https://ai2healthcare.github.io/news/20 ... Dr.Hao_Zhu
Title: MAIB-Talk-019: Applying causal discovery to single-cell analyses using CausalCell
Date:11:00pm US East time, 06/24/2023
Date:11:00am Beijing time, 06/25/2023
Zoom ID:933 1613 9423
Zoom PWD:416262
Zoom: https://uwmadison.zoom.us/meeting/regis ... lnGn06TP2E
Presentation Record(Previous Presentation will be showed here if the video is not released for this talk)
Dr. Hao Zhu
Dr. Hao Zhu was initially graduated from a medical school (community school level) and worked for years in a hospital. He then went to the graduate school of the National University of Defense Technology and was trained in computer science (MS degree) After graduating from NUDT, we joined the First Military Medical University and obtained the PhD degree in Pathology and Pathophysiology. ZHU Hao then got the postdoc training in Singapore (Bioinformatics Institute of Singapore) and UK (University of Nottingham, School of Mathematical Sciences); in these years he worked on computational modeling of developmental signaling. Since 2009 he has worked in Southern Medical University, Guangzhou, working on bioinformatics and genome analysis.
Reference
Yujian Wen, Jielong Huang, Shuhui Guo, Yehezqel Elyahu, Alon Monsonego, Hai Zhang, Yanqing Ding, Hao Zhu (2023) Applying causal discovery to single-cell analyses using CausalCell eLife 12:e81464
https://doi.org/10.7554/eLife.81464
Abstract
Correlation between objects is prone to occur coincidentally, and exploring correlation or association in most situations does not answer scientific questions rich in causality. Causal discovery (also called causal inference) infers causal interactions between objects from observational data. Reported causal discovery methods and single-cell datasets make applying causal discovery to single cells a promising direction. However, evaluating and choosing causal discovery methods and developing and performing proper workflow remain challenges. We report the workflow and platform CausalCell (http://www.gaemons.net/causalcell/causalDiscovery/) for performing single-cell causal discovery. The workflow/platform is developed upon benchmarking four kinds of causal discovery methods and is examined by analyzing multiple single-cell RNA-sequencing (scRNA-seq) datasets. Our results suggest that different situations need different methods and the constraint-based PC algorithm with kernel-based conditional independence tests work best in most situations. Related issues are discussed and tips for best practices are given. Inferred causal interactions in single cells provide valuable clues for investigating molecular interactions and gene regulations, identifying critical diagnostic and therapeutic targets, and designing experimental and clinical interventions.
Editor’s evaluation
This manuscript presents an important tool for causal inference intended for the analysis of single cell datasets but possibly with broader applications. It compares several algorithms and incorporates a number of them in the platform and offers convincing evidence of its usefulness. With the rapid expansion of large datasets, this tool is beneficial in offering several causal inference analysis options and expediting the interpretation of data.
MAIB讲座第19期: 使用 CausalCell 将因果发现应用于单细胞分析
生物制药相关,包括biotech和pharma,股票分析,工作内推,简历评估,职业规划,研发交流,FDA资讯等
版主: Tlexander
-
- 论坛点评
- 帖子: 2975
- 注册时间: 7月 22, 2022, 5:34 pm
前往
- 新闻中心
- ↳ 军事天地(Military)
- ↳ 肚皮舞运动(Joke)
- ↳ 精华区
- ↳ 美国新闻(USANews)
- ↳ 史海钩沉(History)
- ↳ 台海风云(TaiwanStrait)
- ↳ 精华区
- ↳ 中国新闻(ChinaNews)
- ↳ 捕风捉影(Plausible)
- ↳ 美国时政(US Current Affairs)
- ↳ 精华区
- 海外生活
- ↳ 股海弄潮(Stock)
- ↳ 股海弄潮精华区
- ↳ 家居生活(Living)
- ↳ 精华区
- ↳ 车轮上的传奇(Automobile)
- ↳ 二手市场(FleaMarket)
- ↳ 书歌影视美食游
- ↳ 精华区
- ↳ 电脑手机(IT)
- ↳ 精华区
- ↳ 子女教育
- ↳ 精华区
- ↳ 手机计划(Cellular Plan)
- ↳ 信仰天地(Belief)
- ↳ 投资理财退税(Money)
- ↳ 海外鹊桥(Chinese Dating)
- ↳ 医疗与健康
- 学术学科
- ↳ STEM
- ↳ 葵花宝典(Programming)
- ↳ 生物医学(Biomedical)
- ↳ 统计与数据科学(Statistics & DataScience)
- ↳ 前沿科技(Frontier)
- ↳ 金融量化(Invest)
- 职场生涯
- ↳ 生物制药(Pharmaceutical)
- ↳ 绿卡移民(Immigration)
- ↳ 职场讨论
- 情感杂想
- ↳ 梦里花落知多少(Dreamer)
- ↳ 人到中年(Midlife)
- ↳ 性意识(Sex)
- 体育健身
- ↳ 滚吧,足球!(Soccer )
- ↳ 体育博彩
- ↳ 奥运和综合体育
- ↳ 网球(Tennis)
- 休闲娱乐
- ↳ 摄影器材(Photo gears)
- ↳ 网络文学
- ↳ 花鸟鱼虫
- ↳ 枪械射击(Guns & Gear)
- ↳ 新未名博客(Blog)
- 华人世界
- ↳ 加州华人
- ↳ 广告与招聘
- 站务管理
- ↳ 申请新版块或版主
- ↳ 意见与建议
- ↳ 版主专区
- ↳ 账号管理
- ↳ 论坛使用交流
- ↳ 功能测试