Junhyong Kim
@JunhyongKim
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Ex-Chair (yay!) Penn Biology, Single Cell Biology, Genomics, Theoretical Biology, Comp Biology, Evolution, Avatar enthusiast. All tweets, only my opinion.
University of Pennsylvania
Joined December 2015
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Last week I had to talk with my lab about anti-Asian racism. We discussed this Q:
Shocking recent events shed light on rising general anti-Asian racism, but Asians are over-represented by 2X at all levels in academia. Are there anti-racism problems in academia?
A thread..
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Motivated by weekend morning tweets, I'd like to talk about normalization of soft corruption in academia.
First, a story about my advisor, Lev Ginzburg, who fled Russia in the 70's and arrived in US with $50 in his pocket, a wife, and a new born child...
1/x (sorry long)
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A funny thing happened on the way to routine single nucleus ATAC-seq analysis…and after scratching at it for longer than we wanted, we wrote a paper about what we found.
This is a 🧵 about our little paper...(sorry long)
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Every minority group, regardless of their proportional representation, are fighting through “not belonging” in some circle or another.
We still have a lot of work to do.
n/n
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Avatar The Last Airbender is, in fact, the greatest work of cinematic art to EVER grace the TV. I think there is much that we could stand to learn from the young airbender, Aang.
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First, persistent under and over representation are both a clear indication of systemic racism. Under means we are doing something to suppress that group. Over means that group is being excluded from somewhere else and sees refuge in this area.
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HOT take: Single cell field has a junk food prob.
People legit want diff food, but nobody knows how to cook. So now we have diners serving pancakes to sushi & 10 food carts popping up each day with 10 diff amounts of salt.
Stop opening stores and more learning to cook pls.
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but stereotypes of being “sneaky”, “no leadership”, “technical but not creative”, “a sidekick”, are ever present. Names, accents, looks, all create a biased template of roles we are supposed to play.
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Even at my career stage, pretty much weekly, I find myself in situations where I have to fight through these stereotypes at some meeting or another.
Clearly, overrepresentation doesn’t mean all is rosy.
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Asians are overrepresented in green grocers, dry cleaners, nail salon, too—not bc of special talent but bc these are available to them. My children have been told Asians are not attractive, not creative, not leaders. They may want to be movie stars, authors, presidents,
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But, they see no paths. OTOH, if they do well academically, they are told its cause they are Asians.
Asian parents have all experienced their children running away from being Asians or overly attaching themselves to being super-Asians.
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A colleague asked me why Seurat's default so-called CP10k normalization causes inflated false positives with low average UMIs in scRNAseq. Maybe this is already in the literature but here are some thoughts (warning long):
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Well, at least in Academia, with all the overrepresentation, things are good, right? If you think that is true, you can also tell NFL players there’s no racism in sports. Overt anti-Asian racism in academia is rare, though not unheard of,
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I made a comment on this racist shit already, but I see a lot of people asking "WTF, why did he do that?".
Well, I want to explain that this relates to a particular anti-Asian stereotype that is pervasive in academia, not just this racist.
1/3
WTF. Can’t get more racist than this
@PurdueNorthwest
administrator. Who is this person?
#AntiAsianHate
#StopAsianHate
@AcademicChatter
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/PS
I would be remis if I didn't point out all of these hidden cheating rules disproportionately affect minoritized academics, the URMs, women, foreigners..
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Yesterday and today, as dept chair, I tried to say something to the dept and managed to screw it up three times.
In the end all that was needed was just expression of my personal support, bc I had no standing for anything more. This is why diversity in academia is critical.
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See, we've set up a system for the right way to cheat and if you don't know or follow this, you get tarred.
Classic example is the leg up we give on admission to legacies, donors, etc. Do it the wrong way, you go to jail. But, if you do it the right way, $$, all good.
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Like the lobbyists, inside trading, revolving doors all normalized in our poli system, we have a whole host of normalized cheating in our academic system, which when done the right way, nobody cares; when done the wrong way,
well, only those 3rd world countries do that.
/end
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Chair was shocked a new assist prof did this and Lev was forever labeled as selfish.
Lev originally thought everybody gets fixed fair salaries, then when he realized that was not true and tried to work a solution as he was told, everybody thought he was cheating.
4/x
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I saw a post that scorned how certain countries pay profs cash for papers in well-recognized journals...
The horrors! How it must induce people to commit fraud!
But, as a chair, every year I was supposed to look at research productivities (= papers) and determine raises.
6/x
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Luckily, the stereotype doesn’t include devastating assumption of criminality—but the recent COVID agitation shows that is changing too. During the 80’s with the fear of “Japan Invasion” there were a slew of Asian gang stories/movies so “the more things change…”.
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That anti-Asian racism exists is just now making the rounds is the most meta statement about anti-Asian racism.
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Some institutions have a union negotiated "merit process" that explicitly numerically count pubs to convert into "merit units" of salary raises.
But, hey, we are not giving out cash!
Are we?
7/x
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Asians are quiet, do their work, and, hey, smile awkwardly when you talk about "do they really eat dogs?".
Seeing Asians as bland, non-people is not limited to some rare old jerk, it is pervasive in academia.
So, yeah, he said what he did, because he could,
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I thought I would extend what I posted earlier.
I am not aware of any dept that doesn’t think diversity (including gender) is important. So, why doesn’t it happen?
All our processes involve choices and tradeoffs. Examples:
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After almost a year on bioRxiv, our single neuron sub-celllular RNAseq paper is out!!
Thanks to all the reviewers who made the paper better!
We dissect neurites and soma from single neurons to test within-single-cell DE and identify consistently localized RNA.
A comprehensive look at
#RNA
localization within mouse
#neurons
-
@JunhyongKim
and colleagues perform RNA-sequencing for both the soma and
#dendrites
of individual neurons, providing a resource for the sub-cellular localization of transcripts.
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Come to the original! The first single cell meeting since 2009. Deadline Sept 4.
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@IshmailSaboor
I am so sorry this has happened again. I know there is a limit to how much one can accept apologies but, it seems just interminable process to eliminate systemic racism.
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I saw posts decrying compensated secondary positions at foreign unis as "buying citations.".
Yet, every 5 yrs, before UK's REF evals that determine funding, the unis go on a hiring spree & when we pour $$ for hot-shot PI, we are only doing for the deep scholarship, right?
8/x
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The term "foundational" is supposed to mean subsequent models can be built on the model.
This excellent analysis suggests otherwise.
TBH, I cannot see any model in biology, at current data density, being "foundational", so can we stop using this?
How robust are proposed foundation models in single-cell biology?
Here, we assessed two such models: Geneformer and scGPT. We focus on evaluating their zero-shot capabilities.
📄
💻
💪 with
@alexijielu
,
@avapamini
,
@lorin_crawford
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He went to his chair and asked whether he was really the lowest ranked prof in the entire university. His chair told him that he should have negotiated better and unless he has an outside job offer, can't do anything. So he went and got a job offer.
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As we go into grad admit eval, please suppress your instinctive "these people" response to foreign applicants.
They may have sent a form letter, may not know what you or dept really work on, but, all they are doing is trying to better themselves and their lives, just like you.
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Left my computer open to run an errand and got my twitter account hijacked by 17yr old daughter
@kimchikid69
. But, based on the reactions, I should just turn my account over to her.
For real, Avatar holds no candle to Astroboy.
Avatar The Last Airbender is, in fact, the greatest work of cinematic art to EVER grace the TV. I think there is much that we could stand to learn from the young airbender, Aang.
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After arriving in US & tribulations, he managed to get a job at Stony Brook. But, he was financially struggling and tried to find a solution. He learned he could go to th library and find everyone's salaries. To his shock, he found he had the lowest salary in the entire uni.
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Stupid caricatures of any group is racist and we all experience this on the street.
But, why did this presumably well-experienced and well-educated dude feel free to "ching-chong"? Because, he is steeped in the "potted plant" Asian stereo-type in academia.
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After so many years, I am not burned out from grant writing, nor paperwork, nor admin, but tired from
"attention begging"
which is what the chase for glamor journals, speaking slots, various invites, and being on this platform is
The depth of burnout I feel doing anything remotely grant-related is starting to make me question whether I'm actually cut out to be a PI
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11 yrs after F1, OPT, H1-B, I got my green card with 1st job, after years of grief by INS, carrying stacks of papers bc they ask 4 expired docs, "ain't gonna marry an American r u? (Surprise, I did). My 1st thought after green card was "wow, I can quit now and work for MacD".
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For a cluster or metacells from single cell data, how should we compute its average expression?
I've dealt with this problem multiple times so I thought I would share.
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My blog post about the soft corruption of stealing ideas. "The mold in science's bathroom":
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20th joint paper with J. Eberwine's lab. We sequence mtDNA, single mitochondria at a time and find surprising level of within-mitochondria polymorphism.
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@arjunrajlab
I've been advocating getting rid of chalk talks. In my experience, it is one of the most prejudiced part of candidate evaluation process.
It is really hard to get people to layoff (what I call) the Anglo-Saxon model of an intellectual--basically how well can one verbally joust
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Apropos nothing--actually a lot of recent events:
Being a scholar is not a competition…
But, achieving fame/status is a competition.
a thread....
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We dissect dendrites and soma from a single neuron and independently sequence the sub-cellular fractions to comprehensively catalog dendritic transcriptomes. We identify differentially localized iso-forms and computationally annotate 2ndary structures:
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If scientists were honest to themselves, we would admit that 80% of our motivation is game and 20% (just maybe), knowledge.
(Okay, okay, there're unicorns out there, but still...)
The great philosopher 2PAC passed me a piece of paper and said Hammer say this, “ Fame is a narcotic/ the fans want to get a fix but the stars got it /and you’ll being running thru stacks of junk/packs of punks/and still can’t find a track that bumps - let that sink in
#Science
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Still time to apply for our NHGRI R25 Diversity Action Plan, post-bacc program!
If you wanted to further your career in genomics but didn't have access to right courses, this is for you. Fully, paid annual stipend fo $30k.
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We,
@PennBiology
, spent the week shutting down the department and prepare for remote teaching.
Now, we are helping Penn Health System gather personal protection equipment (PPE) from our labs. If Philadelphia area labs have PPEs to donate pls DM me for contact info.
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To all those celebrating
#GRExit
this admissions season, please consider this.
Amongst these things:
1. GRE
2. GPA you understand
3. Pers Statement you understand
4. Letters from people you trust
5. Research Experience
Which is easiest for under-privileged student to access?
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Just dropped off teenage daughter and friends at
#phillyprotest
. Many parents doing the same.
When high schoolers come out is when the tipping point happens.
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Perception of, and reality of, what drives science is, sadly, power dynamics, not some fundamental calculus of depth of science.
Even people who dumped data on me with no hypothesis, think they drove the science after pub, bc they had the money to generate the data.
Are computational biologists the drivers of research? 7 years ago I co-wrote an editorial about how computational biologists are no longer just supportive, but are now running the show. Today I would write how every biologist should also be computational.
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Our paper
with
@jisaacmurray
and Bob Waterston at UW was started with a small R21 project with John. Then we heard that Bob had collected similar data. After a friendly discussion, we all decided we should collaborate rather than compete!
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I have solved my problem of needing to zoom 6 hours a day...
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@lpachter
Read and approved the 1st time.
By the 5th journal, titles changed, authors changed, text changed, and we've all stopped asking coauthors to read/edit and hate the paper anyway.
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We are excited to announce "Center for Sub-Cellular Genomics" under
@genome_gov
Center of Excellence in Genome Sciences (CEGS) with Jim Eberwine (MPI),
@DavidIssadore
, Daeyeon Lee at Penn; Jonathan Sweedler (U Illinois) & James Zou (Stanford) & others:
.
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Wow, two passages stand out:
"...point of science is what is discovered, not how it was discovered or by whom"
"One psychiatrist who saw your collection of pictures said it could only have been made by a man who hated women."
In the interest of promoting an understanding of the history, this scathing letter from Crick to Watson in 1967 is a remarkable document. Crick lays out a detailed criticism of the draft of Watson's "Double Helix" (provisionally titled "Honest Jim" here).
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All agree diversity in acad is important. But, it is always 2nd important. 2nd when compared to "fit" in grad stud, 2nd to interview skills, 2nd to search directions...
Yes, sometimes those other things can be primary, but if diversity's always 2nd, then it's not important.
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More out of 10X?
@Jmurray
pointed out this nice paper as we are starting some comparative scRNAseq together:
They run barcoding on cells prior to overloading a 10X flow cell. Multiplets with high prob, have distinct barcodes, yielding usable data.
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I know PIC seems trivial but we went through ten different rounds of how one might reasonably quantify snATAC-seq data within features and in the end decided PCI had the cleanest conceptual basis.
Code:
/end
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Here with our wonderful Genome Sciences T32 and R25 trainees at Duke for the
@genome_gov
Annual Training meeting. First in person meeting since 2019.
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Looking forward to seeing everybody again at the 10th CSHL Single Cell Analysis meeting next week! Hard to believe the small meeting we started 10 years ago has grown to this kind of global community
#cshlsca
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Sitting in my son's 2yr pandemic delayed graduation..every time somebody talks about taking risks, importance of failure, following meandering career path, I just see swarms if survivor bias graphic flying around.
Grrr, don't anybody actually talk to young people?
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I was very proud that my children made independent decisions to participate in the Philly protests.
I worried for their safety, but I didn't worry much about them not coming home. That's the difference.
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Jim Eberwine and I am happy to post our 26th joint paper (and Jim's first pre-print) describing our method called Chex-seq to assay open single-stranded DNA regions from single cells in fixed tissue.
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Happy to finally see this paper out led by
@zhenmiao
who conceived of the study and did all of the development work. 1/n
A new study demonstrates the need and advantage of uniformly quantifying single nucleus ATAC-seq data using Paired-Insertion-Counting (PIC).
@ZhenMiao2
,
@JunhyongKim
,
@PennMedicine
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Tfw teaching summer undergrads some phylogenetics:
CRISPR and whatnot new techniques to create genetic markers for single cell lineage tracing is wonderful, but why are people reinventing comp methods that already have 50 yrs of development?
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I took my daughter to a neurologist in Seoul to get a migraine consultation and CGRP inhibitor shot.
Appt:
Korea --same day
US -- 3-6 month with our Cadillac insurance
Drug
Korea--$300 (imported)
US-- $300
Doc fee
Korea -- $12 (full cost)
US -- $$$$? (Lots zeros)
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Penn Biology is recruiting a new Plant Biologist at the level of Assistant Professor.
We are proud to be a single biology department with a long history of collegial interdisciplinary interactions
Please share..
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First talk of 2023 Cold Spring Harbor Labs Single Cell Analysis Meeting starting with Nikolai Slavov. Looking forward to three exciting days of interdisciplinary talks!
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We are one of the few still integrated Biology departments and looking forward to your applications.
The Department of Biology at the University of Pennsylvania will be accepting applications for the PhD program during the 2020-21 admissions cycle. For more details please read the full statement on our website:
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When I was in grad school on Long Island, I'd go into NYC and always feel some kind of weight lift that I didn't know was there--the change from homogeneity of LI to diversity of NYC.
Now, I feel a weight lift I forgot about.
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@KordingLab
@ianholmes
There is a lot of evolutionary biology literature, both experimental and theoretical on this topic--not necessarily asking existence of GD.
First, nobody claims uniform randomness of variants, whether by mutations or recombination. Background mutation rates vary by 2-3 fold,
1/
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This is just amazing work. Wow.
Out work about "Single Cortical Neurons as Deep Artificial Neural Networks" was finally published in Neuron
With
@mikilon
and
@Segev_Lab
@NeuroCellPress
paper:
code:
data:
All new results in thread below
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Tsundoku is the Japanese word for books you collect but never read.
What do you call twitter links you like so you can read the paper later but never get to...
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Uh, now MC HAMMER is a single cell biologist? Neat! I am gonna have to name our next method MC-HAMMER..(called it first, all you single cell people out there).
🤔💭 A single-cell method to map higher-order 3D genome organization in thousands of individual cells reveals structural heterogeneity in mouse ES cells | bioRxiv
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30+ yrs ago when I left, Korea was a regressive, dictatorial, police state.
I now sit here visiting a vibrant, free soc of BTS and shiny public infrastructure, I remember how we talked about “becoming America.”
Oh, where are you now, land of my children?
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This is a bit of distraction, but recent events have lowered by tolerance for dumb shit in academia and I have to say something that I might have let go a month ago.
(I guess this is my first subtweet--is that what this is called?)
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TFW you tease your teen daughter everybody else is getting Happy Father's day tweets and she posts a pic of you trophying a kimchi jar (beats me why)
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What is upsetting about the Harvard/Asian news:
is not the idea of quotas. I think representative balance is to be desired, neither under nor over. (Although, what trait to balance is a more difficult issue.) /1
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Today
@PennBiology
held zoom graduation for all our majors. While we were uncertain and inexperienced doing this, it all turned out great. In some ways more real and moving than the real thing. One of few good things to come out of this...
Congrats to all our Class of 2020!!
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Tomorrow is this talk by talented Paul Magwene. He is one of the deepest thinker of my former trainees.
@lpachter
kindly pointed Paul, Paul Lizardi, and I conceptualized pseudotime and I want to use this to talk about method dev in compbio
1/n
ATTN
#ComputationalBiology
Community: Last
#BlackInCompBio
series of 2020!
Tune in for a community chat with Dr. Paul Mgawene of
@DukeU
@magwenelab
over a unique journey in computational biology. RSVP today:
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In this new work by
@ZhenMiao2
with Jianqiao Wang,
@kernyupark
, and
@DaKuangDerek
we develop a probabilistic linear model testing framework for snATAC data called PACS.
1/n
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Last week we concluded our
@genomedotgov
genomics summer internship program with these fantastic students: Lana Abdi, Adetola Alonge, Donovan Brown, Da’Shira Brown, Savoya Joyner, Wara Laura
@Wara73375043
, Jose Malaret, Eric Mendoza, Sebastian Plasencia, Meghan Wachira.
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Not only reinventing the wheel, but going through exactly the same sequence of reinventing the wheel that ecology did 50 years ago: PCA -> CA -> Factor analysis -> Path analysis
Excellent paper showing that many of us in the single cell dimension reduction world have been reinventing the wheel. Correspondence analysis deserves to be widely known as an alternative to PCA. Congratulations!
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It seems strange so many seem to think the "other side" of all this cost (which is approximately correct) is the PI. The entity carrying the cost is the tax payers (and a bit subsidized by unis).
How much does a graduate student cost per year?
Salary: $35,793
Benefits + Tuition: $26,463
Supplies: $12,000
Travel: $3,000
Overhead: $42,491
Total: $119,747
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@Caroline_Bartma
Following you is so exciting.
Because every day I think "is this the day I unfollow
@Caroline_Bartma
"
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80% of things appearing as a "new method" paper are things that used to be in the Methods section of a biology paper--100% for Dana's sentiment.
@vallens
3) This is why I like to work centered around a concrete biological application, then I can say "my method discovered exciting new biology that other methods fail to find". This is what gives me the scientific high, even if some of my methods might not be the sexiest new ML
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But, this became one of the main factors by which my student dropped out of science.
To all the unprofessional reviewers out there—the people you are really hurting are trainees. To the unethical editors/reviewers out there FU. Stop driving young people out of science.
/end
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Like other minorities, many Asians in academia know they have to act "non-Asian" to be admitted to leadership pos and inner circles. "Hard working", "technically good", may seem positive, but this can be akin to calling female scientists "collaborative" instead of "dynamic" /3
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I generally agree with this and the OP. The problem, I think, is more on the side of "modeling the method"
1/n
The confidence interval shown here is not quite right, but sadly, yeah.
The reason is a reluctance to model the data, which is surprising given the number of biologists, physicists, and statisticians in the room.
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Since this morning's tweet from my colleague
@IshmailSaboor
, I spent the whole day thinking of what I can say...no words. Is this really the world we are okay living in?
Today my mom will give me the same speech she’s been giving me since I was a young boy: she’ll say be careful, be vigilent, because many people will only ever see you as a threat. Today I will respond to my mom and say there is nothing I can do.
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Wonderful recognition of tremendous talent and dedication of
@ZhenMiao2
!
Huge congratulations to
@ZhenMiao2
of the
@JunhyongKim
Lab for being awarded a 2022 Blavatnik Family Fellowship in Biomedical Research!
@pennbgs
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We are now accepting applications for NHGRI Diversity Action Plan at Penn for paid summer internships and stipend funded postbacc program in Genomics and Computational Biology. Please see:
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With some exceptions, most people I know with true fame and status are not nice people. We all implicitly know this--which is why we get "not only was he famous, he was such a nice person" as if this was an unexpected bonus.
Yeah, don't look too close at your heroes.
end
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@theosysbio
@arjunrajlab
Kimura's neutral model based on load of selection is the most successful predictive mathematical model in biology. Kimura predicted codon third position variation before the invention of sequencing. Every time a conservation arg is made for function, this is Neutral theory.
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It is this kind of propping up the cult of personality that perpetuates the corrupt culture
Last night the genomics community applauded a disgraceful normalization of racism and sexism as Jim Watson was toasted on his 90th birthday. /1
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