Sumaiya Nazeen
@snz20.bsky.social
Postdoctoral Research Fellow, DBMI, HMS, Neurology, BWH
Sudarsky Scholar'22
MIT EECS SM'14, PhD'19
Fulbright S&T Fellow'12
Ludwig Center Fellow'15
She/Her/Hers
Sudarsky Scholar'22
MIT EECS SM'14, PhD'19
Fulbright S&T Fellow'12
Ludwig Center Fellow'15
She/Her/Hers
Pinned
Sumaiya Nazeen
@snz20.bsky.social
· Jan 28
NERINE reveals rare variant associations in gene networks across multiple phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease https://www.biorxiv.org/content/10.1101/2025.01.07.631688v1
Check out the latest preprint from @j-e-mitchel.bsky.social on a new single-cell genetic colocalization tool, scJLIM, which shows significant power gain over bulk colocalization. It has been a pleasure being part of the effort!
Super excited that my paper describing the scJLIM single-cell genetic colocalization tool is finally out on bioRxiv! scJLIM enables you to identify the specific cell states where GWAS genetic variants impact gene expression. Check it out! www.biorxiv.org/content/10.1...
A single-cell genetic colocalization test improves power and resolves disease-mediating cell types
Statistical colocalization testing methods can determine if the same single-nucleotide polymorphism (SNP) underlies both a genome-wide association study (GWAS) locus as well as an expression quantitat...
www.biorxiv.org
October 20, 2025 at 4:18 PM
Check out the latest preprint from @j-e-mitchel.bsky.social on a new single-cell genetic colocalization tool, scJLIM, which shows significant power gain over bulk colocalization. It has been a pleasure being part of the effort!
Reposted by Sumaiya Nazeen
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by Sumaiya Nazeen
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
September 30, 2025 at 2:19 AM
Do you know ~60% of human SVs fall in ~1% of GRCh38? See our new preprint: arxiv.org/abs/2509.23057 and the companion blog post on how we started this project and longdust: lh3.github.io/2025/09/29/o.... Work with Alvin Qin
Reposted by Sumaiya Nazeen
We are deeply saddened to hear of the passing of Jane Goodall.
Jane was a much-loved member of the conservation community in Cambridge and worldwide. She completed her PhD at @darwincollegecam.bsky.social and was an Honorary Fellow at @newnhamcollege.bsky.social.
www.youtube.com/watch?v=ZIzR...
Jane was a much-loved member of the conservation community in Cambridge and worldwide. She completed her PhD at @darwincollegecam.bsky.social and was an Honorary Fellow at @newnhamcollege.bsky.social.
www.youtube.com/watch?v=ZIzR...
Jane Goodall - Finding our way to a better future
YouTube video by Cambridge University
www.youtube.com
October 1, 2025 at 8:59 PM
We are deeply saddened to hear of the passing of Jane Goodall.
Jane was a much-loved member of the conservation community in Cambridge and worldwide. She completed her PhD at @darwincollegecam.bsky.social and was an Honorary Fellow at @newnhamcollege.bsky.social.
www.youtube.com/watch?v=ZIzR...
Jane was a much-loved member of the conservation community in Cambridge and worldwide. She completed her PhD at @darwincollegecam.bsky.social and was an Honorary Fellow at @newnhamcollege.bsky.social.
www.youtube.com/watch?v=ZIzR...
Reposted by Sumaiya Nazeen
Yup. This was me 10 years ago.
Why is this horrible for Universities?
Just about everyone who isn't a citizen or green card holder already who's hired for a tenure track faculty position is hired through an H1B and then, after 3-5 years, applies for a green card.
This is literally "No more foreign professors can be hired"
Just about everyone who isn't a citizen or green card holder already who's hired for a tenure track faculty position is hired through an H1B and then, after 3-5 years, applies for a green card.
This is literally "No more foreign professors can be hired"
Those on an H1B cannot return to the US from tomorrow (Sunday) unless paying $100K. This is an out-of-the blue presidential action. We’ll see software engineers stranded abroad.
One easy to predict outcome: those on US visas will travel less… for work, for conferences etc.
One easy to predict outcome: those on US visas will travel less… for work, for conferences etc.
September 20, 2025 at 4:03 PM
Yup. This was me 10 years ago.
Reposted by Sumaiya Nazeen
The 2025 Ig Nobel-winning research was as wacky as ever. But wars, visa restrictions, Trump's border and research policies, and even an all-too-frequent airplane incident kept nearly half the winning teams from traveling to Boston @science.org www.science.org/content/arti...
The Ig Nobels are science’s most lighthearted event. This year is ‘not typical’
Amid Trump research cuts, visa restrictions, and international conflicts, some winners sit out the celebration of whimsical science
www.science.org
September 19, 2025 at 4:44 PM
The 2025 Ig Nobel-winning research was as wacky as ever. But wars, visa restrictions, Trump's border and research policies, and even an all-too-frequent airplane incident kept nearly half the winning teams from traveling to Boston @science.org www.science.org/content/arti...
Reposted by Sumaiya Nazeen
In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
September 17, 2025 at 3:12 PM
In a new preprint from @brianhie.bsky.social's lab, the team reports the first generative design of viable bacteriophage genomes.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Leveraging Evo 1 & Evo 2, they generated whole genome sequences, resulting in 16 viable phages with distinct genomic architectures.
Reposted by Sumaiya Nazeen
Brilliant paper by Visscher et al.
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Direct effect of genetic ancestry on complex traits in a Mexican population
Human populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...
www.medrxiv.org
September 11, 2025 at 5:57 AM
Brilliant paper by Visscher et al.
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Populations differ in traits/disease burden. Are these differences due to genetics?
Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.
1/3
www.medrxiv.org/content/10.1...
Reposted by Sumaiya Nazeen
More of "The AI Coming For Us". Well, one way it's going to take us out is if the next generation of folks relies on this slop for anything serious ....
"The reference genome is essentially folded using the BWT, which allows the search for read alignments to take on a bow-tie shape in the index"
Hmmm... @benlangmead.bsky.social
Hmmm... @benlangmead.bsky.social
September 9, 2025 at 2:51 PM
More of "The AI Coming For Us". Well, one way it's going to take us out is if the next generation of folks relies on this slop for anything serious ....
Reposted by Sumaiya Nazeen
Whether we like it or not, AI is here and not going anywhere. The excellent colleagues behind @callingbullshit.bsky.social (@jevinwest.bsky.social & @carlbergstrom.com) now have a great resource to help us understand AI and how to deal with it. Highly recommended!
thebullshitmachines.com/index.html
thebullshitmachines.com/index.html
September 6, 2025 at 7:54 PM
Whether we like it or not, AI is here and not going anywhere. The excellent colleagues behind @callingbullshit.bsky.social (@jevinwest.bsky.social & @carlbergstrom.com) now have a great resource to help us understand AI and how to deal with it. Highly recommended!
thebullshitmachines.com/index.html
thebullshitmachines.com/index.html
Reposted by Sumaiya Nazeen
❗ I clearly consider this result as THE most important result achieved over this last decade for exploiting and democratizing genomic data.
I think there will be a "before" and an "after" logan and logan-search
github.com/IndexThePlan...
logan-search.org
Have a look at this thread
I think there will be a "before" and an "after" logan and logan-search
github.com/IndexThePlan...
logan-search.org
Have a look at this thread
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 4, 2025 at 12:35 PM
❗ I clearly consider this result as THE most important result achieved over this last decade for exploiting and democratizing genomic data.
I think there will be a "before" and an "after" logan and logan-search
github.com/IndexThePlan...
logan-search.org
Have a look at this thread
I think there will be a "before" and an "after" logan and logan-search
github.com/IndexThePlan...
logan-search.org
Have a look at this thread
Reposted by Sumaiya Nazeen
New York Times story with profiles of researchers whose grants were terminated.
[Gift Link]
www.nytimes.com/2025/08/24/o...
[Gift Link]
www.nytimes.com/2025/08/24/o...
Opinion | America First? Not When It Comes to Your Health.
www.nytimes.com
August 24, 2025 at 1:08 PM
New York Times story with profiles of researchers whose grants were terminated.
[Gift Link]
www.nytimes.com/2025/08/24/o...
[Gift Link]
www.nytimes.com/2025/08/24/o...
Reposted by Sumaiya Nazeen
Even superintelligent AI cannot simply replace humans for most of what we do, nor can it perfect or ruin our world unless we let it, AI Snake Oil’s @randomwalker.bsky.social tells EFF’s Cindy Cohn and @thejasonkelley.com on the new “How to Fix the Internet.”
Podcast Episode: Separating AI Hope from AI Hype
If you believe the hype, artificial intelligence will soon take all our jobs, or solve all our problems, or destroy all boundaries between reality and lies, or help us live forever, or take over the w...
www.eff.org
August 19, 2025 at 5:17 PM
Even superintelligent AI cannot simply replace humans for most of what we do, nor can it perfect or ruin our world unless we let it, AI Snake Oil’s @randomwalker.bsky.social tells EFF’s Cindy Cohn and @thejasonkelley.com on the new “How to Fix the Internet.”
Reposted by Sumaiya Nazeen
Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities
August 20, 2025 at 4:58 PM
Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities
Reposted by Sumaiya Nazeen
This is also quite good. The "doing more with less" definition of intelligence (and "doing less with more" definition of stupidity) has an appeal. Reminds me of an old philosophy professor I had. Brilliant guy. Barely was on email. But his work never suffered for it.
youtu.be/jXa8dHzgV8U?...
youtu.be/jXa8dHzgV8U?...
Intelligent Humans vs. Smart AI: The Ultimate Showdown
YouTube video by Machine Learning Street Talk
youtu.be
August 13, 2025 at 8:56 PM
This is also quite good. The "doing more with less" definition of intelligence (and "doing less with more" definition of stupidity) has an appeal. Reminds me of an old philosophy professor I had. Brilliant guy. Barely was on email. But his work never suffered for it.
youtu.be/jXa8dHzgV8U?...
youtu.be/jXa8dHzgV8U?...
Reposted by Sumaiya Nazeen
Dijkstra’s is not optimal anymore for finding shortest paths!?
Breaking the Sorting Barrier for Directed Single-Source Shortest Paths
arxiv.org/abs/2504.17033
Breaking the Sorting Barrier for Directed Single-Source Shortest Paths
arxiv.org/abs/2504.17033
August 11, 2025 at 3:37 PM
Dijkstra’s is not optimal anymore for finding shortest paths!?
Breaking the Sorting Barrier for Directed Single-Source Shortest Paths
arxiv.org/abs/2504.17033
Breaking the Sorting Barrier for Directed Single-Source Shortest Paths
arxiv.org/abs/2504.17033
Reposted by Sumaiya Nazeen
At the same time, we made thousands of synonymous mutations in endogenous yeast genes and measured their growth. We used careful statistics and controls. Only 3%, 204 of 6874, had a fitness effect! This goes against a controversial recent result that most synonymous mutations had fitness effects.
August 7, 2025 at 8:29 AM
At the same time, we made thousands of synonymous mutations in endogenous yeast genes and measured their growth. We used careful statistics and controls. Only 3%, 204 of 6874, had a fitness effect! This goes against a controversial recent result that most synonymous mutations had fitness effects.
Reposted by Sumaiya Nazeen
‘Seek Funding’ Step Added To Scientific Method
‘Seek Funding’ Step Added To Scientific Method
PARIS—In an effort to modernize the principles and empirical procedures of examining phenomena and advancing humanity’s collective knowledge, the International Council for Science announced Thursday t...
theonion.com
August 5, 2025 at 3:15 PM
‘Seek Funding’ Step Added To Scientific Method
thought of this episode from Recess
www.youtube.com/watch?v=1mLo...
www.youtube.com/watch?v=1mLo...
Disney's Recess - Gus's Last Stand
YouTube video by iVideoXD
www.youtube.com
July 20, 2025 at 7:55 PM
thought of this episode from Recess
www.youtube.com/watch?v=1mLo...
www.youtube.com/watch?v=1mLo...
Reposted by Sumaiya Nazeen
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
No, AlphaFold has not completely solved protein folding
Biology is hard. Yes, even for AI.
clauswilke.substack.com
July 12, 2025 at 6:19 PM
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
clauswilke.substack.com/p/no-alphafo...
Reposted by Sumaiya Nazeen
“There is a cult of ignorance in the United States and there always has been.” — Isaac Asimov.
July 11, 2025 at 10:42 PM
“There is a cult of ignorance in the United States and there always has been.” — Isaac Asimov.
Reposted by Sumaiya Nazeen
No you cannot determine which drugs are safe and effective with machine learning. You cannot. It will not work. People will die.
"At FDA we're accelerating drug approvals so that you don't need to use primates or even animal models. You can do the drug approvals very, very quickly with AI."
July 1, 2025 at 9:15 PM
No you cannot determine which drugs are safe and effective with machine learning. You cannot. It will not work. People will die.
Reposted by Sumaiya Nazeen
Pleased to share our ICML Spotlight with @eberleoliver.bsky.social, Thomas McGee, Hamza Giaffar, @taylorwwebb.bsky.social.
Position: We Need An Algorithmic Understanding of Generative AI
What algorithms do LLMs actually learn and use to solve problems?🧵1/n
openreview.net/forum?id=eax...
Position: We Need An Algorithmic Understanding of Generative AI
What algorithms do LLMs actually learn and use to solve problems?🧵1/n
openreview.net/forum?id=eax...
June 20, 2025 at 3:48 PM
Pleased to share our ICML Spotlight with @eberleoliver.bsky.social, Thomas McGee, Hamza Giaffar, @taylorwwebb.bsky.social.
Position: We Need An Algorithmic Understanding of Generative AI
What algorithms do LLMs actually learn and use to solve problems?🧵1/n
openreview.net/forum?id=eax...
Position: We Need An Algorithmic Understanding of Generative AI
What algorithms do LLMs actually learn and use to solve problems?🧵1/n
openreview.net/forum?id=eax...
Reposted by Sumaiya Nazeen
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
June 24, 2025 at 4:52 PM
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Reposted by Sumaiya Nazeen
The NIH has not issued a single new call for proposals since the end of January.
June 9, 2025 at 10:07 PM
The NIH has not issued a single new call for proposals since the end of January.