木双日记：请问有计算生物学方面的资料吗？计算基因组和计算神经科学之类的。 谢谢

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私信

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概念

计算生物学 http://en.wikipedia.org/wiki/Computational_biology Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems.

生物信息学 http://en.wikipedia.org/wiki/Bioinformatics Bioinformatics Listeni/ˌbaɪ.oʊˌɪnfərˈmætɪks/ is an interdisciplinary field that develops methods and software tools for understanding biological data.

计算基因 http://en.wikipedia.org/wiki/Computational_genomics Computational genomics (often referred to as Computational Genetics) refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data,[1] including both DNA and RNA sequence as well as other "post-genomic" data (i.e. experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays).

http://en.wikipedia.org/wiki/Computational_and_Statistical_Genetics The interdisciplinary research field of Computational and Statistical Genetics uses the latest approaches in genomics, quantitative genetics, computational sciences, bioinformatics and statistics to develop and apply computationally efficient and statistically robust methods to sort through increasingly rich and massive genome wide data sets to identify complex genetic patterns, gene functionalities and interactions, disease and phenotype associations involving the genomes of various organisms.

计算神经科学 http://en.wikipedia.org/wiki/Computational_neuroscience Computational neuroscience is the study of brain function in terms of the information processing properties of the structures that make up the nervous system.

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http://www.bio-complexity.com/QUBsscb13/QUBsscb.html Summer School in Computational Biology (2013)

• check out related lectures
• http://www.bio-complexity.com/QUBsscb14/Home.html 2014 version

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问题209进展 https://github.com/memect/hao/issues/209 想必你已经看过维基百科相关介绍了，可以先看看这个 http://www.bio-complexity.com/QUBsscb13/QUBsscb.html Summer School in Computational Biology (2013) 不用都读，先过一遍达成初步印象再细读

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Recommendation from expert in this domain

Here some some slides from books (both are great):

1. http://bix.ucsd.edu/bioalgorithms/ (They don't maintain it anymore. but still have a lot slides)
2. http://www.comp.nus.edu.sg/~ksung/algo_in_bioinfo/ (they also have all the slides)

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https://www.coursera.org/course/bioinformatics Bioinformatics Algorithms (Oct 10,2014-Jan 12, 2015)

This course is the first in a two-part series covering some of the algorithms underlying bioinformatics. It will cover some of the algorithms underlying the following fundamental topics in bioinformatics: assembling genomes, comparing DNA and protein sequences, finding regulatory motifs, analyzing genome rearrangements, identifying proteins, and many other topics.

Course Syllabus The course will be based on six "chapters" covering the following central questions, with the algorithmic ideas that we will use to solve them in parentheses:

Where Does DNA Replication Begin? (Algorithmic Warm-up)
How Do We Sequence Antibiotics? (Brute Force Algorithms)
Which DNA Patterns Act As Cellular Clocks? (Greedy and Randomized Algorithms)
How Do We Assemble Genomes? (Graph Algorithms)
How Do We Compare Biological Sequences? (Dynamic Programming Algorithms)
Are There Fragile Regions in the Human Genome? (Combinatorial Algorithms)

The grading for the course will be based on several weekly programming challenges, as well as a comprehension quiz at the end of each chapter.

Bioinformatics Algorithms (Part 2) will be based around the following questions:

Which Animal Gave Us SARS? (Evolutionary Trees)
How Do We Locate Disease-Causing Mutations? (Combinatorial Pattern Matching)
How Did Yeast Become Such a Good Wine Brewer? (Clustering Algorithms)
Why Do We Still Not Have an HIV Vaccine? (Hldden Markov Models)
Was T-Rex Just a Big Chicken? (Computational Proteomics)
What Genetic Characteristics Do Human Populations Share? (Principal Components Analysis)

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textbook "Bioinformatics Algorithms: an Active Learning Approach" http://bioinformaticsalgorithms.com/

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old book "An Introduction to Bioinformatics Algorithms"

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一张图表解析生物信息学中算法的实际应用(摘自"An Introduction to Bioinformatics Algorithms"）同时推荐该书作者Pavel Pevzner (UCSD教授, ACM院士) Coursera公开课Bioinformatics Algorithms (今年10月开课) http://memect.co/LXVPbgn YouTube教学视频 http://memect.co/r5gosNm 需要较强的数学及算法基础

http://www.weibo.com/5220650532/BorSV49Fo?ref=

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http://www.zhihu.com/question/20543692/answer/30117762 如何自学生物信息学？

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http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002632 An Online Bioinformatics Curriculum （2012） David B. Searls

Abstract

Online learning initiatives over the past decade have become increasingly comprehensive in their selection of courses and sophisticated in their presentation, culminating in the recent announcement of a number of consortium and startup activities that promise to make a university education on the internet, free of charge, a real possibility. At this pivotal moment it is appropriate to explore the potential for obtaining comprehensive bioinformatics training with currently existing free video resources. This article presents such a bioinformatics curriculum in the form of a virtual course catalog, together with editorial commentary, and an assessment of strengths, weaknesses, and likely future directions for open online learning in this field.

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问: 有计算生物学方面的资料吗？计算基因组和计算神经科学之类的。 答: David Searls 总结了一个比较全面的列表,覆盖几十门名校(MIT, Stanford, Harvard, Berkeley, Yale, ...)四大类(生物系，计算机写，数学写，其他写) 的生物信息学相关课程 (An Online Bioinformatics Curriculum, 2012) http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002632

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http://www.computational-genomics.net/ Introduction to Computational Genomics: A Case Studies Approach Nello Cristianini, Matthew W. Hahn

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http://biochem218.stanford.edu/

• Computational Molecular Biology

Biochemistry 218 - BioMedical Informatics 231

Doug Brutlag, Rhiju Das, Gavin Sherlock, Mike Snyder, and Peter Karp

Spring Quarter 2013-2014

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我在 @知乎 回答了【如何自学生物信息学？】：现在又诸多的网络课程，所以你可以自学的。 PLOS Computational Biology: An Online Bioinformatics Curriculum 这个链接很全，很实用 http://t.cn/RhUiysg

http://www.weibo.com/1862168475/Blps2fFDK

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计算神经科学 Computational Neuroscience 资源整理

http://home.earthlink.net/~perlewitz/ Computational Neuroscience on the Web

• 资源门户网站(学者,论文,课程一网打尽)
• This site provides an annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. One can locate modeling software and that for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. There are links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.

http://www.ccnss.org/

• 计算神经科学暑期学校(2010至2014共5期)

https://www.coursera.org/course/compneuro

• 华盛顿大学公开课 "Computational Neuroscience"

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http://www.ccnss.org/materials.html

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http://www.frontiersin.org/computational_neuroscience

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问: 求计算神经科学资料? 答: 1. 资源门户网站(学者,论文,课程一网打尽) "Computational Neuroscience on the Web" http://home.earthlink.net/~perlewitz/ 2. 暑期学校(2010至2014共5期) http://www.ccnss.org/index.html 3. 还有华盛顿大学公开课 "Computational Neuroscience" 谢 @苏梦Neuro-Gatsby @课程图谱 @要有光LTBL 推荐

http://www.weibo.com/5220650532/BoAQg5kj6?ref=

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@苏梦Neuro-Gatsby ：Cold Spring Harbor Asia, Suzhou, Computational and Cognitive Neuroscience Summer School http://t.cn/8F8yTcu http://www.weibo.com/1650783775/AxIRUqq3b

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@课程图谱

公开课点评# 华盛顿大学的 Computational Neuroscience @要有光LTBL 大神的点评：“印度老师很幽默，女老师有点像冷血女杀手酷酷的感觉，讲得很细致，尤其指出了现有神经网络模型和人脑之间的一些区别，我觉得在这方面改进可能是未来的发展方向”http://t.cn/zRVGVUG 相关视频http://t.cn/z82mFrz

http://www.weibo.com/3369755644/AeqCoitt6