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DNA Ghost:

This note based blog covers bioinformatics and cancer genomics 

June 4, 2019

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

Logistic regression

Let's recall how logistic regression...

January 30, 2019

When comes to a general bioinformatics task, there are alway 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 whi...

December 27, 2018

Ghost recently did some reseach 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-based...

December 3, 2018

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

A route towards tumorigenesis

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

November 30, 2018

Ghost encountered dimension reduction problem while designing a model aiming to describe patient's immuno-oncology (IO) status. The model is suppose 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...

May 14, 2018

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...

April 10, 2018

Frequentist's approach: Assume sequencing error distribution.

Frequentist's method makes the null hypothesis that non-reference allele is caused by sequencing error and the sequencing error follows either binomial or Poisson distribution. Then we fit error rate into pro...

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