molecule using a computer and computer data bases, which accounts for the increase in energy required where docking disrupts water molecules that are localized at ligand hydration sites. The method uses computer-stored data representing a predicted ligand-receptor structure (preferably one that is validated). The computerized scoring analysis includes determining whether the receptor includes one or more hydration sites occupied by localized water, and, if so, assessing a penalty if docking the ligand into the receptor results in unfavorable interaction of the ligand with a localized water molecule remaining at the receptor hydration site (i.e. after docking).10-04-2012
20130096017Digital Holographic Method of Measuring Cellular Activity and of Using Results to Screen Compounds - 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.04-18-2013
20130102480PREDICTION DEVICE, PREDICTION METHOD, PROGRAM, AND RECORDING MEDIUM - 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 04-25-2013
20130123120Highly Multiplex PCR Methods and Compositions - 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.05-16-2013
20100279881Epitope-mediated antigen prediction - 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. In this study, we identified the protein target of paraproteins from a number of patients with multiple myeloma. These methods will be useful in biomarker discovery, clinical diagnostics, and therapeutic drug lead identification.11-04-2010
20080207461Devices for Conducting and Analyzing Microarray Experiments - The present invention relates to devices for the simultaneous performance of microarray experiments for detecting specific interactions between probe and target molecules in a microtiter plate as well as to methods for manufacturing such devices. Furthermore, the present invention relates to the use of such devices in a method for qualitatively and/or quantitatively detecting specific interactions between probe and target molecules.08-28-2008
20100304983METHOD FOR PROTEIN STRUCTURE DETERMINATION, GENE IDENTIFICATION, MUTATIONAL ANALYSIS, AND PROTEIN DESIGN - 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.12-02-2010
20100317537BIOPHYSICAL PARAMETERS FOR SYSTEMS BIOLOGY - 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.12-16-2010
20100317536CRYSTAL STRUCTURE OF HUMAN GPVI AND APPLICATIONS THEREOF - 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.12-16-2010
20120283112Systems and Methods for Identifying Cosmetic Agents for Skin Care Compositions - Provided are methods and systems for determining functional relationships between a cosmetic agent and a skin tissue condition of interest. Also provided are methods and systems for identifying cosmetic agents that affect a skin aging tissue condition, as well as the use of agents identified by such methods and systems for the preparation of cosmetic compositions, personal care products, or both.11-08-2012
20110312510High-Throughput Complement-Mediated Antibody-Dependent and Opsonic Bactericidal Assays - The disclosure provides methods and kits for performing automated high-throughput assays to measure bactericidal activity in samples, such as plasma or sera from vaccinated subjects to evaluate the efficacy of vaccines against bacterial pathogens. The method combines obligatory linear-range data analysis, plate sealing and liquid volume handling for all assay steps to provide an automated, high-throughput measurement of bactericidal activity with favorable inter-assay and inter-operator variability.12-22-2011
20130196864DESIGN, SYNTHESIS AND ASSEMBLY OF SYNTHETIC NUCLEIC ACIDS - 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.08-01-2013
20130210648RATIO BASED BIOMARKERS AND METHODS OF USE THEREOF - 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.08-15-2013

Patent applications in class In silico screening