Vega Shah
@dr_alphalyrae
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AI for life sciences & health @nvidia | trained as a scientist from @jgi @uw @cal, working in product strategy | building community @techbi0 | views all mine
San Francisco Bay Area
Joined December 2013
we’re not quitting science, we’re quitting academia. I am still very much in science and will remain here forever
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What do you call feeling both burnt out and not feeling like you did enough work to deserve a burn out?.
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USPS just dropped forever stamps for 2023 and one of the themes is microscopic images 🦠
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Recently heard ‘it costs nothing to be nice’ at a meeting. And I strongly disagree. Continuing to be nice to people with harmful/toxic behaviors only creates a reward feedback loop encouraging them. And that is a heavy cost indeed.
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still one of the top christmas gifts i have ever received 🧬
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after years of pouring gels in lab, i can confidently say the skills are transferable to creme brûl��e making
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I had to double check. TIL Matlab is a $1.2B business?! Can someone in engineering explain the secret sauce? I tried to use Matlab once in grad school and quickly decided it wasn’t a good fit for genomics/biology data.
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by age 30, most of your friends and family should have no idea what your job is exactly.
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Grad students thinking about a career industry, TA-ing is a highly underrated role in phd programs, often considered a burden in addition to research. But being a teaching assistant can provide several industry-specific transferable skills 🧵.
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so is Nobel just a nepobaby club?.
An absolutely bonkers stat from this Nature article on Nobel Prize winners. "702 out of 736 researchers who have won science and economics prizes up to 2023 are part of the same academic family".
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anyone ever wonder how useful parafilm would be outside of lab? and yet it doesn’t exist as a household product. this keeps me up at night.
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grad students, if you’re not sure what jobs are applicable for your skillsets out of phd, just search the name of your grad program in Linkedin. It will show you all the alumni with non-academic career trajectories that faculty won’t tell you about #AltAcChats.
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@Prokaryota lmfao my science degree is why i have a lit 10 step beauty routine. I read papers. That’s commitment baby 💅.
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Curious about compensation in biotech and pharma? This massive spreadsheet of crowdsourced data from r/biotech is a fantastic resource capturing types of roles, types of orgs and experience levels across various geographic locations -
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dating app for scientists that shows people in your area that have access to instruments or reagents you need.
dating app for academics showing hot singles in your area of expertise.
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a sisterhood forged by science. images made using memories of labwork with friends in grad school and postdoc
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@soumya_goblue @jrstateamerica @Stanford if you’ve ever walked past a college campus you should probably put it on there.
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Starting next week I’ll be doing a weekly twitter thread about startups in biotech. Focusing on software, sequencing, drug discovery, and lab automation. Goals are to evangelize innovations and help grad students/postdocs find interesting places to apply for industry roles 1/2.
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grad students and postdocs planning to transition to data science/comp bio roles in industry - Python is pretty cool but please learn some boring SQL. It’s ubiquitous and necessary. Also there’s a strong possibility you won’t be using much of R.
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why are kitchen parafilm and pipettes not a thing? is anyone working on this.
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subtweet: if all PI-related issues in academia can be boiled down to lack of funding the well funded labs would be known for positive culture and work-life balance.
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phds/postdocs applying for industry roles, some ways to translate academic tasks into jobs:. • lab work ➡️ r&d scientist. • planning/timelines/budgets ➡️ project manager. • ideas/experimental design ➡️ product manager. • teaching/sci comm ➡️ product marketing 1/2.
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Scientists with a deep appreciation for art and aesthetics are rare and should be celebrated more.
In science and engineering, I feel like having a sense of aesthetics is dramatically more useful than being marginally more intelligent.
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evergreen tweet.
sharing notes with someone that started their career in biotech in the 80s and finding that all the problems are still the same
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visiting a friend in seattle and she handed me coffee in this mug 🤔
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Modern Statistics for Modern Biology and includes R packages for data analyses in the ebook
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during a postdoc interview:. PI: Do you get scared and confused when you see large excel files or datasets?. Me: No.
What’s the worst question you’ve been asked in a job interview?.
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grad students and postdocs planning to transition to computational/data roles in industry - Python is pretty cool but please learn some boring SQL. It’s ubiquitous and necessary.
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going to grad school genuinely delays a key realization that being successful and happy for that matter has nothing to do with being a good student or extremely technically skilled.
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One of the sad parts about being in academia was the general derision towards fashion. I spent at least a few years wearing super boring clothes to fit in. Why do academics deny themselves self expression and art?.
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Being a TA in grad school turned out to be the most useful source of translatable skill for industry. TAing is underrated and often considered a burden for PhD students. But it can prepare you for a great career outside academia 🧵.
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Big day today - @nvidia is open-sourcing the BioNeMo Framework, a toolkit of programming resources, libraries, and AI models designed for drug discovery. This release equips academic labs and biotech companies with advanced tools for protein design, small molecule generation, and
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The global postdoc shortage is in part because people are leaving for industry roles but also because academic PIs continue to be ultra-selective based on metrics like first author papers, “culture fit” and whether candidates are from prestigious labs/universities.
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subtweet: people with ostensibly successful careers telling undergrads not to do a PhD is gatekeeping. It’s quite hard to predict what your future job needs. Do a doctoral if you can have sustained interest in a topic for 5-6 years.
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It’s 🧬Startup Saturday🧬and today i’m talking about @plasmidsaurus 🦖🦕. Plasmidsaurus is solving a common cloning problem for lab scientists by providing fast, affordable (~$15) whole plasmid sequencing 🧵(1/4)
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Nobody talks about how labwork is actually physically taxing and inefficient. We need more practical solutions to make the life of scientists better. Is anyone automating simple things like washing beakers, test tubes or reusable pipette tips?.
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grad students, if you’re ambivalent about industry vs. academia - start doing informational interviews in 3rd/4th year instead of right before defense. Then you can incorporate job-relevant skills into your last dissertation chapter.
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I can’t describe how important it is to establish roles, responsibilities and a general ethos for research labs. Especially in academia where so many labs turn dysfunctional due to internal competition and lack of structure.
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it’s official, @nvidia swag now has life sciences representation! With a DNA structure and chemical structure 🧬👩🏻🔬
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@jgschraiber @sebatlab Exactly. Also the assumption that postdocs remain trainees for their entire time at a lab is absurd. They probably require the same ‘onboarding’ time as new hires in industry, somewhere between 3-6months. Labeling experienced scientists trainees for years is exploitative.
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An observation from the industry side, a lot of companies prefer not to hire academic scientists because they are prone to spending too much time in ideation as opposed to building+experimentation. I struggled in my job search early on due to this belief about phds in industry.
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Excel is an extremely common tool in genomics. Often used to enumerate and annotate genes. With one massive caveat, Excel mistakes gene names for dates and automatically updates them. A recent paper in @Nature provides a tool to resolve this issue:
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It is becoming clear that the AI and biotech intersection holds 3 big opportunities:.1) discovery of molecules and novel drug+target pairings .2) using data to guide clinical experimental design to speed phase I/II and beyond.3) operational efficiency via faster protocols, better.
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on a scale of 1 to 10, how nerdy is to own watercolors of plasmids?
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454 Bio just launched an open source DNA sequencing platform that could be a game changer in a space that has been previously controlled by a few companies @454Bio 🧬👀
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Engineering bacteria as interactive cancer therapies | Science
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1) project management: planning a course calendar, syllabus and regular meetings. 2) public speaking/scicomm: translating complex topics into a presentation and delivering it . 3) people management/support: making sure the grading is fair, answering questions, office hours.
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Humans are literally walking around with novel, undiscovered proteins inside their gut. There is so much we don't know yet about the living world and that's incredible.
A new type of microbe discovered in the human gut! Called obelisks, they can create their own proteins that are entirely new to science. The team named their proteins “oblins.” Scientists scratching their heads about it .
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trying to explain to new phd grads/postdocs that industry is not the 'easy alternative' to tenure track
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Perfectly timed with today's Nobel Prize announcement for AlphaFold. The @NVIDIAHealth & Life Sciences team has released 2 downloadable inference microservices: AlphaFold2-multimer & RFDiffusion. AlphaFold2-multimer allows for prediction of multimeric protein structures faster
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When I switched from being a postdoc to a scientist at a biotech startup, I realized my previous work habits were useless. In this article, I describe 4 mental models to work more effectively in a company, especially for folks coming from a postdoc or phd. Link in bio👆
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anyone that thinks industry is the dark side should just follow the Sabatini timeline. I am terrified for young graduate students right now.
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Curious about biotech salaries? Every year r/biotech does an anonymous survey, results below 👇 In 2023 the annual base ranged from 350k-20k. Leadership pays orders of magnitude more than individual contributor roles. Yet another incentive to develop soft skills!
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Curious about salaries in biotech? .r/biotech's annual survey data for 2024 is out. With 700+ entries showing a range from $400k - $30k in annual base. Leadership roles earn significantly more and the inflection point is at director level and up. Link below👇
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A curated set of 241,118 genomes from the human gut microbiome including 310 novel species 🦠🧬
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the entire field of biology is *it depends*.
Man, I'm getting real sick of "it depends".
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The @nvidia holiday sweater with DNA on it should tell you how hard we’re cooking in digital biology 🧬
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my mom said it’s not too late to take the MCAT a few weeks before my phd defense 💀.
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My career got infinitely better when I stopped looking for low stress jobs or projects and started getting better at differentiating good stress from bad stress. Good stress comes from working on complex, impactful problems and bad stress often comes from difficult people.
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people in academia applying for industry roles, the order of items on the résumé should be:. - brief description & goals.- job experiences w/ specific projects.- skills (technical and soft skills).- degrees.- publications/presentations/awards.
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sharing notes with someone that started their career in biotech in the 80s and finding that all the problems are still the same
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the age of bio has begun.
Medicine is biology.Physics is computer science that mimics biology.Chemistry is using that computer science that mimics biology to model biology. Literature, peace, and economics are all biological constructions so looks like a clean sweep for bio this year.
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Last 3 years I have been an active member of a community on software for bio. Today I have to face the reality that this community, that used to consist of thoughtful operators wanting to talk about science+tech has now become overrun with loud, obnoxious and generally ignorant.
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‘many proteins not predicted by the genetic code’. Remember when we thought sequencing the entire human genome would solve all medical problems.
We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability.
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If you are headed to industry, expect this progression👇. skillset 5 years ago: molecular/genomic techniques in lab, python and R, writing papers. skillset today: making an idea a reality with a cross-functional team, problem solving, removing blockers and breaking ties.
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Many bioinformatics programming tasks can be automated with ChatGPT 👀
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phds/postdocs headed to industry roles -- something nobody tells you is that 1st author papers will have little to no impact on your success whereas how you make people feel is going to become a significant determining factor in promotion, salary, title.
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Deep embedding and alignment of protein sequences | Nature Methods
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Grad students planning to transition to industry - one major cultural difference between academia and industry is how much your success depends on being a low stress entity+likable. Some things that will actively hamper progress -. 1) not doing small talk.2) interrupting people.
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@ScientistsLift there is way more academic fraud and data fabrication than people realize. My guess is that a very small fraction is actually caught, usually when it’s very blatant or in a high profile paper.
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@pdhsu the concept of lineages is seriously one of the oddest academic rituals. its just a job, chill.
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Today we launch @NVIDIA’s Virtual Screening for Drug Discovery implemented via inference microservices or NIMs. Leading biotechnology software providers such as @Benchling, @Dotmatics, @Schrödinger, @TetraScience and @Terray_Tx to use NIMs in their computer-aided drug discovery
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One of the negative experiences of my training as a scientist was being judged for being interested in fashion and art. Why is caring about aesthetics considered orthogonal to pursuing science?.
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@jmc_rhet millennials complaining about their postdoc salaries when all they need to do is just roll their sleeves up and pick up that phone when Dartmouth search committee’s director calls you!!.
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Disruptive science is now happening in the startup space instead of academia. Propelled by scientist founders and mission driven investors.
It’s pretty clear that the current model of science and scientific funding is a dead-end.
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@ZJAyres when I was in grad school the people classified as average or non-starters were simply the most different compared to the professors in thought and demographics.
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@ScientistsLift the HR and labor law violations alone would be enough to get some PIs fired in any other type of job outside academia.
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genuinely don’t understand the sharp line drawn across bioinformatics and molecular bio wet lab roles. When so many scientists do both, across industry (usually in startups) and also in academic labs.
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Folks are always surprised to learn that @NVIDIAHealth has been working on a foundation model for cell segmentation called Vista 2D that can be trained on a variety of cell imaging outputs, including brightfield, phase-contrast, fluorescence, confocal, or electron microscopy. I
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engineers and UI/UX people laid off by twitter, meta and other big tech companies should join life sciences software building efforts. their skills are precious here and can contribute to something more meaningful to humanity compared to adtech and social media.
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Does anyone know why biological experiments are often done with 3 replicates as opposed to 4, 5 or 6? Looking for studies that show 3 is the magic number 🦠.
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Most of biotech software problems are at their core, software problems - legacy code, scalability, observability, security, skill gaps etc. But the biotech software workforce and leadership is disproportionately made up of bio experts versus software experts. (1/2).
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AlphaFill: enriching AlphaFold models with ligands and cofactors | Nature Methods
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‘Errors in the genome database and the associated computational methods led to millions of false-positive findings of bacterial reads across all samples’.
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De novo design of protein interactions with learned surface fingerprints | Nature
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@AnupamAich4 @TheBcellArtist came here to say exactly this ☝️why in the world would anyone pick a postdoc over 3-4x higher comp, higher impact at work and generally better work culture?.
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JPM Healthcare is in a week. Although this is an investment conference, it’s also the highest number of biotech events per square mile anywhere in the world—more parties than your bioRxiv-addled brain can comprehend. So the @TechBi0 community has crowdsourced events in a single
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Should biologists use agile/scrum? I wrote a short article on the successful use of LabScrum (link in bio). Key reasons why LabScrum works - 1) Breaking down monumental tasks to digestible chunks 2) Creating a safe space to share imperfect drafts and results 3) Embracing
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When I read news like this, it’s an example of why tech driven ethos ‘move fast, break things’ doesn’t quite work for biotech. A sense of cautious urgency is probably a better choice.
7 children developed blood cancer after Bluebird Bio gene therapy, @Jasonmmast writes.
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