Abstract: Disclosed herein are formulations, substrates, and arrays. In certain embodiments, substrates and arrays comprise a porous layer for synthesis and attachment of polymers or biomolecules. Also disclosed herein are methods for manufacturing and using the formulations, substrates, and arrays, including porous arrays. Also disclosed herein are formulations and methods for one-step coupling, e.g., for synthesis of peptides in an N?C orientation. In some embodiments, disclosed herein are formulations and methods for high efficiency coupling of biomolecules to a substrate.

Abstract: A method is provided for detecting one or more analytes in a sample. The method relies, in part, on the ability of functionalized particles added to the sample to partially or completely inhibit the transmission of electromagnetic radiation into and out of the sample through a detection surface in a reaction vessel containing the sample. In a microarray format, the invention can be used to screen millions, billions or more biological elements, such as an organism, cell, protein, nucleic acid, lipid, saccharide, metabolite, or small molecules. Methods, apparatuses and kits are described.

Abstract: Provided herein are products and processes for the quantitation of mitochondrial nucleic acid in a sample from a subject. In certain aspects are multiplex methods for determining dosage of mitochondrial nucleic acid relative to genomic nucleic acid for a sample from a subject including amplifying sets of mitochondrial polynucleotides and genomic polynucleotides from nucleic acid for a sample under amplification conditions. In certain aspects are multiplex methods for determining dosage of mitochondrial nucleic acid relative to genomic nucleic acid for a sample from a subject including amplifying sets of mitochondrial polynucleotides and amplifying sets of nuclear polynucleotides from nucleic acid for a sample under amplification conditions.

Abstract: Provided herein are encoded split pool libraries useful, inter alia, for forming highly diverse and dense arrays for screening and detection of a variety of molecules.

Abstract: Provided herein are encoded split pool libraries useful, inter alia, for forming highly diverse and dense arrays for screening and detection of a variety of molecules.

Abstract: The present invention is directed to a method of quantifying intracellular metabolite effluxes in permeabilized cancer cells for selecting cancer patients responsive for a cancer treatment, the method comprising the steps of: a) providing a sample of cancer cells taken from a patient; b) permeabilizing said cancer cells; c) incubating said permeabilized cancer cells in a reaction medium for a period of time allowing biological activity of intracellular organelles and accumulation of metabolites produced by said activity into the reaction medium in the presence of a substrate or substrates relating to a metabolite efflux or effluxes of interest, wherein said substrates used are at least glutamine and pyruvate; d) determining the quantity of metabolites relating to said metabolite efflux or effluxes of interest accumulated in the reaction medium during step c); and e) comparing the amounts of metabolites determined in step d) to equal measurements performed on control samples of the same tissue type and assessi

Abstract: Provided herein are method and kits for elucidation of immunological repertoires (comprising functional pairs of immune cell receptors and antigens). In some embodiments, an immune cell receptor and an antigen that it binds to are isolated, and sequence information is obtained about the immune cell receptor and antigen. In some embodiments, an antigen expressed on a first cell and an immune cell receptor expressed on a second cell can form a synapse, mRNAs can be isolated from the resulting doublet of cells, and sequences of the functional immune cell receptor and its antigen can be obtained from the mRNAs.

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: 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: 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: 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: 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: 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: 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