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DNA Ghost:

This note based blog covers bioinformatics and cancer genomics 

February 7, 2020

  Bioinformatics is an interdisciplinary of biology (clinical medicine), computer science as well as statistics. To enable an in-depth biomedical / bioinformatics research, especially data driven research, researchers ought to have robust and intuitive understanding to...

January 20, 2020

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...

June 4, 2019

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...

January 30, 2019

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...

December 27, 2018

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...

December 3, 2018

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...

November 30, 2018

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...

October 26, 2018

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...

June 11, 2018

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...

June 5, 2018

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...

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