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There's a whole branch of CS, bioinformatics, which would be more confused if you did NOT ask the questions with biological structures involved. The field of s

There's a whole branch of CS, bioinformatics, which would be more confused if you did NOT ask the questions with biological structures involved. The field of string algorithms, or "stringology" as they whimsically call it, is also heavily focused on DNA. I was planning to study bioinformatics in my youth. Life events intervened and I had to do a regular software engineering degree instead, but I still have an unreasonable love for the Burrows-Wheeler transform.

dekhn 5y ago
What you say doesn't really make sense. For example, BWT has nothing specific to do with bioinformatics. It's used in bzip compression, of course, but a wide range of other things, predating its use for genome analysis. I think the way I'd put it is, DNA sequence analysis benefitted greatly from the wide range of algorithms creatd for string processing- everything from fast string search (boyer moore) to dynamic programming to forward-backward alogirhtm for HMMs. But there's very little, if at all, stringology done that's purely DNA specific.
- vintermann 5y ago
  Yes, I know BWT has nothing specific to do with bioinformatics, but BWT-based compressed indices for bioinformatics is its main practical application today (bzip2 isn't competitive any longer, no one is more sorry about that than me!) But it's a good example of the thing I say: Even for pure math papers related to BWT, odds are good they use DNA as an example. I wouldn't be "thrown for a loop" at all from your clever bio-themed interview questions, and there are a lot of people like me. Maybe not who love BWT as much, but who in exchange have actually studied bioinformatics. I'm not sure we're better candidates for it, so you're bringing in some questionable bias.
  - dekhn 5y ago
    Maybe. But since you're a BWT nerd, you'll enjoy my story. I used to work at Google and was well-placed at a key time, sitting near Jeff Dean and Sanjay Ghemawat while launching Google Cloud Genomics. One day, I invited Richard Durbin (one of the innovators in using BW for genomics) to stop by and give Jeff and Sanjay a quick update on his work in sequence compression and indexing. it was great to be a fly on that wall. At the end of the talk I mentioned that Burrows of Burrows-Wheeler was just down the hall if Richard wanted to chat with him as well. Unfortunately Mike wasn't in the office that day, otherwise I would have been able to cross "Be present when the inventor of an important and subtle algorithm meets a user who has applied it for state of the art research in an unexpectedly productive way" off my bucket list. As for the bias, sure, but it's fairly small, and I can adjust on the fly to give every candidate a reasonable attempt to solve the problem. I can also give the problem without any reference to biology

dekhn 5y ago

What you say doesn't really make sense. For example, BWT has nothing specific to do with bioinformatics. It's used in bzip compression, of course, but a wide range of other things, predating its use for genome analysis. I think the way I'd put it is, DNA sequence analysis benefitted greatly from the wide range of algorithms creatd for string processing- everything from fast string search (boyer moore) to dynamic programming to forward-backward alogirhtm for HMMs. But there's very little, if at all, stringology done that's purely DNA specific.

vintermann 5y ago
Yes, I know BWT has nothing specific to do with bioinformatics, but BWT-based compressed indices for bioinformatics is its main practical application today (bzip2 isn't competitive any longer, no one is more sorry about that than me!) But it's a good example of the thing I say: Even for pure math papers related to BWT, odds are good they use DNA as an example. I wouldn't be "thrown for a loop" at all from your clever bio-themed interview questions, and there are a lot of people like me. Maybe not who love BWT as much, but who in exchange have actually studied bioinformatics. I'm not sure we're better candidates for it, so you're bringing in some questionable bias.
- dekhn 5y ago
  Maybe. But since you're a BWT nerd, you'll enjoy my story. I used to work at Google and was well-placed at a key time, sitting near Jeff Dean and Sanjay Ghemawat while launching Google Cloud Genomics. One day, I invited Richard Durbin (one of the innovators in using BW for genomics) to stop by and give Jeff and Sanjay a quick update on his work in sequence compression and indexing. it was great to be a fly on that wall. At the end of the talk I mentioned that Burrows of Burrows-Wheeler was just down the hall if Richard wanted to chat with him as well. Unfortunately Mike wasn't in the office that day, otherwise I would have been able to cross "Be present when the inventor of an important and subtle algorithm meets a user who has applied it for state of the art research in an unexpectedly productive way" off my bucket list. As for the bias, sure, but it's fairly small, and I can adjust on the fly to give every candidate a reasonable attempt to solve the problem. I can also give the problem without any reference to biology