Provided herein are methods of identifying gene expression levels in specific cell types based on bulk gene expression levels measured in tissue samples comprising a plurality of cell types.

Provided herein are methods of identifying gene expression levels in specific cell types based on bulk gene expression levels measured in tissue samples comprising a plurality of cell types.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Provided herein are automated apparatus for the identification of microorganisms in various samples. The disclosure solves existing challenges encountered in identifying and distinguishing various types of microorganisms, including viruses and bacteria in a timely, efficient, and automated manner by sequencing.

Methods and computer systems related to image-based data analysis such as mass spectrometric data analysis. Methods and computer systems herein utilize multiple micro-processes operating concurrently to carry out rapid, efficient, and automated analysis of mass spectrometry data.

Methods and computer systems related to image-based data analysis such as mass spectrometric data analysis. Methods and computer systems herein utilize multiple micro-processes operating concurrently to carry out rapid, efficient, and automated analysis of mass spectrometry data.

The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.

Cell free nucleic acids from a test sample obtained from an individual are analyzed to identify possible fusion events. Cell free nucleic acids are sequenced and processed to generate fragments. Fragments are decomposed into kmers and the kmers are either analyzed de novo or compared to targeted nucleic acid sequences that are known to be associated with fusion gene pairs of interest. Thus, kmers that may have originated from a fusion event can be identified. These kmers are consolidated to generate gene ranges from various genes that match sequences in the fragment. A candidate fusion event can be called given the spanning of one or more gene ranges across the fragment.

Cell free nucleic acids from a test sample obtained from an individual are analyzed to identify possible fusion events. Cell free nucleic acids are sequenced and processed to generate fragments. Fragments are decomposed into kmers and the kmers are either analyzed de novo or compared to targeted nucleic acid sequences that are known to be associated with fusion gene pairs of interest. Thus, kmers that may have originated from a fusion event can be identified. These kmers are consolidated to generate gene ranges from various genes that match sequences in the fragment. A candidate fusion event can be called given the spanning of one or more gene ranges across the fragment.

The present invention provides compositions and methods that can be used to identify an antigen or epitope region of an antigen specific for a disease or other condition. Such methods incorporate k-mer binding statistics to serum antibody from condition and control cohort samples to predict the suitability of antigen sequences identified as relevant to the disease or condition as antigen markers. Also disclosed herein are systems for performing the same.