Abstract: An algorithm for determining the viral antigenic protein variants to be used to construct vaccines designed to immunize against variable viral populations (quasispecies) is described. The method entails analyzing multiple nucleotide sequences of viral proteins and identifying those variants that provide selective advantage to the virus. Examples are given for influenza A hemagglutinin 3 and HIV-1 gp120.

Abstract: The present invention relates to a arrays of nucleic acid and methods of screening these arrays for desired nucleotide sequences. In a preferred embodiment of the invention, a desired cDNA clone can be obtained in three or less rounds of PCR screening. A master plate containing a population of cDNA, distributed in a plurality of wells, is screened for a desired clone by PCR. After a master well containing the desired cDNA is identified, a second plate containing a cDNA array of the master well can then be screened using the same PCR primers. Since the second plate contains about 50-fold to 100-fold fewer clones than the master plate, an expedient reduction in the number of candidates can be achieved in a single PCR step. The invention also relates to a super-master plate containing at least two, preferably more, different populations of cDNA obtainable from different sources of mRNA.

Abstract: The invention provides Response regulator polypeptides and polynucleotides encoding Response regulator polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing Response regulator polypeptides to screen for antibacterial compounds.

Abstract: One embodiment of the present invention provides methods for detecting known blocks of functionally aligned protein sequences in a test nucleic acid sequence, e.g., in an uncharacterized EST. The method can include the following steps. A) Reverse translate the set of protein sequences to a set of functionally aligned nucleic acid sequences using codon-usage tables and create a profile from the set of functionally aligned nucleic acid sequences. B) Construct a first indicator function for the profile. The first indicator function corresponds to adenine. The first indicator function allows the value at a given position to be continuous between 0 and 1 as a function of the percentage presence of adenine at a particular position. C) Construct a second indicator function for the test nucleic acid sequence. The second indicator function also corresponds to adenine. D) Compute the Fourier transform of each of the indicator functions. E) Complex conjugate the Fourier transform of the second indicator function.

Abstract: A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known. Profiling methods and other methods for characterizing polynucleotides are presented.

Abstract: The disclosed invention provides a novel method for analyzing genomic DNA and expressed sequences using auxiliary oligonucleotides, preannealed to the single-stranded target nucleic acid to form a partially duplex target molecule, offers several advantages in the analysis of nucleic acid sequences by hybridization to genosensor arrays or “DNA chips”. Also provided is a method for directly analyzing and comparing patterns of gene expression at the level of transcription in different cellular samples.

Abstract: This invention relates to novel human genes, to proteins expressed by the genes, and to variants of the proteins. The invention also relates to diagnostic assays and therapeutic agents related to the genes and proteins, including probes, antisense constructs, and antibodies. The subject nucleic acids have been found to be differentially regulated in tumor cells, particularly in colon cancer tissue.

Abstract: This invention relates to novel human genes, to proteins expressed by the genes, and to variants of the proteins. The invention also relates to diagnostic assays and therapeutic agents related to the genes and proteins, including probes, antisense constructs. and antibodies. The subject nucleic acids have been found to be differentially regulated in tumor cells, particularly colon cancer cell lines and/or tissue.

Abstract: The present invention relates to systems, integrated computer software programs, and related methods for manipulation and analysis of gene expression data. The methods of the invention are particularly suited for use with gene expression data generated with microarray and genechip technologies. A particular embodiment of the invention relates to systems utilizing clustering algorithms, which may be used to correlate temporal patterns of gene expression. The invention also relates to graphical tools, search and sort functions for viewing both the original and processed gene expression data. The present invention also relates to a graphical user interface for data clustering, graphical viewing, and browsing.

Abstract: The present invention relates to a method for the amplification of or creation of A signalling event for detection of a probe which reacts with a test substance, the method comprising causing the test substance to react with the probe and identifying the reaction of the test substance with the probe by release of a signalling moiety from a vesicle. The invention also relates to a kit for the detection of a probe which reacts with a test substance, the kit comprising a vesicle which contains a signalling moiety.

Abstract: A method of analyzing DNA fragments separated electrophoretically is presented. The method includes the use of an expert system that interprets raw or preprocessed signal from the separation. The expert system can be used for real-time base-calling, or applied offline after data acquisition is complete. The expert system is directly applicable to all types of electrophoretic separation used for DNA sequencing, i.e. slab gel, capillary and microchip. Each lane of a multiplex system can consist of 1 to 4 (or even more) different fragment labels. The expert system may also be used with other base-coding schemes, such as those in which more than one base is labeled with a given dye, but the amount of label is different for each base. When the presently disclosed method is applied to DNA sequencing, the resulting interpretation comprises a DNA base sequence with numerical confidences assigned to each base.

Abstract: The invention is directed to constitutively active Stat proteins and methods for their preparation. The modified Stat proteins have at least one cysteine residue which may interact with the corresponding cysteine residue on another modified Stat protein to form a dimer. The constitutively active Stat proteins are capable of binding to DNA and activating transcription in the absence of tyrosine phosphorylation. Cell lines expressing the modified Stat protein exhibit a transformed phenotype and are capable of forming tumors in nude mice. Methods are describe utilizing the modified Stat proteins of the invention in the absence and presence of tyrosine phosphorylation in identifying agents capable of modulating Stat protein dimerization, transcriptional activity, and cellular transformation in vitro and in vivo. The invention is also directed to polynucleotides encoding modified, constitutively active Stat proteins.

Abstract: A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Abstract: The present computer-implemented process involves a methodology for determining properties of ligands which in turn can be used for designing ligands for binding with protein or other molecular targets, for example, HIV targets. The methodology defines the electrostatic complement for a given target site and geometry. The electrostatic complement may be used with steric complement for the target site to discover ligands through explicit construction and through the design or bias of combinatorial libraries. The definition of an electrostatic complement, i.e., the optimal tradeoff between unfavorable desolvation energy and favorable interactions in the complex, has been discovered to be useful in ligand design. This methodology essentially inverts the design problem by defining the properties of the optimal ligand based on physical principles.

Abstract: This invention provides methods for determining drug specificity, therapeutic index and effective doses for individual patients. According to the methods of the invention, graded levels of drug are applied to a biological sample or a patient. A plurality of cellular constituents are measured to determine the activity of the drug on a target pathway and at least one off-target pathway. A drug specificity is determined by comparing the target and off target activities of the drug. A therapeutic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the target pathway. A toxic concentration (or dose) is defined as a concentration (or dose) of the drug that induces certain response in the off target pathway. Therapeutic index is the ratio of the toxic concentration over therapeutic concentration. Methods are also provided to determine an effective dose of a drug for a patient by measuring the activity of the drug on the particular patient.

Abstract: A computerized method is described for assembling DNA sequence determined for small DNA fragments, called fragment reads, into larger fragments of DNA sequence called contigs. The method used makes a table of occurrences or counts for each mer appearing in any of the fragment reads and then picks from among those mers specific mers to use as mer tags. Following checking, the mer tags are used to assemble fragment reads into contigs. A feature of this method is that the processing time necessary to perform this process on a computer varies linearly with the number of fragment reads rather than with the square or cube of the number of fragment reads.

Abstract: The present invention relates to a method for the detection of gene expression and analysis of both known and unknown genes. The invention is a highly sensitive, rapid and cost-effective means of monitoring gene expression, as well as for the analysis and quantitation of changes in gene expression for a defined set of genes and in response to a wide variety of events. It is an important feature of the present invention that no single molecular species of cDNA gives rise to more than one fragment in the collection of products which are subsequently amplified and representative of each expressed gene. This achievement is facilitated by immobilizing the cDNA prior to digesting and then digesting with sequentially with two frequently cutting enzymes. Linker oligomers are ligated to each cut site following the respective digestion. Primers, complementary to the oligomer sequence with an additional 3′ variable sequence are used to amplify the fragments.

Abstract: A subject of the invention is a modified yeast strain in which the acetyl-CoA pregnenolone acetyltransferase (APAT) activity is eliminated by altering the gene coding for this activity with resultant stabilization of 3&bgr;-hydroxysteroids.

Abstract: The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject so that a diagnostic profile is obtained, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects so that perturbation response profiles are obtained which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profile or profiles which best fit the diagnostic profile according to some objective measure.

Abstract: A new technology is described that allows for the rapid and efficient construction of complex cDNA libraries from cultured eukaryotic cells. The technology exploits eukaryotic biology by using transgenic constructs that have been nonspecifically inserted into the genome to facilitate the expression of nuclear genes as fusion transcripts. The invention further allows one to specifically subclone the corresponding fusion transcripts into highly complex cDNA libraries. The libraries are easily characterized by molecular analysis techniques such as hybridization, and individual clones can be directly sequenced to generate a sequence database of the cellular portion of the fusion transcripts.