Shengxin weekly issue 33

Health letter lovers weekly （ The first 33 period ）： Scientific research and life

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This week's topic ： Scientific research and life

During the period of Shubo , You may not feel the meaning of this topic , But officially enter the work , Full access to human life , Worry about eating and drinking Lazar , Life is inevitable , Life must also be dealt with and faced . If you choose scientific research , How would you handle your life in your research career ？ How to put the family position ？

There is an impressive passage in the article linked to this topic ：“ It doesn't really matter whether you have time to spend with your children and family or how busy you are with your work , The key is whether you really put your child's family first , Reluctant to give them time .” We have learned to be loved since childhood , But you and I will also learn to love .

Shengxin technology trends

1、Cell｜ This is the first large-scale high-resolution discovery of the whole process from a single cell carrying a carcinogenic mutation to an invasive tumor

The research team will be based on single cells RNA-seq The evolutionary pedigree tracing system of KP In a mouse model , The whole process of a single cell carrying a carcinogenic mutation evolving into an invasive tumor was continuously and comprehensively monitored , It is revealed that rare subclones can drive tumor expansion through a unique transcription program . Besides , The research team also found that the tumor passed through the typical 、 Unique evolutionary trajectory development , Interfering with additional tumor suppressors can accelerate tumor progression . The study reconstructed the transformation from single transformed cells to complex cells with unprecedented scale and resolution 、 The whole process of tumor evolution of invasive tumor population .

2、Nature | 30 Kinds of cancer 2583 Genome wide data analysis revealed staining in vitro DNA Mutation and 10% Cancer related

The research team analyzed the data from 30 It's a cancer 2500 Multiple genome-wide data , The most comprehensive map of known aggregated somatic mutations 、 The most detailed atlas , Reveals ecDNA in APOBEC3 The mutation characteristics of , This previously undetected mutation pattern leads to about 10% The development of human cancer . The study found that ,kataegic In the event 76.1% It is shown to be associated with activation induced deaminase （AID） and APOBEC3 Mutations associated with the deaminase family . stay 31% Of ecDNA Found in the sample APOBEC3 dependent kataegis Events and staining in vitro DNA（ecDNA） Co emergence , This situation is called kyklonas event .

3、NBT | Wang jun, / Chenyihua group used AI High throughput mining of functional macromolecules of enabling microbiome

Researchers have integrated natural language analysis in a variety of artificial intelligence fields （Natural Language Processing） Neural network method , Take antibacterial peptide as the first research object , After studying the existing thousands of antibacterial peptide sequences , Constructed with an accuracy of more than 90% Prediction method of antimicrobial peptides , It is far beyond the previously published model for determining antimicrobial peptides based on amino acid composition and properties .

article

1、 Different evolutionary models of tumor clonal evolution

Different models of tumor clonal evolution are summarized , And the study of the existing evolutionary patterns of various cancer species , The whole series is worth reading .

@mugpeng contribution .

2、11 Tumor like antigen

This article summarizes 11 Production and characteristics of tumor like antigens , Hope to be able to study the target 、 Accurate diagnosis 、 Immunotherapy, etc .

3、 Free and easy to use blog comment system plug-in -- utterances

4、 Use glmnet Carry out regularized generalized linear model regression

5、 Tumor microbial microenvironment

The role of tumor microbial microenvironment in tumor immune microenvironment is multifaceted ： May act as an immune activator 、 Inhibitor or bystander . Tumor microbial microenvironment regulates tumor immune microenvironment , Make it a potential target for improving immunotherapy . This is a new field facing major challenges , It is worth exploring further .

Tools

1、SwiftBar - Powerful macOS Menu bar customization tool

Write a Shell Script , Then add to SwiftBar, You can have one MacOS plug-in unit .

2、Proksee - A genome assembly 、 Annotation and visual expert system

It can be used to divide the macrogenome （binning） Visualization of the sketch of a single bacterium obtained after （ The web version only supports fasta Format nucleic acid sequence , After comments is not supported temporarily faa or gff3 Visualization of results . Can choose linux edition , Support conda install ：https://anaconda.org/bioconda/proksee, Support from scratch assembly and annotation ）.

@15521271731 contribution .

3、charpente - Seamless design robust Shiny Expand

4、plottify - A simple matplotlib Wrappers , Auto zoom font size 、 Scatter size and row width , Make it proportional to the size of the drawing

5、janitor - R Simple data cleaning tools in

Janitor It has the function of simply checking and cleaning dirty data . It is for elementary and intermediate R User built , And optimized for user friendliness . senior R Users can already complete everything involved here , But use janitor They can do it faster , And leave their ideas for something interesting .

The main function ：

• Perfect formatting data.frame Name ;
• Create a 、 Frequency table of two or three variables and format it ;
• Provide other tools for cleaning and inspection data.frame

resources

1、A profile of differential DNA methylation in sporadic human prion disease blood: precedent, implications and clinical promise

2019- Doctoral thesis of the University of London , Elaborate the methylation content in a comprehensive way , Contains the recurrence code .

@ylchenchen contribution .

2、Unraveling population heterogeneity using single-cell analysis

2022- Doctoral Dissertation of the University of Washington , Introduction of single cell classification algorithm .

@ylchenchen contribution .

3、 Medical data science course

Great based on Rmd Open course materials for , Infer assumptions from , The data distribution , Batch processing , And the processing of genomic data .

@mugpeng contribution .

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