Abstract: Disclosed herein are systems and methods for identifying biomarkers. Biomarker identification can be achieved while increasing efficiency and decreasing data and computation complexity but maintaining accuracy. Such biomarker identification can be achieved via analysis of differential gene expression, such as determined using single cell RNA-sequencing data sets.

Abstract: Disclosed herein are methods of identifying and treating subjects with cancer, and methods of predicting a survival outcome in a subject with cancer, such as pancreatic cancer. In one aspect, the application provides methods for detecting the presence of cancer or infectious disease in a subject by collecting and analyzing sequencing information from the subject, such as by performing single cell RNA sequencing analysis of individual cells obtained from a sample from the subject. In a further aspect, the application provides methods for detecting the presence of cancer or infectious disease in a subject by determining microbial diversity and/or assessing the presence or absence of particular microbes in individual cells from the subject as compared to a control. Also provided are methods of determining T-cell microenvironment reaction, for example by sequencing nucleic acid molecules in individual T-cells obtained from the subject.