The invention relates to a method for determining whether a subject with an infection has a viral infection. The invention further relates to method for determining the cellular immune response to a viral infection or a vaccine. The methods may be performed on a blood sample obtained from a subject, and is based on the finding that specific cellular signaling pathways are active. The invention further relates to components for performing the methods and use of those components in a method of diagnosis.

Provided herein are methods, systems, and storage media that may find use, e.g., in sequencing (e.g., via NGS) polymorphic alleles, such as detecting loss-of-heterozygosity (LOH) of a human leukocyte antigen (HLA) gene or another polymorphic human gene. In some embodiments, the methods and systems comprise obtaining observed allele frequencies and observed binding propensities for the alleles to one or more bait molecule(s), then applying an optimization model to determine adjusted allele frequencies that take into account these binding propensities, thereby adjusting for and/or minimizing any potential bias rooted in differential allele: bait binding propensities with regard to determination of allele frequency.

Provided herein are methods, systems, and storage media that may find use, e.g., in sequencing (e.g., via NGS) polymorphic alleles, such as detecting loss-of-heterozygosity (LOH) of a human leukocyte antigen (HLA) gene or another polymorphic human gene. In some embodiments, the methods and systems comprise obtaining observed allele frequencies and observed binding propensities for the alleles to one or more bait molecule(s), then applying an optimization model to determine adjusted allele frequencies that take into account these binding propensities, thereby adjusting for and/or minimizing any potential bias rooted in differential allele: bait binding propensities with regard to determination of allele frequency.

Disclosed herein include systems, devices, and methods for determining a variable number tandem repeat (VNTR) status. Haplotypes of a VNTR can be determined using long sequence reads of reference samples aligned to the VNTR in a reference. Short reads of a test sample of a test subject can be aligned to the haplotypes determined using the long sequence reads to determine a VNTR status (e.g., one or more haplotypes or a genotype of the test subject) of the test subject based on the probability indications of the haplotypes.

Disclosed herein include systems, devices, and methods for determining a variable number tandem repeat (VNTR) status. Haplotypes of a VNTR can be determined using long sequence reads of reference samples aligned to the VNTR in a reference. Short reads of a test sample of a test subject can be aligned to the haplotypes determined using the long sequence reads to determine a VNTR status (e.g., one or more haplotypes or a genotype of the test subject) of the test subject based on the probability indications of the haplotypes.

Provided herein are methods and systems for the analysis of biomarkers, and methods of providing diagnoses and/or prognoses therewith. In particular, methods and systems for performing biomarker ratio imaging microscopy (BRIM) are provided, as well as methods of using BRIM for the analysis of biomarker pairs (e.g., CD44/CD24, N-cadherin/E-cadherin, CD74/CD59, etc.) diagnosis and/or prognosis of cancer (e.g., ductal carcinoma in situ).

Provided herein are methods and systems for the analysis of biomarkers, and methods of providing diagnoses and/or prognoses therewith. In particular, methods and systems for performing biomarker ratio imaging microscopy (BRIM) are provided, as well as methods of using BRIM for the analysis of biomarker pairs (e.g., CD44/CD24, N-cadherin/E-cadherin, CD74/CD59, etc.) diagnosis and/or prognosis of cancer (e.g., ductal carcinoma in situ).

The disclosure provides a process of designing and optimizing supramolecular therapeutics. The disclosure also provides a method for designing and optimizing antibody drug conjugates.

The disclosure provides a process of designing and optimizing supramolecular therapeutics. The disclosure also provides a method for designing and optimizing antibody drug conjugates.

Embodiments facilitate generation of a prediction of long-term survival (LTS) or short-term survival (STS) of Glioblastoma (GBM) patients. A first set of embodiments discussed herein relates to training of a machine learning classifier to determine a prediction for LTS or STS based on a radiographic-deformation and textural heterogeneity (r-DepTH) descriptor generated based on radiographic images of tissue demonstrating GBM. A second set of embodiments discussed herein relates to determination of a prediction of disease outcome for a GBM patient of LTS or STS based on an r-DepTH descriptor generated based on radiographic imagery of the patient.