Abstract: Provided herein are systems and methods for identifying alternative splicing derived cell surface antigens. Also provided are methods and compositions for using the identified cell surface antigens. Further provided are methods, compositions, and systems for diagnosing diseases in a subject using the identified cell surface antigens or treating diseases using the same.

Abstract: Disclosed herein are systems and methods for identifying candidate targets that may be used for therapeutic developments. The systems and methods may comprise receiving and analyzing biologically relevant data to identify information or events such as splicing events that may be statistically significant or specific to certain diseases, illnesses or conditions. Also provided are systems and methods for modulating the statistically significant events using compositions or molecules including small molecule compounds, oligonucleotides, proteins or cells.

Abstract: Disclosed herein are systems and methods for quantification and analysis of alternative splicing events, and prediction of biological relevance of alternative splicing events comprising a software module: quantifying alternative splicing events using biological data related to a genome, a transcriptome, or both provided by a user; processing the quantified alternative splicing events with information stored in a database; identifying statistically significant alternative splicing events, predicting functional impact of alternative splicing events on protein structures, protein functions, RNA stability, RNA integrity, or biological pathways, predicting druggability and reversibility of aberrant splicing events as well as controllability of splicing in general using statistical modeling and machine learning algorithms

Abstract: A method of determining responsiveness to cancer treatment is disclosed. The method comprises analyzing a frequency of tumor infiltrating lymphocytes (TILs) having a CD8+CD28?CD152? signature in a sample of the subject, wherein a frequency of TILs having the CD8+CD28?CD152? signature above a predetermined level is indicative of a positive responsiveness to cancer treatment. Other signatures reflecting responsiveness to cancer treatment are also disclosed. In addition, methods of treating cancer based on these signatures are also disclosed.

Abstract: A method of determining responsiveness to cancer treatment is disclosed. The method comprises analyzing a frequency of tumor infiltrating lymphocytes (TILs) having a CD8+CD28?CD152? signature in a sample of the subject, wherein a frequency of TILs having the CD8+CD28?CD152? signature above a predetermined level is indicative of a positive responsiveness to cancer treatment. Other signatures reflecting responsiveness to cancer treatment are also disclosed. In addition, methods of treating cancer based on these signatures are also disclosed.