Onur
@eonurkara
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Featuring random thoughts. Computational Biology PhDc @ LUMC • TU Delft. Aging, AML and AI.
Amsterdam, NL
Joined April 2020
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@Uzaktan_Gelen_
Orada oturunca insanın aklına gelmeyebiliyor bazı şeyler. “Çorba ne ile konur?” diye sorduklarında kaşık mı lan acaba diye düşünmüştüm birkaç saniye 😂
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Happy to be nerding and presenting first year of my PhD work at
#ECCB2022
. Interested in leukemia or how single cell technology can help guiding its future theparies? Come and see me at P127 today!
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I still remember wandering around in Bushnell park with
@duyguucar
(obv 6 feet apart) and her saying “this disease makes you realize how important our work is”.
I agreed and so do other people.
Today in Cell.
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At the end of my PhD if I have a poster, at each section I will just put the title and a QR code to the related publication. I like how people don’t get the meta-humor in this, I think it is brilliant and serves the purpose (advertisement).
"The only thing more full than the auditorium tonight is
@ManolisKellis
poster"
@LB_Barreiro
intro at
#BoG22
... Ahem... you be the judge. Poster
#135
, come say hi! Full res here:
#Alzheimers
#SingleCell
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I have created a simple generic mail template with the links of official rescue organizations. If you would like to send it around to your organization or company, just reach out to me.
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@davidasinclair
I don’t have access but apperantly they have been critisized for their analyses, please have a look:
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Boredom makes you wonders. I created a simple word game a month ago as a joke while we had nothing else to do. It stick in my mind so we decided to implement it:
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What are the most common signatures conserved during aging?
If you’re curious, then you can read our new study which is just published in
@AgingCell
.
👇🏻
In this new study led by
@eonurkara
and Neerja Katiyar, we uncovered the most conserved immune signature conserved between short (NZO) and long living (B6) strains of mice.
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#Rejected
#AcademicTwitter
We could not make it to the cover of Aging Cell :(
Congratulations to the authors who made it. However, I don't want our cover image to be thrown away as I spent few days on it. So, there you go! 😄
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I just learnt Jun-Fos heterodimers are structrually more stable than Jun homodimers and Fos proteins can’t even f*cking homo-dimerize.
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I haven’t had a chance to promote our work (cinaR) with
@duyguucar
yet but other people already started doing it for us! It is so motivating! We created a CRAN/R package for computational analyses of bulk ATAC-seq (and RNA-seq) profiles.
📦🖥 "cinar • a single wrapper function for end-to-end computational analyses of bulk ATAC-seq (or RNA-seq) profiles"
👤 Onur Karakaslar
@eonurkara
#rstats
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I will forever be grateful and in his debt for broadening my horizon and enabling me to become a world citizen.
#Atat
ürk
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I wrote my first recommendation letter for one of my previous collegues for a position in
@broadinstitute
and it worked lol. Life is full of surprises...
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Hartford’da dışarı çıkmışken dedemi aramışımdır.
Dedem: Carcurt’ta havalar nasıl?
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With this, I also would like to thank at first my mentor
@duyguucar
, and my co-author Neerja Katiyar and all other authors and former interns who contributed to this story. 👏🏻
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Canı evde sıkılan dost edinin.
Şu hayatta hissettiğim en büyük eksikliklerden biri hiç kartpostal almamış olmak sanırım...
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Just happy to be involved in this project with awesome scientists.
#Preprint
Alert from our very own
@Jin_Q_Cheong
, a 5th yr PhD candidate in
@WCM_IMP
, and
@arjunrshankar
, a post-doc in the lab, on long-lasting epigenetic memory of
#COVID19
in hematopoietic stem cells and their mature progeny cells!
#thread
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Do you want to use R & Python on a HPC cluster with a Jupyter notebook from your laptop?
You may want to check this out:
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Had an “Eureka” moment in my PhD yesterday, now need to work couple of years to share it with all of you guys (if it is true) 😂
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I realized last week that I made a mistake in my code, which made me to arrive false conclusions. I presented these findings during our weekly work discussions, and defended them… finally when I realized, I felt terribly embarresed.
But there were some stories which cheered me
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My friend
@JeppeSeverens
just published this piece in
@LeukemiaJnl
. Check it out!!!
Congrats to Jeppe and the whole team (special kudos to
@erikvandenakker
)! It was truly amazing to see how this story unfolded over the last three years and I am truly
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Favorite moments so far
#LK99
• Kwon going rogue at a random conference
• Russian anime girl cooking LK-99 at her basement and refusing to share a video lol
• Mic drop by Sinead Griffin
Global scientific K-drama 😂
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My computer loading 5 single cell experiments to environment and throwing a memory error one hour later
Me:
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I think I am mature enough not to make ‘see you next year’ jokes now.
Hmm.
Just kidding, see y’all next year haha
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Is this a common theme that such a study does not share their transcriptional data till the drug is approved?
@Nature
I have a hunch that running their RNA-seq data on our pipeline (), we might actually see why those NPM1 patients are not responding!
Nature research paper: The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia
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Is there a drought in Istanbul? Should people be worried?
I was curious what the data tell us, so here it is:
@iski_destek
@istanbulbld
@ekrem_imamoglu
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I don’t know if I should be happy that the creator of UMAP liked my tweet or be sad that he’s the only one 😂
Thanks
@leland_mcinnes
!
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Speaking of posters... If you want to learn more about what I did in the first year of my PhD, apparently I will be in Madison in July at
#ISMB2022
!
@TransMedISMB
At the end of my PhD if I have a poster, at each section I will just put the title and a QR code to the related publication. I like how people don’t get the meta-humor in this, I think it is brilliant and serves the purpose (advertisement).
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It may be stupid but I am still blown away by what you can do using *free stuff* on internet.
Learn, write, ask questions, get feedback, publish your work, promote your work... it is incredible.
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Evet bilmiyoruz çünkü içerisinde milyonlarca “Perceptron” var. Aşağıda gördüğün mor bir perceptron’u temsil ediyor. Bu resimde içerisine üç tane sayı giriyor (x1, x2, x3) ve dolayısıyla 3 tane de “ağırlık” var (w1, w2,w3). y ise çıktısı, ve bunların her biri sadece bir sayı.
Şu an piyasadaki pek çok AI araştırmacısının (buna GPT’yi geliştiren Ilya ve ekibi de dahil) akıl hocası, Turing ödüllerini kazanan Prof Hinton’un söyledikleri çok ürkütücü.
Diyor ki; GPT gibi modellerin nasıl çalıştığını tam bilmiyoruz.
Sunucu da şaşırıyor tabii. Bunu söyleyen
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People I tell this to laughs at me but I do feel like a modern day artist while doing my job, specifically like a sculptor. Shaping out a sculpture (story/figures) out of mud (data) backed up by ideas of others (literature).
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Starting from consensus peaks (or a count matrix), cinaR runs differential and enrichment analyses and provides users with various configurable plotting options.
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* me when someone I don’t want to respond texts me *
unbothered, moisturized, in my lane, focused, flourishing
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Our profanity detection tool Sinkaf was cited and these results were presented at LREC2022 in Marsille lol. How do I get my citation counted? 🤣🤣
Congrats to the authors from
@Turkcell
:
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People are not looking forward to struggling with money at their 30s. Such a big surprise! 🙃
Many U.S. academics are reporting widespread challenges in recruiting
#postdocs
, finds an investigation by
@ScienceCareers
.
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Fun Fact:
B-cells are NOT named after Bone marrow, the name comes from Bursa, which is actually a city in Turkey and nothing to do with B-cells. Apperantly, Bursa of Fabricius is an organ near birds’ ass where these cells are discovered.
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sinkaf’ın 5000’den fazla indirilmesi ve en çok yıldız alan repom olması beni buruk bir mutluluğa sevk ediyor. Hayat komik kuşlar uçuyor.
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Marbless is finally here!
Create 5-letter words by dropping down 🟡.
Clear all marbless to win the daily challenge.
#Marbless
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I was reading
@benfrederickson
's blog post on numerical optimizations and I got really really jealous of the last example where he found the north American city locations based on pairwise distances. Soo, I wrote my own version of it on
@p5xjs
lol.
Link:
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Hayatımda yaşadığım en komik anılardan biridir. İtalyan arkadaş Bruschetta yapıp getirir. Türk bir arkadaş bunu görür ve İtalyan’a seslenir:
- Aaa Bruşetta mı yaptın?
+ “Brusketta”
- Bruşetta o. Emin misin?
+ İtalyanım.
bruşetta ❌(aurait ete ecrite: bruscietta)
brusketta ✅
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My last month:
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Türkiye'de 1950'den bu yana en popüler kadın ve erkek isimlerinin değişimi.
Evet, evde sıkılınca böyle şeyler yapıyorum...
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US corner of biomedical research
Really excited to present new work by
@ritagonmar
: we visualized the entire PubMed library, 21 million biomedical and life science papers, and learned a lot about --
THE LANDSCAPE OF BIOMEDICAL RESEARCH
Joint work with
@CellTypist
and
@benmschmidt
. 1/n
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Half of my job is “cleaning the data”, trying to understand the column names in an excel sheet. Quarter is “running a pipeline”, looking for a random comment that would help me understand the code, and the rest is “plotting”, ggplot ruining my day because of an x-axis tick.
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Congrats to both teams, specially to
@Jin_Q_Cheong
and
@arjunrshankar
! Amazing work. Be proud to be a small contributor :)
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Shameless self promotion.
Our paper on warning surgeons during tumor excision surgeries about left-over tumor cells, is now published at
@PLOSCompBiol
.
@cakmakcid
&
@eonurkara
use an RF model to pinpoint glioma cells using HRMAS NMR signal. Great collaboration with
@mnmsPlatform
.
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Users can choose from different state-of-art algorithms for both analyses, correct for unknown and known batch effects, add covariates to account for confounding factor and do much more.
Check it out, it is cool! :)
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@Tim_TLBL
@Sleutelstad
There were dozens of police officers, fire fighters, ambulances and even a helicopter… but it’s not reported at any sort of media resources. Just a tweet. Thanks Tim.
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Life is boring without games. 🙃
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Sayın
@kilicdarogluk
,
Ben siyasetle yakından ilgilenen biri değilim. İşim bilim ama yine de ülkem adına birkaç kelam etmek istiyorum. Biz sizi iyi bir insan olarak bildik ve bu ülkenin geleceği için çalıştığınıza hepimiz şahidiz. Fakat bugün de açıkça gösterdi ki, artık emekli
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When you see your game gets an instant fame… 😂
We’re also feature by Michael DiCostanzo few days ago on tiktok!
Michael has more than 720K followers and he reviews games. Here is his reactions to our game 😂
link:
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After spending more than 2 years on AML in my PhD, I can clearly say that... AML is a heterogeneous disease.
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Şu hayatta hissettiğim en büyük eksikliklerden biri hiç kartpostal almamış olmak sanırım...
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The logic is dead simple, there is a 5-letter secret word and you know the sum of the letters. At each guess, you learn whether a letter is in (blue) or not (gray).
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So far I have seen couple of bombings, one coup, a troll being US president and a global pandemic, can’t wait for the next
#20yearsoldchallenge
!
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I would like to thank all of my supervisors, specifically
@erikvandenakker
for the super cool project, mentoring, and enduring my constant nagging! Also, kudos to my fellow
@DanieleBizzarr2
for getting a 10 min talk!
Let's go!
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This one looks cool, people should write ML frameworks with this one.
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Have no creativity whatsoever 🥲
🟧
🟥🟧
🟥🟥🟥
🟧🟥🟥🟥
🟥🟥🟥🟥🟥
🟥🟥🟥🟥🟥🟥
Percentile: 1
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I’ve found an actual human bug.
Just put on a headset, and talk to a microphone such that you hear your own voice with 100 ms delay.
YOU CAN’T TALK.
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I present the following paradox: no one believes that GO term enrichment is interesting or useful and yet everyone does it 🤔
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Turtle = *me every lab meeting*
“what is going on here guys?”
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Sometimes the ones love you most, hurts you most. Such irony.
News & Views: Immune cells called neutrophils can support the spread of cancer. How neutrophils aid this process now comes into focus through insights into the function of structures called neutrophil extracellular traps, according to a Nature paper.
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My friend
@DanieleBizzarr2
and I are studying Dutch for more than a year now. We've recently discovered this amazing collection of Donald Ducks, might be useful for those who want to practice their dutch skills or would like to have some nostalgia :)
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I was so hyped out about my recent finding for two days! Then I found out that it was published in a 39 impact factor journal in 2020 🥲
(They even used my slide title as their article name lol)
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Finally had a chance to play with Dall•E. Here is a penguin in Istanbul looking for a bus stop:
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Today I looked at the output folder of my current project, so far there are 307 pdf files mostly containing more than one plot inside. We created 40 panels from those to form the story of the paper. That means only 13% of my work (or less) will be out there. Such inefficiency lol
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“If you lose 10kg of fat, precisely 8.4kg comes out through your lungs....”
Never thought about this one before.
*exhales harder*
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I got the idea from the runaway species of
@davideagleman
. I see a resemblance between the alternative endings Hemingway wrote and shaping out of our story from the data we analyzed.
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We need to start thinking about utilising mobile phones more for bioinformatics problems.
Just think about a future where you can make couple of bucks lending your phone’s idle time to help out researchers to figure out solutions for the next pandemic.
Genopo, a tool enabling nanopore sequence analysis on Android devices. Potential for revolutionizing disease monitoring in underfunded locations and labs worldwide
@GarvanInstitute
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