Abstract: Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer and/or the likelihood of a beneficial response to chemotherapy for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene expression-tumor region ratios, tumor-associated stromal surface area, and gene cliques, i.e. genes that co-express with a validated biomarker and thus may be substituted for that biomarker in an assay, are also provided.

Abstract: The present invention relates to the use of genes differentially expressed in benign thyroid lesions and malignant thyroid lesions for the diagnosis and staging of thyroid cancer.

Abstract: There are many clinical instances in which, during the course of a disease, a patient may produce an antibody directed to unknown protein target(s). The targeted antigen(s) may be autoantigens (e.g., autoimmune diseases), microbial antigens (e.g., infectious diseases), allergens or, as in the case of B lymphoproliferative disorders and monoclonal gammopathies, antigens of unknown identity. When the antigen source is known or suspected, it may be feasible to construct a cDNA expression library and identify it. However, with no clues as to the antigen's origin, expression screening is impossible. We describe a new search strategy to overcome this limitation. We term the approach Epitope-Mediated Antigen Prediction (E-MAP). The technology enables one to link antibodies of unknown specificity to their cognate/target antigens in the protein database without requiring prior knowledge of their cellular source. We also describe a clinical application of the E-MAP technology to the study of multiple myeloma.

Abstract: Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or comparative genome hybridization microarray, comprising selecting a plurality of potential target sequences, generating a plurality of candidate probes from the target sequences, filtering the plurality of candidate probes by analyzing candidate probes for selected probe properties in silico. Microarrays comprising probes selected by the methods of the invention are particularly useful for comparative genome hybridization and location analysis.

Abstract: The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to nucleic acid sequencing.

Abstract: The present invention relates to the determination of intra- or intermolecular interaction between molecules in aqueous solution, said method comprising the steps of: (a) determining the dehydration (?Gdehydration) of all atoms in the intermolecular interface, (b) adding the vacuum hydrogen bond energy (?H-bond), and (c) further adding the change in the free enthalpy of the interacting partners upon their interaction. The obtained results can be used for the prediction if and to what extent two molecules of various origin fit to each other.

Abstract: A method of analyzing wound samples is provided. The analysis typically involves the use of mass spectrometry.

Abstract: The present invention provides a sensor apparatus based on 2D films or 3D assemblies of cubic nanoparticles capped with an organic coating. The apparatus is used to determine the composition and preferably measure the concentration of volatile and non-volatile compounds in a sample, with very high sensitivity. Methods for use of the apparatus in applications such as diagnosis of disease, food quality and environmental control are disclosed.

Abstract: The present invention relates to nucleic acid sequences from Bacillus thuringiensis and, in particular, to genomic DNA sequences. The invention encompasses nucleic acid molecules present in non-coding regions as well as nucleic acid molecules that encode proteins, fragments of proteins, tRNA's, fragments of tRNA's, rRNA's and fragments of rRNA's. In addition, proteins and fragments of proteins so encoded and antibodies capable of binding the proteins are encompassed by the present invention. The invention also relates to methods of using the disclosed nucleic acid molecules, proteins, fragments of proteins, RNA's, and antibodies, for example, for gene identification and analysis, and preparation of constructs.

Abstract: Quantitative expression datasets are created and used in the identification, monitoring and treatment of disease states and characterization of biological conditions. Quantitative datasets are derived from subject samples and enable evaluation of a biological condition. Such quantitative datasets may be used to provide an output score indicative of the biological state of a subject through analysis against a profile dataset.

Abstract: A crystal, a preparation method and 3D structure of CD147 extracellular region are provided. Such 3D structure is useful in the determination of the active site of CD147 extracellular region by computer modeling or molecular docking method. The crystal and/or 3D structure are useful in a structure-based drug design and the selection of an antibody, a ligand or an interacting molecule of CD 147 extracellular region.

Abstract: As disclosed herein, the present invention provides for kits and a composition for diagnosis, prognosis, drug discovery, drug development, and patient stratification. The kits can comprise a plurality of binding elements for cell surface markers, and a plurality of binding elements for state-specific intracellular markers. The kits can further comprise a plurality of modulators directed for the particular cell function or signaling pathways. The kits can further include fixatives, permeabilizing agent, buffers, containers, instructions, and software for data analysis/compilation.

Abstract: The invention provides isolated pyruvate dehydrogenase kinase nucleic acids and their encoded polypeptides. The present invention provides methods and compositions relating to altering pyruvate dehydrogenase kinase levels in plants. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions.

Abstract: The present invention relates to methods for drug repositioning. More particularly, this invention relates to methods for selecting approved drugs or combinations of approved drugs for use in new therapeutic indications. This approach is situated in a cross section between drug repositioning and disease treatment by combinations of drugs with additive or synergistic action. The invention also allows to define drugs or drug combinations for treating the unmet medical need in diseases neglected by majority of Pharma companies, such as orphan diseases.

Abstract: The present invention provides methods and compositions related to genomic profiling, and in particular, to assigning probabilistic measure of clinical outcome for a patient having a disease or a tumor using segmented genomic profiles such as those produced by representational oligonucleotide microarray analysis (ROMA).

Abstract: This invention contemplates an accurate and efficient estimation of gene copy number using oligonucleotide microarrays. The method integrates gene copy number data obtained from perfect match and mismatch probe sequence structure intensities and probe binding affinities. In one embodiment, an accurate determination of single nucleotide polymorphisms (SNPs) sequences is obtained. In another embodiment, an accurate detection and determination of DNA copy number alteration is obtained. In another embodiment, an accurate estimation for RNA gene expression is obtained.

Abstract: The present invention is directed to a method and apparatus that satisfies the need for a bioelectronic tongue for food allergy detection. The method of detecting concentration of food allergen incorporates antibodies into an electronic tongue to create a bioelectronic tongue. Additionally the method uses impedance, capacitance, and/or other related electrochemical methods for detecting analyte in complex media. Furthermore the method additionally includes methods to subtract out non-specific interactions. The method also subtracts non-specific interactions. The device/apparatus is a Bioelectronic Tongue for detecting allergen in diluted food samples. The device includes: a sensor array; an impedance or capacitance analyzer; a preprocessor; a feature extractor; a pattern recognizer; and an output device indicating an allergen concentration.

Abstract: The present invention includes biomolecules and use of these biomolecules for differential diagnosis of prostate cancer and/or non-malignant disease of the prostate. In an embodiment, the present invention provides methods for detecting biomolecules within a biological sample as well as a database comprising of mass profiles of biomolecules specific for healthy subjects, subjects having a non-malignant disease of the prostate and subjects having prostate cancer. The invention further includes kits for differential diagnosis of prostate cancer and/or non-malignant disease of the prostate in a biological sample.

Abstract: The present invention discloses variants that are predictive of human pigmentation patterns. The invention furthermore relates to variants that are useful for determining risk of skin cancer, including melanoma and basal cell carcinoma. The disclosed variants can be utilized for the determination of the natural pigmentation patterns of a human individual, and for determining a susceptibility to melanoma and basal cell carcinoma, from a sample of genetic material. Methods and kits including the variants described are useful in e.g. forensic testing and diagnostic applications.

Abstract: The present invention relates to a protein crystal of at least one binding site of a human aromatase. The present invention also relates to a fully processed human cytochrome P450 aromatase and a protein crystal thereof. The present invention further relates to methods of making and using the aromatase and the protein crystal thereof.

Abstract: The present invention discloses novel macromolecule transduction domain (MTD) peptides which facilitate the traverse of a biologically active molecule across the cell membrane. Also disclosed are polynucleotides encoding the MTD peptides, methods of identifying the MTD peptides; methods of genetically engineering a biologically active molecule to have cell permeability by using the MTD peptides, methods of importing a biologically active molecule into a cell by using the MTD peptides, and uses thereof.

Abstract: A system, a method and a computer-readable medium are provided for associating a nucleic acid profile or proteomic profile with a patient state, to utilize a healthcare protocol or guideline for decision support, in which the patient state provides a description of a current status and a history of a patient, and the nucleic acid profile or proteomic profile is an analysis of characteristics including genetic constitution, gene expression, or modification of the protein content of the tissue or cell, all of which aid in diagnosis of the disease state of a patient. The nucleic acid profile or proteomic profile shows a molecular indicator of the patient state. The invention also provides a method for associating a stage in the healthcare protocol or guideline with the nucleic acid profile or proteomic profile.

Abstract: Systems and methods collect and screen a biological material to facilitate its selection and use for therapeutic and/or research purposes. The systems and methods take into account both objective and semi-objective attributes manifest in a biological material, such as genetic, phenotypic, clinical, and genealogic attributes. The diverse array of the objective and semi-objective attributes enhances the level of confidence that the biological material can be best matched with a particular research or therapeutic purpose.

Abstract: It is proposed by the present invention the use of ternary matrices as an adapter of molecular biological information for integration of the said biological information. Another exclusive aspect of the present invention consists in a method of search and visualization of molecular biological information stored in at least one database, wherein a preferred implementation of the method is made using a computer program and wherein the same may be accessed using a computer network such as the Internet.

Abstract: Methods and kits are provided for determining the probability of lung cancer, for managing treatment of subjects with potential lung cancer and for molecular staging of lung tumors. The methods include determining an amount of each member of a panel of biomarkers in a sample from the subject, wherein the panel of biomarkers comprises at least two of the proteins alpha-1-antitrypsin, carcinoembryonic antigen, squamous cell carcinoma antigen, retinol binding protein, transferrin, and haptoglobin; and assigning the subject to a group having a higher or lower probability of lung cancer based on the determined amount of each biomarker the panel.

Abstract: The present invention relates to the gut microbiome as a biomarker and therapeutic target for energy harvesting, weight loss or gain, and/or obesity in a subject. In particular, the invention provides methods of altering and monitoring the relative abundance of Bacteroides and Firmicutes in the gut microbiome of a subject.

Abstract: 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.

Abstract: 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.

Abstract: Compositions, methods and related uses are provided relating to cleaving modified DNA. For example, a set of DNA fragments obtainable by enzymatic cleavage of a large DNA is described where at least 50% are similarly sized and have a centrally positioned modified nucleotide. In addition, an enzyme preparation is provided that includes one or more enzymes that recognize a modified nucleotide in a DNA and cleave the DNA at a site that is at a non-random distance from the modified nucleotide. The one or more enzymes are further characterized by an N-terminal conserved domain with greater than 90% amino acid sequence homology to WXD(X)10YXGD. The related uses include creating a methylome, methods of purifying DNA fragments containing a modified nucleotide and diagnostic applications.

Abstract: The present invention provides methods of predicting protein aggregation and designing aggregation inhibitors. One such method for predicting potential protein aggregation inhibiting peptide sequences, includes the steps of: a) identifying a peptide sequence forming at least part of an aggregation region in a target protein; b) testing whether said peptide sequence forms part of a ?-sheet; c) if a positive result is achieved in step b), extracting the adjacent strands of that sheet; d) identifying residues in the adjacent strands to said peptide sequence whose side chains interact with said peptide sequence, those residues forming a potential protein aggregation inhibiting peptide sequence. The present invention also provides methods of designing compounds using the residues identified in the above method; compounds produced by the methods and computer programs for carrying out the above methods.

Abstract: The present invention relates to a system of multi-stage stem cell carcinogenesis and a method of generating such multi-stage stem cell carcinogenesis system. Various stages of cancer stem cells can be generated from normal stem cells via mutagenesis. The system of the present invention enables monitoring changes in the ability of cells to transition from one stage of carcinogenesis to another and to identify genetic pathways and molecules that influence carcinogenesis. The present invention also enables a high-throughput and nonbiased screening for targets that preferentially affect cancer stem cells relative to non-cancer stem cells or their derivatives during stem cell carcinogenesis, thus is useful in developing anti-cancer therapeutics.

Abstract: Methods and systems of DNA sequencing that compensate for sources of noise in next-generation DNA sequencers are described.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: Drug discovery is a complex undertaking facing many challenges, not the least of which is a high attrition rate as many promising candidates prove ineffective or toxic in the clinic owing to a poor understanding of the diseases, and thus the biological systems, they target. Therefore, it is broadly agreed that to increase the productivity of drug discovery one needs a far deeper understanding of the molecular mechanisms of diseases, taking into account the full biological context of the drug target and moving beyond individual genes and proteins. The present methods rely on the use of label-free cellular assays, particularly the DMR index, to systematically display the mode of actions, the toxicity, and the target(s) and pathway(s) of any molecules.

Abstract: 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.

Abstract: 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.

Abstract: Drug discovery is a complex undertaking facing many challenges, not the least of which is a high attrition rate as many promising candidates prove ineffective or toxic in the clinic owing to a poor understanding of the diseases, and thus the biological systems, they target. Therefore, it is broadly agreed that to increase the productivity of drug discovery one needs a far deeper understanding of the molecular mechanisms of diseases, taking into account the full biological context of the drug target and moving beyond individual genes and proteins. The present methods rely on the use of label-free cellular assays, particularly the DMR index, to systematically display the mode of actions, the toxicity, and the target(s) and pathway(s) of any molecules.

Abstract: The present invention relates to compositions, kits, and methods for molecular profiling and cancer diagnostics, including but not limited to gene expression product markers, alternative exon usage markers, and DNA polymorphisms associated with cancer. In particular, the present invention provides molecular profiles associated with thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.

Abstract: 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.

Abstract: The present invention relates to methods of identifying small molecule candidate agents capable of modulating transcription factor function such that the function/expression of a target transcription factor and/or proteins downstream of this target protein comprises the screening of small molecule libraries using in silico high throughput docking for candidate small molecules/agents that are selectively identified for their ability to target and disrupt the transcription factor-DNA interface through unique transcription factor and/or DNA descriptors that are defined within a pharmacophore, and then testing/evaluating the candidate agents identified above through one or more in vitro assays for their ability to modulate transcription factor function including expression of this target protein and/or proteins that are downstream of the target transcription factor.

Abstract: 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.

Abstract: 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.

Abstract: The invention provides methods, databases and systems for making glycoprotein products having defined properties.

Abstract: 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.

Abstract: 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.

Abstract: A data processing method for an estimation of compound-protein interaction using both chemical substance information, such as a chemical property of the compound, and biological information, such as sequence information of genes to rationally and efficiently screen compounds. First space representing space coordinates of a first chemical substance group and second space representing space coordinates of a second chemical substance group are defined, and the first chemical substance group is characterized by a first characteristic amount and the second chemical substance group is characterized by a second characteristic amount, and map transformation of the coordinates of the first space and the coordinates of the second space results in the solution so as to increase the correlation between the first space and the second space using a multivariable analysis technique or a machine learning method.