4 ms·

Our lab (http://www.hammerlab.org http://www.hammerlab.org) solves computational problems in the domain of cancer immunotherapy. Our open source software (https

Our lab (http://www.hammerlab.org http://www.hammerlab.org) solves computational problems in the domain of cancer immunotherapy. Our open source software (https://github.com/hammerlab https://github.com/hammerlab) is used to create personalized therapeutic vaccines that we are testing in a phase i clinical trial right now. If you are an experienced machine learning engineer and would like to help improve the quality of our vaccines, please send me an email at hammer at hammerlab dot org. We are located in NYC.

chrisamiller 10y ago
I can vouch that the hammerlab is legit and doing solid science! I've had great interactions with members of their lab and have been impressed by their work, as well as their committment to open source and open science (preprints, etc). To piggyback, if you are interested in personalized cancer vaccines, we're also hiring at WashU for a senior scientist position that will be working at least part time on immunotherapy and personalized cancer vaccines. If you're an interdisciplinary person, who knows cancer and can code, drop me a line (c.a.miller at wustl.edu)
teekert 10y ago
Nice work, but as you say, the following: It is common to see these gene sets being referred as pathways and it is for this reason that GSEA is also known as pathway analysis. Will really lead to communication problems with biologist, but you already admit that in the sentence following this one :) For a very long long time, Pathways are the word used by biologists for defined signalling cascades inside cells, to used the same word for a clustered gene set is quite confusing. Your approach is very data driven and as it is you are ignoring a vast sea of literature out there that investigates the relation between signalling pathways and target mRNAs by doing research into (among others) transcription complexes directly (i.e. using CHIP [0]) (like they do i.e. here: [1]). I get that for computer scientists this is perhaps the fastest way to results but I feel such research can be done in a smarter way, by teaming up with biologists. Don't you agree? [0] https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation [1] http://www.ncbi.nlm.nih.gov/pubmed/24695361 http://www.ncbi.nlm.nih.gov/pubmed/24695361
LeicesterCity 10y ago
I'm a recent Biology undergrad. Do you have any advice for learning Comp Bio/Bioinformatics? Can it be self-taught, or does one need a PhD?
- eru 10y ago
  The programming part can definitely be self-taught, that's basically how virtually everybody actually goes about learning programming successfully. You already know some biology, so you can probably say more about that side of the equation.
- sn9 10y ago
  It can definitely be self-taught! A promising path would be to self-teach as much as possible and then apply for an MS program in bioinformatics or something similar. Apart from the usual advice for teaching yourself programming, you can practice bioinformatic-specific skills at the wonderful Rosalind Project [0]. [0] http://rosalind.info/about/ http://rosalind.info/about/

chrisamiller 10y ago

I can vouch that the hammerlab is legit and doing solid science! I've had great interactions with members of their lab and have been impressed by their work, as well as their committment to open source and open science (preprints, etc). To piggyback, if you are interested in personalized cancer vaccines, we're also hiring at WashU for a senior scientist position that will be working at least part time on immunotherapy and personalized cancer vaccines. If you're an interdisciplinary person, who knows cancer and can code, drop me a line (c.a.miller at wustl.edu)

teekert 10y ago

Nice work, but as you say, the following: It is common to see these gene sets being referred as pathways and it is for this reason that GSEA is also known as pathway analysis. Will really lead to communication problems with biologist, but you already admit that in the sentence following this one :) For a very long long time, Pathways are the word used by biologists for defined signalling cascades inside cells, to used the same word for a clustered gene set is quite confusing. Your approach is very data driven and as it is you are ignoring a vast sea of literature out there that investigates the relation between signalling pathways and target mRNAs by doing research into (among others) transcription complexes directly (i.e. using CHIP [0]) (like they do i.e. here: [1]). I get that for computer scientists this is perhaps the fastest way to results but I feel such research can be done in a smarter way, by teaming up with biologists. Don't you agree? [0] https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation [1] http://www.ncbi.nlm.nih.gov/pubmed/24695361 http://www.ncbi.nlm.nih.gov/pubmed/24695361

LeicesterCity 10y ago

I'm a recent Biology undergrad. Do you have any advice for learning Comp Bio/Bioinformatics? Can it be self-taught, or does one need a PhD?

eru 10y ago
The programming part can definitely be self-taught, that's basically how virtually everybody actually goes about learning programming successfully. You already know some biology, so you can probably say more about that side of the equation.
sn9 10y ago
It can definitely be self-taught! A promising path would be to self-teach as much as possible and then apply for an MS program in bioinformatics or something similar. Apart from the usual advice for teaching yourself programming, you can practice bioinformatic-specific skills at the wonderful Rosalind Project [0]. [0] http://rosalind.info/about/ http://rosalind.info/about/