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by persephone74
Dec 6 20201 min read3 answers 2

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I am finishing my first semester of a PhD in genetics with a focus on computational biology, and I'm looking for high-impact thesis topics. I expect that the most impactful areas to research are in alternative proteins or bio security, but I'm not sure. 

I have an undergraduate and master's degree in bioinformatics, and have done several fellowships, most recently at the California Department of Public Health where I focused on antibiotic resistance. 

I'm only interested in dry lab work. I'm most interested in the development of computational methods and models. 

If anyone has thesis topic suggestions, they would be greatly appreciated! 

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Sindy_Li

Dec 19, 2020

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Hey, I'm working on some research on the most impactful areas within ML-aided drug and vaccine discovery. I can share that with you once I'm done.

EdoArad3y2
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Sounds amazing! Could you write a post about it when you're done?

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Tessa

Dec 20, 2020

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I have some biosecurity-related ideas:

You could look into genetic engineering attribution! There were a bunch of EA authors on the The biosecurity benefits of genetic engineering attribution, a useful background paper that came out two weeks ago. altLabs just finished running a data science contest on this problem using AddGene data. They got great results on that contest, so I think now the problem is around how to extend it beyond the AddGene database, how to

There's a ton of interesting work happening in metagenomics for infectious disease surveillance and modelling. I'm no expert in this, but Nextstrain and IDSeq both seem like useful projects.

You could also look into the projects being pursued under IARPA's FunGCAT (can we tell if DNA encodes for something dangerous) and FELIX (can we detect whether an organism was engineered) programs, and look for interesting ways to complement and build upon those projects / publications?

Tessa3y2
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A few more thoughts:

Improving sequence screening tools for gene synthesis providers. NTI is working on a common mechanism to prevent illicit gene synthesis and I think they recently hired a comp bio consultant on that project.

You might also be interested in modelling for environmental use of gene editing? This is maybe more into evolutionary biology, but I'm thinking of some of the groups funding under DARPA's Safe Genes program and people working on reversible or limited-range gene drives.

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BrownHairedEevee

Dec 22, 2020

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Hi! I just took a computational genetics class and I'm really interested in this topic, so I'm glad you're excited to use compgen for social good!

How about using computational methods to study environmental DNA (eDNA)?

1 Related Questions

21
What are the most relevant subdomains of software for biosecurity?
David M
· 2y ago · 1m read
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3Answer by David M1y
Update: 80,000 Hours has now moved 'infosecurity' from a 'sometimes recommended' path to a 'recommended' one
2Answer by Rory Greig1y
I just wrote a relevant forum post on how simulation models / Agent-based models could be highly impactful for pandemic preparedness: https://forum.effectivealtruism.org/posts/2hTDF62hfHAPpJDvk/simulation-models-could-help-prepare-for-the-next-pandemic A crucial aspect of this is better software tools for building large scale simulations, so I would say this is a large opportunity for someone who wants to work in software engineering.  Even just working as a research engineer in an existing academic group building epidemiological models would be impactful in my opinion. The role of research engineer within academia is quite neglected because it tends to pay less than equivalent industry jobs. 
2Answer by Chris Kerr1y
If you have a software engineering background but no particular expertise in biology or information security, then I would suggest trying to find some existing open-source software project which is helpful to biosecurity work and then help to make it more robust and user-friendly. I haven't worked in biosecurity myself, but I can tell you from experience in other areas of biology that there are many software packages written by scientists with no training in how to write robust and usable software, and so there is a lot of low-hanging fruit for someone who can configure automatic testing, use a debugger or profiler, or add a GUI or web front end.  
2
Chris Kerr
1y
Nowadays the amounts have to be extremely large before it is worth the effort of setting up a distributed system. You can fit 1 TB of RAM and several hundred TB of disk space in a commodity 4U server at a price equivalent to a couple of weeks of salary + overhead for someone with the skills to set up a high performance cluster, port your software to work on it, or debug the mysterious errors.
2Answer by Yonatan Cale2y
I have mysterious answers to this which I can't say publicly but people may contact me privately
3
Yonatan Cale
2y
I'd like to point out that often conversations like this in EA send people the wrong way: Things that are "known" to be useful for certain domains are often misleading.  A good example is the misconception that devs need ML experience to contribute to AI Safety (which is wrong).  To avoid this kind of mistake, I recommend finding one or more concrete jobs that seem appealing to you (or companies and ask what they need, or something like that).
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EdoArad3y16
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Did you apply for coaching with Effective Thesis? They can give advice and connect you to experts in the field. See also their topic profile on life science.

You might also be interested in contacting the Cultivated Meat Modeling Consortium for modeling related work. 

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persephone743y1
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I've applied to effective thesis, thanks!

I had not heard of CMMC though – I will have to check it out. Thanks for passing that on.

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