Professor of Medicine at @UChicago. Decoding the human microbiome. BlekhmanLab.org
Chicago
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These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today!
We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe
The new issue is out👉cell.com/cell/current
Featuring an engineered Newcastle disease virus that selectively and safely lysed tumors in refractory cancer patients, the identification of rhodoquinone as a mammal mitochondrial electron carrier, and a metagenome-informed metaproteomics approach unravelling the interplay between the host, gut microbiome, and diet to identify disease biomarkers.
📷credit: SciStories
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still the best example of how AI works
The story of Nigel Richards, the man from New Zealand who memorized every French word in the French scrabble dictionary and won the French Scrabble Championship without speaking any French buff.ly/2rK5wi4
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Kamala's mother immigrated from India to pursue a PhD & stayed to work as a cancer researcher
Kamala's father immigrated from Jamaica to pursue a PhD & stayed to work as a professor
Immigrant scientists contribute not only to science but to society at large -- for generations
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Congratulations, you invented taxes and public education
Silicon Valley is backing a novel idea: Instead of charging students tuition, students go to school for free and are required to pay back a percentage of their income after graduation, but only if they get a job with a good salary nyti.ms/2FeBUOp
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Do US citizens understand how stressful it is to be an immigrant scientist in the US?
Far from family/friends, never ending visa bureaucracy & payments, constant fear of not being allowed back in the US, or being forced to leave your home/job/PhD due to some ban
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As a professor at a public university, my job is 60% research, 20% teaching, 20% service, 20% paperwork, 20% grant writing, 20% mentoring, 10% reviewing, 5% organizing, and 5% letter writing, so there's really not a lot of time for radical left indoctrination
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Stuck at home with small kids due to #COVID19? Here are some fun activities you can enjoy together:
- Write a research paper
- Teach a class via zoom
- Write a grant proposal
- Email
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My biologist origin story is that when I was a young child I found out I was fascinated by grant applications
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reading about people taking ivermectin for covid and the stories are really heartworming
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Just got an email that one of my grants got an automatic 1 year no-cost extension, without even requesting it, due to #COVID19
Grant admins and funding agencies: this is a great way to support your investigators during this crisis
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Basically how machine learning works
The story of Nigel Richards, the man from New Zealand who memorized every French word in the French scrabble dictionary and won the French Scrabble Championship without speaking any French buff.ly/2rK5wi4
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I am not an expert in epidemiology or virology, have never researched vaccination strategies, and find immunology uninterpretable, but here is my thoughts on whether we should delay the 2nd vaccine dose (1/79)
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If you are annoyed by being called a trainee as a PhD student, wait till you're a professor and still called "early career" in your 40s
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Just did the calculation: my household has saved $4,932 by not paying for parking on campus over the last 18 months
The university parking system -- making employees pay large amounts to park at work -- is a scam, plain and simple
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Not to mention a constant uphill battle to advance your career.
You think writing papers or giving talks is hard? Try doing it in a different language. Oh, and you're ineligible for most fellowships and funding opportunities
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Why does every computer science professor have a webpage that looks like it was built in 1995 by writing HTML from scratch?
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Breakdown of PhD student cost on a grant:
tuition $45K
stipend $35K
fringe $10K
indirects $60K
--
total paid by NIH to university: $150K
total paid by university to student: $35K
(this is just a toy example to illustrate a point, not real numbers but same ballpark)
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Hello, I'd like to invite you to do my laundry for me. If you accept, I ask that you do my laundry in the next 7 business days. If you decline, please give a reason, and recommend 2-3 colleagues who can do my laundry instead.
No, of course there's no payment, what a crazy idea
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The first 90% of a paper takes 90% of the work. The remaining 10% of a paper accounts for the other 90% of the work.
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New proposed postdoc salary scale in the Boston area, based on data from a salary and benefits survey
nature.com/articles/s41587-0…
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Work from home update --
Number of papers I've read: 0
Number of times I've watched Frozen 2: 137
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Imagine a job where once you're hired your boss says "welcome! Now go do whatever you want. We'll check back in 5 years, and then either fire you or give you the job for life"
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Received dozens of replies that say "go back to your country, free up your job for Americans"
If I go, I take my lab with me. This not only won't free up jobs, but would actually take away several job opportunities for Americans.
(Also I'm not going anywhere)
Time to relieve your stress. Return to your country of origin. Use your skills to help develop your own country. There you will live close to your family and within your traditions and culture. Especially during this time of high unemployment, we need those jobs for Americans.
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As a reviewer, my goal is to find critical flaws, not to "improve" the paper. Every paper can be improved in 100 different ways, many of them subjective. The authors have already decided they're happy with the paper as is. A reviewer is not a co-author or a collaborator.
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A gentle reminder that graduate students who are immigrants/international are ineligible for the GRFP -- just like they're excluded from almost all other graduate and postdoc fellowships in the US.
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Mind blowing.
The FTO gene is associated with obesity in humans. Plants don't have a homolog. What happens when you transgenically express the human FTO in plants?
Giant potatoes and rice
nature.com/articles/s41587-0…
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Incoming PhD students: joining a new PI's lab as their first graduate student could be one of your best career choices. Lots of 1:1 mentoring, seeing how a lab is built first hand, tons of other advantages. The opposite of a red flag.
Imposter syndrome is hitting hard this morning. I recently found out that graduate students have been told by more established PIs that I am a “red flag” because I have not yet secured external funding and because I haven’t recruited other graduate students. 1/
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Both of these can be true:
1. Grad students and postdocs are underpaid
2. Faculty are underpaid
Instead of fighting each other, faculty and trainees should work together to raise salaries in academia
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In my experience a CNS is required for a faculty position, so far I haven't seen anyone hired without a central nervous system
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It sucks not being able to visit your family
Just ask immigrant scientists who haven't seen their family in years because of visa issues & costs, and the very real possibility they would not be allowed back in the country
It's time to fix the US visa system
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Instead of saying "they got covid despite of being vaccinated", say "they got covid with only mild/no symptoms thanks to being vaccinated" 👍
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If you ever read a paper and get to a part where you ask yourself "why is this part even here? Seems unrelated to the rest of the paper" the answer is almost always "because a reviewer asked for it"
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Weird getting an email with a $10K bill for a journal publication fee, followed by an email requesting to review a paper for the same journal for free. Feels like being a victim in some kind of a pyramid scheme
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RT if you went to a public school and was never attacked by a bear #DeVosHearing
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#FireFauci implies the existence of an Earth Fauci and a Wind Fauci
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Kamala Harris's mother immigrated from India to pursue a PhD & stayed to work as a cancer researcher
Kamala Harris's father immigrated from Jamaica to pursue a PhD & stayed to work as a professor
Not sure if they would have been able to do this under the current administration
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Is it just me? When I complete a task and realize it was not on my to-do list, I add it to the list so I can immediately check it off.
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There's a confusion, seems that Pence was referring to a different company, Pfizer Total Landscaping
As Pence claims credit, Pfizer says it did NOT join in the administration's partnership.
Pfizer head of vaccine development Dr. Kathrin Jansen told the NY Times: “We were never part of the Warp Speed ... We have never taken any money from the U.S. government, or from anyone.”
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📢Big news: my lab is moving to @UChicago!
I'm thrilled to join the superb genomics and microbiome research community at UChicago, and beyond excited about new research directions and collaborations!
And we're recruiting at all levels! 👇
blekhmanlab.org/
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I can't even read a paper every 5 days
Publish a paper every 5 days?! Profile of the 9000 hyper-prolific researchers
nature.com/articles/d41586-0… @NatureNews by John Ioannidis @METRICStanford @StanfordMed R Klavans K Boyack #OA
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About 50% of my lab's collaborative papers started from discussions in in-person conferences
So far we have 0 new collaborations that started in a virtual conference
Not saying virtual meetings don't have advantages, but for driving collaborative science, in-person >>> virtual
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Really appreciate editors who, when sending you back the reviews for your paper, also include a summary of critical points to address -- and more importantly, points you _don't_ have to address, despite what reviewer 3 says
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Wow -- faculty are 25 times more likely to have a parent with a PhD.
Almost 50 times more likely in "prestigious universities"
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If there is a single advice I can give to grad students it will be this:
Back up your computer. Every file. At least daily. In multiple locations. One of which is off-site or in the cloud.
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Transitioning between scientific fields is challenging but twitter just did a seamless transition from epidemiology to explosives research
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As a scientist, the best thing to hear from a colleague is "we discussed your paper in journal club and everyone liked it". Makes my day every time
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An example of how useful twitter can be as a tool for scientists:
After posting a postdoc ad here 4 days ago I've seen thousands of people visiting our lab website (100x more than usual) from all over the world.
I did not post an ad anywhere else.
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This is taking off so on a serious note, a request: if you are evaluating colleagues for tenure/ promotion in the coming year, please be kind and mindful of this weird situation we are all living through
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To the reporters looking for comments on the space twin study:
1. There's no study, just a press release.
2. Changes are in RNA levels, not DNA (unless he came back as a different species)
3. Is this 7% difference a lot? No - literally everything causes changes in RNA levels
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Types of peer review:
1) 3 anonymous scientists write secret reviews in a process that takes a few months
2) dozens of known experts write comments that anyone in the world can see hours after a paper is posted (e.g this thread 👇)
Explain to me again why is 1 >> 2?
Based on the content of my mentions, I feel like I need to further debunk crazy #nCoV2019 / HIV conspiracy preprint. This is a thread doing so. 1/9
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Mother’s milk is a critical, dynamic biological system
We show that maternal genetics controls milk gene expression and composition, which in turn shape the infant gut microbiome
Our latest, led by @kelsey_EJ, great collab w/ @frankwalbert @DemerathE
biorxiv.org/content/10.1101/…
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You think professors are scatterbrained or have a bad memory? Ask them about their grad school rejections from 30 years ago
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If you were a professor of virology when the pandemic started, by now you either have 100,000 followers or you deleted your account
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How do bacteria and host genes interact in the gut? How do these interactions change across disease? We integrating microbiome and host RNA-seq data to find out!
Our latest is now out @NatureMicrobiol:
nature.com/articles/s41564-0…
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These are the most common questions about scientists?? I'll try to answer:
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Something that's almost never discussed here, and maybe should be: the experiences of trainees when the PI moves to another institution or leaves academia.
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"How did this get past the reviewers??"
I am again asking that we stop blaming reviewers for bad papers. Reviewers spend time & effort with no compensation, and their suggestions are often overlooked. The people responsible are those who actually wrote the paper -- the authors
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Say you pick 100 random bioinformatics software tools -- how many will you actually be able to access, install, and run?
Our new paper: biorxiv.org/content/early/20…
1/5 Our preprint about software crisis in computational biology is live! We have performed a review of usability and archival stability of published omics tools and resources. We have found that 28% of the tools are impossible to install. bit.ly/2yAphZX
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"We are drowning in information, while starving for wisdom. The world henceforth will be run by synthesizers, people able to put together the right information at the right time, think critically about it, and make important choices wisely."
- E. O. Wilson
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Yes -- give every PhD a green card!
This is exactly what the U.S needs to do to be competitive again for international scientists
The America COMPETES Act would exempt STEM PhD graduates from green-card caps, effectively stapling a green card to the doctoral diploma of every international student in STEM. It also would charge these applicants an extra fee to fund scholarships for U.S. STEM students 2/
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Unpopular opinion (?): universities, scientific societies, and journals don't need to have a position or comment on geopolitical events
All they should do is offer support to those impacted, and allow their members to express their opinions without fear of retaliation
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Just checked the twitter bylaws and it is indeed required that a "CNS paper for faculty position" discussion is always followed by a "working on weekends" discussion
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I don’t get the concern about scientists moving to industry.
1. Having more career options is good for everyone!
2. It’s not like there’s a shortage of brilliant scientists who want a career in academia
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Thinking about all the international/immigrant scientists who haven't seen their family in years and had to cancel travel plans yet again this year. Such a discouraging situation.
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Every BioRxiv preprint includes a warning that it "has not been certified by peer review", but PNAS contributed papers have no disclaimer?
How about "This paper has been through a fake peer review process to achieve the illusion of validity; skepticism is advised"
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Looking at the full range of GRE scores --> no correlation between GRE and graduate outcomes
biorxiv.org/content/early/20…
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Definitely happy that I finally caved in and got TSA precheck in November 2019 in anticipation for all the upcoming travel in 2020
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To the hundreds of new followers after my Kamala tweet: welcome! I hope you like genetics
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Impressive new results on COVID19 showing that 28% of the population are susceptible to trusting numbers reported in a tweet with no citation or link
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Dear editor, we have addressed reviewer 2's concerns and have revised figure 1 as requested
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📣Postdoc positions available in my lab!
Research at the interface of microbiome + human genomics. Exciting projects and collaborations, wonderful place to live, lots of flexibility (remote work ok)
BlekhmanLab.org
Informal inquiries welcome - email/DM me. Please RT!
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How heritable is the gut microbiome? What influences its heritability?
Our latest, where we answer these questions using >16,000 microbiome profiles from wild baboons
Work by @ferocious_sloth, wonderful collab with @ArchieLab @jtung5 @AmboseliBaboons
science.sciencemag.org/conte…
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FYI, all immigrants to the US are *required* to have these vaccines:
Mumps
Measles
Rubella
Polio
Tetanus and diphtheria
Pertussis
Haemophilus influenzae type B (Hib)
Hepatitis A
Hepatitis B
Rotavirus
Meningococcal disease
Varicella
Pneumococcal disease
Seasonal influenza
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So far, the only concrete steps by the federal government to fight COVID:
1) ban H1B and J1 visas
2) do less testing
3) cancel a funded NIH grant for bat coronavirus research
Did I miss anything?
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In -omics studies, understudied genes are systematically abandoned in favor of better-studied genes in the paper writing stage
elifesciences.org/reviewed-p…
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Mother's milk is often the sole source of nutrition for the baby. Milk also contains diverse bacterial communities -- but how to these bacteria impact the infant gut microbiome?
Our latest: biorxiv.org/content/10.1101/…
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We keep hearing that it's critical to take a long break after grad school
So this is a gentle reminder that many can't do this, either because they don't have the financial ability to not work, or they're immigrant scientists whose legal visa status relies on employment
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Cool new paper with associations between gut microbes and specific dietary components
Top associated foods:
1. Coffee
2. Unsalted nuts
3. Dark chocolate
nature.com/articles/s41591-0…
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Unpopular opinion: graphical abstracts are great! A good graphical abstract can be the most useful visual in a paper
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Very strange -- ordered some shrink-wrapped dead cats as usual, but instead got a bunch of conical tubes??? WTF
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Confession: I don't really care about the origin of covid and whether or not it's a "lab leak"
We should shift the discussion to the U.S fumbled response that lead to 600,000 dead and how we avoid this in future pandemics, which are definitely coming -- lab leak or otherwise
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Famous senior dude at a fancy university: "I don't know why you young folks are complaining about funding, when I started as PI the first 5 grant proposals I wrote were all funded on first try"
Me:
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Comparing preprints to their final published versions:
- 93% of articles do not change their main conclusions
- only 1 out of 184 published papers contradicted a conclusion made by its preprint
journals.plos.org/plosbiolog…
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