Abstract: Basis motifs are determined from an input sequence through an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.

Abstract: A method and apparatus for searching a gene sequence. The gene sequence search method includes receiving the gene sequence from a user, generating extended sequences including the received gene sequence, partial sequences included in the gene sequence and an inverse sequence complementary to the gene sequence, storing the gene sequence, the extended sequences, the partial sequences, the inverse sequence and input-related record information in a database, integrated-searching the gene sequence using a gene sequence search server, estimating a gene sequence search ranking for a predetermined period using the database and outputting an integrated and searched result of the gene sequence and a gene sequence search ranking result to the user.

Abstract: Basis motifs are determined from an input sequence through an iterative technique that begins by creating small solid motifs and continues to create larger motifs that include “don't care” characters and that can include flexible portions. The small solid motifs, including don't care characters and flexible portions, are concatenated to create larger motifs. During each iteration, motifs are trimmed to remove redundant motifs and other motifs that do not meet certain criteria. The process is continued until no new motifs are determined. At this point, the basis set of motifs has been determined. The basis motifs are used to construct redundant motifs. The redundant motifs are formed by determining a number of sets for selected basis motifs. From these sets, unique intersection sets are determined. The redundant motifs are determined from the unique intersection sets and the basis motifs. This process continues, by selecting additional basis motifs, until all basis motifs have been selected.

Abstract: Structure-based processing includes a method of diagnosing diseases that works by arranging diseases, symptoms, and questions into a set of related disease, symptom, and question structures, such as objects or lists, in such a way that the structures can be processed to generate a dialogue with a patient. A structure-based processing system organizes medical knowledge into formal structures and then executes those structures on a structure engine to automatically select the next question. Patient responses to the questions lead to more questions and ultimately to a diagnosis.

Abstract: Described are methods and systems for designing target-specific oligonucleotides of L-length. The method comprises a) parsing a polynucleotide target into overlapping sequences of N-length nucleotides, creating a kernel set; b) performing step a) reiteratively for each target until each it is associated with its own kernel set; c) removing N-length kernels from the kernel sets which are redundant; d) concatenating X-length nucleotide suffixes to each N-length nucleotide kernel to create L-length oligonucleotide sets; e) ordering L-length nucleotides within each set of step d) by their nucleotide position within the target; f) retaining or rejecting an L-length oligonucleotide, based on the presence or absence of each of the X consecutive and overlapping N-length kernels; and g) performing step f) reiteratively.

Abstract: In one aspect, the present invention provides methods of determining whether an agent is more like a partial agonist of a target molecule than a full agonist of the same target molecule. In another aspect, the present invention provides methods to select a candidate compound that may reduce blood plasma glucose concentration in a mammal. Populations of genes are provided that are useful in the practice of the present invention.

Abstract: Methods, computer systems, and computer program products for biopolymer engineering. A variant set for a biopolymer of interest is constructed by identifying, using a plurality of rules, a plurality of positions in the biopolymer of interest and, for each respective position in the plurality of positions, substitutions for the respective position. The plurality of positions and the substitutions for each respective position in the plurality of positions collectively define a biopolymer sequence space. A variant set comprising a plurality of variants of the biopolymer of interest is selected. A property of all or a portion of the variants in the variant set is measured. A sequence-activity relationship is modeled between (i) one or more substitutions at one or more positions of the biopolymer of interest represented by the variant set and (ii) the property measured for all or the portion of the variants in the variant set.

Abstract: A transcript mapping method according to an embodiment of the invention is described hereinafter and combines short tag based (SAGE and MPSS) efficiency with the accuracy of full-length cDNA (flcDNA) for comprehensive characterization of transcriptomes. This method is also referred to as Gene Identification Signature (GIS) analysis. In this method, 5? and 3? terminal tags are obtained from a transcript and the terminal tags are for identifying 5? and 3? sites located on a genome sequence. Further, occurring segments and thus feasible gene locations are identified along the genome sequence after the 5? and 3? sites are identified. A data structure is also generated for indexing the genome sequence so that the terminal tags can be mapped to the genome sequence.

Abstract: Structure-activity methods based on molecular descriptors that are a combination of structural information about the through-space and through-bond relationships between components of a molecule's structure and spectral data attributable to those components are disclosed. In some embodiments, a molecule is described by multiple sets of such descriptors to account for flexibility in the structure of the molecule. In a particularly disclosed embodiment, predicted 13C—13C COSY data and 13C—13C distance data are used as descriptors. Models of molecular properties may be established using the disclosed spectral data-activity methods and used to predict the properties of molecules.

Abstract: The present invention provides a biochip microarray, with multiple properties for use in identification of gene- and protein-induction or repression by drugs, the evaluation of efficacy and toxicity of any drug of choice, prediction of efficacy and toxicity of newly-discovered drugs, families of drugs or classes of drugs. Experimental information acquired from the biochip is inputted into a Drug-Gene-Protein-Biology (DGPB) database from which experimental data can be mined and analyzed based on the users preferences. A method for predicting the effect of a test composition for the treatment of a disease also is described. An animal model for the disease is selected. A biochip array for evaluating the effect of the test composition for the treatment of the disease is provided. The test composition is tested in the animal model to obtain a first set of biological markers representative of the effect of the test composition in the animal model.

Abstract: A method and system for morphology based mitosis identification and classification of digital images. Luminance parameters such as intensity, etc. from a digital image of a biological sample (e.g., tissue cells) to which a chemical compound (e.g., a marker dye) has been applied are analyzed and corrected if necessary. Morphological parameters (e.g., size, elongation ratio, parallelism, boundary roughness, convex hull shape, etc.) from individual components within the biological sample are analyzed. A medical conclusion (e.g., type and count of mitotic cells) or a life science and biotechnology experiment conclusion is determined from the analyzed luminance and morphological parameters. The method and system may be used to develop applications for automatically obtaining a medical diagnosis (e.g., a carcinoma diagnosis).

Abstract: “In silico” nucleic acid recombination methods, related integrated systems utilizing genetic operators and libraries made by in silico shuffling methods are provided.

Abstract: This invention relates to novel general methods and compositions that provide cancer-specific or highly cancer-associated antigens useful for diagnosis and treatment of cancer.

Abstract: Disclosed is a crystalline human CR2 protein in complex with C3d, and the three dimensional structure of the crystalline complex. Also disclosed are methods of use of the structure, particularly for structure-based identification of compounds that bind to CR2 and inhibit or enhance the binding of CR2 to a natural ligand, that bind to CR2 and agonize or antagonize the receptor, that bind to CR2 and inhibit or enhance CR2 dimerization, or that use the C3-binding ability of CR2 as a drug delivery vehicle. Also disclosed are therapeutic compounds obtained by such methods and uses for such compounds.

Abstract: The present invention relates to a method for the detection of biological agents and, in particular, biological agents that may present a health hazard. In one embodiment, the invention identifies the unidentified biological agent, assesses the reliability of the identification, and if determined to be reliable, outputs the identification. Initially, data that relates to the biological composition of an unidentified biological agent is received. The data is then analyzed with a machine learning procedure to identify the unidentified biological agent in the sample. The reliability of the identification is then assessed with, for example, an analysis of MS/MS data on the unidentified biological agent. If the identification is found to be reliable, the identification is output.

Abstract: The invention is a solid state process for analyzing genomes by visualizing sequence specific markers (e.g., proteins that bind a defined DNA sequence elements) by scanning probe microscopy. The method includes linear display of the nucleic acid on a solid surface, image acquisition by the scanning probe microscope, and digital data analysis. The acts of the method result in a bar code type display of each fragment of the DNA sample. These bar codes are then used to place the fragments in the order they appear on the original DNA sample.

Abstract: The invention provides isolated polypeptide and nucleic acid sequences derived from Streptococcus pneumoniae that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.

Abstract: The present invention relates to methods for separating nucleic acids from other cellular debris, especially substances that carry a net positive charge at low pH, by electrophoresis under acid conditions. In the purification method of the present invention, nucleic acids are separated from proteins found in the same biological sample by applying the sample to an electrophesis gel and subjecting the sample to electrophoresis under acid conditions to separate the nucleic acids from the proteins. The optimum pH may differ for different sample types but can be readily determined by those skilled in the art. Preferably, the separation is performed at a pH of about 2 to about 4. More preferably, electrophoresis is carried out at a pH of 2.

Abstract: Compositions and methods for the therapy and diagnosis of cancer, such as ovarian cancer, are disclosed. Compositions may comprise one or more ovarian carcinoma proteins, immunogenic portions thereof, polynucleotides that encode such portions or antibodies or immune system cells specific for such proteins. Such compositions may be used, for example, for the prevention and treatment of diseases such as ovarian cancer. Methods are further provided for identifying tumor antigens that are secreted from ovarian carcinomas and/or other tumors. Polypeptides and polynucleotides as provided herein may further be used for the diagnosis and monitoring of ovarian cancer.

Abstract: An unliganded form of Staphylococcus aureus thymidylate kinase (S. aureus TMK) has been crystallized, and the three dimensional x-ray crystal structure has been solved to 2.3 Å resolution. The x-ray crystal structure is useful for solving the structure of other molecules or molecular complexes, and designing inhibitors of S. aureus TMK activity.