EpiDISH web toolkit is online

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The EpiDISH web toolkit is based on Bioconductor package EpiDISH. The originial BioC package contains functions to infer cell-type fractions from DNAm profiles of heterogeneous tissues, DNAm reference matrix for common tissue types, and CellDMC algorithm to identify differentially methylated cell-types in EWAS. In addition to all functionalities provided in the BioC R package, the web toolkit provides interactive visiulizatio tools, which are more user-friendly to those who are not familiar with R programming.

Please visit Here for further detail.
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2019-2-21

Welcome Professor Colin Collins

We are privileged that Prof Colin Collins is visiting Shanghai again.

This month. Details below about his seminar at PICB which is being jointly organized with the Institute for Health Sciences:

Speaker: Prof. Colin Collins, PhD, Professor, University of British Columbia and Senior Scientist Vancouver Prostate Centre

Time: 11:00-12:00 AM, Tue Dec. 16th, 2014 Place: Room 300 (PICB) Host: Dr Andrew Teschendorff (PICB) & Prof Sun Yu (IHS) Title: Mechanistic Insights To Therapeutic Resistance In Prostate Cancer

Dr Collins' lab spans computer science, bioinformatics and biology. The Web Site for Vancouver Prostate Centre: http://www.prostatecentre.com/ and Dr Collins' webpage is http://www.prostatecentre.com/about-us/people/clinical-research-scient ists/dr-colin-collins

Written by Yuan Tian

2014-12-18

Three PHD Student passed their Thesis report

Congraduate to three PHD students in our lab for their effort on the Thesis report!!

On Nov 24, Professor Shao Zhen, Professor Luonan Chen were invited to acting as judgers for our students' Thesis Report. Totally, there are five PDH students attended the report and to be honset it's not easy to understand what the other group is doing. So many equations and picture on the PPT that it's hard for me to catch up with the main ponit.

Anyway, A harder way is just in front of us.

Written by Yuan Tian

2014-12-7

Joint Seminar

On Apirl 25th, our second joint seminar with Professor Zhen Shao's Group and Professor Luonan Chen's Group was successfully applied in room 300.

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In this seminar, Yang Gao from Andrew's groups, Mushan Li from Zhen Shao's group and Hao Kang from Luonan Chen's groups made presentation for their recent work.

Written by Yuan Tian

2015-4-27

Our lab Website

For a long time I want to establish a website for our lab, but to be honest I am to lazy. Finally I save some time for it.

Before I started to write this website, I actually know nothing, I indeed leared some thing about HTML and PHP when I was in collage but to be honest they are not well quilified until now. So I went to some help from Bootstrap. Alt text

At the beginning, everything went well since I merely know how to write css, javascript and get more and more tips from Google. But then, I decided to create more modal than Bootstrap offered, Things suddently become complicated becasue most moduls given by Bootstrap are well packaged which means it's becomning harder for freshman who want to change some CSS codes because for one single div, there are sometimes 4 or 5 CSS file involved.

I turned my direction back and went to W3school, bought a very good PHP book and start to Google small code's script instead of big modules. Finally, after two or three days, I can understand how to create a nice layout without helpers like Bootstrap.

Then I links MySQL, to be honest, the database is not very useful here because I can easily access all pictures or files by direction. However, on the purpers of do some excersise, I link mySQL up.... Problem like this can be seen for many many times, but with the help of Google, I finally overcomed most of them.

Alt text This is the Main Page for our group which I think is not bad! I love it realy.

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Well, so far, I have coded about one week, and I have finished most part of front, but I need some script to help me to manage this website. There are still many things to be done.

Written by Yuan Tian

2014-12-7

Welcome Professor Colin Collins

We are privileged that Prof Colin Collins is visiting Shanghai again.

This month. Details below about his seminar at PICB which is being jointly organized with the Institute for Health Sciences:

Speaker: Prof. Colin Collins, PhD, Professor, University of British Columbia and Senior Scientist Vancouver Prostate Centre

Dr Collins' lab spans computer science, bioinformatics and biology. The Web Site for Vancouver Prostate Centre: http://www.prostatecentre.com/ and Dr Collins' webpage is http://www.prostatecentre.com/about-us/people/clinical-research-scient ists/dr-colin-collins

Written by Yuan Tian

2014-12-18

Chinese R languange Meeting

On Dec 5 th, I attended the 7th Chinese R languange Meeting holded by Huadong Normal University. Out of my expectation I met little people who are doing research there, instead, there are a lot of engineers and students who study programming there. As far as I know, wherever there are programmers, lies great chances.

Above all speakers, I love the one who focus on Shiny most. Shiny is a newly published R tools can help costumers put their research output on the Internet, so, to be honest, it's the first time when statistic scientist have a chance to tell the world what they are doing. Alt text

This is the main page of R studio, the company who developed Shiny.

As far as I see, most students and engineer showing on the meetin indeed regard R as a king of languange, but for PICB student, we have the advantage that we can develop much more complicated modals and statsitic method to dealing with large data set when they can somehow use most advanced tools to show figures generated by linear regression.

In the Winter vocation, I will focus on Shiny for sure.

Written by Yuan Tian

2014-12-10

Journal Club List

Network reconstruction for trans acting genetic loci using multi-omics data and prior information

They demonstrated, that existing biological knowledge can be leveraged for the integrative analysis of networks underlying trans associations to deduce novel hypotheses on cell regulatory mechanisms.

Tianyu Zhu 2020/06/11

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

They developped an evaluation framework called BEELINE. They found that the area under the precision-recall curve and early precision of the algorithms are moderate. The methods are better in recovering interactions in synthetic networks than Boolean models. BEELINE will aid the development of gene regulatory network inference algorithms.

Ning Wang 2020/07/02

Supervised classification enables rapid annotation of cell atlases

They described Garnett, a tool for rapidly annotating cell types in single-cell transcriptional profiling and single-cell chromatin accessibility datasets, based on an interpretable, hierarchical markup language of cell type-specific genes. Garnett successfully classifies cell types in tissue and whole organism datasets, as well as across species.

Weiyan Chen 2020/07/09

Putative cell type discovery from single-cell gene expression data

They presented the Single-Cell Clustering Assessment Framework, a method for the automated identification of putative cell types from single-cell RNA sequencing (scRNA-seq) data. Their method automatically identifies the 'ground truth' cell assignments with high accuracy.

Xue Hu 2020/07/16

A meta-analysis of genome-wide association studies of epigenetic age acceleration

They identified novel SNPs and genes associated with epigenetic age acceleration, and highlighted differences in the genetic architecture of Horvath-based and Hannum-based epigenetic ageing measures.

Chenglong You 2020/07/30

Single-Sample Node Entropy for Molecular Transition in Pre-deterioration Stage of Cancer

They have successfully developed a dynamic node entropy model based on single case data to find out tipping point and possible mechanism for cancer progression.

Qi Luo 2020/08/06

Bayesian reassessment of the epigenetic architecture of complex traits

Here, a statistical approach is presented to infer the epigenetic architecture of complex disease, determine the variation captured by epigenetic effects, and estimate phenotype-epigenetic probe associations jointly.

Han Jing 2020/08/27

scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens

They presented scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout.

Alok 2020/08/13

We are small but productive.

Invited speakers, Group Achivement, Students performance....

EpiDISH web toolkit is online

Welcome Professor Colin Collins

Three PHD Student passed their Thesis report

Joint Seminar

Our lab Website

Welcome Professor Colin Collins

Chinese R languange Meeting

Journal Club List