Abstract: Methods of treating a disease by leveraging positive and negative correlations between tRNA-derived fragments (tRF) and messenger RNA (mRNA) wherein said correlations can be used to establish a level of granularity that is specific to a disease of interest wherein said disease-specific positive and negative correlations can allow a level of therapeutic intervention that will be unprecedented because it will have been informed by three dimensions: at least one mRNA of interest; at least one tRF that are positively/negatively correlated with it; and, the identity of the disease in which one wishes to modulate the abundance of the at least one mRNA of interest.

Abstract: The present invention includes a method for analyzing RNA fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of rRNA fragments. The invention also includes diagnosing, identifying or monitoring a disease or condition, and a method for identifying rRNA fragments. The invention also includes diagnosing, identifying or monitoring a glaucoma in a subject in need thereof by characterizing the identity of rRNA or tRNA fragments.

Abstract: The present invention includes a method for analyzing RNA fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of rRNA fragments. The invention also includes diagnosing, identifying or monitoring a disease or condition, and a method for identifying rRNA fragments. The invention also includes diagnosing, identifying or monitoring a glaucoma in a subject in need thereof by characterizing the identity of rRNA or tRNA fragments.

Abstract: Disclosed herein are novel compositions, methods, and systems for determining whether a subject has, or is at risk of developing, or is at a given stage of a condition afflicting a tissue of interest, or determining the tissue or cell provenance of a biological sample, based on expression level of one or more of the novel miRNA and isomiR sequences disclosed herein. The compositions, methods, and systems described herein can be used to diagnose a disease or disorder, or prognose a given stage and/or progression of the disease or disorder, or determine the identity of the tissue or cell in a sample. In some embodiments, the compositions, methods, and systems described herein can be used to develop a treatment for the disease or disorder. For example, in some embodiments, the novel miRNAs can be used as therapeutics for treatment of a disease or disorder.

Abstract: The present invention includes a method for analyzing tRNAHisGTG fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat and/or prevent a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of tRNAHisGTG fragments. The invention further includes diagnosing, identifying or monitoring a disease or condition, a panel of engineered oligonucleotides, a kit for a high-throughput assay, and a method and system for identifying tRNAHisGTG fragments.

Abstract: Disclosed herein are novel compositions, methods, and systems for determining whether a subject has, or is at risk of developing, or is at a given stage of a condition afflicting a tissue of interest, or determining the tissue or cell provenance of a biological sample, based on expression level of one or more of the novel miRNA and isomiR sequences disclosed herein. The compositions, methods, and systems described herein can be used to diagnose a disease or disorder, or prognose a given stage and/or progression of the disease or disorder, or determine the identity of the tissue or cell in a sample. In some embodiments, the compositions, methods, and systems described herein can be used to develop a treatment for the disease or disorder. For example, in some embodiments, the novel miRNAs can be used as therapeutics for treatment of a disease or disorder.

Abstract: The present invention includes a method for analyzing tRNA-derived fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat a disease or condition, disease recurrence, or disease progression comprising characterizing the identity of tRNA fragments. The invention also includes diagnosing, identifying or monitoring a disease or condition, and a method for identifying tRNA fragments. The invention also includes diagnosing, identifying or monitoring Parkinson's disease in a subject in need thereof by characterizing the identity of tRNA fragments.

Abstract: In various aspects and embodiments the invention provides a method of detecting SARS-CoV-2 in a sample obtained from a subject, the method comprising contacting the sample with a with a composition comprising a plurality of PCR primers targeting at least one sequence selected from the group consisting of SEQ ID NOS: 1-559, thereby forming a PCR mixture; conducting PCR amplification of the PCR mixture and detection of the at least one sequence selected from the group consisting of SEQ ID NOS: 1-559; wherein an elevated level of the at least one sequence selected from the group consisting of SEQ ID NOS: 1-559 indicates the presence of SARS-CoV-2 in the sample.

Abstract: The present disclosure provides a method for assessing whether a uveal melanoma (UVM) patient has, or is at risk of developing a condition, the method comprising measuring the abundance of at least two isomiRs, and/or at least one tRNA derived fragment (tRF), in a biological sample obtained from the patient, and computing the difference in abundance of the at least two isomiRs and at least one tRF as an indication that the subject either has, or is at risk of developing, or is at a given stage of the condition.

Abstract: The present invention includes a method for analyzing tRNAHisGTG fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat and/or prevent a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of tRNAHisGTG fragments. The invention further includes diagnosing, identifying or monitoring a disease or condition, a panel of engineered oligonucleotides, a kit for a high-throughput assay, and a method and system for identifying tRNAHisGTG fragments.

Abstract: The present invention includes a method for analyzing RNA fragments. In one aspect, the present invention includes a method of identifying a subject in need of therapeutic intervention to treat a disease or condition, disease recurrence, or disease progression comprises characterizing the identity of rRNA fragments. The invention also includes diagnosing, identifying or monitoring a disease or condition, and a method for identifying rRNA fragments. The invention also includes diagnosing, identifying or monitoring a glaucoma in a subject in need thereof by characterizing the identity of rRNA or tRNA fragments.

Abstract: Methods of treating a disease by leveraging positive and negative correlations between tRNA-derived fragments (tRF) and messenger RNA (mRNA) wherein said correlations can be used to establish a level of granularity that is specific to a disease of interest wherein said disease-specific positive and negative correlations can allow a level of therapeutic intervention that will be unprecedented because it will have been informed by three dimensions: at least one mRNA of interest; at least one tRF that are positively/negatively correlated with it; and, the identity of the disease in which one wishes to modulate the abundance of the at least one mRNA of interest.

Abstract: A method of identifying a subject in need of therapeutic intervention to treat a disease or condi-tion or disease recurrence or disease progression comprising, isolating isomiRs or miRNAs from a sample obtained from the subject; and characterizing the isomiRs or miRNAs and their presence or absence in the sample to identify a signature, wherein when the signature is indicative of a di-agnosis of the disease then treatment of the subject is recommended.

Abstract: The present invention includes a method for analyzing tRNA fragments. In one aspect, the present invention includes Sa method of identifying a subject in need of therapeutic intervention to treat a disease or disease progression comprises characterizing the identity of tRNA fragments. The invention further includes diagnosing identifying or monitoring a disease or condition, a panel of engineered oligonucleotides, a kit for a high-throughput assay, and a method and system for identifying tRNA fragments.

Abstract: Disclosed herein are novel compositions, methods, and systems for determining whether a subject has, or is at risk of developing, or is at a given stage of a condition afflicting a tissue of interest, or determining the tissue or cell provenance of a biological sample, based on expression level of one or more of the novel miRNA and isomiR sequences disclosed herein. The compositions, methods, and systems described herein can be used to diagnose a disease or disorder, or prognose a given stage and/or progression of the disease or disorder, or determine the identity of the tissue or cell in a sample. In some embodiments, the compositions, methods, and systems described herein can be used to develop a treatment for the disease or disorder. For example, in some embodiments, the novel miRNAs can be used as therapeutics for treatment of a disease or disorder.

Abstract: Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 3,197 and one or more corresponding mature sequences having SEQ_ID NO: 3,198 through SEQ_ID NO: 6,565 is provided. Techniques are also provided for regulating gene expression.

Abstract: Sequences of ribonucleic acid interference molecules are provided. For example, in one aspect, at least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ_ID NO: 1 through SEQ_ID NO: 11,928 and one or more corresponding mature sequences having SEQ_ID NO: 11,929 through SEQ_ID NO: 24,555 is provided. Techniques are also provided for regulating gene expression.

Abstract: Disclosed herein are novel methods, assays and systems for determining a given state of a cell or a tissue by detecting the presence or absence of a short RNA molecule originating from (a) at least one or more exons of at least one or more protein-coding genes, or from (b) at least one or more segments of at least one or more non-coding transcripts, or from (c) both (a) and (b), in a biological sample from a subject. In some embodiments, the methods, assays and systems described herein can be used to identify an origin and/or a type of a cell or tissue, and/or distinguish a cell or tissue from another cell or tissue. In some embodiments, the methods, assays and systems described herein can also be used to diagnose a disease or disorder, or prognose a given stage and/or progression of the disease or disorder in a subject.

Abstract: A method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA will bind thereto is provided. For example, in one aspect of the invention, a method for determining whether a nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto is comprised of the following steps. One or more patterns are generated by processing a collection of known mature microRNA sequences. The reverse complement of each generated patter is then computed. One or more attributes are then assigned to the reverse complement of the one or more generated patterns. The one or more patterns that correspond to a reverse complement having one or more assigned attributes that satisfy at least one criterion are thereafter subselected. Each subselected pattern is then used to analyze the nucleotide sequence, such that a determination is made whether the nucleotide sequence contains a microRNA binding site and which microRNA sequence will bind thereto.

Abstract: Ribonucleic acid interference molecules are provided. In one aspect of the invention, a method for regulating gene expression comprises the following step. At least one nucleic acid molecule comprising at least one of one or more precursor sequences having SEQ ID NO: 1 through SEQ ID NO: 103,948, each one of the precursor sequences containing one or more mature sequences having SEQ ID NO: 103,949 through SEQ ID NO: 230,447, is used to regulate the expression of one or more genes.