Abstract: Disclosed herein are methods of detecting a target viral nucleic acid sequence, determining the localization of the target viral nucleic acid sequence, and/or quantifying the number of target viral nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH or viral Nano-FISH.

Abstract: The present disclosure provides methods and compositions for image based analysis and quantification of a protein load from protein (e.g., p53BP1) accumulation, induced by a cellular perturbation, such as administration of a genome editing tool comprising a DNA binding domain and a nuclease domain, a gene repressor, or a gene activator.

Abstract: Provided herein are polypeptides, compositions, and methods for use thereof for genetic and epigenomic engineering, including, genome editing and gene regulation. These polypeptides and compositions include nucleic acid binding domains that bind to a target nucleic acid of interest. The nucleic acid binding domains include repeat units derived from repeat units identified in proteins from animal pathogens such as bacterium of the order Legionellales and the species Legionella and Francisella.

Abstract: Methods and apparatus to test and screen compounds in a multiplexed manner, using a mixture of genetically or functionally heterogeneous cells in common conditions.

Abstract: Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.

Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.

Abstract: The present disclosure is in the field of genome engineering, particularly targeted modification of the genome of a hematopoietic cell.

Abstract: Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.

Abstract: Disclosed herein are methods for solubilizing and isolating nuclear proteins from cells.

Abstract: This application provides a system and related methods that determine residue sequences for engineered proteins that facilitate genome engineering, including transcription activator-like effector nucleases. The system may receive an input DNA sequence for a region of a given genome and desired cleavage positions within the region. The system may determine candidate residue sequences for proteins that bind to the region and cleave the region at the desired cleavage positions, such as transcription activator-like effector nucleases (TALENs). The determination may be based on how the proteins may interact with the region and perform other biological functions. A selection can be made from the candidate residue sequences to achieve high accuracy and efficiency in the genome engineering tasks. The system may thus allow development of proteins that incorporate the selected residue sequences to perform the genome engineering tasks.

Abstract: Disclosed herein are methods of detecting a target nucleic acid sequence, determining the localization of the target nucleic acid sequence, and/or quantifying the number of target nucleic acid sequences in a cell. This method may be used on small V target nucleic acid sequences, and may be referred to as Nano-FISH.

Abstract: Disclosed herein are methods of detecting a regulatory element, determining the localization of a regulatory element, and/or measuring the activity of a regulatory element.

Abstract: The present disclosure is in the field of genome engineering, particularly targeted modification of the genome of a hematopoietic cell.

Abstract: The present disclosure is in the field of genome engineering, particularly targeted modification of the genome of a hematopoietic cell.

Abstract: Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.

Abstract: The presently disclosed subject matter provides for expression cassettes that allow for expression of a globin gene or a functional portion thereof, vectors comprising thereof, and cells transduced with such expression cassettes and vectors. The presently disclosed subject matter further provides methods for treating a hemoglobinopathy in a subject comprising administering an effective amount of such transduced cells to the subject.

Abstract: The present disclosure is in the field of genome engineering, particularly targeted modification of the genome of a hematopoietic cell.

Abstract: Described herein are methods and compositions for analyzing regulatory regions within polynucleotides, particularly within genomic DNA. The methods provided herein include cleaving the polynucleotides with a cleaving agent such as DNase1 and using the cleavage patterns for such applications as identifying regulatory states of a cellular or polynucleotide sample; identifying novel regulatory elements; generating maps of binding patterns of regulatory factors along a polynucleotide; generating maps of regulatory networks; and identifying topologic features of a polynucleotide sample, particularly samples of polynucleotides bound to proteins. The methods provided herein may also be used in a myriad of other applications including predicting risks of diseases or disorders, diagnostics, drug screening, and therapeutic development.

Abstract: The present invention provides a method for globally mapping a genome for its protein-binding pattern. A computer system useful for this purpose is also described.