Abstract: Provided herein are methods of detecting responses of bio-artificial tissues to agents by performing assays using three-dimensional bio-artificial tissues. The methods are adaptable to high-throughput platforms.

Abstract: The present invention features biomarkers capable of diagnosing inflammatory bowel disease and methods of using such biomarkers to diagnose and selecting treatments for inflammatory bowel diseases.

Abstract: Methods and systems for identifying binding sites in macromolecules using small molecule mimics of naturally occurring molecules is disclosed. A reactive probe is provided that mimics small molecule cofactors. A target macromolecule is irreversibly bound to the probe in vivo to selectively pull down or precipitate probe-bound macromolecules. The macromolecules may be, but are not limited to, DNA, RNA, and proteins.

Abstract: The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.

Abstract: A method for the repair of a unit, by specific diagnosis of the undesired state, and its appropriate repair, using said specific diagnosis as a means to repair in an appropriate way said unit. The diagnosis and repair processes may involve chemical, physical, or mechanical means. The units being diagnosed and repaired include live matter (e.g. human beings, animals, plants) as well as non-live matter (e.g. buildings, electronic equipment, polymer materials).

Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, or two different sheared polynucleotides as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described method.

Abstract: The present invention provides a sequencing library, and the sequencing library has an inserted fragment which is an equidirectional alternating concatemer of a sequence to be tested and a tag sequence. The present invention further provides a method for preparing the sequencing library. The present invention also provides a sequencing method. The sequencing library and sequencing method as provided in the present invention are capable of removing DNA amplification errors and sequencing errors under any sequencing depths, so that mutations of DNA molecules could be ultra-accurately determined. The sequencing library of the present invention is suitable for construction of a sequencing library of trace short DNA fragments and even of single-strand DNAs.

Abstract: Processes, oligonucleotides, and kits for amplifying RNA. In particular, the processes generate and amplify cDNA libraries in which the orientation of the input RNA molecule is preserved in the products. Among the various aspects of the present disclosure is the provision of process for directionally amplifying RNA. The process comprises reverse transcribing at least one RNA molecule in the presence of a plurality of first synthesis primers to generate a plurality of first strands of complementary DNA (cDNA), wherein each of the first synthesis primers comprises a 3? sequence having complementarity to a portion of the RNA molecule, a non-complementary 5? sequence corresponding to one or more amplification primers, and optionally an internal tag sequence comprising a first tag sequence.

Abstract: Methods for measuring a panel of biomarkers in a subject suspected of having breast cancer are provided. The methods include obtaining a biological sample from the subject and determining a measurement for a panel of biomarkers in the biological sample, the panel comprising at least 5 biomarkers selected from the group comprising LPC(18:3), LPC(20:2), LPC(20:1), LPC(20:0), PC(32:1), PC(34:4), PC(38:3), PC(40:5), PC(40:3), PC(44:11), ePC(32:2), ePC(38:3), C19:1 CE, C19:0 CE, and C20:0 CE, wherein the measurement comprises measuring a level of each of the at least 5 biomarkers.

Abstract: The invention generally relates to methods of performing a capture reaction. In certain embodiments, the method involves obtaining a nucleic acid, fragmenting the nucleic acid, and capturing a target sequence on the nucleic acid fragment using a capture moiety, such as a molecular inversion probe.

Abstract: The present invention relates to improved yeast transformation of yeast cells and yeast cell libraries transformed thereby. More specifically, the present invention relates to the transformation of yeast by electroporation.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Disclosed herein include systems, methods, compositions, and kits for sample identification. A sample indexing composition can comprise, for example, a protein binding reagent associated with a sample indexing oligonucleotide. Different sample indexing compositions can include sample indexing oligonucleotides with different sequences. Sample origin of cells can be identified based on the sequences of the sample indexing oligonucleotides. Sample indexing oligonucleotides can be barcoded using barcoded and lengthened using daisy-chaining primers.

Abstract: Disclosed herein are systems and methods for detecting Chemical Species, Biomolecules and Biotargets (Analytes) using receptor functionalized metal nanoparticles and Dynamic Light Scattering.

Abstract: A method of in vivo mutagenesis of a preselected target region (PTR) of an intracellular DNA within a cell culture, which PTR comprises at least one sequence of interest (SOI) which is at least 60 nucleobases long, the method comprising: a) providing a pool of partially overlapping single stranded DNA (ssDNA) oligonucleotides which upon alignment form a continuous sequence that is complementary to the SOI, wherein the pool contains a diversity of mutagenizing oligonucleotides covering nucleobase mismatches at every position of said SOI and combination of said nucleobase mismatches, wherein each mutagenizing oligonucleotide is hybridizing with the PTR and comprises at least one mismatching nucleobase up to 20% mismatching nucleobases, compared to the SOI; b) integrating the pool into said intracellular DNA by homologous recombination and inducing in vivo mutagenesis of the intracellular DNA through hybridizing the oligonucleotides to the PTR, thereby producing a cell library comprising a repertoire of variant

Abstract: Replicable libraries having discrete members in defined locations for screening for antigens to a pathogenic organism are provided. Also provided are methods for using such libraries as well as a specific antigen, CT788, which induces T-cell activation during a Chlamydia infection.

Abstract: An in vitro method for the identification and quantification of glycated human serum albumin to assess the extent of diabetic complications in diseased individuals. Further, a diagnostic kit for identifying the extent of diabetes in a diseased individual by estimating glycated serum albumin levels in such individuals.

Abstract: Methods for the identification of agents the bind to exo-sites of proteins are provided. Agents identified by the methods described herein and pharmaceutical compositions comprising the identified agents are also provided. Methods of using an identified agent for the treatment or prevention of a disease, disorder, or condition are also provided, including methods of treating or preventing a disease associated with reduced, elevated, or ectopic expression or aberrant activity of a protein comprising an exo-site.

Abstract: The present disclosure relates to the field of G protein coupled receptor (GPCR) structural biology and signaling. In particular, the present disclosure relates to binding domains directed against and/or specifically binding to GPCR:G protein complexes. Also provided are nucleic acid sequences encoding such binding domains and cells expressing or capable of expressing such binding domains. The binding domains of the present disclosure can be used as universal tools for the structural and functional characterization of G-protein coupled receptors in complex with downstream heterotrimeric G proteins and bound to various natural or synthetic ligands, for investigating the dynamic features of G protein activation, as well as for screening and drug discovery efforts that make use of GPCR:G protein complexes.

Abstract: Provided herein are affinity reagents having affinity for particular target, each reagent having a unique DNA barcode, and methods for using the same to measure the abundance of targets in a sample. In particular, methods are provided in which unique barcodes linked to affinity reagents are contacted to a sample to bind antigens if present in said sample. In cases in which the affinity reagents are antibodies and the targets are antigens, antibodies that are bound to their target antigens can be separated from unbound antibodies and the DNA barcode associated with the affinity reagent is amplified, such as with a PCR reaction. In some cases, amplified barcode DNA is subjected to DNA sequencing as a measure of the levels of the target protein in the sample.