Abstract: The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Abstract: A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.

Abstract: Disclosed herein is a method of utilizing an enzyme in a nucleic acid manipulation process, the method comprising: a) transforming a microorganism with a non-native enzyme; b) inducing expression of the enzyme in the microorganism, thereby producing the non-native enzyme; c) adding the microorganism of step b) directly to a non-naturally occurring nucleic acid manipulation process, wherein the non-native enzyme is not purified from the microorganism prior to addition to the nucleic acid manipulation process; and carrying out the nucleic acid manipulation process using the enzyme. Importantly, this method can be carried out without the need to purify the enzyme from the cell producing it before it is used in the nucleic acid manipulation method. Also disclosed herein is a kit for carrying out a nucleic acid manipulation process, the kit comprising a) a microorganism expressing a non-native enzyme; b) nucleic acids of interest; and c) reagents for use in the nucleic acid manipulation process.

Abstract: Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.

Abstract: Disclosed herein is a method of utilizing an enzyme in a nucleic acid manipulation process, the method comprising: a) transforming a microorganism with a non-native enzyme; b) inducing expression of the enzyme in the microorganism, thereby producing the non-native enzyme; c) adding the microorganism of step b) directly to a non-naturally occurring nucleic acid manipulation process, wherein the non-native enzyme is not purified from the microorganism prior to addition to the nucleic acid manipulation process; and carrying out the nucleic acid manipulation process using the enzyme. Importantly, this method can be carried out without the need to purify the enzyme from the cell producing it before it is used in the nucleic acid manipulation method. Also disclosed herein is a kit for carrying out a nucleic acid manipulation process, the kit comprising a) a microorganism expressing a non-native enzyme; b) nucleic acids of interest; and c) reagents for use in the nucleic acid manipulation process.

Abstract: A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.

Abstract: Disclosed are compositions and methods for nucleic acid amplification and detection. Specifically, disclosed herein are compositions and methods that allow for amplification of nucleic acids at a wide variety of temperatures. This includes a polymerase which is thermostable at high temperatures, and a method of amplification that can be conducted at relatively low temperatures.

Abstract: Disclosed are compositions and methods for nucleic acid amplification and detection. Specifically, disclosed herein are compositions and methods that allow for amplification of nucleic acids at a wide variety of temperatures. This includes a polymerase which is thermostable at high temperatures, and a method of amplification that can be conducted at relatively low temperatures.

Abstract: A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.

Abstract: The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Abstract: Disclosed herein is a method of utilizing an enzyme in a nucleic acid manipulation process, the method comprising: a) transforming a microorganism with a non-native enzyme; b) inducing expression of the enzyme in the microorganism, thereby producing the non-native enzyme; c) adding the microorganism of step b) directly to a non-naturally occurring nucleic acid manipulation process, wherein the non-native enzyme is not purified from the microorganism prior to addition to the nucleic acid manipulation process; and carrying out the nucleic acid manipulation process using the enzyme. Importantly, this method can be carried out without the need to purify the enzyme from the cell producing it before it is used in the nucleic acid manipulation method. Also disclosed herein is a kit for carrying out a nucleic acid manipulation process, the kit comprising a) a microorganism expressing a non-native enzyme; b) nucleic acids of interest; and c) reagents for use in the nucleic acid manipulation process.

Abstract: Disclosed are compositions and methods for nucleic acid amplification and detection. Specifically, disclosed herein are compositions and methods that allow for amplification of nucleic acids at a wide variety of temperatures. This includes a polymerase which is thermostable at high temperatures, and a method of amplification that can be conducted at relatively low temperatures.

Abstract: Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.

Abstract: Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.