Recommended reading for bioinformatics

Question

I'm keen on learning about bioinformatics.

I am ideally looking for a short course introduction, with some practical tasks I can get my teeth into immediately to see if there is any interest in it for me.

I already have a good understanding of molecular biology, so I should be able to skip most of the foundational work.

Any suggestions?

Answer 1

Try MIT OpenCourseware. I see they have a Bioinformatics course here. The course is using MATLAB, so if you have it, it might be interesting.

Answer 2

As unlikely as it sounds, the Bioinformatics for Dummies book is a really good introduction to the tools and practices being used currently, as well as a good intro to the common problems that people are looking to solve and what kind of frameworks they use to solve them.

Answer 3

Essential Bioinformatics by Jin Xiong.

Answer 4

Start by writing a basic sequence-alignment program. You'll get some dynamic programming practice in, as well.

Answer 5

Here's a list:

• collaborate on a research project with a friend or someone that you can meet on the Internet.
• contribute to an open-source Bioinformatics project, like BioPerl or BioRuby.
• read a journal that discusses an algorithm that you find interesting, and try to replicate their results. If you're not at a University, some of the good open-access journals include the PLOS series of journals, old issues of PNAS, and Bioinformatics. Keep in mind that in computer science terms, many bioinformatic algorithms are a little bit boring.
• take your favorite problem from your experience in molecular biology, and do research on it at some of the large databases, like the EMBL or the NCBI. There's a great deal of data out there.

In general it's hard to know what questions to ask when you come to a new field, so if you can find a mentor/collaborator that would be optimal. Barring that, read a lot and pursue what you find interesting. Good luck!

Edit: Since you asked for reading requests, I would recommend this book:

Biological Sequence Analysis

This book is suitable for upper-level undergraduates and graduate students with moderate experience in computation. It's a good reference, and does a very good job explaining the motivating ideas behind some of the more important algorithms in Bioinformatics.

Answer 6

Do you have any special interest in any particular area of "bioinformatics", e.g. sequence analysis, structure, expression, networks, proteomics, population genetics, evolutionary/phylogenetic analyses, ecological modelling, etc.? If so, please say, and you could get more specific pointers.

Answer 7

I'd second the recommendation for Biological Sequence Analysis by Durbin et al, and I'd add a recommendation for Introduction to Computational Genomics by Cristianini and Hahn. It's a slim volume that introduces several of the primary areas of Bioinformatics at a sophmore or junior level. There is an associated web site. I agree that Bioinformatics for Dummies is a useful book, and I own a copy, but I think its focus is really on wet-lab researchers who need to know how to use some of the common bioinformatics tools. The books I recommended are oriented more to folks who want to write their own software, and need to know the gritty details of how the important algorithms work.

Answer 8

Are you a computer scientist or a biologist?

In the latter case, a very good reading is Software Carpentry for bioinformatics:

• http://swc.scipy.org/index.html

it introduces a lot of best practices to programming and to bioinformatics, which usually are not explained in the other textbooks.

Answer 9

Probably the best book in stringology ever made:

• Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology

Quite old, but still very relevant today, especially for bioinformatics.

Answer 10

Hello Matt,

I suppose that you've gotten a good overview of some of the things bioinformaticians do by now. The best next step towards getting into bioinformatics is to dive in by developing a tool that can be useful to people. I'm a bioinformatician surrounded mostly by molecular and behavioral biologists (we work on social behavior in ants) and can think of many small projects that would be appropriate because their aim is to making a bioinformatic approach accessible to non-computational people. Don't hesitate to get in touch if you'd be interested in working together on something.

Answer 11

Because you are asking on Stackoverflow, I assume you want to learn bioinformatics as a programmer and not as a user. An Introduction to Bioinformatics Algorithms may be a good start. It's quite accessible to the novice programmer.

Answer 12

If you are interested in perl programmimg , I suggest you to read Beginning Perl for Bioinformatics.
You can follow the example in this book to study the perl programming and learn how to use this language to solve problems.

Answer 13

"beginning perl for bioinformatics" and "mastering perl for bioinformatics" are two books I use a lot as well as the before mentioned "Bioinformatics Algorithms" I hope that helps.

Answer 14

Late answer, but if you're also interested in getting up to speed on current research, I would recommend taking a look at BMC Bioinformatics and PLoS Computational Biology, both of which are reputable and, more importantly, open access (i.e., you don't need to pay or have a university site license in order to read them). Given your background in molecular biology, they should be very readable to you. Both journals cover a large spectrum of topics in computational biology and bioinformatics.

Edit: One of my favorite books on the subject that is both readable and comprehensive of the field: Understanding Bioinformatics by Zvelebil and Baum.

Answer 15

Equivalent question on biostar (Stack Overflow for bioinformatics): Recommend your favorite bioinformatics books.