3 ms·

More specifics about what you're interested in? I work in the space (human genetics - we analyse the output of 1000 Genomes) and happy to help, but "bioinformat

by bthomas 15y ago

More specifics about what you're interested in? I work in the space (human genetics - we analyse the output of 1000 Genomes) and happy to help, but "bioinformatics" is pretty broad. I'll also note so much of the human genetics space is so new that most knowledge is still couped up in academic papers - there aren't very good resources for the general public. A colleague helped edit a textbook in 2007 on genetic analysis (which would still be considered "new" in textbook space), and none of the tools in that book can be used with 1000 genomes data.

mlwarren 15y ago
Maybe some broad-sweeping entry level books or literature reviews would be good. For me (and possibly many others on hn), the extent of my knowledge in the field as a whole is pretty small so I think some introductory resources geared towards someone coming from a strong software or math background would be best.
- aheilbut 15y ago
  "Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by Durbin, Eddy, Krogh, and Mitchison is a classic, very readable intro to sequence analysis algorithms (dynamic programming, HMMs) that would be interesting for someone coming from a math/cs background.
- bthomas 15y ago
  (The following are all for genetics, others can chime in on other areas or bioinformatics in general.) -- I'm bias, but I think the best entry level book is still from 1998 - Genome by Matt Ridley [1]. It's what got me interested in genomics as a CS undergrad (I read it in 2009). Another decent one is The $1000 Genome [2], it gives a good cross section of genetics in 2010. -- Our group has a series of intro lecture videos from last academic year [3]. They are fairly up to date, and this year's videos will probably be posted soon. -- Genomes Unzipped is great if you prefer a blog [4] -- I think the best way to actually learn this stuff is to just play with the software tools. They all point to open data in the tutorials. Biopython's tutorial is particularly good - just google the biological terms as you go. Bioconductor has some good (though more targeted) tutorials too. -- Going to talks can be a great way to get a broad overview of the space. Drop me a note if you happen to be located in Boston. -- Finally, this goes without saying, but don't take articles in the mainstream media at face value. (Including, and in fact in particular, the NYT.) Every time I get together with relatives I have to argue against the latest grand prediction. [1] http://www.amazon.com/Genome-The-Autobiography-Species-Chapters/dp/0060932902 http://www.amazon.com/Genome-The-Autobiography-Species-Chapt... [2] http://www.amazon.com/The-000-Genome-Revolution-Personalized/dp/1416569596 http://www.amazon.com/The-000-Genome-Revolution-Personalized... [3] http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/primers/primer-medical-and-pop http://www.broadinstitute.org/scientific-community/science/p... [4] http://www.genomesunzipped.org/ http://www.genomesunzipped.org/
  - joeroot 15y ago
    Thanks a lot for these - been looking for a solid set of resources on this for a while.

by bthomas 15y ago

mlwarren 15y ago

Maybe some broad-sweeping entry level books or literature reviews would be good. For me (and possibly many others on hn), the extent of my knowledge in the field as a whole is pretty small so I think some introductory resources geared towards someone coming from a strong software or math background would be best.

aheilbut 15y ago
"Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids" by Durbin, Eddy, Krogh, and Mitchison is a classic, very readable intro to sequence analysis algorithms (dynamic programming, HMMs) that would be interesting for someone coming from a math/cs background.
bthomas 15y ago
(The following are all for genetics, others can chime in on other areas or bioinformatics in general.) -- I'm bias, but I think the best entry level book is still from 1998 - Genome by Matt Ridley [1]. It's what got me interested in genomics as a CS undergrad (I read it in 2009). Another decent one is The $1000 Genome [2], it gives a good cross section of genetics in 2010. -- Our group has a series of intro lecture videos from last academic year [3]. They are fairly up to date, and this year's videos will probably be posted soon. -- Genomes Unzipped is great if you prefer a blog [4] -- I think the best way to actually learn this stuff is to just play with the software tools. They all point to open data in the tutorials. Biopython's tutorial is particularly good - just google the biological terms as you go. Bioconductor has some good (though more targeted) tutorials too. -- Going to talks can be a great way to get a broad overview of the space. Drop me a note if you happen to be located in Boston. -- Finally, this goes without saying, but don't take articles in the mainstream media at face value. (Including, and in fact in particular, the NYT.) Every time I get together with relatives I have to argue against the latest grand prediction. [1] http://www.amazon.com/Genome-The-Autobiography-Species-Chapters/dp/0060932902 http://www.amazon.com/Genome-The-Autobiography-Species-Chapt... [2] http://www.amazon.com/The-000-Genome-Revolution-Personalized/dp/1416569596 http://www.amazon.com/The-000-Genome-Revolution-Personalized... [3] http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/primers/primer-medical-and-pop http://www.broadinstitute.org/scientific-community/science/p... [4] http://www.genomesunzipped.org/ http://www.genomesunzipped.org/
- joeroot 15y ago
  Thanks a lot for these - been looking for a solid set of resources on this for a while.