Abstract: This invention relates to microbiome markers for healthy aging. There is provided, inter alia, a method of predicting or determining healthy aging in an individual, the method comprising: (a) determining the presence or an amount of at least one microorganism in a sample representing the individual's gut microbiome, wherein the at least one microorganism is selected from Table 1A, wherein an enrichment of said microorganisms is indicative of healthy aging; and/or (b) determining the presence or an amount of at least one microorganism in a sample representing the individual's gut microbiome, wherein the at least one microorganism is selected from Table 1 B, wherein a depletion of said microorganisms is indicative of healthy aging.

Abstract: Systems and methods for outbreak analysis by performing taxonomic classification of the first LRS data to assign one or more taxonomic identifiers to each record in the first LRS data; identifying a plurality of species-specific candidate genomes from a reference genome database based on the assigned taxonomic identifiers; aligning the first LRS data with each of the plurality of species-specific candidate genomes to determine a first species identity of a microorganism species present in the sample; identifying a first nearest strain of the identified microorganism species present in the first sample by aligning the first LRS data with a plurality of strain-specific candidate genome dataset.

Abstract: Clinical decision support systems and methods for microorganism identification in a sample by determining long-read nucleic acid fragment sequence data (LRS data) originating from a plurality of species in the sample; performing taxonomic classification of the LRS data; determining an abundance levels of a plurality of reference genomes based on taxonomic identifiers of the LRS data; aligning the LRS data with a subset of the reference genomes; performing coverage analysis to determine an identity of one or more microorganism present in the sample based on the coverage analysis.

Abstract: The invention relates to a method for analysing ribonucleic acid (RNA) interactions comprising: a) cross-linking base-paired nucleotides of at least one RNA molecule and/or at least one pair of RNA molecules using a tagged, reversible cross-linking agent (preferably tagged-psoralen) under ultraviolet irradiation; b) fragmenting the said cross-linked RNA molecule(s); c) using said tag to extract said cross-linked RNA fragment(s); d) ligating the said cross-linked RNA fragment(s) to produce cross-linked ligated RNA chimera(s); e) reversing the cross-linking of the said agent to the said RNA molecule(s); f) preparing a sequence library by sequencing the ligated RNA chimera molecule(s) or pair(s); and g) analysing the sequence library to determine RNA interactions. Also disclosed is a method of studying a subject by analysing RNA interactions and attributing them to a clinical picture, or a drug discovery method by attributing an efficacy score to the drug based upon determined RNA interactions.

Abstract: The invention relates to using a class of microbial species that can contribute to robust recovery of the microbiome after antibiotic usage. In particular, the inventors of this invention have identified 21 bacterial species exhibiting robust association with ecological recovery post antibiotic therapy.

Abstract: The invention relates to a method for analysing ribonucleic acid (RNA) interactions comprising: a) cross-linking base-paired nucleotides of at least one RNA molecule and/or at least one pair of RNA molecules using a tagged, reversible cross-linking agent (preferably tagged-psoralen) under ultraviolet irradiation; b) fragmenting the said cross-linked RNA molecule(s); c) using said tag to extract said cross-linked RNA fragment(s); d) ligating the said cross-linked RNA fragment(s) to produce cross-linked ligated RNA chimera(s); e) reversing the cross-linking of the said agent to the said RNA molecule(s); f) preparing a sequence library by sequencing the ligated RNA chimera molecule(s) or pair(s); and g) analysing the sequence library to determine RNA interactions. Also disclosed is a method of studying a subject by analysing RNA interactions and attributing them to a clinical picture, or a drug discovery method by attributing an efficacy score to the drug based upon determined RNA interactions.

Abstract: Disclosed is a computer-implemented method of determining at least one optimal alignment of at least part of a first map to at least part of a second map or a plurality of second maps, wherein the maps are physical genome maps and/or restriction maps. The method comprises: receiving first map data indicative of a first ordered list of distances between features of the first map, receiving second map data indicative of a second ordered list of distances between features of the second map or second maps; generating, from the second map data, seed data indicative of a plurality of seeds, each seed comprising at least one of the distances in the second ordered list, wherein the features are restriction sites and distances are fragment sizes.