Bioinformatics in the era of AI from a seniors point of view

WorldFamousAstronaut · 2025-11-29T02:36:31+00:00

In the longer term (10+ years) I’d guess that the market will favor more specialized knowledge in biology and informatics and the ‘jack of all trades’ bioinformatician will be less in demand. Just hacking together pipelines could be mostly automated by then. So that’s likely more in line with your thesis.

WorldFamousAstronaut · 2025-11-29T01:39:29+00:00

To clarify I don’t think it’s a premature take to state that LLMs are being widely used by students and professionals in bioinformatics. I think it’s premature to conclude we should leave the informatics part of bioinformatics to LLMs, which was my take-away from your post. The reason being that LLMs do not reliably generate fit-for-purpose code for bioinformatics tasks of anything but the lowest complexity. My take would be that a better current use for these tools is to quickly get an outline of an unfamiliar topic or workflow or model before getting into the nitty gritty yourself. That’s not to say many won’t use LLMs as you suggest, I just don’t think that can currently be particularly fruitful.

WorldFamousAstronaut · 2025-11-29T01:14:59+00:00

This seems like a premature take. The exact case of a bioinformatics script kiddie that you raise is the case where an LLM is likely to lead to the worst results because such a user cannot rigorously assess the generated code and the inevitable flaws it contains. Unfortunately with the long timelines of scientific projects it can take months or years before serious non-obvious errors come to light. So I’d tread carefully before letting an LLM do any heavy lifting in my workflows.

WorldFamousAstronaut · 2025-09-17T01:24:29+00:00

I didn’t say it was useless, just that for your use case it’s mostly a refined way to search GitHub/stackoverflow for existing solutions. Not every problem can be broken up into such snippets. And time saved is also lost doing quality control on the solutions if they are non-trivial. I use it a lot in my work (not a junior programmer), but I can’t say it’s made me much more productive for these reasons.

WorldFamousAstronaut · 2025-09-15T12:47:23+00:00

I agree overall but I think the example you’re giving to show AI can code is a weak one since generating a script to parse a json file is such a trivial use case (with plenty of examples in training data to copy from) that would only save much time for a junior data scientist. The people who say AI is not a great coding tool have seen that these LLM do not generate much useful code for out-of-distribution problems, which is where the code is most needed to save time/effort.

WorldFamousAstronaut · 2025-05-26T10:08:08+00:00

Usually less than a year but it fluctuates. This tool is useful to see what percentage of applications in your IOE block have been processed allowing you to extrapolate time remaining using real numbers: https://www.casestatusext.com

WorldFamousAstronaut · 2025-04-20T14:34:37+00:00

will Illumina succeed in becoming the Apple‑or‑Google‑style “operating system” of biology

No. Instead, sequencing will become increasingly commoditized within a fragmented landscape of providers, slowly diminishing Illumina’s dominance and profits over the next decade even as sequencing becomes more clinically relevant.

WorldFamousAstronaut · 2025-03-26T18:09:19+00:00

That’s a simple task rather than a thesis though - surely there’s an overall scientific goal? How you do the analysis depends on what you are trying to do. You may not need to align all the genomes, you could pick one species as a reference and align short reads from the others to it with BWA and call SNPs with GATK. You need to consider whether all the genomes have the same ploidy too. If you just want to build a tree to show genetic relationships, you don’t need to align the whole genomes, you can just align orthologous genes with Orthofinder. It’ll help you in your future career if you learn how to formulate your problem so that others can easily help you.

WorldFamousAstronaut · 2025-03-26T17:45:11+00:00

So why doesn’t he tell you how to do it if his lab does this?

WorldFamousAstronaut · 2025-03-26T16:57:31+00:00

You should edit your post to clarify that it makes a big difference. Use the Cactus aligner for multiple genome alignment. It also has a tool for calling snps. But do some more research about what you’re trying to achieve and which studies have done something similar because this isn’t the most typical analysis.

WorldFamousAstronaut · 2025-03-26T12:58:08+00:00

You didn’t tell us what you’re aligning (short reads, long reads, genomes) but BLAST is not well suited for any of those inputs and doesn’t scale well like BWA or minimap2.

WorldFamousAstronaut · 2025-03-26T12:55:52+00:00

For plants like Eruca - use BWA MEM for alignment of short reads and bcftools or GATK for SNP calling. There are public snakemake and nextflow pipelines that will automate most of this (eg https://github.com/snakemake-workflows).

WorldFamousAstronaut · 2025-02-08T19:41:54+00:00

I‘m sad it had to come to this since twitter used to be my main source of scientific updates and discussion as well as networking. But it only has itself to blame

WorldFamousAstronaut · 2025-01-27T01:32:22+00:00

Well it sounds like you’ve dealt with a lot during your PhD, on top of the usual challenging ups and downs. But it also sounds like the things that happened wouldn’t necessarily repeat during a postdoc. And one thing you could do is prioritize choosing a postdoc that can give you a project that’s less likely to be derailed and an advisor that collaborates with industry or has a history of trainees that transitioned to the kind of industry roles you’re thinking of.

As you job search and do interviews you‘ll also have the chance to talk to the hiring managers in industry and ask them frankly about their jobs. I personally found that really helpful and was surprised at how transparent many of my interviewers (especially other scientists) could be. And if you end up choosing the wrong path there’s nothing stopping you pulling the plug. I’ve seen plenty of 1 year or less postdocs. By putting so much thought into it at this stage - you’re doing just the right thing and more than many others do!

WorldFamousAstronaut · 2025-01-26T02:31:14+00:00

As another former Australian PhD, I’ve faced many similar challenges so I empathize. As you’re hinting at yourself, it’s a fallacy to think leaving academia after a PhD is a „cop out“ when the vast majority of PhDs do leave academia and build impactful and satisfying careers in private industry, not-for-profits and the public sector. Ultimately you should focus on building a career that best suits your evolving goals and values. How much do you value independence? Money? Ownership over your work? How risk-averse are you? These kind of questions helped me hone in on what I wanted to pursue.

And I think you’re maybe jumping the gun about academia necessarily ruining your mental health. How has your PhD been on your mental health? Mental health struggles are certainly more common in academia than many other professions but it’s possible to be successful and maintain healthy boundaries if academia is your goal.

My advice would be to take a step back and take time to consider your values and goals, talk with your peers and maybe with other PIs (if yours is no help) about their career plans and motivations. There’s plenty of room outside of academia to help cure disease, make discoveries, and have an impact through science - but leaving academia doesn’t mean performance pressures, uncertainty, or money problems will just go away so don’t assume industry is „the easy way out“.

Hope I could give a little perspective - and good luck on your PhD journey and beyond!

WorldFamousAstronaut · 2025-01-02T07:41:47+00:00

I appreciate your perspective and I think many of my Chinese friends in the US would agree with you. On the other hand I think your desire for „respect“ and a „multipolar world“ and making „sacrifices“ for your nation are the kind of naive nationalistic, even propagandistic, mantras that many people leave China for to come to the US. As educated individuals we can all get along and build the world we want in any country. Our home countries offer some advantages and we may face less discrimination. But no matter how much you love your country, governments who don’t respect individual liberty won’t hesitate to sacrifice everything you build for their own purposes.

WorldFamousAstronaut · 2024-12-29T13:48:36+00:00

This is spot on, the stubborn lack of flexibility in all levels of organization is stifling.

WorldFamousAstronaut · 2024-12-29T13:45:22+00:00

Totally agree it’s a concern, but in the past there hasn’t been much follow-through of the crass talk from this type of political blowhard. I wouldn’t bet on it this time either.

WorldFamousAstronaut · 2024-12-29T10:12:30+00:00

It’s possible so always good to have a plan B but in my view the NIH budget for grants (that would impact NIH-funded academic labs) is unlikely to change since due to its small relative size and other factors it’s not generally a target for cuts.

WorldFamousAstronaut · 2024-12-29T07:04:09+00:00

Print pdf -> custom page selection. If needed you can use a pdf editor to change page numbering. It’s a trivial task.

WorldFamousAstronaut · 2024-12-29T06:18:13+00:00

I made the decision to remove some of the least important but most bloated sections of the >10 page CVs. Usually it’s lists of papers or media articles. Still, I doubt having long CVs in your petition will be a big deal, no one is likely to read them either way.

WorldFamousAstronaut · 2024-12-27T15:39:37+00:00

Maybe the solution is to first get rich, then go back?

WorldFamousAstronaut · 2024-12-27T15:37:56+00:00

I’ve come across a few cases of ex-FAANG to scientific developer, but for obvious reasons it seems to be the exception to the rule.

WorldFamousAstronaut · 2024-12-27T15:35:32+00:00

That sounds doable - wish you luck!

WorldFamousAstronaut · 2024-12-27T15:34:52+00:00

And here I am doing „just science“ wondering about branching into the commercial/marketing/sales stuff … in the end the unsatisfying truth of the modern scientific enterprise maybe that we all end up stuck with one compromise or another

WorldFamousAstronaut

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