F. B. Dincaslan
@dincaslan.bsky.social
Post-Doc in 🇪🇺 | Research 👩🏻🔬👩🏻💻
📚 Books | Travelling 🧭 | Chess ♟️
Skeets in TR/ENG Views are my own
📚 Books | Travelling 🧭 | Chess ♟️
Skeets in TR/ENG Views are my own
Pinned
Hi, folks! I am Betul. I completed my PhD in Biomedical Eng. in 🇸🇬.
I enjoy doing both wet&dry research (as expected from my background), discovering new ways of visualising the data, reading books while travelling, hiking and rapid chess.
I enjoy doing both wet&dry research (as expected from my background), discovering new ways of visualising the data, reading books while travelling, hiking and rapid chess.
Reposted by F. B. Dincaslan
Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Group Leader - Generative Biology and AI
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
tinyurl.com
January 1, 2026 at 12:08 PM
Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Reposted by F. B. Dincaslan
As I hope for a successful and productive 2026, my thoughts revolve around the core prerequisites:
◼️ They are both simple & challenging:
blog.slavovlab.net/2019/12/31/r...
◼️ They are both simple & challenging:
blog.slavovlab.net/2019/12/31/r...
Research success
We — the research community — can be much more successful if we invest more time and effort in what matters: Coming up with original new leads and helping each other grow as scientists …
blog.slavovlab.net
January 1, 2026 at 3:00 PM
As I hope for a successful and productive 2026, my thoughts revolve around the core prerequisites:
◼️ They are both simple & challenging:
blog.slavovlab.net/2019/12/31/r...
◼️ They are both simple & challenging:
blog.slavovlab.net/2019/12/31/r...
Reposted by F. B. Dincaslan
2025 was the year we stopped debating whether paying peer reviewers might work and started showing that it does.
December 31, 2025 at 10:13 PM
2025 was the year we stopped debating whether paying peer reviewers might work and started showing that it does.
Reposted by F. B. Dincaslan
5. Data Visualization socviz.co/ by Kieran Healy. I've read book 4 and 5.
Data Visualization
A practical introduction.
socviz.co
December 28, 2025 at 2:45 PM
5. Data Visualization socviz.co/ by Kieran Healy. I've read book 4 and 5.
Reposted by F. B. Dincaslan
4. Fundamentals of Data Visualization clauswilke.com/dataviz/
Fundamentals of Data Visualization
A guide to making visualizations that accurately reflect the data, tell a story, and look professional.
clauswilke.com
December 28, 2025 at 2:45 PM
4. Fundamentals of Data Visualization clauswilke.com/dataviz/
Reposted by F. B. Dincaslan
10/ The truth? Feeling like a beginner again is normal. The best bioinformaticians aren’t the ones who “know it all.” They’re the ones who adapt.
December 25, 2025 at 2:45 PM
10/ The truth? Feeling like a beginner again is normal. The best bioinformaticians aren’t the ones who “know it all.” They’re the ones who adapt.
Reposted by F. B. Dincaslan
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 17, 2025 at 12:46 AM
Organelles do NOT have a single uniform pH.
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
And if you think they must, because “protons diffuse fast,” this paper is for you.
A thread on why that assumption is wrong; and what we found instead. 🧵 1/n
Reposted by F. B. Dincaslan
So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?
December 17, 2025 at 6:46 PM
So question for single-cell peeps. It seems that ParseBio is even more locked-down than 10x! Is it the case that if I'm not a "registered" ParseBio customer, I can't even access their splitpipe software? Is there any archived version of splitpipe available?
Reposted by F. B. Dincaslan
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
https://ds.dfci.harvard.edu/postdocs/
t.co
December 1, 2025 at 6:59 PM
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
Reposted by F. B. Dincaslan
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 8, 2025 at 4:53 PM
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
Reposted by F. B. Dincaslan
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 7, 2025 at 4:11 PM
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
Reposted by F. B. Dincaslan
#AMC2025 is almost here (Oct 28–29, Jena) and we’ve opened a few more seats! If you work on host-microbiome interactions, aging, or age-related diseases, bring a poster and join this amazing crowd!
amc25.leibniz-fli.de/registration/
✨ Highlights 👇 🧵 (1/4)
amc25.leibniz-fli.de/registration/
✨ Highlights 👇 🧵 (1/4)
October 6, 2025 at 2:49 PM
#AMC2025 is almost here (Oct 28–29, Jena) and we’ve opened a few more seats! If you work on host-microbiome interactions, aging, or age-related diseases, bring a poster and join this amazing crowd!
amc25.leibniz-fli.de/registration/
✨ Highlights 👇 🧵 (1/4)
amc25.leibniz-fli.de/registration/
✨ Highlights 👇 🧵 (1/4)
Reposted by F. B. Dincaslan
🇬🇧 Introducing ISCB UK! Join us April 21–22, 2026, in Cambridge for the first #ISCBUK conference connecting the #bioinformatics and #computationalbiology community in the UK.
✨ Abstract submissions now open!
🗓️ Deadline: Feb 5, 2026
🔗 https://www.iscb.org/uk2026/call-for-submissions/abstracts
✨ Abstract submissions now open!
🗓️ Deadline: Feb 5, 2026
🔗 https://www.iscb.org/uk2026/call-for-submissions/abstracts
October 3, 2025 at 10:16 AM
🇬🇧 Introducing ISCB UK! Join us April 21–22, 2026, in Cambridge for the first #ISCBUK conference connecting the #bioinformatics and #computationalbiology community in the UK.
✨ Abstract submissions now open!
🗓️ Deadline: Feb 5, 2026
🔗 https://www.iscb.org/uk2026/call-for-submissions/abstracts
✨ Abstract submissions now open!
🗓️ Deadline: Feb 5, 2026
🔗 https://www.iscb.org/uk2026/call-for-submissions/abstracts
Reposted by F. B. Dincaslan
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 11:07 AM
We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue.
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
As an academic without any industry experience, I was not good at asking about my rights or salary negotiations. However, I have been learning from EU-ECRs regarding that. Even PhDs know their rights very well. Impressive and hopeful ✨
August 30, 2025 at 9:10 AM
As an academic without any industry experience, I was not good at asking about my rights or salary negotiations. However, I have been learning from EU-ECRs regarding that. Even PhDs know their rights very well. Impressive and hopeful ✨
Reposted by F. B. Dincaslan
Free course: Intro to Computational Biology by Mike Love, author of DESeq2.
biodatascience.github.io/compbio/
biodatascience.github.io/compbio/
August 26, 2025 at 1:45 PM
Free course: Intro to Computational Biology by Mike Love, author of DESeq2.
biodatascience.github.io/compbio/
biodatascience.github.io/compbio/
Reposted by F. B. Dincaslan
There and back again... A few months ago I wrote an essay on moving from academia to biotech. Today I published a follow-up: moving from biotech to academia. doi.org/10.59350/004...
August 9, 2025 at 11:56 AM
There and back again... A few months ago I wrote an essay on moving from academia to biotech. Today I published a follow-up: moving from biotech to academia. doi.org/10.59350/004...
Reposted by F. B. Dincaslan
You can not live without Rmarkdown if you use R for genomics data analysis. Cheatsheet from Posit:
rstudio.github.io/cheatsheets...
rstudio.github.io/cheatsheets...
July 28, 2025 at 2:15 PM
You can not live without Rmarkdown if you use R for genomics data analysis. Cheatsheet from Posit:
rstudio.github.io/cheatsheets...
rstudio.github.io/cheatsheets...
Thanks Science&Jennifer Sills for making all these struggles visible.
#NextGenSci gave young scientists this prompt: When pursuing science education or work abroad, what is the biggest challenge you face? What one change would help scientists from your country or region overcome this challenge?
Here's how they responded: scim.ag/4llEPGf
Here's how they responded: scim.ag/4llEPGf
Supporting scientists who study and work abroad
scim.ag
July 25, 2025 at 5:35 PM
Thanks Science&Jennifer Sills for making all these struggles visible.
Reposted by F. B. Dincaslan
🔬 A new study in NAR Genomics and Bioinformatics compares short-read and long-read sequencing, aligning results at the cDNA level using UMIs 🧬
📖 Dive into the full article: doi.org/10.1093/narg...
#Sequencing #Bioinformatics #GeneExpression #Genomics #UniqueMolecularIdentifier #NARGAB
📖 Dive into the full article: doi.org/10.1093/narg...
#Sequencing #Bioinformatics #GeneExpression #Genomics #UniqueMolecularIdentifier #NARGAB
July 16, 2025 at 1:44 PM
🔬 A new study in NAR Genomics and Bioinformatics compares short-read and long-read sequencing, aligning results at the cDNA level using UMIs 🧬
📖 Dive into the full article: doi.org/10.1093/narg...
#Sequencing #Bioinformatics #GeneExpression #Genomics #UniqueMolecularIdentifier #NARGAB
📖 Dive into the full article: doi.org/10.1093/narg...
#Sequencing #Bioinformatics #GeneExpression #Genomics #UniqueMolecularIdentifier #NARGAB
Reposted by F. B. Dincaslan
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
July 14, 2025 at 1:45 PM
String manipulation is a critical daily task for bioinformaticians.
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
Here is a cheatsheet using stringr: rstudio.github.io/cheatsheets...
I probably use stringr::str_replace() once every other day...
to clean up metadata (of course!) #rstats
I made a list of books to read in 2025 before NY. I’ve read 10 books so far (couldn’t complete a few more as i left them at home).
Today, I checked out the list. I read only one book from that list (& have been reading 2 more).
Although I still have time, I enjoyed the serendipity of the process.
Today, I checked out the list. I read only one book from that list (& have been reading 2 more).
Although I still have time, I enjoyed the serendipity of the process.
July 13, 2025 at 9:14 PM
I made a list of books to read in 2025 before NY. I’ve read 10 books so far (couldn’t complete a few more as i left them at home).
Today, I checked out the list. I read only one book from that list (& have been reading 2 more).
Although I still have time, I enjoyed the serendipity of the process.
Today, I checked out the list. I read only one book from that list (& have been reading 2 more).
Although I still have time, I enjoyed the serendipity of the process.
Even if you’ve certain goals about your paper (e.g., preprint, data-sharing, more details), the corresponding author(s)-a.k.a the PI-decides what to do with it.
Some people expect a lot from PhDs in this regard. There is a power imbalance in academia. Convince PIs by incentives or pressuring, idc.
Some people expect a lot from PhDs in this regard. There is a power imbalance in academia. Convince PIs by incentives or pressuring, idc.
July 12, 2025 at 11:23 AM
Even if you’ve certain goals about your paper (e.g., preprint, data-sharing, more details), the corresponding author(s)-a.k.a the PI-decides what to do with it.
Some people expect a lot from PhDs in this regard. There is a power imbalance in academia. Convince PIs by incentives or pressuring, idc.
Some people expect a lot from PhDs in this regard. There is a power imbalance in academia. Convince PIs by incentives or pressuring, idc.
Reposted by F. B. Dincaslan
🧵 1/ In bioinformatics, cutoffs rule everything.
What’s “significant”? What’s not?
Let’s talk thresholds—and how they shape your science.
What’s “significant”? What’s not?
Let’s talk thresholds—and how they shape your science.
July 5, 2025 at 1:45 PM
🧵 1/ In bioinformatics, cutoffs rule everything.
What’s “significant”? What’s not?
Let’s talk thresholds—and how they shape your science.
What’s “significant”? What’s not?
Let’s talk thresholds—and how they shape your science.
Duolingo’s constant expansion of courses that I have already completed reminds me that nothing in language learning lasts without (daily) practice.
June 29, 2025 at 9:57 PM
Duolingo’s constant expansion of courses that I have already completed reminds me that nothing in language learning lasts without (daily) practice.