The present disclosure discloses a DNA matrix processing method based on a combined restriction digestion mechanism, including the following steps: constructing a single auxiliary strand-mediated combined restriction digestion mechanism; introducing an auxiliary strand based on the single auxiliary strand-mediated combined restriction digestion mechanism, to obtain a dual auxiliary strands-mediated combined restriction digestion mechanism; and constructing DNA matrix processing and a weighted sum of Boolean matrix multiplication with the dual auxiliary strands-mediated combined restriction digestion mechanism; in which the two auxiliary strands are directly used as elements involved in the matrix processing, and the 2N auxiliary strands are combined into N.sup.2 four-pronged restriction digestion structures in the presence of E6 type DNAzymes to cleave N.sup.2 substrate strands. Meanwhile, due to high-efficiency catalysis and specific recognition, the E6 type DNAzymes make the matrix processing rapid and accurate.

The disclosure provides genetically engineered C1-fixing microorganisms capable of producing nanobodies. Additionally, the disclosure provides engineered microorganisms comprising one or more disrupted genes to strategically divert carbon flux away from nonessential or undesirable products towards products and/or co-products of interest. The disclosure enables co-production of useful chemicals from gaseous substrates.

The disclosure provides genetically engineered C1-fixing microorganisms capable of producing nanobodies. Additionally, the disclosure provides engineered microorganisms comprising one or more disrupted genes to strategically divert carbon flux away from nonessential or undesirable products towards products and/or co-products of interest. The disclosure enables co-production of useful chemicals from gaseous substrates.

The techniques and/or systems described herein are directed to improvements in genomic prediction using homomorphic encryption. For example, a genomic model can be generated by a prediction service provider to predict a risk of a disease or a presence of genetic traits. Genomic data corresponding to a genetic profile of an individual can be batch encoded into a plurality of polynomials, homomorphically encrypted, and provided to a service provider for evaluation. The genomic model can be batch encoded as well, and the genetic prediction may be determined by evaluating a dot product of the genomic model data the genomic data. A genomic prediction result value can be provided to a computing device associated with a user for subsequent decrypting and decoding. Homomorphic encoding and encryption can be used such that the genomic data may be applied to the prediction model and a result can be obtained without revealing any information about the model, the genomic data, or any genomic prediction.

An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.

An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.

The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient’s tumor mutation burden.

The invention provides oncogenomic methods for detecting tumors by identifying circulating tumor DNA. A patient-specific reference directed acyclic graph (DAG) represents known human genomic sequences and non-tumor DNA from the patient as well as known tumor-associated mutations. Sequence reads from cell-free plasma DNA from the patient are mapped to the patient-specific genomic reference graph. Any of the known tumor-associated mutations found in the reads and any de novo mutations found in the reads are reported as the patient’s tumor mutation burden.

Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.

Disclosed herein are designed heterodimer proteins, monomeric polypeptides capable of forming heterodimer proteins, protein scaffolds including such polypeptides, and methods for using the heterodimer proteins and subunit polypeptides for designing logic gates.