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

Abstract: Disclosed is a process to construct multi-component biomolecule or cellular arrays suitable for use in SPR imaging studies of large molecule, cellular/molecular, and cell/cell interactions. Also disclosed are the resulting arrays. The success of the procedure hinges on the use of a reversible protecting group to modify reversibly ?-functionalized alkanethiols self-assembled on metal substrates. The arrays themselves include a metal substrate, a continuous layer of an identical ?-modified alkanthiol adhered to the metal substrate, and one or more discrete spots of biomolecules or cells directly bonded to the continuous layer of ?-modified alkenthiol. The areas of the continuous layer of ?-modified alkenthiol not covered by one of the discrete spots are covered by a background material resistant to non-specific protein binding.

Abstract: Disclosed are methods and systems for applying independent component analysis (ICA) and other advanced signal processing techniques to automatically identify an optimal number of independent gene clusters and to efficiently separate gene expression data into biologically relevant groups. Embodiments of the methods and systems of the present invention provide an interface that allows the user to review the results at various stages during the analysis, thereby optimizing the type of analysis performed for a specific experiment. Also disclosed are methods and systems to mathematically define the relationship for gene expression within a group of interrelated genes.

Abstract: The present invention provides amino acid sequences of peptides that are encoded by genes within the human genome, the kinase peptides of the present invention. The present invention specifically provides isolated peptide and nucleic acid molecules, methods of identifying orthologs and paralogs of the kinase peptides, and methods of identifying modulators of the kinase peptides.

Abstract: The expression data of specimen genes are processed using the SWEEP operator method and the parameter increasing method, and genes are selected. A FNN model is constructed by making the expression data of the selected genes as input variables.

Abstract: The present invention relates to methods for identifying novel genes comprising: (i) generating one and/or more specialized databases containing information on gene/protein structure, function and/or regulatory interactions; and (ii) searching the specialized databases for homology or for a particular motif and thereby identifying a putative novel gene of interest. The invention may further comprise performing simulation and hypothesis testing to identify or confirm that the putative gene is a novel gene of interest. The present invention also relates to natural language processing and extraction of relational information associated with genes and proteins that are found in genomics journal articles. To enable access to information in textual form, the natural language processing system of the present invention provides a method for extracting and structuring information found in the literature in a form appropriate for subsequent applications.

Abstract: Compositions and methods for the therapy and diagnosis of cancer, particularly prostate cancer, are disclosed. Illustrative compositions comprise one or more prostate-specific polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of diseases, particularly prostate cancer.

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 provides a computer based method for preparing a stem cell factor (SCF) analog comprising the steps of: (a) providing computer expression of the three dimensional structure of an SCF molecule using its crystal structure; (b) selecting from the computer expression of step (a) at least one site on the SCF molecule for alteration; (c) preparing a SCF molecule having an alteration at said at least one selected site; and (d) optionally, testing the SCF molecule for a desired characteristic. This invention also provides SCF analogs and SCF ligand analogs prepared according to the above-described method. Compositions comprising SCF analogs or SCF ligand analogs prepared according to the above-described method effective to treat a subject and a pharmaceutically acceptable carrier are provided, as are methods of treating a subject comprising administration of pharmaceutical compositions comprising the prepared SCF analogs and SCF ligand analogs prepared by the described methods.

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: Compositions and methods for the therapy and diagnosis of cancer, particularly ovarian cancer, are disclosed. Illustrative compositions comprise one or more ovarian tumor polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of diseases, particularly ovarian cancer.

Abstract: This invention provides a method for protein structure alignment. More particularly, the present invention provides a method for identification, classification and prediction of protein structures. The present invention involves two key ingredients. First, an energy or cost function formulation of the problem simultaneously in terms of binary (Potts) assignment variables and real-valued atomic coordinates. Second, a minimization of the energy or cost function by an iterative method, where in each iteration (1) a mean field method is employed for the assignment variables and (2) exact rotation and/or translation of atomic coordinates is performed, weighted with the corresponding assignment variables.

Abstract: A molecule surrounding surface (20) is set so as to be reflected in the spatial dimension of a molecule. A molecule surrounding space surrounded by the molecule surrounding surface is divided into a plurality of component spaces (22), by which the reaction characteristic of the molecule is characterized. Probe points are provided on a frontier surrounding surface (5) on the molecule surrounding surface, and a space occupied rate is derived for each of the component spaces. Electrostatic energies are derived for each of the probe points on the frontier surrounding surface, and the sum of the electrostatic energies on the frontier surrounding surface is derived as a enelectrostatic factor of each of the component spaces. In addition, van der Waals energies are derived for each of the probe points, and the sum of the van der Waals energies on the frontier surrounding surface is derived as a steric factor of each of the component spaces.

Abstract: The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of murine genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. As such, the invention related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.

Abstract: The sequences of 5′ ESTs derived from mRNAs encoding secreted proteins are disclosed. The 5′ ESTs may be to obtain cDNAs and genomic DNAs corresponding to the 5′ ESTs. The 5′ ESTs may also be used in diagnostic, forensic, gene therapy, and chromosome mapping procedures. Upstream regulatory sequences may also be obtained using the 5′ ESTs. The 5′ ESTs may also be used to design expression vectors and secretion vectors.

Abstract: The invention provides novel polynucleotides and polypeptides encoded by such polynucleotides and mutants or variants thereof that correspond to a novel human secreted semaphorin-like polypeptide. These polynucleotides comprise nucleic acid sequences isolated from cDNA library from fetal liver-spleen (Hyseq clone identification numbers 5688868 (SEQ ID NO: 1)). Other aspects of the invention include vectors containing processes for producing novel human secreted semaphorin-like polypeptides, and antibodies specific for such polypeptides.

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: This invention relates to novel molecular constructs that act as various logic elements, i.e., gates and flip-flops. The constructs are useful in a wide variety of contexts including, but not limited to, computation and control systems. The basic functional unit of the construct comprises a nucleic acid having at least two protein binding sites that cannot be simultaneously occupied by their cognate binding protein. This basic unit can be assembled in any number of formats providing molecular constructs that act like traditional digital logic elements (flips-flops, gates, inverters, etc.).

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.