Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: The present disclosure is directed to methods for assessing the severity and progression of a SARS-CoV2 infection in a subject using cell-free DNA (cfDNA). The present disclosure is further directed to methods for assessing tissue damage as a result of SARS-CoV2 infection. In addition, the present disclosure provides methods for treating a SARS-CoV2 infection in a subject. Finally, the disclosure also provides methods for detecting a microbial co-infection of a subject suffering from a SARS-CoV2 infection.

Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.

Abstract: Described herein are methods for rapid, highly multiplexible detection of nucleotides in samples and constructs made to be used in said methods.

Abstract: The present disclosure is directed to novel methods for detecting tissue damage, graft-versus-host disease (GVHD), microbial infections, presence of a tumor, and loss of engraftment in a subject using cell-free DNA (cfDNA) profiling. The methods of the disclosure are in part based on the recognition that damaged tissues, microbes during an infection, tumors, and donor cells (e.g., in a hematopoietic cell transplantation) shed small fragments of cfDNA into blood circulation.

Abstract: The present disclosure provides multiplexed methods, and constructs made to be used in said methods, for characterizing microbes from a biological sample to both rapidly identify the microbe and characterize drug susceptibility or resistance and perform microbial taxa identification and nucleic acid target detection at high multiplexity. The methods can also be used to predict future microbe drug susceptibility or resistance.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Prediction of allograft rejection is provided based on the quantification of transplant-derived circulating cell-free DNA (dd-cfDNA levels) in the absence of a donor genotype. The technology provided herein alleviates some of the barriers to the implementation of Genome Transplant Dynamics (GTD), which will further widen its clinical application.

Abstract: Micron scale biogeography is a major driver of physiology and ecology of complex microbial biofilm communities, which remains elusive largely due to the lack of tools for spatially resolved phylogenetic mapping. This disclosure provides methods, computer-readable storage devices and kits that allow highly multiplexed and spatially resolved imaging of microbial community spatial organization. The disclosure provides a highly-multiplexed approach to resolve the spatial structure of complex microbial community at high taxonomic resolution.

Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: Methods and apparatus in the field of single molecule sensing are described, e.g. for molecular analysis of analytes such as molecular analytes, e.g. nucleic acids, proteins, polypeptides, peptides, lipids and polysaccharides. Molecular spectroscopy on a molecule translocating through a solid-state nanopore is described. Optical spectroscopic signals are enhanced by plasmonic field-confinement and antenna effects and probed in transmission by plasmon-enabled transmission of light through an optical channel that overlaps with the physical channel.

Abstract: In one aspect of the invention, a method or apparatus is described for determining concentration(s) of one or more analytes in a sample using plasmonic excitations. In another aspect, a method relates to designing systems for such concentration determination, wherein metallic nanostructures are used in combination with local electrical detection of such plasmon resonances via a semiconducting photodetector. In certain aspects, the method exploits the coupling of said metallic nanostructure(s) to a semiconducting photodetector, said detector being placed in the “metallic structure's” near field. Surface plasmon excitation can be transduced efficiently into an electrical signal through absorption of light that is evanescently coupled or scattered in a semiconductor volume. This local detection technique allows the construction of sensitive nanoscale bioprobes and arrays thereof.

Abstract: In one aspect of the invention, a method or apparatus is described for determining concentration(s) of one or more analytes in a sample using plasmonic excitations. In another aspect, a method relates to designing systems for such concentration determination, wherein metallic nanostructures are used in combination with local electrical detection of such plasmon resonances via a semiconducting photodetector. In certain aspects, the method exploits the coupling of said metallic nanostructure(s) to a semiconducting photodetector, said detector being placed in the “metallic structure's” near field. Surface plasmon excitation can be transduced efficiently into an electrical signal through absorption of light that is evanescently coupled or scattered in a semiconductor volume. This local detection technique allows the construction of sensitive nanoscale bioprobes and arrays thereof.