Vega Shah @dr_alphalyrae Twitter profile

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Vega Shah

@dr_alphalyrae

10 months

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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Vega Shah

@dr_alphalyrae

1 year

USPS just dropped forever stamps for 2023 and one of the themes is microscopic images 🦠

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Vega Shah

@dr_alphalyrae

1 year

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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Vega Shah

@dr_alphalyrae

5 months

still one of the top christmas gifts i have ever received 🧬

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Vega Shah

@dr_alphalyrae

3 years

after years of pouring gels in lab, i can confidently say the skills are transferable to creme brûlée making

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Vega Shah

@dr_alphalyrae

2 years

by age 30, most of your friends and family should have no idea what your job is exactly

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Vega Shah

@dr_alphalyrae

1 year

Santa got me a sequencing mug and lego bouquet of flowers 🌸

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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

4 years

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

11 months

still got those lab hands 👩🏻‍🔬

Jon

@BiggestttHater

11 months

what is y’all most liked tweet?

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Vega Shah

@dr_alphalyrae

11 months

@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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

1 year

a sisterhood forged by science. images made using memories of labwork with friends in grad school and postdoc

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Vega Shah

@dr_alphalyrae

11 months

POV: when i say ‘advanced bioinformatics’ on my résumé

David Sünderhauf

@davvi36

11 months

well, ctrl+f and search for spaces and boom - the gaps are highlighted for you 😁

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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

3 years

serious question, how to make new friends in your 30s?

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Vega Shah

@dr_alphalyrae

1 year

why are kitchen parafilm and pipettes not a thing? is anyone working on this

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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

1 year

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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Vega Shah

@dr_alphalyrae

2 years

@AdamMGrant don’t take criticism from people you wouldn’t take advice from

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Vega Shah

@dr_alphalyrae

8 months

no comments

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Vega Shah

@dr_alphalyrae

2 years

visiting a friend in seattle and she handed me coffee in this mug 🤔

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Vega Shah

@dr_alphalyrae

1 year

Modern Statistics for Modern Biology and includes R packages for data analyses in the ebook

Modern Statistics for Modern Biology

If you are a biologist and want to get the best out of the powerful methods of modern computational statistics, this is your book.

www.huber.embl.de

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Vega Shah

@dr_alphalyrae

1 year

during a postdoc interview: PI: Do you get scared and confused when you see large excel files or datasets? Me: No

Adam Karpiak

@Adam_Karpiak

1 year

What’s the worst question you’ve been asked in a job interview?

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Vega Shah

@dr_alphalyrae

1 year

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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Vega Shah

@dr_alphalyrae

10 months

zoom call at 4pm on friday

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Vega Shah

@dr_alphalyrae

2 years

i did my taxes on powerpoint

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Vega Shah

@dr_alphalyrae

11 months

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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Vega Shah

@dr_alphalyrae

2 months

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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Vega Shah

@dr_alphalyrae

4 months

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

6 months

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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Vega Shah

@dr_alphalyrae

1 year

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

11 months

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.

Research Culture: Why every lab needs a handbook

By explaining how a lab works, outlining what is expected of everyone, and describing the culture the lab is aiming for, a good lab handbook will benefit all the members of a research group.

elifesciences.org

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Vega Shah

@dr_alphalyrae

2 years

@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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

3 years

on a scale of 1 to 10, how nerdy is to own watercolors of plasmids?

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Vega Shah

@dr_alphalyrae

4 months

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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Vega Shah

@dr_alphalyrae

1 year

Engineering bacteria as interactive cancer therapies | Science

Engineering bacteria as interactive cancer therapies

With increasing evidence that microbes colonize tumors, synthetic biology tools are being leveraged to repurpose bacteria as tumor-specific delivery systems. These engineered systems can modulate the...

www.science.org

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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

10 months

trying to explain to new phd grads/postdocs that industry is not the 'easy alternative' to tenure track

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Vega Shah

@dr_alphalyrae

7 months

@mbeisen @eLife @TheOnion this is astounding. what a mistake.

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Vega Shah

@dr_alphalyrae

3 months

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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Vega Shah

@dr_alphalyrae

1 year

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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Vega Shah

@dr_alphalyrae

9 months

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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Vega Shah

@dr_alphalyrae

29 days

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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Vega Shah

@dr_alphalyrae

2 years

A curated set of 241,118 genomes from the human gut microbiome including 310 novel species 🦠🧬

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species

Nature Communications - Here, Leviatan et al. produce 241,118 genome assemblies to produce a new human gut microbiome reference set of 3,594 species genomes, of which 310 represent previously...

www.nature.com

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Vega Shah

@dr_alphalyrae

6 months

the entire field of biology is *it depends*

Demetri

@PhDemetri

6 months

Man, I'm getting real sick of "it depends"

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Vega Shah

@dr_alphalyrae

9 months

my mom said it’s not too late to take the MCAT a few weeks before my phd defense 💀

Roshan Patel

@roshanpateI

9 months

When you have immigrant parents as a startup founder

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Vega Shah

@dr_alphalyrae

1 month

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

1 year

Many bioinformatics programming tasks can be automated with ChatGPT 👀

Many bioinformatics programming tasks can be automated with ChatGPT

Computer programming is a fundamental tool for life scientists, allowing them to carry out many essential research tasks. However, despite a variety of educational efforts, learning to write code...

arxiv.org

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Vega Shah

@dr_alphalyrae

11 months

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

8 months

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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Vega Shah

@dr_alphalyrae

5 months

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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Vega Shah

@dr_alphalyrae

7 months

@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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Vega Shah

@dr_alphalyrae

1 year

Deep embedding and alignment of protein sequences | Nature Methods

Deep embedding and alignment of protein sequences

Nature Methods - DEDAL is a deep learning-based protein sequence alignment method that improves the quality of predicted alignment for remote homologs and better discriminates remote homologs from...

www.nature.com

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Vega Shah

@dr_alphalyrae

2 years

@pdhsu the concept of lineages is seriously one of the oddest academic rituals. its just a job, chill.

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Vega Shah

@dr_alphalyrae

3 years

@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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Vega Shah

@dr_alphalyrae

8 months

Disruptive science is now happening in the startup space instead of academia. Propelled by scientist founders and mission driven investors.

Maxim Ziatdinov

@MaximZiatdinov

8 months

It’s pretty clear that the current model of science and scientific funding is a dead-end

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Vega Shah

@dr_alphalyrae

1 year

@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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Vega Shah

@dr_alphalyrae

7 months

@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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Vega Shah

@dr_alphalyrae

7 months

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

2 years

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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Vega Shah

@dr_alphalyrae

1 year

missed opportunity to call this paper phast and phurious

PHASTEST: faster than PHASTER, better than PHAST

Abstract. PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST

academic.oup.com

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Vega Shah

@dr_alphalyrae

7 months

‘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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Vega Shah

@dr_alphalyrae

1 year

AlphaFill: enriching AlphaFold models with ligands and cofactors | Nature Methods

AlphaFill: enriching AlphaFold models with ligands and cofactors

Nature Methods - The AlphaFill algorithm transplants missing small molecules and ions from experimentally determined structures to predicted protein models in the AlphaFold protein structure...

www.nature.com

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Vega Shah

@dr_alphalyrae

2 years

@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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Vega Shah

@dr_alphalyrae

1 year

De novo design of protein interactions with learned surface fingerprints | Nature

De novo design of protein interactions with learned surface fingerprints

Nature - A surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling the de novo design of protein interactions and of artificial proteins with...

www.nature.com

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Vega Shah

@dr_alphalyrae

11 months

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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Vega Shah

@dr_alphalyrae

1 year

my bookmarked list of papers to read *later*

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Vega Shah

@dr_alphalyrae

1 year

Software in the life sciences is experiencing a moment of disruption much like fintech and edtech did, more than a decade ago. People working in biotech should consider joining software companies because the coming years will be transformative. Some indicators of change 🧵1/3

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Vega Shah

@dr_alphalyrae

2 years

@TrumanLab 👆and usually they are not weeding out bad students, they are weeding out people *not* like themselves. People that might not come from the same background, culture or socioeconomic classes as them. This is hugely detrimental to innovation and progress.

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Vega Shah

@dr_alphalyrae

11 months

A biological camera that captures and stores images directly into DNA | Nature Communications

A biological camera that captures and stores images directly into DNA

Nature Communications - DNA data storage has gained recent interest due to the high information density of DNA. Here, the authors have developed a method to directly capture information in the form...

www.nature.com

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Vega Shah

@dr_alphalyrae

2 years

phds/postdocs looking at industry roles right now are probably discouraged by the layoffs and uncertainty around jobs - a few things to remember: - layoffs are accompanied with severance and a buffer period to find your next job. Postdoc roles rarely offer this.🧵1/3

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Vega Shah

@dr_alphalyrae

3 years

@stacyfarina This thread is very inspirational, albeit a bit optimistic. Speaking from experience, the culture of academia is changing in that younger faculty are quickly learning the correct optics while still perpetuating the same toxic/abusive lab policies behind the scenes.

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Vega Shah

@dr_alphalyrae

3 months

i used matlab for 2 months in grad school and later decided i would do anything to avoid matlab

json

@JsonBasedman

3 months

Name a programming language worse than R. You can't. You literally can't do it.

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Vega Shah

@dr_alphalyrae

1 year

subtweet: doing your statistical analyses using R vs any software with a GUI doesn’t make it more right 🧐 conversely a poor grasp of statistics can’t be saved with command lines. stay awake folks.

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Vega Shah

@dr_alphalyrae

2 years

subtweet: industry vs. academia debates feel circular because both sides are arguing from a point of survivorship bias. The most useful tweets are people sharing their lived experiences from various roles to help grad students make a choice.

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Vega Shah

@dr_alphalyrae

3 years

@Dey_Gautam Let me get this right, you’d like underpaid postdocs to put *more* effort into doing free work while they tackle the stress and anxiety of academia? sounds great.

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Vega Shah

@dr_alphalyrae

1 year

@academic_exit The real question here is - how many fold increase is your post-academic salary? the answer is 3-4x of postdoc.

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Vega Shah

@dr_alphalyrae

5 years

10^8 friends per mL

Zymo Research

@ZymoResearch

5 years

Comforting yourself after a failed experiment like: the real discovery was the friends we made along the way

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Vega Shah

@dr_alphalyrae

1 year

by mid-30s most of your family and friends should have no idea what your job is exactly

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Vega Shah

@dr_alphalyrae

1 year

aliquot

Sarah Haider 👾

@SarahTheHaider

1 year

What is a word/phrase specific to your field that you think should be used widely?

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Vega Shah

@dr_alphalyrae

2 years

A coworker that is out of the loop on the academia vs industry discussion asked me how they are different culturally. My response was an anecdote from a previous role, a play in 3 acts. Act 1 - Company hires a postdoc from Famous Lab™ with multiple CNS papers + v.good recs 🧵

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Vega Shah

@dr_alphalyrae

1 year

i think my life got better when I stopped looking for low stress jobs/projects and started getting better at differentiating good stress from bad stress. good stress comes from solving difficult problems and bad stress seems to come from working with difficult people.

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Vega Shah

@dr_alphalyrae

1 year

the smartest and kindest people I know have two key personality traits: 1) learners for life, they are always studying, reading and teaching 2) strict boundaries around their time and effort

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Vega Shah

@dr_alphalyrae

3 years

if you went to biotech trade shows just to get these, raise your hand

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Vega Shah

@dr_alphalyrae

9 months

I have 3 1) your PI shouldn’t be the single source of truth for science or your performance. Find other faculty or people in power that can be your mentors. 2) create a strong network of collaborators. 3) listen more than you talk. But when you talk make it count.

Dr. Catharine Young

@catgyoung

9 months

What’s the one piece of advice for entering PhD students that you wish someone had shared with you?

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Vega Shah

@dr_alphalyrae

3 years

@markwbudde stolen data

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Vega Shah

@dr_alphalyrae

4 years

@GradInSoup I opted to quit academia and I’d say my experience is the exact opposite. I was always a workaholic. In industry I see direct rewards in the form of training, opportunities and compensation when I work beyond the 9to5. Something that was unheard of in academia.

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Vega Shah

@dr_alphalyrae

1 year

De novo design of luciferases using deep learning | Nature

De novo design of luciferases using deep learning

Nature - A deep-learning-based strategy is used to design artificial luciferases that catalyse the oxidative chemiluminescence of diphenylterazine with high substrate specificity and catalytic...

www.nature.com

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Vega Shah

@dr_alphalyrae

1 year

CMV: Is there really a need to retain postdocs? If the supply of TT roles is lower than number of postdocs, there isn’t a retention problem. Unless of course the goal is to extract cheap labor indefinitely with no career prospects.

Retaining postdocs by recognizing their worth

Nature Biotechnology - Data from a postdoc salary and benefits survey may assist in retaining PhD holders interested in academia but considering alternate options owing to financial considerations.

www.nature.com

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Vega Shah

@dr_alphalyrae

3 years

@professorkao @jmc_rhet smallviolin.jpeg

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Vega Shah

@dr_alphalyrae

1 year

product management concepts i wish i knew when i was a lab researcher: 1) MVP: creating a minimum viable product. this allows you to stop being perfectionist and keep making steady progress. one time i took 6 months to write a first draft for a pub, should have been weeks. 1/3

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