Abstract: The disclosure provides for methods to form compact cross-linked polynucleotide/protein structures that can then be labeled using a barcoded oligonucleotide array in order to reconstruct physical linkage and/or genomic proximity (and phase) of polynucleotide fragments.

Abstract: This application provides a bead with a covalently attached chemical compound and a covalently attached DNA barcode and methods for using such beads. The bead has many substantially identical copies of the chemical compound and many substantially identical copies of the DNA barcode. The compound consists of one or more chemical monomers, where the DNA barcode takes the form of barcode modules, where each module corresponds to and allows identification of a corresponding chemical monomer. The nucleic acid barcode can have a concatenated structure or an orthogonal structure. Provided are method for sequencing the bead-bound nucleic acid barcode, for cleaving the compound from the bead, and for assessing biological activity of the released compound.

Abstract: High-throughput methods for screening large populations of variant proteins are provided. The methods utilize large-scale arrays of microcapillaries, where each microcapillary comprises a solution containing a variant protein, an immobilized target molecule, and a reporter element. Immobilized target molecules may include any molecule of interest, including proteins, nucleic acids, carbohydrates, and other biomolecules. The association of a variant protein with a molecular target is assessed by measuring a signal from the reporter element. The contents of microcapillaries identified in the assays as containing variant proteins of interest can be isolated, and cells expressing the variant proteins of interest can be characterized. Also provided are systems for performing the disclosed screening methods.

Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Abstract: Various approaches for generating read-sets from nucleic acid molecules and segments and phasing are disclosed. Nucleic acids are assembled into complexes using binding moieties and exposed nucleic acid ends are tagged with nucleic acid tags. Read-sets can be generated from tagged nucleic acid molecules and segments. Physical linkage relationships between nucleic acid molecules and segments can be examined using the nucleic acid tags. Various approaches to generating read-sets and phasing are presented.

Abstract: Described are DNA molecules which can be transcribed into an mRNA harbouring novel UTR sequences combining the advantages of being extremely short and at the same time allowing for high translation efficiencies of RNA molecules containing them. Further, described are vectors comprising such a DNA molecule and to host cells comprising such a vector. Moreover, described are corresponding RNA molecules containing such UTRs. Further, described is a pharmaceutical composition comprising the described RNA molecule and optionally a pharmaceutically acceptable carrier as well as to the use of the described UTRs for translating a coding region of an RNA molecule into a polypeptide or a protein encoded by said coding region.

Abstract: Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence ?X?, wherein X is the desired peptide epitope, wherein each of ? and ? comprise an amino acid, using the peptide library to select an affinity reagent.

Abstract: Disclosed herein are methods and compositions for the detection of small RNAs in a sample. The methods and compositions disclosed herein may be used for preparing sequencing libraries of the small RNAs, fragments of RNAs and DNAs.

Abstract: One aspect of the present invention describes materials and methods of quantitatively measuring the density or percent occupancy of DNA binding proteins such as histones, histone variants, histone post translational modifications and transcription factors in chromatin at given DNA loci. One embodiment measures a factor's average quantity at specific gene loci, and controls for a number of pitfalls concerning antibody quality and handling issues. Other embodiments include calibrating and quantifying chromatin immunoprecipitation assays, assessing an affinity reagent specificity, as well as required reagents and their formulation in kits. Another embodiment allows for the diagnosis of a condition or disease by measuring the density of a histone modification at a genomic locus.

Abstract: The present disclosure relates to methods for constructing polynucleotide libraries and/or polynucleotide sequencing. Related kits and devices are also disclosed. The present disclosure also relates to compositions, kits, devices, and methods for conducting genetic and genomic analysis, for example, by polynucleotide sequencing. In particular aspects, provided herein are compositions, kits, and methods for constructing libraries with improved ligation efficiency and conversion rate during sequencing. In certain embodiments, the compositions, kits, and methods herein are useful for analyzing polynucleotide fragments, such as circulating polynucleotide fragments in the body of a subject, including circulating tumor DNA.

Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid using one-sided transposition, sequencing the template library, and capturing the contiguity information.

Abstract: Provided herein are methods for capturing a connected probe and/or a capture handle sequence to a capture domain of a capture probe.

Abstract: Compositions and methods, systems, and kits for detecting and quantifying variations in numbers of molecules, particularly variations in gene dosage, e.g., due to gene duplication, or to variations from the normal euploid complement of chromosomes, e.g., trisomy of one or more chromosomes that are normally found in diploid pairs, without digital sequencing.

Abstract: A method for analyzing macromolecules, including peptides, polypeptides, and proteins, employing nucleic acid encoding is disclosed.

Abstract: The invention relates to a method for screening a library of peptide ligands, said library comprising a plurality of polypeptides covalently linked to a molecular scaffold at two or more amino acid residues, comprising the steps of displaying said library of peptide ligands in a genetic display system, wherein the polypeptide comprises two or more reactive groups which form a covalent linkage to the molecular scaffold, and at least one loop which comprises a sequence of amino acids subtended between two of said reactive groups; exposing the peptide ligands to one or more cells which display one or more target molecules on the cell surface; and screening the peptide ligands for binding against the target, and selecting the ligands which bind to the target.

Abstract: The present invention relates to genomic analysis. In particular, the present invention provides methods and compositions for mapping genomic interactions.

Abstract: An example of an array includes a support, a cross-linked epoxy polyhedral oligomeric silsesquioxane (POSS) resin film on a surface of the support, and a patterned hydrophobic polymer layer on the cross-linked epoxy POSS resin film. The patterned hydrophobic polymer layer defines exposed discrete areas of the cross-linked epoxy POSS resin film, and a polymer coating is attached to the exposed discrete areas. Another example of an array includes a support, a modified epoxy POSS resin film on a surface of the support, and a patterned hydrophobic polymer layer on the modified epoxy POSS resin film. The modified epoxy POSS resin film includes a polymer growth initiation site, and the patterned hydrophobic polymer layer defines exposed discrete areas of the modified epoxy POSS resin film. A polymer brush is attached to the polymer growth initiation site in the exposed discrete areas.

Abstract: The invention provides a method for predicting whether a binding peptide, which binds to a target peptide presented by a Major Histocompatibility Complex (MHC) and is for administration to a subject, has the potential to cross react with another peptide in the subject in vivo. The method comprises the steps of identifying at least one binding motif in the target peptide to which the binding peptide binds; and searching for peptides that are present in the subject that comprise the at least one binding motif and that are not the target peptide. The presence of one or more such peptides indicates that the binding peptide has the potential to cross react in vivo.

Abstract: This disclosure describes methods and compositions for protein and peptide sequencing.