Current overview of bioinformatics?

November 9, 2021 12:49 PM

What are some good current introductions to the enormous field of bioinformatics? I've had recommended Biological sequence analysis: probabalistic models of proteins and nucleic acids, Durbin et al., but this came out in 1998. Is it a classic I should read anyway? What else should I look at? Fairly technical is OK. Thanks!
posted by 8603 to Science & Nature (6 answers total)

IMO it's really not much of a field for classic textbooks unless you want to understand how certain algorithms work rather than how to use programs that depend on those algorithms. New tools replace old ones fairly frequently, and the sheer number of tools expands and fragments all the time. A key skill set for me right now is being able to locate and troubleshoot poorly documented software that is definitely not covered in books, because it was written by like, one lab's postdoc who's now moved on to other things. But I've heard decent things about The Biostar Handbook, and there's a very active community at r/bioinformatics.
posted by deludingmyself at 1:10 PM on November 9, 2021 [7 favorites]

I second The Biostar Handbook and would also recommend biostars.org more generally for troubleshooting and tutorials (I personally don't look at r/bioinformatics much).

A more up to date textbook in line with the Durbin et al. one you mention might be Bioinformatics Algorithms by Compeau and Pevzner that goes along with the exercises on rosalind.info. This text is also used in a popular Coursera specialization on bioinformatics. I would only recommend this text if you want a more hands-on learning experience though, and not all types of bioinformatics work require such an in-depth understanding of algorithms (though it's beneficial).

The textbook I was assigned in my undergrad "intro to genomics and bioinformatics" course back in ~2012 was "Introduction to Genomics" by Arthur Lesk but I don't know if I'd say it's a definitive text so much as a broad overview (which sounds like it might be what you're looking for?).
posted by Oliva Porphyria at 1:57 PM on November 9, 2021 [1 favorite]

I did my PhD with a heavy focus on bioinformatics (but notably, in an academic department where bioinformatics is not normally used so I had no resources in the forms of fellow researchers/professors), so I basically taught myself everything.

Here was my approach to learn bioinformatics and do research using those tools:

- Took a survey course in bioinformatics (which used this textbook by Pevsner... it was fine, although very wordy and basically instantly out-of-date). This was somewhat good for understanding the broad strokes, but it didn't really help me figure out what *I* needed to do.
- Read a LOT of journal articles. There's a lot of good review articles, but it depends on what you're looking for. Clinical epidemiology using whole genomes? Environmental monitoring of DNA (i.e. metagenomics)? Something more on the protein/metabolomics side (I know less about that)?
- Got comfortable using command line.
- Worked through the Biostar Handbook to understand *how* to do things on the computer, through command line. I'll note that the Biostar Handbook skews heavily toward clinical stuff, whole genome analysis, but it is highly recommended if you want to actually do analysis.
- Looked back at the articles I read to piece together how to do the kinds of analyses I saw in publications.
- Learned python to write my own scripts for analysis, on top of using software that's available.
- Googled every error message I got until things worked. Biostars.org as also mentioned is also great.

Obviously YMMV depending on whether you need to actually *do* bioinformatics or if you just want to understand it conceptually and read about fun new research.
posted by Paper rabies at 2:19 PM on November 9, 2021 [3 favorites]

Woot! I reviewed Durbin's book for embnet.news when it came out in 1998. tl;dr: "You get a lot of meat for your 20 pounds but you have to chew it well to benefit." If your definition of "Bioinformatics" is "the analysis of biological sequences" - which is quite old style - then I found Claverie & Notredame's Bioinformatics for Dummies is easier to digest. I don't think either of them cover genomes and the -omics. It's an exponential world out there. My first [1992] binfo paper was a considered analysis of all 45 available gene sequences from one species of fungus. Exactly 10 years later, I got the half-share of a PhD student who'd just completed a similar analysis for their MSc on 40 genomes of thermophilic bacteria. Kids now are probably knocking off biomes on their phones.
posted by BobTheScientist at 3:28 PM on November 9, 2021 [4 favorites]

I second The Biostar Handbook and would also recommend biostars.org more generally for troubleshooting and tutorials (I personally don't look at r/bioinformatics much).

Yeah, to clarify: r/bioinformatics has a lot of people who are in a similar position of trying to figure out whether this field is for them. biostars.org has a lot of people trying to figure out how to solve a specific problem.
posted by deludingmyself at 6:07 PM on November 9, 2021 [2 favorites]

Response by poster: Thanks, folks! I got a copy of the Biostar Handbook and an older edition of Bioinformatics Algorithms (Compeau and Pevsner). The other Pevsner book is available online at my library, so I'll take a look after I get done with the others.
posted by 8603 at 8:50 AM on November 14, 2021