Abstract: The present invention provides RNA-guided endonucleases, which are engineered for expression in eukaryotic cells or embryos, and methods of using the RNA-guided endonuclease for targeted genome modification in eukaryotic cells or embryos. Also provided are fusion proteins, wherein each fusion protein comprises a CRISPR/Cas-like protein or fragment thereof and an effector domain. The effector domain can be a cleavage domain, an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. Also provided are methods for using the fusion proteins to modify a chromosomal sequence or regulate expression of a chromosomal sequence.

Abstract: Computer programs, algorithms, and methods for identifying TALE-activator binding sites, and methods for generation and use of TALE-activators that bind to these sites.

Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.

Abstract: The present invention provides compositions and methods for detecting the expression and/or activation levels of components of signal transduction pathways in tumor cells such as triple-negative metastatic breast tumor cells. Information on the expression and/or activation levels of components of signal transduction pathways derived from use of the present invention can be used for cancer diagnosis, prognosis, and in the design of cancer treatments.

Abstract: Provided are methods, compositions, reagents, kits that are useful for detecting a specific nucleic acid region in genome with high efficiency and high sensitivity.

Abstract: Disclosed herein are methods and compositions for targeted cleavage of a genomic sequence, targeted alteration of a genomic sequence, and targeted recombination between a genomic region and an exogenous polynucleotide homologous to the genomic region. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain and polynucleotides encoding same. Methods for targeted cleavage include introduction of such fusion proteins, or polynucleotides encoding same, into a cell. Methods for targeted recombination additionally include introduction of an exogenous polynucleotide homologous to a genomic region into cells comprising the disclosed fusion proteins.

Abstract: Computer programs, algorithms, and methods for identifying TALE-activator binding sites, and methods for generation and use of TALE-activators that bind to these sites.

Abstract: Disclosed herein are methods and compositions for targeted deletion of double-stranded DNA. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain, and polynucleotides encoding same. Methods for targeted deletion include introduction of such fusion proteins, or polynucleotides encoding same, into a cell such that two targeted cleavage events occur. Subsequent cellular repair mechanisms result in deletion of sequences between the two cleavage sites.

Abstract: The present disclosure, in some aspects, provides compositions, systems and methods for proximity-based detection of target biomolecules of interest.

Abstract: Methods and systems for encoding digital information in nucleic acid (e.g., deoxyribonucleic acid) molecules without base-by-base synthesis, by encoding bit-value information in the presence or absence of unique nucleic acid sequences within a pool, comprising specifying each bit location in a bit-stream with a unique nucleic sequence and specifying the bit value at that location by the presence or absence of the corresponding unique nucleic acid sequence in the pool But, more generally, specifying unique bytes in a bytestream by unique subsets of nucleic acid sequences. Also disclosed are methods for generating unique nucleic acid sequences without base-by-base synthesis using combinatorial genomic strategies (e.g., assembly of multiple nucleic acid sequences or enzymatic-based editing of nucleic acid sequences).

Abstract: Compositions and methods for using nucleosome interacting protein domains to increase accessibility of programmable DNA modification proteins to target chromosomal sequences, thereby increasing efficiency of targeted genome/epigenetic modification in eukaryotic cells.

Abstract: A method includes: (1) applying stimulations to a system, wherein applying the stimulations includes modulating, over time, characteristics of the stimulations; (2) measuring a time-varying response of the system to the stimulations; (3) fitting the time-varying response of the system into a model of the system; and (4) using the model of the system, identifying an optimized combination of characteristics of the stimulations to yield a desired response of the system.

Abstract: A protein reporter system comprising at least one reporter including a response element responsive to the binding of a transcription factor, a secreted enzyme backbone and a recognition region for specific binding of an antibody. Multiplexed assays for binding, assaying and quantifying the activity of transcription factors are also described, in which the assays use protein reporters in sets, libraries or other groupings, as necessary to achieve desired quantification.

Abstract: Methods for diagnosis of sepsis are disclosed. In particular, the invention relates to the use of biomarkers for aiding diagnosis, prognosis, and treatment of sepsis, and to a panel of biomarkers that can be used to distinguish sepsis from noninfectious sources of inflammation, such as caused by traumatic injury, surgery, autoimmune disease, thrombosis, or systemic inflammatory response syndrome (SIRS).

Abstract: The present invention relates to the field of analysis of the three-dimensional structure of the genome, i.e., for genome architecture mapping (GAM). The invention provides a method of determining spatial proximity of a plurality of nucleic acid loci in a compartment such as the cell nucleus, by exploiting their co-segregation amongst fractions of that compartment, identified upon separation of the nucleic acid loci from each other depending on their localization in the compartment to obtain a collection of fractions, e.g., by cryo-sectioning or cryo-milling the compartment; determining the presence or absence of the plurality of loci in the fractions; and determining the co-segregation of the plurality of loci. Co-segregation may then be analysed with statistical methods to determine spatial proximity. The method can be used e.g., for determining physical distance between a plurality of loci; and mapping loci and/or genome architecture, e.g.

Abstract: Unbiased, genomewide and highly sensitive methods for detecting mutations, e.g., off-target mutations, induced by engineered nucleases.

Abstract: In one embodiment, a method of encoding variation data for a population comprises receiving, by a variant encoding engine executing on a processor, information describing genetic variation of a population of individuals. The information comprises a plurality of variable sites within the reference genome of the population and the genotypes of a plurality of individuals in the population with respect to those variable sites. The method further comprises selecting an encoding strategy for the information based on the characteristics of the genetic variation across the population, and encoding the information according to the selected encoding strategy. In certain embodiments, selecting an encoding strategy may comprise determining the variability of a variable site within the population, and encoding information associated with the variable site based on the variability.

Abstract: The present invention relates to a method for determining an uterine receptivity profile in order to increase implantation success in assisted fertilization.

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

Abstract: The present invention relates to a nucleic acid of the general formula (I): GIXmGn, which may be modified by a lipid. The invention relates further to a pharmaceutical composition containing an immune-stimulating agent according to the invention in combination with a pharmaceutically active carrier/vehicle (and, optionally, further auxiliary substances, additives and/or further adjuvants). The present invention can relate to a vaccine, which corresponds to a pharmaceutical composition of the invention, wherein the pharmaceutically active component induces a specific immune response (e.g. an antigen). The present invention can relate to the use of a nucleic acid of the invention or a pharmaceutical composition according to the invention for the treatment of infectious diseases, autoimmune disease, allergies or cancer diseases.