14 12 2011



New era of DNA sequencing and related bioinformatics

9 12 2011

I can say the passed week is a week full of great news.

Wednesday (Nov 30, 2011)
“DNA Sequencing Caught in Deluge of Data” — You must want to read this article.

Monday (Dec 5, 2011)
UK will invest £75M for a new BIOINFORMATICS HUB in current EBI, as part of the ELIXIR project. I guess this must be within the framework of the HORIZON 2020, which the EU’s new programme for research and innovation running from 2014 to 2020 with an €80 billion budget. €80 billion!! OMG!

Tuesday (Dec 6, 2011)
The National Human Genome Research Institute (NHGRI), as part of NIH, announced to invest $416 million on research of using genomic data for medical clinical research, including rare inherit disease. Three genome sequencing centers are funded, including the Broad Institute, Genome Institute at Washington University, and Human Genome Sequencing Center, Baylor College of Medicine.

Whole-genome sequencing seems becoming more and more popular since it’s becoming cheaper and faster. Citing what the ELIXIR website says, “Modern sequencers are capable of analysing the equivalent of a human genome every 14 minutes at a cost of US $5,000.” We cannot imagine how easy to get a personal genome sequenced in next 5 years.

So, next question is: What would you do if it became possible to sequence the equivalent of a full human genome for only $1,000? This is the Question of the Year of Nature in 2007, when the whole-genome sequencing is still quite expensive. Personally I like the Ewan’s answer there: Full employment in bioinformatics. Think about it: if you can get your genome sequence in $1, what would you do to that 3,000,000,000 DNA nucleotides?
First of all, you may want to store it (or maybe not, since it’s too large). There are already companied coming out to store the DNA data, like the startup recently invested by Google Ventures, DNAnexus. But question is: who really wants to store all 3G data file, even though the 3G USB just costs less than $1? To only store the difference (between a particular genome and some reference genome), instead of every bit, might be the final solution.
Next, you want to see/visualize it. “Viewing your genomic data on iPhone” is one of such bleeding topics. I am quite serious, Illumina is working on the project with Apple, and even there are working Apps out already.
The most informative thing next is to analysis the data. It’s also the most challenging one. People including myself are working hard on it (That’s why the Uncle Sam invest money on it). Let’s think about this in a non-academic way. More and more companies smell the big cake (first let’s assume it’s a big cake), for example the genotyping-phenotype company like 23andme, the bioinformatics company like GenomeRequest, and just yesterday I read news about a new company called Spiral Genetics (who collect the open source software to do bioinformatics for customers, in a very smart way). Last week, Nature News blog reports the OpenSNP, a website (maybe a company next month) designed by several undergraduate students from U. Washington, they try to build the website to let people share their personal genotype data (from 23andme, deCODEme etc.). It’s a very cool idea!

OK. I know some people might be still questioning whether we need whole-genome sequencing. For individual research, it’s true that not every case needs whole-genome sequencing. But like from old phone to iphone, or from iphone to iphone3G, 4G, 4Gs… do you really need to change your iphone to Iphone 4Gs? You may not, or I am sure practically you don’t need at all. I am still using my wife’s old Nokia, no touch-screen, but very practical. Then why iphone 4Gs are so popular? Because it’s the trend! The lower cost and human’s desire/curiosity/greediness makes it popular. So the same for personal genome sequencing data. The only thing is to show this in an elegant way that even your grandma can understand. That’s the business!

The tide: personal genome sequencing

14 10 2011

I cannot be more excited to share what I read today, all about the personal genome sequencing.

First let’s watch the TED talk by Richard Resnick, CEO of GenomeQuest.

Also, several related companies additional the well-known 23andMe:

Of course, I want to broadcast a blog, http://www.genomesunzipped.org/, written by a group of graduate students, postdoc, and professor etc. from different countries. They wrote very good quality blogs (including the one excited me today, about discussion the possible error in a recent Science paper), and more interesting is that they post their personal SNP data (from above companies) online and you can download and browse the data. Cool?

Ending with what Rick said in his TED talk, “And at the time — this was a few years ago — it cost $100,000. Today it’s $10,000. Next year it’s $1,000. The year after it’s $100, give or take a year. That’s how fast this is moving.” Exactly, that’s how fast this is moving! How about us? and how about me?


18 06 2011



其实自己最近发生了很多事情,只是懒于动笔。人还是应该向前看,像刚刚看完老罗的视频(youku|YouTube),讲他创业2年来的一些感想收获,我每每都看得心有兮兮焉——创业又何尝不是我心中的一个梦?很赞同老罗说的,“我从来都不觉得我有多么勇敢,我只是有一点点勇敢。在普遍怂货的局面下你就显得非常勇敢。就好像你生理上只是正常,但在一群阳痿面前,你就是一个猛男。”很多时候人缺少的就是那么一点点勇气,敢于做自己,敢于去尝试,然后你就显得非常勇敢。像王琦,敢于放下PhD一年去做旅行,我相信他有一天能走到那个岛的(抱歉我总是记不住名字OK, I could finally remind myself — it’s Madagascar)。30岁怎么啦?结婚有孩子又怎么啦?人要怂永远都会怂,人要敢于改变自己永远都有机会改变自己。也借机祝福Akhil,虽然你看不到这些文字(看到也看不懂),祝福你继续走下去,等我稍有心情的时候给你回信。




27 05 2010

btw, 我一直重建一个专门的blog(或者网站),收集各种好玩的小游戏,或者经典笑话,clips,可以让不开心的人进去之后就能开心起来!之前在东大lmbe博客里建了一个,后来跟我的个人blog一起关掉了。现在很多做社区的,做网游的,来头很大,很热闹,但是生活往往并没有那么复杂,就想一个人呆着,就想重温一下超级玛丽,不想去花时间去看那些鱼目混珠的社区网站,简单点,纯粹点,再加上精致点,一切就完美了!


24 03 2010
[16:30:02] … 给你讲个笑话
[16:30:22] … 有两个人去钓鱼
[16:30:56] … 其中一个人钓上来一条美艳的美人鱼
[16:31:02] … 非常漂亮
[16:31:16] … 那个人欣赏了半天
[16:31:31] … 决定把它放回大海
[16:31:41] … 另外一个人很奇怪,问:why?
[16:32:16] … 他耸耸肩,答道:how?

// 听懂了没?今天给老外讲,居然没有人明白,唉!


11 02 2010