188results about "Library member identification" patented technology

The present disclosure relates to methods for high-throughput analysis of proteins and peptides employing a set of engineered binders that recognize terminal amino acid residues of peptide analytes. In particular, disclosed herein is the analysis of occupancy of N-linked glycosylation sites in proteins and peptides. The disclosure finds utility at large-scale profiling of N-linked glycosylation sites, as well as monitoring changes in glycosylation patterns associated with numerous disease conditions.

Provided are antibodies that include amino acid sequences of SEQ ID NOs: 2, 4, and 6-12, or amino acid sequences that are about 95% identical thereto, and fragments thereof. Also provided are scFv peptides that include a VH segment having a first amino acid sequence of amino acids 4-113 of any one of SEQ ID NOs: 2 and 8-12, a VL segment having a second amino acid sequence having amino acids 113-237 of SEQ ID NOs. 2 and 8-12, or both; nucleic acids encoding the same; methods for using the same to detect and / or target conformational states of FN in samples; methods for treating diseases and / or disorders and / or for meliorating at least one symptom of consequence of a disease or disorder associated with abnormal expression of a force-induced conformational state of FN in subjects; and methods for screening for compounds having selective binding activities for conformational states of FN.

This application relates to reagents and methods for analyzing associated nucleic acids. Specifically, reagents and methods are provided for analyzing nucleic acids (e.g., genomic DNA) of circulating particles (i.e., particles derived from blood). The method includes associating at least two target nucleic acid fragments of the circulating particles to produce a group of at least two associated target nucleic acid fragments. In the method, the target nucleic acid fragments can be associated by techniques such as barcoding, partitioning, ligation, and / or individual sequencing. Sequencing of the group of associated fragments provides a group of informationally associated sequence reads corresponding to the sequences of the fragments from a single particle.

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

This disclosure provides a powerful screening platform that combines pre-templated instant partitions with DNA-encoded library (DEL) technologies to identify target small molecule interactions and analyze their intracellular effects in single cell resolution using methods that require minimal sample preparation and affordable sequencing costs. These methods are well suited for rapidly evaluating drug candidates by simultaneously detecting novel target-binding molecules while screening their transcriptional effects with a single affordable, high throughput workflow.

The systems and methods described herein are directed to methods of making spatially barcoded surfaces by a spatially restricted release of unique oligonucleotide barcodes from beads.

The present invention relates to peptides, proteins, nucleic acids, and cells for use in immunotherapeutic methods. Specifically, the present invention relates to the immunotherapy of cancer, particularly hematological tumors such as acute myeloid leukemia (AML). Furthermore, the present invention relates to tumor-associated T cell peptide epitopes that can be used, for example, as active pharmaceutical ingredients in vaccine compositions to stimulate anti-tumor immune responses or that can stimulate ex vivo T cells for transfer into patients. Peptides bound to major histocompatibility complex (MHC) molecules, and even the peptides themselves, may be targets for antibodies, soluble T cell receptors, and other binding molecules.

The present disclosure provides methods and systems for nucleic acid processing. A method for preparing a sequencing set may include providing a template nucleic acid and amplifying the template nucleic acid to provide a complementary nucleic acid. Next, the complementary nucleic acid may be fragmented and barcoded to produce a first set of barcoded fragments comprising a plurality of first barcoded fragments. Next, the plurality of first barcoded fragments may be fragmented to yield a second set of barcoded fragments comprising a plurality of second barcoded fragments.

The present disclosure provides methods for non-invasive prenatal screening (NIPS) of fetal aneuploidies. The present methods are based on analyzing cell-free fetal DNA (cff DNA) found in a pregnant woman's circulation through the next generation sequencing (NGS) technology. Particularly, the present methods analyze the relative abundance of different fetal genomic fragments present in the maternal sample, where the fragments can be aligned to particular chromosomal locations of the fetal genome. The relative abundance information is indicative as to whether a particular chromosome is overrepresented or underrepresented in a fetal genome as compared to normal individuals, and thus can be used to detect fetal aneuploidy. Additionally, methods for increasing the positive predictive values (PPV) of NIPS by excluding false-positive detections are also provided.

The present disclosure relates to methods and kits for analyzing a macromolecule. In some embodiments, the present disclosure relates to macromolecule analysis methods which employ barcoding and nucleic acid encoding of molecular recognition events. Also provided herein is a method and related kits for transferring information using a plurality of enzymes, including for performing a ligation, extension, and cleavage reaction with nucleic acid molecules associated with the macromolecule for analysis. In some embodiments, the macromolecule for analysis comprises a peptide, a polypeptide, or a protein.

Micron scale biogeography is a major driver of physiology and ecology of complex microbial biofilm communities, which remains elusive largely due to the lack of tools for spatially resolved phylogenetic mapping. This disclosure provides methods, computer-readable storage devices and kits that allow highly multiplexed and spatially resolved imaging of microbial community spatial organization. The disclosure provides a highly-multiplexed approach to resolve the spatial structure of complex microbial community at high taxonomic resolution.

The present disclosure provides methods, compositions, and systems for evolving virus-like particles (VLPs) having one or more desired properties such as increased production levels, increased cargo packaging efficiency, and / or increased transduction of particular target cell types of interest. The present disclosure also provides libraries for use in such methods, and methods for producing the libraries. Group specific antigen (gag) proteins comprising nucleocapsid protein variants evolved using the methods described herein are also provided herein. The present disclosure also provides VLPs comprising such gag proteins comprising nucleocapsid protein variants. Polynucleotides, vectors, cells, and kits useful for performing the methods described herein are also provided.

The present disclosure relates, in general, to methods for improving preparation of a spatial transcriptomics RNA, library, for example a mRNA library, by improving capture of RNA transcript information from a tissue sample in situ. The spatial transcriptomics library from a tissue sample is useful to determine a genetic profile and help diagnose a person who has or is at risk of having a disease, such as cancer, genetic disease, autoimmune disease, and other indications, and improve treatment of the subject.

This disclosure relates to reversible affinity selection methods useful for the isolation and enrichment of covalent peptide inhibitors directly from large synthetic peptide libraries. Also disclosed herein are synthetic peptides for targeting HPV16 E6 and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 protein.

The present application provides a nucleic acid array for detecting spatial information of nucleic acids in a sample, a method for detecting spatial information of nucleic acids in a sample on the basis of the array, and a method for producing the nucleic acid array.

Methods for controlling non-systematic error in an amplification-based next generation sequencing (NGS) library preparation are described, which method includes using an internal amplification control (IAC) sharing identical priming sites to a native nucleic acid target template of interest in a NGS library preparation.

A machine-readable medium and methods of reading and writing same are disclosed. The machine-readable medium comprises a substrate having an array of addressable locations thereon, each addressable location adapted to be physically associated with a collection of non-polymeric molecules. The molecules in each collection are selected from a set of unambiguously identifiable molecules, each molecule uniquely associated with a predetermined position in a numerical value, wherein the presence of the molecule in the collection indicates a predetermined digit at the associated position and the absence of said molecule in the collection indicates a zero at said associated position.

Methods and compositions are provided to identify oligonucleotides that bind targets of interest. The targets include tissues, cells, circulating biomarkers such as microvesicles, including those derived from various diseases. The oligonucleotides can be used in diagnostic and therapeutic applications.

The technology described herein is directed to compositions and methods for delivery of nucleic acids to cells of interest, e.g., in vivo. Methods are described for the identification of viral envelope sequences that mediate infection or transduction of a target cell type using virus-like particles in a high-throughput manner. The methods and compositions described herein permit the delivery of, e.g., RNA encoding therapeutic polypeptides and / or gene editing machinery to cells of interest. Such delivery can be in a manner that limits, avoids or circumvents accumulation in or clearance of the delivery vehicles by the liver.

The present application provides a method of producing a “liquid” array of ligand (such as glycan) modified bacteriophage where the ligand modification is encoded genetically within the bacteriophage genome. This method will allow for the determination of the ligand binding profile of biomacromolecules and cells. Furthermore the method allows the elucidation of ligand-protein interactions where ligand binding is co-operative and synergistic.

The present invention features a number of methods for identifying one or more compounds that bind to a biological target. The methods include synthesizing a library of compounds, wherein the compounds contain a functional moiety having one or more diversity positions. The functional moiety of the compounds is operatively linked to an initiator oligonucleotide that identifies the structure of the functional moiety.

Provided herein are systems and methods for screening desirable biological variants using a high-throughput integrated system. The integrated system may be configured to input a plurality of parameters from functional studies of biological variants under applied conditions, in conjunction with integrated libraries of biological variants, and filter the inputs to produce desirable biological variants based on an input performance requirement. The system may output optimized strains, molecules, or novel molecules expected to have a desirable functional characteristic. Accordingly, the methods and systems disclosed herein enable multi-parametric studies of biological diversity and conditional diversity in systems biology.

To provide polypeptides that bind to a transferrin receptor.SOLUTION: Provided herein are polypeptides that bind to a transferrin receptor, methods of producing such polypeptides, and methods of using the polypeptides to target a composition to a transferrin receptor-expressing cell.SELECTED DRAWING: None

Provided herein are methods, systems, compositions, and kits that can determine spatial information between a plurality of analytes in a sample by tagging such analytes with tags, where identities and / or locations of such tags are previously unknown prior to tagging. Each of a plurality of analyte sequences may be tagged with multiple spatial tags, such that each analyte sequence is associated with a set of two or more spatial tags. The sets of spatial tags may be analyzed to generate a map of analyte sequences. The map may comprise information about the respective absolute positions of each of a set of sequences with respect to a reference sequence. The map may comprise information about the respective probability cloud (or likely location) of each of a set of sequences with respect to a reference sequence.

Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.

Methods and compositions for generating sequencing readings by initiating partitions. Unique molecular identifiers and bead-specific barcodes can be introduced into targeted nucleic acid fragments, and combinations of bead-specific barcodes, UMIs, and fragments can be used to identify when multiple bead-specific barcodes originate from the same partition, thereby improving deconvolution of partition-based sequence analysis.