In oncology research, it is a common goal to uncover specific molecular pattern of cancer. High-throughput sequencing has been become the routine approach to start with. However, sequencing technique such as RNA-Seq and bisulfite sequencing generates high dimension dat...

Survival analysis and logistic regression share certain similarities. The use of logistic regression for survival analysis, although not strictly correct due to data censoring in survival data, provides intuitive understanding. 

Logistic regression

Let's recall how...

When comes to a general bioinformatics task, there are always a bunch of tools on which we have to evaluate based on their underlying algorithm. Moreover, when we are about to build a model on our own, we again have to pick from a variety of ML model. How do we know wh...

Ghost recently did some research on cell type decomposition technique, specifically TIL decomposition in tumor sample. TIMER and CIBERSORT came across alone with their technical debates published on correspondence of Genome Biology. Li in Revisit linear regression-base...

Ghost came across this interesting figure on Cell Science and would like to take this opportunity to talk about tumor microenvironment. 

A route towards tumorigenesis

Tumor microenvironment is dynamic battlefield between tumor and immune system. This long-lasting ba...

Ghost encountered dimension reduction problem while designing a model aiming to describe patient's immuno-oncology (IO) status. The model is supposed to incorporate well-known immune related factors listed in the figure below (for factor selection details, please read...

First things first, the proposed classification are immune suppressing and immune escaping. Now let's go back for some specifics.

Immuno-oncology cycle

The whole immuno-oncology (IO) process can be briefly described as the following cycle. 

Tumor cells release neoantigen...

Immunotherapy has been the hot spot in cancer treatment in recent years. As a key component, neoantigen identification is usually done bioinformatically. If you are not familiar with concept of immunotherapy or neoantigen, please read THIS article first. Here Ghost wan...

Tumor clonal evolution

Cancer is stubborn largely due to its nature of heterogeneity: they evolve to adjust the changes of surrounding environment.

Figure above shows tumor clonal evolution. During the long lasting tumorigenesis period, tumor generates heterogeneous clo...

Identifying somatic mutation has always been challenging.

Tumor heterogeneity

The major challenge of calling somatic mutation is heterogeneity of tumor tissue. Unlike germline variants usually having allele frequency (AF) around either 50% or 100% with a little deviation...