Abstract: Disclosed are methods for the practice of systems pharmacology, systems toxicology, and systems pathology using patterns, such as images, reflective of the biological state of subjects such as humans or experimental mammals. The patterns are generated from data obtained from one or more samples from one or more subjects by applying certain data treatment techniques, and are reflective of the biochemistry of the subjects. The patterns are used in drug selection and discovery, assessment of toxicity and drug efficacy, segmentation of populations, discovery of disease subtypes, as surrogate end points, in the assessment of therapeutic options, and for diagnosis and prognosis of disease.

Abstract: The invention involves generating and presenting, typically electronically, a number of design alternatives to persons who are participating in the design, selection, or market research exercise. The participants (referred to as “selectors”) transmit data indicative of their preferences among or between the presented design alternatives, and that data is used to derive a new generation of design alternatives or proposals. The new designs are generated through the use of a computer program exploiting a genetic or evolutionary computational technique. The process is repeated, typically for many iterations or cycles.

Abstract: The present invention provides Modular Molecular Clasps and methods of using these Modular Molecular Clasps in a wide range of applications in the health care industry, e.g., in therapy, in clinical diagnostics, in in vivo imaging or in drug discovery. The Modular Molecular Clasps of the present invention also have industrial and environmental applications, e.g., in environmental diagnostics, industrial diagnostics, food safety, toxicology, catalysis of reactions or high-throughput screening; as well as applications in the agricultural industry and in basic research. Methods of designing the Modular Molecular Clasps, as well as arrays and biosensors comprising these Modular Molecular Clasps are also provided.

Abstract: Disclosed are methods of manufacturing synthetic DNAs, that is, DNAs made at least in significant part by chemical synthesis of nucleic acid polymers. Also provided are methods for assembling plural DNAs in the same pool by multiplexed assembly of synthetic oligonucleotides. In exemplary embodiments, the methods involve pre-amplification of one or more oligonucleotides using “universal” primers, reduction of the error rate in oligonucleotide and/or nucleic acid products, and sequence optimization and oligonucleotides design. Also provided are low-purity arrays of nucleic acids and methods for assembling nucleic acids using oligonucleotides obtained from low-purity arrays.

Abstract: The invention provides a family of nucleotide analogs useful in sequencing nucleic acids containing a homopolymer region comprising, for example, two or more base repeats, and to sequencing methods using such nucleotide analogs.

Abstract: A sample holder comprises a substrate microfabricated to define a multiplicity of microscopic islands defining sample support surfaces. At least one sump separates adjacent island surfaces and inhibits transport of samples between adjacent island surfaces.

Abstract: Disclosed are methods for the practice of systems pharmacology, systems toxicology, and systems pathology using patterns, such as images, reflective of the biological state of subjects such as humans or experimental mammals. The patterns are generated from data obtained from one or more samples from one or more subjects by applying certain data treatment techniques, and are reflective of the biochemistry of the subjects. The patterns are used in drug selection and discovery, assessment of toxicity and drug efficacy, segmentation of populations, discovery of disease subtypes, as surrogate end points, in the assessment of therapeutic options, and for diagnosis and prognosis of disease.

Abstract: The invention involves generating and presenting, typically electronically, a number of design alternatives to persons who are participating in the design, selection, or market research exercise. The participants (referred to as “selectors”) transmit data indicative of their preferences among or between the presented design alternatives, and that data is used to derive a new generation of design alternatives or proposals. The new designs are generated through the use of a computer program exploiting a genetic or evolutionary computational technique. The process is repeated, typically for many iterations or cycles.

Abstract: The present invention provides methods and systems for developing profiles of a biological system based on the discernment of similarities, differences, and/or correlations between biomolecular components, of a single biomolecular component type, of a plurality of biological samples. Preferably, the method comprises utilizing hierarchical multivariate analysis of spectrometric data at one or more levels of correlation.

Abstract: The present invention provides methods and systems for developing profiles of a biological system based on the discernment of similarities, differences, and/or correlations between biomolecular components, of a single biomolecular component type, of a plurality of biological samples. Preferably, the method comprises utilizing hierarchical multivariate analysis of spectrometric data at one or more levels of correlation.

Abstract: Disclosed are competition assay methods for reliably detecting the presence and/or quantitation of small molecules (e.g., metabolites) and peptides/proteins in a sample by the use of capture agents specific for immobilized small molecules and/or peptides/proteins. Arrays comprising these small molecules and/or peptides/proteins are also provided.

Abstract: Methods and systems are disclosed for developing profiles of a state of a biological system based on the discernment of similarities, differences, and/or correlations between a plurality of data sets that are derived from one or more biomolecular component types, one or more biological sample types, and/or one or more types of measurements.

Abstract: Disclosed is a family of novel protein constructs, useful as drugs and for other purposes, termed “adzymes,” comprising an address moiety and a catalytic domain. In some types of disclosed adzymes, the address binds with a binding site on or in functional proximity to a targeted biomolecule, e.g., an extracellular targeted biomolecule, and is disposed adjacent the catalytic domain so that its affinity serves to confer a new specificity to the catalytic domain by increasing the effective local concentration of the target in the vicinity of the catalytic domain. The present invention also provides pharmaceutical compositions comprising these adzymes, methods of making adzymes, DNA's encoding adzymes or parts thereof, and methods of using adzymes, such as for treating human subjects suffering from a disease, such as a disease associated with a soluble or membrane bound molecule, e.g., an allergic or inflammatory disease.

Abstract: Disclosed are methods for reliably detecting the presence of proteins, including proteins with various post-translational modifications (phosphorylation, glycosylation, methylation, acetylation, etc.) in a sample by the use of one or more capture agents that recognize and interact with recognition sequences uniquely characteristic of a protein or a set of proteins (Proteome Epitope Tags, or PETs) in the sample. Arrays comprising these capture agents or PETs are also provided.

Abstract: The invention provides novel methods for screening a sample to select a ligand to a target of interest and for obtaining information about the ligand and its binding characteristics. Specifically, the claimed multi-dimensional methods involve combining a solution of heterogeneous ligands with the target of interest to screen the ligands on the basis of one or more binding characteristics. Ligands having the first binding characteristic bind to the target of interest thereby to form a target/ligand complex. The complex then optionally is separated from the unbound components using any of a variety of separation techniques, e.g., size exclusion. At least one of the complex or unbound components then is introduced to a second “dimension”. The second dimension is capable of separating components based upon a second binding characteristic. One then elutes the ligand having the desired binding characteristics.

Abstract: The invention provides novel methods for screening a sample to select a ligand to a target of interest and for obtaining information about the ligand and its binding characteristics. Specifically, the claimed multi-dimensional methods involve combining a solution of heterogeneous ligands with the target of interest to screen the ligands on the basis of one or more binding characteristics. Ligands having the first binding characteristic bind to the target of interest thereby to form a target/ligand complex. The complex then optionally is separated from the unbound components using any of a variety of separation techniques, e.g., size exclusion. At least one of the complex or unbound components then is introduced to a second “dimension”. The second dimension is capable of separating components based upon a second binding characteristic. One then elutes the ligand having the desired binding characteristics.

Abstract: The invention provides novel methods for screening a sample to select a ligand to a target of interest and for obtaining information about the ligand and its binding characteristics. Specifically, the claimed multi-dimensional methods involve combining a solution of heterogeneous ligands with the target of interest to screen the ligands on the basis of one or more binding characteristics. Ligands having the first binding characteristic bind to the target of interest thereby to form a target/ligand complex. The complex then optionally is separated from the unbound components using any of a variety of separation techniques, e.g., size exclusion. At least one of the complex or unbound components then is introduced to a second “dimension”. The second dimension is capable of separating components based upon a second binding characteristic. One then elutes the ligand having the desired binding characteristics.

Abstract: The invention features an apparatus for the separation and analysis of proteins, which includes a sample input, a first liquid chromatography column, a multiport injection valve connecting the sample input to the column, a pump for providing variable pressure delivery of a solution to the column via the multiport valve, and a program for specifying a sequence of system control programs.