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Shengxin Weekly Issue 38

2022-07-31 11:36:00 【Wang Shixiang】

生信爱好者周刊（第 38 期）：The candidates don't option purpose「基石项目」Whether on the road to success？

这里记录每周值得分享的生信相关内容,周日发布.

本杂志开源（GitHub: ShixiangWang/weekly）,欢迎提交 issue,投稿或推荐生信相关内容.

「生信周刊讨论区（语雀）」 | 「生信讨论区（Gitter）」

封面图

本周话题：The candidates don't option purpose「基石项目」Whether on the road to success？

它面向中国内地及港澳地区全职工作的科研人员,每人每年最高500万经费,连续资助5年.5年周期一过,还有机会再续！And it only candidate,不选项目.换言之,它专注于支持富有创造力的科学家开展探索性与风险性强的基础研究.
如何选？Scientists leading principle.由施一公带头,潘建伟、谢晓亮、张杰等知名科学家组成的科学委员会来决定.

@ShixiangWang - From the scientific exploration prize to a new foundation,We see more and more enterprises begin to found in basic scientific research force to send money,The new foundation projects focused on from“0”到“1”的研究,即「项目耗时长,风险性高,本身成果就不容易产出,也就不那么容易得到资助」,To what extent is in the process of actual application and review“0”的开始,China's outstanding young talents in real how many people have to do“0”到“1”Research ideas and courage all have no data to support,So the state should wait success now：第1-2The idea of the selected topic、Content and how the progress of the next five years will directly affect the project success degree.Will be stillborn,Step by step out of the complete system of Chinese commercial support for basic research,值得期待.

生信研究

1、Science | Massive parallel analysis（MPRA）Determine a variety of causal mutation associated with human phenotype of

Temple university school of medicine research team proved that,MPRAsProvides an extensible platform to separate and drawing complex phenotypic correlation natural genetic variation regulation of events,And highlights the limitations of existing methods.研究发现,Significant and significant alleleMPRAGenome-wide distribution of variation relative to the corresponding is the characteristics of the highly mobile.This effect shows that,Function prediction may be able to easily distinguish from genome backgroundeQTL区域,At the same time to distinguish the same regulation of highly related and common significant variation in the area of.These results for, including gene expression and complex phenotype, hundreds of independent genetic related specific mutation study provides new evidence.

论文链接：https://www.science.org/doi/10.1126/science.abj5117

2、Nature Biotechnology | cfDNAThe fragmentation patterns new methodEPIC-seqCancer, high detection sensitivity and subtypes to distinguish

cfDNAIs released into the blood plasma degradation ofDNA片段,Can with tissue injury、Concentration changes such as cancer and inflammation reaction,In the early diagnosis of disease、预后、Monitoring has important potential value.

发表在Nature BiotechnologyA study introduces a kind of based oncfDNAA new approach to cancer detection——EPIC-seq.By capturing the target gene transcription start siteTSS区域,Implement targeted sequencing depth;机器学习结合cfDNA分子特征——The promoter fragment entropy（PFE）And absence of nucleosome area （NDR）深度,构建预测模型,预测目标RNA表达.在非小细胞肺癌（NSCLC）和弥漫性大BCell lymphoma in,The method realizes high sensitivity detection and subtypes to distinguish.

论文链接：https://www.nature.com/articles/s41587-022-01222-4

3、Nature Review Immunol. | MHCⅠSuch molecules and tumor immune surveillance and immune escape

在这篇综述中,The author reviewed the limitCD8+TCellular immune therapy used two factors：①难以识别MHC ISuch molecules on tumor-specific peptide;②The tumor cells inTCells choose next evolutionary damage antigen presenting ability.The author describes in detail the defective product ribosome non-canonical translation of the latest progress on how to produce peptide,It is associated with as carcinogenic characteristics of translation disorders,And put forward the imbalance of translation as an important new source of tumor-specific peptide.另外,The author also discussed the composition and presenting antigen processing way（Including recently described immune ribosome）The synthesis and function of how the manipulation for tumor immune escape,And points out the common drug targets may enhance the immune therapy.

论文链接：https://www.nature.com/articles/s41577-020-0390-6

4、Nature Communication | One thousand people in our country colorectal cancer genome new parting

Sun yat-sen university cancer prevention and control center rui-hua xu/Wang feng team inNature Communications发表的研究,全面分析了1015Cases of Chinese patients with colorectal cancer genome chromosome mutation events、Immunogenicity and mitochondrial genome characteristics,And in combination with clinical information to explore the molecular characteristics and clinical features of colorectal cancer relationship. Sequencing the raw data has been uploaded to the China national biological information center national center for genome data（HRA000873）,Clinical information inSupplementary Data2（OSOnly to a state of survival,Didn't find time to live）,The database provides processing goodmaf文件.

数据库链接：https://changkang.hapyun.com/

论文链接：https://www.nature.com/articles/s41467-022-30062-8

5、iMeta | Majorbio Cloud：一站式多组学数据分析平台

Majorbio CloudIs a high-throughput omics analysis online platform,Own analysis process includes micro ecology、转录组、蛋白与代谢及基因组等多组学.Through detailed online documentation and online classes,Users can use more simple and quick to fit.此外,The platform also provides users with rich visualization plugin library.目前Majorbio Cloud已有1200+文章引用了.

论文链接：https://onlinelibrary.wiley.com/doi/10.1002/imt2.12

话说这个imetaJournal recently always like to push some commercial companies raw letter cloud platform into article.

博文资讯

6、Single-cell transcriptome one-stop data analysis process ofpopsicleR

In this paper, through sample data,From a single cell to control the quality of annotation to the final cell,展示了如何使用popsicleRTo analyze single-cell transcriptome one-stop package

Github: https://github.com/bicciatolab/popsicleR

7、推荐 10 个好用到爆的 Jupyter Notebook 插件

Jupter Notebook 是基于网页的用于交互计算的应用程序,Can write and run the code directly in your web page,具有灵活、The characteristics of highly extensible,Users can easily implement some practical function by installing plugins,This paper introduces several injupyter notebook中被广泛用到的插件,Better able to help you analyze data visualization,Greatly improve the efficiency of daily work！！

8、如何监测 Linux 的磁盘 I/O 性能

9、10 Minutes to understand micro service、容器和 Kubernetes

Through this tweet,You can learn what is micro service、容器和Kubernetes,As well as the relationship and difference between them.

工具

10、https://github.com/hpc/Spindle

11、simpr - 模拟数据生成

SimprPackage provides a general、Simple and clear and friendly framework,用于生成模拟数据,Fitting model and the result,The complete workflow can be in a singlepipeline中完成,And does not need external functions to create and use global variables and circulation,The package function for some power analysis、设计分析、The simulation research and the teaching of statistical data is very useful~

12、shinybusy - State of load calculationShiny拓展

13、R包：Communication algorithm based on gene expression of cell——NicheNet

Most of the current study the calculation method of intercellular communication is different,NicheNet Based on the ligand gene regulation effect,Using the presupposition and the combination of the intracellular signal transduction and transcription regulation.NicheNet Can predict which of ligands affect another cells express,What kind of target genes is affected by each ligand and may involve which signal transduction medium.

R包链接：https://github.com/saeyslab/nichenetr

14、rcli - 简化的R版本处理

In all the major operating system,安装多个RThe interpreter and switch between them is a very tiring task,This tool is convenient to solve this matter.

资源

15、BookChapter-RNA-Seq-Analyses - RNAThe design of the sequencing data and analysis

This chapter content forRNASeqData analysis provides a comprehensive overview of,Including quality evaluation,reads的预处理、reads比对,Genetic quantitative、Variable shear and variance analysis, etc,This book also provides a brief description of the code and data format,To use the workflow steps,详见Github文档.

Github：https://github.com/grimmlab/BookChapter-RNA-Seq-Analyses

Book：https://doi.org/10.1007/978-3-030-62490-3_11

Amazon link: https://www.amazon.com/Generation-Sequencing-Analysis-Materials-Biosciences/dp/3030624897

16、Windows开发环境配置指南