Abstract: The present invention is directed to a method for treating cancer in a subject determined as having the presence of a G600>A substitution, a C601>T substitution, or both, in the B cell lymphoma 2 (BCL2) gene of a cell.

Abstract: Methods of determining a type of cancer in a subject or estimating survival time after diagnosis of a subject comprising employing a machine learning model to evaluate mutations that are not exonic non-synonymous mutations are provided. Methods comprising training a machine learning model are also provided.

Abstract: Methods of storing information in a living organism are provided. Systems and computer program products for performing the methods are also provided.

Abstract: Computerized methods for engineering a nucleic acid molecule comprising a coding region optimized for expression in a first set of organisms and deoptimized for expression in a second set of organisms are provided.

Abstract: A system and method of whole-cell process simulations may include: using at least one first hardware module, to produce a first predicted value, representing an expected behavior of a plurality of resource entities in a simulated biological cell; using at least one second hardware module, to produce a second predicted value, representing an interaction of a plurality of client entities with at least one of the plurality of resource entities in the simulated biological cell; using at least one third hardware module, to produce a third predicted value, representing an arbitration of interactions between the plurality of resource entities and the plurality of client entities in the simulated biological cell; and producing a simulated value of a product of a natural process in the simulated biological cell, based on said first, second and third predicted values.

Abstract: Nucleic acid molecules comprising a coding sequence with at least one codon substituted to a synonymous codon, a modified form of a virus comprising the nucleic acid molecules of the invention, and methods for producing these nucleic acid molecules, and viruses, are provided.

Abstract: Attenuated viruses and methods of designing them are disclosed. In one embodiment, there is disclosed an attenuated form of a virulent virus comprising an RNA encoding a viral protein or a nucleic acid sequence transcribable to said RNA, wherein the folding energy or structure of the RNA is changed at positions of evolutionarily conserved RNA structures with respect to that of said RNA encoding said viral protein in the virulent virus so as to bring about attenuation of the virus.

Abstract: Methods of designing a polynucleotide sequence for expressing a polypeptide-of-interest in a cell are provided. Also provided are artificial transcript sequences generated according to the present teachings. Further provided are methods of estimating the adaptiveness of a transcript sequence encoding a polypeptide-of-interest to a gene expression machinery in a cell.

Abstract: Nucleic acid molecule comprising a coding sequence and a region of increased folding energy upstream of a stop codon are provided. Expression vectors and cells comprising the nucleic acid molecule are also provided. Methods for optimizing a coding sequence comprising increasing folding energy in a region upstream of the stop codon are also provided.

Abstract: The present invention is directed to a chimeric polypeptide including a polypeptide of interest N-terminal to an essential protein of a target cell. Further provided is a polynucleotide encoding the chimeric polypeptide, a method of producing thereof, and a method for producing a protein of interest. The chimeric polypeptide of the invention improves the genetic stability of the polypeptide of interest ensuring its expression over time.

Abstract: Modified genomes of an organism comprising at least one coding sequence comprising at least one mutation, wherein the mutation generates an underrepresented sequence that is underrepresented in the unmodified genome of the organism are provided. Organism and cells comprising the modified genomes of the invention, pharmaceutical compositions comprising the organisms and cells of the invention, as well as methods of making the modified genomes are also provided.

Abstract: Methods of designing a polynucleotide sequence for expressing a polypeptide-of-interest in a cell are provided. Also provided are artificial transcript sequences generated according to the present teachings. Further provided are methods of estimating the adaptiveness of a transcript sequence encoding a polypeptide-of-interest to a gene expression machinery in a cell.

Abstract: Nucleic acid molecule and vectors comprising regions of high or low folding energy are provided. Methods of producing coding sequences optimized for protein expression comprising introducing a mutation that increases or decreased folding energy are also provided.

Abstract: Nucleic acid molecules comprising a mutation that mutation modulates the interaction strength of the nucleic acid molecule to a 16S ribosomal RNA are provided. Methods of improving the translation process of a nucleic acid molecule and producing a nucleic acid molecule optimized for translation, as well as cells comprising the nucleic acid molecules are also provided.

Abstract: Genetically modified cells with at least one codon substituted to a synonymous codon, and with modified replicative fitness as compared to the unmodified cell, wherein a slower translating synonymous codon increases replicative fitness and a faster translating codon decreased replicative fitness are provided. Further, vaccine composition comprising those cells as well as methods for modifying replicative fitness of a cell are provided.

Abstract: The present invention is directed to a method for treating cancer in a subject determined as having the presence of a G600>A substitution, a C601>T substitution, or both, in the B cell lymphoma 2 (BCL2) gene of a cell.

Abstract: Genetically modified cells with at least one codon substituted to a synonymous codon, and with modified replicative fitness as compared to the unmodified cell, wherein a slower translating synonymous codon increases replicative fitness and a faster translating codon decreased replicative fitness are provided. Further, vaccine composition comprising those cells as well as methods for modifying replicative fitness of a cell are provided.

Abstract: Attenuated viruses and methods of designing them are disclosed. In one embodiment, there is disclosed an attenuated form of a virulent virus comprising an RNA encoding a viral protein or a nucleic acid sequence transcribable to said RNA, wherein the folding energy or structure of the RNA is changed at positions of evolutionarily conserved RNA structures with respect to that of said RNA encoding said viral protein in the virulent virus so as to bring about attenuation of the virus.

Abstract: Attenuated viruses and methods of designing them are disclosed. In one embodiment, there is disclosed an attenuated form of a virulent virus comprising an RNA encoding a viral protein or a nucleic acid sequence transcribable to said RNA, wherein the folding energy or structure of the RNA is changed at positions of evolutionarily conserved RNA structures with respect to that of said RNA encoding said viral protein in the virulent virus so as to bring about attenuation of the virus.

Abstract: Nucleic acid molecules comprising a coding sequence with at least one codon substituted to a synonymous codon, a modified form of a virus comprising the nucleic acid molecules of the invention, and methods for producing these nucleic acid molecules, and viruses, are provided.