Abstract: A computer implemented method of generating new chemical compounds is provided. The method includes preparing a data-driven substructure feature vector for each of a plurality of chemical compounds for which a chemical or physical property is known. The method further includes preparing a predefined component feature vector, creating a regression model to predict a target value for the chemical or physical property, and performing a search algorithm to identify substructure features that affect the target value for the chemical or physical property. The method further includes generating a candidate structure having the target value for the chemical or physical property, and synthesizing the candidate structure.

Abstract: A method for making a polynucleotide is provided including (a) delivering one or more reaction reagents including an error prone or template independent DNA polymerase, cations and a selected nucleotide to a reaction site including an initiator sequence having a terminal nucleotide for a time period and under conditions capable of covalently adding one or more of the selected nucleotide to the terminal nucleotide at the 3? end of the initiator such that the selected nucleotide becomes a terminal nucleotide, and (b) determining whether the selected nucleotide has been added to the terminal nucleotide, wherein if the selected nucleotide has not been added to the terminal nucleotide, then repeating step (a) until the selected nucleotide has been added, and (c) repeating steps (a) and (b) until the polynucleotide is formed.

Abstract: The present disclosure provides methods for optimizing barcode design for multiplex DNA sequencing. Also disclosed are DNA barcodes optimized for use with particular sequencing technologies.

Abstract: The present invention provides miniaturized instruments for conducting chemical reactions where control of the reaction temperature is desired or required. Specifically, this invention provides chips and optical systems for performing and monitoring temperature-dependent chemical reactions. The apparatus and methods embodied in the present invention are particularly useful for high-throughput and low-cost amplification of nucleic acids.

Abstract: The present invention relates to compositions and methods for delivery of siRNA to specific cells or tissue. More particularly, the present invention relates to compositions and methods for cell type-specific delivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer.

Abstract: A method of modeling phase characteristics of thermodynamic systems utilizing pseudo-properties strategy and a reduced number of variables is disclosed herein. The method describes a means of determining the probability of phase splitting of mixtures of materials at a given temperature, pressure, and composition by characterizing the functions that describe the system via pseudo-properties, and also by describing the system in n?1 or fewer variables, where n represents the number of components in the system of interest. In an embodiment, a multi-component system is characterized in one variable, thereby providing simplified thermodynamic models in a time-efficient manner. In addition, the information generated by this reduced-variable calculation can further be used as a starting point for calculations of equations of state.

Abstract: The systems and methods of the invention provide a guided approach to pyrosequencing (i.e., hybrid pyrosequencing). A de novo nucleic acid sequence may compared to a library of possible results and the next nucleotide to be dispensed is selected based on the comparison of the de novo sequence and the library of possible results. In another example, at least the first nucleotide to be dispensed is selected based on a query of a database(s) of non-sequence parameters (e.g., incidence of infection, diagnostic symptoms, sample source) and subsequent dispensations determined based on a comparison of the de novo sequence and the library of possible results (e.g., candidate sequences). The systems and methods of the invention may be performed using a droplet actuator.

Abstract: A substance identification method includes combining substances into four or more intermediate subpools in wells of a subpool plate and repooling the intermediate subpools into a number of final screening pools based on a repooling design providing the subpooled substances in at least three different final screening pools. The repooling design determines coordinates locating well positions for the substances. Another substance identification method includes using a two-dimensional array of wells arranged in rows and a number of columns that is at least 1.5 times the rows. Substances in the wells are combined into a number of screening pools. Individual screening pools include substances from wells having a row identifier in common with one other well. A pooling design provides the pooled substances in two different screening pools. The pooling design determines coordinates locating well positions for the substances.

Abstract: The present invention relates to screening methods and, in particular, to methods of screening anti-ligands libraries for identifying anti-ligands specific for differentially and/or infrequently expressed ligands. The method comprises the steps of providing a library of anti-ligands; providing a first subtractor ligand; providing a second target ligand; determining the amount of the first and second target ligands using one or more equations derived from the universal law of mass action; providing the determined amount of a first subtractor ligand; providing the determined amount of a second target ligand; providing separation means capable of use to isolate anti-ligand bound to the second target ligand from anti-ligand bound to the first subtractor ligand; exposing the library of to the first and second target ligands to permit binding of anti-ligands to ligands; and using the separation means to isolate the anti-ligand bound to second target ligand.

Abstract: The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer-readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries.

Abstract: The present invention relates to a method of identifying one or more genes encoding one or more proteins having an optimized property. In particular, the method comprises expressing a collection of genes and screening for a desired property, identifying a plurality of genes having the desired property, and replacing one or more one or more sub-sequences of each of said genes with a different, compatible genetic sub-sequence, and screening again in order to identify genes encoding proteins having an optimized property.

Abstract: Methods and compositions are disclosed for introducing molecular switch functionality into a protein affinity reagent to render its binding to a target molecule sensitive to an environmental trigger, such as pH, while maintaining binding affinity to the target molecule. Combinatorial libraries created by the method are also disclosed.

Abstract: The systems and methods of the invention provide a guided approach to pyrosequencing (i.e., hybrid pyrosequencing). A de novo nucleic acid sequence may compared to a library of possible results and the next nucleotide to be dispensed is selected based on the comparison of the de novo sequence and the library of possible results. In another example, at least the first nucleotide to be dispensed is selected based on a query of a database(s) of non-sequence parameters (e.g., incidence of infection, diagnostic symptoms, sample source) and subsequent dispensations determined based on a comparison of the de novo sequence and the library of possible results (e.g., candidate sequences). The systems and methods of the invention may be performed using a droplet actuator.

Abstract: Antigen-specific immunoglobulin V-regions are identified from a library of nucleic acids amplified using polymerase chain reaction using leader sequence-specific forward primers. The use of leader sequence primers allows all V-region sequences to be amplified (including those with extensive 5? end mutations) without loss of the original 5? V gene segment sequence. A second V-region library is made using a larger than conventional set of 5? V-region primers. The sequence errors introduced into the amplification products by this method are corrected using sequence information obtained in the products amplified by the V-region primers to screen the library created using the leader sequence primers. Amino acid sequence information from fragments of donor immunoglobulins can be used to assist in the identification of nucleic acids encoding the heavy and light chains of donor antibodies as well as to design primers to amplify such nucleic acids.

Abstract: Methods for identifying modified proteases with modified substrate specificity or other properties are provided. The methods screen candidate and modified proteases by contacting them with a substrate, such as a serpin, an alpha macroglobulins or a p35 family protein or modified serpins and modified p35 family members or modified alpha macroglobulins, that, upon cleavage of the substrate, traps the protease by forming a stable complex. Also provided are modified proteases.

Abstract: The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag.

Abstract: The present invention includes composition and methods for making and using a combinatorial library to identify modified thioaptamers that bind to, and affect the immune response of a host animal, transcription factors such as IL-6, NF-?B, AP-1 and the like. Composition and methods are also provided for the treatment of viral infections, as well as, vaccines and vaccine adjuvants are provided that modify host immune responses.

Abstract: Individual patient- and disease-specific test results are obtained from a mixture of one or more distinct tests from multiple combined and distinct patient samples or reactions. In an especially preferred aspect, multiple reaction products from oligonucleotides having unique identifier portions are prepared or received from a clinician and combined for hybridization on a chip. Test results are deconvoluted using a deconvolution table in which associative data are employed to provide access to the individual patient- and disease-specific test results.

Abstract: In some aspects, the invention provides a genetically tractable in situ non-human animal model for hepatocellular carcinoma. The model is useful, inter alia, in understanding the molecular mechanisms of liver cancer, in understanding the genetic alterations that lead to chemoresistance or poor prognosis, and in identifying and evaluating new therapies against hepatocellular carcinomas. The liver cancer model of this invention is made by altering hepatocytes to increase oncogene expression, to reduce tumor suppressor gene expression or both and by transplanting the resulting hepatocytes into a recipient non-human animal. The present invention also provides methods for identifying and validating tumor suppressor genes by screening pools of shRNAs that target genomic regions deleted in human cancers, such as human hepatocellular carcinomas.

Abstract: A total forensic DNA casework management system and method for the deconvolution of mixed DNA samples using a novel, 3-rule algorithm to determine the proportional allele sharing of the sample's contributors. The process is fully document, can assess and process DNA anomalies and artifacts, and transforms raw STR data to produce final DNA profile types, peak height ratios, proportions, fitting criteria and associated graphs.

Abstract: Described is a method for determining a nucleotide sequence within cDNA, the frequency of a nucleotide sequence in a cDNA sample, as well as a method for (unbiased) determination of relative transcript levels of genes without sequence information of these genes being required, said methods using complexity reduction and (high throughput) sequencing.

Abstract: The present invention is related generally to analysis of polynucleotides, particularly polynucleotides derived from genomic DNA. The invention provides methods, compositions and systems for such analysis. Encompassed by the invention are arrays of polynucleotides in which the polynucleotides have undergone multiple rounds of amplification in order to increase the strength of signals associated with single polynucleotide molecules.

Abstract: Methods for identifying modified proteases with modified substrate specificity or other properties are provided. The methods screen candidate and modified proteases by contacting them with a substrate, such as a serpin, an alpha macroglobulins or a p35 family protein or modified serpins and modified p35 family members or modified alpha macroglobulins, that, upon cleavage of the substrate, traps the protease by forming a stable complex. Also provided are modified proteases.

Abstract: The present invention is a cell-based method of identifying a set of signal transduction proteins having an intracellular localization pattern responsive to toxic compounds. The method requires identifying and screening an initial set of signal transduction proteins against a set of toxic compounds, and determining changes in intracellular localization pattern of each of the proteins. Proteins whose changes in intracellular localization pattern are redundant are discarded from the initial set, and new proteins are added to provide a new set of proteins. I repeat the method steps with new sets of proteins until the set of proteins provides me at least 5 principal components with respect to the range of compounds marketed as small organic molecules.

Abstract: Methods of identifying specific target molecules for design of anti-angiogenic and vascular targeting approaches are disclosed. Transcriptional profiles of tumor endothelial cells were compared with that of normal resting endothelial cells, normal but angiogenically activated placental endothelial cells, and cultured endothelial cells. Although the majority of transcripts were classified as general angiogenesis markers, 17 genes were identified that show specific overexpression in tumor endothelium. Antibody targeting of four cell-surface expressed or secreted products (vimentin, CD59, HMGB1 and IGFBP7) inhibited angiogenesis in vitro and in vivo. Finally, targeting endothelial vimentin in a mouse tumor model significantly inhibited tumor growth and reduced microvessel density. The results demonstrate the utility of the identification and subsequent targeting of specific tumor endothelial markers for anticancer therapy.

Abstract: A system and method for cleanup of biological samples from contaminants prior to spectroscopy analysis. The system includes a support configured to hold a sample including a liquid having at least one group of biological molecules with a surface of the support binding the molecules at a surface tension angle to the liquid of less than 180 degrees. The system includes an evaporator configured to evaporate liquid from the support, a solvent applicator configured to apply a solvent for dissolution of the contaminants in the sample, and a solvent removal device configured to remove applied solvent from the sample and thereby at least partially remove the contaminants.