为了更好了了解表观遗传学(Epigenetics)，在这里放了些图例，以方便理解。如果你想了解更多关于Epigenetics的相关背景你可以访问 University of Utah’s Epigenetics training site 或者全能的wikipedia

 

How to become a bioinformatics expert

Why become a bioinformatics expert?

Recent years have seen an explosive growth in biological data. Large sequencing projects are producing increasing quantities of nucleotide sequences. The contents of nucleotide databases are doubling in size approximately every 14 months. The latest release of GenBank (V.102) exceeded one billion base pairs. Not only the size of sequence data is rapidly increasing, but also the number of characterized genes from many organisms and protein structures doubles about every two years. To cope with this great quantity of data, a new scientific discipline has emerged: bioinformatics, biocomputing or computational biology.

But how to become a bioinformatics expert?

Bioinformatics combines the tools and techniques of mathematics, computer science and biology in order to understand the biological significance

A reasonably thorough table of next-gen-seq software available in the commercial and public domain
Source: http://seqanswers.com/forums/showthread.php?t=43

Integrated solutions
1. CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux.
2. Galaxy - Galaxy = interactive and reproducible genomics. A job webportal.
3. Genomatix - Integrated Solutions for Next Generation Sequencing data analysis.
4. JMP Genomics - Next gen visualization and statistics tool from SAS. They are working with NCGR to refine this tool and produce others.
5. NextGENe - de novo and reference assembly of

    今年还是犒劳一下自己买了一辆自行车，主要是想运动一下。工作的地除了早上走30分钟的路程，基本不知道这儿是长啥样的（晚上通常都一两点才回去，看到的只能是星空了）。

    昨日，吃过午饭就出发了，没有计划，来次无目的无方向的小旅程。首先穿过的是邻近的小区，那有个绿葱葱的大草坪，自然少不了富家女在溜狗，我想在这里看书也不错，不过还欠点静谧。出到公路，看到对面已是中央美院，我被旁边整齐的柳树道吸引了过去，这些柳树都剪得齐刷刷的，就像小时候剪的窝盖头，骑着车，头刚好在柳叶子下，风吹一下，宛若一缕绿丝划过。走到了尽头，折返，寻觅他处。没有选择却迂回的走过长长的公路，看到出现了一条村庄土路，虽然都是土石路，却不喜在公路上吸尾气，就拐了进去。颠颠跛跛，就进村了，看来北京的农村跟南方的差不多，只是墙矮了些，里面都是那么破落，带总能感觉到些暖和，有时能看到些节日的彩带烟花爆竹散落的碎纸片，鸡犬相鸣，妇人们七嘴八舌的谈话，只是在这里比南方安静了很多。不一会儿我就穿梭出去了，村落很小，但很平和。

    走出了村路，看到远处，原来还有几个很漂亮的小区，估

大多数开发人员通常都有这个观点，即汇编语言和 C 语言适合用来编写对性能要求非常高的程序。而 C++ 语言的主要应用范围是编写复杂度非常高的程序，但是对性能要求不是那么严格的程序。但是事实往往并非如此，很多时候，一个程序的速度在框架设计完成时大致已经确定了，而并非是因为采用了C++语言才使其速度没有达到预期的目标。因此当一个程序的性能需要提高时，首先需要做的是用性能检测工具对其运行的时间分布进行一个准确的测量，找出关键路径和真正的瓶颈所在，然后针对瓶颈进行分析和优化，而不是一味盲目地将性能低劣归咎于所采用的语言。事实上，如果框架设计不做修改，即使用C语言或者汇编语言重新改写，也并不能保证提高总体性能。
因此当遇到性能问题时，首先检查和反思程序的总体框架。然后用性能检测工具对其实际运行做准确地测量，再针对瓶颈进行分析和优化，这才是正确的思路。
但不可否认的是，确实有一些操作或者C++的一些语言特性比其他因素更容易成为程序的瓶颈，一般公认的有如下因素。
（1）缺页：如第四章中所述，缺页往往意味着需要访问外部存储。因为外部存储访问相对于访问内存或者代码执行，有数量级的差别。因此只要有可能

    昨晚，工作到11点，独自跨度走回小区住处。外面下着蒙蒙细雨，雾（可能是霭）很大。临近门口，一只白乎乎的东西“啾”一声从路面穿进草丛，直到一层楼房下的避荫住。夜很静，连灯光都已像星空一样稀疏，所以本能的愣了一下。往下面寻觅，只听一声细腻而腼腆的声音“喵”，我好奇心起，我喜欢小动物，尤其是猫科的。于是也应声叫了一声，伸过手去向它招了招，没想到它竟走了过来，用它的胡须和脸在我的指端和手侧轻抚了一下。我捊了一下它的头毛，跟它玩了起来。然后就离开了。没想，我上楼时，它也跟了上来，我打开了门，它犹豫了一下，我想起前天还有吃泡面剩下的火腿肠，于是赶紧撕开了一根，诱使它一下，果然，它就进屋了。我把门关上后，它开始有点紧张，环绕着房子四处打探了一下，就躲在沙发里了，我把火腿肠弄成一小段一小段，唤了几次它，就马上凑过来，屡试不爽，于是我跟它玩闹在一起。因为它长得很像我以前养过的一只白猫，叫“大白”，我叫了它好几个名字都不怎么搭理，只好不客气的叫“小白”了，可能因为食物之故它也适应了。

    我把它捧上沙发，玩起来，没多久它就睡着了，唯一调皮的是，只要你抓它的爪

Introductory Books
 1. Introduction to Bioinformatics: A Theoretical and Practical Approach by Stephen A., Krawetz and David D.
 2. Introduction to Computational Molecular Biology by Joao Carlos Setubal, Joao Meidanis, Jooao Carlos Setubal
 3. Bioinformatics for Dummies by Jean-Michel Claverie, Cedric Notredame
 4. Developing Bioinformatics Computer Skills by Cynthia Gibas, Per Jambeck
 5. Beginning Perl for Bioinformatics by James Tisdall
General Bioinformatics Books (Including Genomics)
 1. A Primer of Genome Science by Gibson G and Muse SV
 2. Bioinformatics : A Biologist's Guide to Biocomputing and the Internet by Stuart M. Brown
 3. Bioinformatics Basics Applications in Biological Science and Medicine by Hooman H. Rashidi, Lukas K. Buehler
 4. Bioinformatics: Methods and Protocols by Stephen Misener, Stephen A. Krawetz
 5. Bioinformatics : Sequence

2007

High-throughput Paired-End Sequencing like 454, solexa, and SOLiD. Paired-End Mapping to the reference genome to find structural variation.
Korbel et al., Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome Science, 27 September 2007 (10.1126/science.1149504).
Structural rearrangements were identified as significant differences between the fragments identified by the paired-end reads and the corresponding regions of the reference sequence.
Strategies:
Five different signatures(i-v)were used to predict SVs.
(i)Deletions relative to the reference genome were identified by paired-ends spanning a genomic region in the reference genome longer than a specified cutoff;
(ii)Simple insertions relative to the reference genome werepredicted with paired-ends that spanned a region shorter than a cutoff;
(iii)Mated insertions contained sequences connected to a distal locus on the basis of their paired-ends;
(

(1)GTG-banded karyotype
The gold standard for clinical cytogenetic testing still remains the GTG-banded karyotype, where a genomewide analysis usually identifies chromosomal rearrangements or aberrations of 3–5 Mb and larger.


(2)Array-based approach (array CGH/ROMA, SNP oligonucleotide microarray)
*ROMA, representational oligonucleotide microarray analysis

2004 Two initail studies using CGH technology:
used a bacterial artificial chromosome (BAC)-based array, with clones chosen at 1-megabase (Mb) intervals throughout the human genome, together with a technique called array-based comparative genomic hybridization (array CGH);

Comparative genomic hybridization (CGH) is a molecular-cytogenetic method for the analysis of copy number changes (gains /losses) in the DNA content of tumor cells. The method is based on the hybridization of fluorescently labeled tumor DNA (frequently Fluorescein - FITC) and normal DNA (frequent

Principles of Genome Analysis and Genomics. Blackwell Science, Inc.. 1405101202.

Proceedings -1st Intl Conf on Intelligent Systems for Molecular Biology. 1993. The AAAI Press. 0929280474.

Proceedings -2nd Intl Conf on Intelligent Systems for Molecular Biology. 1994. The AAAI Press. 0929280687.

Proceedings- 3rd Intl Conf on Intelligent Systems for Molecular Biology. 1995. The AAAI Press. 0929280830.