Abstract: The presently-disclosed subject matter includes methods and systems for identifying biomarkers of interest, diagnosing and/or monitoring conditions of interest, assessing the efficacy of a treatment program, and composition screening. Exemplary methods include providing a sample of interest, fractionating the sample, generating thermograms, and comparing thermograms.

Abstract: A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 210 24mers is described.

Abstract: The invention relates to the field of molecular biology, nucleic acid chemistry and medical diagnostics. More specifically, it relates to methods and compositions for promoting the hybridization of a nucleic acid probe with a target nucleic acid sequence which is not perfectly matched to the probe.

Abstract: A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 210 24mers is described.

Abstract: Methods for processing sequences so as to be capable of selecting a family of polynucleotide sequences in which any two sequences with in the family meet predetermined criteria, particularly with respect to the degree of homology between the sequences.

Abstract: Methods for detecting the presence or absence of an analyte in a sample are disclosed. Kits for performing the analysis methods of the invention are also disclosed.

Abstract: The invention includes methods of representing polymer sequences in a way that reveals important position-specific contextual information. The representations can be used to determine a number of properties of polymers, such as protein and nucleic acid sequences, including the identification of secondary domain structures, folding rate constants, and the effects of altering (e.g., mutating) monomers. In addition, the representations can be used to compare polymers and thereby identify important structural and functional characteristics of polymers.

Abstract: The present invention provides methods and means for analyzing, designing, selecting and generating oligomer sequences, such as those for use in multiplex array-based nucleic acid probe systems, down to the selection of a single pair of optimal primer/target oligomers. Sequences are represented by a function of sequence context, called the context functional descriptor. In addition to the consideration of base pairing and nearest-neighbor analysis, the present computational methods incorporate the use of context functional descriptors and correlation matrices to account for higher-order thermodynamic interactions between nucleic acid sequences.

Abstract: The methods of the invention allow for the construction and/or use of modular computational models to accurately predict the therapeutic properties, including both therapeutic potency and one or more ADMET properties, of all or part of a chemical compound. The modular computational models can be used to rapidly screen libraries of chemical compounds, and reliably identify small subsets of those chemical compounds that have desirable therapeutic potency and ADMET properties, and are thus the best overall drug candidates.

Abstract: Methods, compositions, and kits for modulating the stability of at least one nucleic acid duplex, are disclosed.

Abstract: Methods for detecting the presence or absence of an analyte in a sample are disclosed. Kits for performing the analysis methods of the invention are also disclosed.

Abstract: Methods, compositions, and kits for modulating the stability of at least one nucleic acid duplex, are disclosed.

Abstract: Methods for identifying a site on a nucleic acid sequence having a desired free energy variability are disclosed. The methods are useful for, e.g., selecting antisense oligonucleotides, e.g., for therapeutic use.

Abstract: A method of providing the sequence of a single stranded nucleic acid molecule, which, when hybridized to a complementary single stranded molecule, results in a double stranded (duplex) structure having a preselected value for a free energy parameter.

Abstract: Methods for detecting the presence or absence of an analyte in a sample are disclosed. Kits for performing the analysis methods of the invention are also disclosed.

Abstract: Nucleic acid capture moieties, methods of using nucleic acid capture moieties, reaction mixtures including nucleic acid capture moieties, and kits including nucleic acid capture moieties are disclosed.

Abstract: A method for determining at least one DNA sequence that can be employed as a flanking sequence to a DNA binding site for a ligand, wherein the DNA binding site is located within a preselected DNA sequence, to provide a relative increase, decrease, or approximate equality in binding constant of the ligand for its DNA binding site, or relative composite reaction rate for the ligand and a DNA sequence. Also provided are applications of the method to determine DNA primers useful in conjunction with DNA amplification to detect the presence or absence of DNA sequences and to diagnose diseases related to viral DNA, such as human immunodeficiency virus.