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Sumaiya Nazeen

@snz20.bsky.social
98 followers 418 following 14 posts

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

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Reposted by Sumaiya Nazeen
Waggoner Lab @labwaggoner.bsky.social · 09/07/2026
NERINE, a probabilistic rare variant burden test that integrates gene and protein networks to improve statistical power and biological interpretability @harvardmed.bsky.social www.cell.com/cell-genomic... www.cell.com/cell-genomic... @snz20.bsky.social t.co/vh5U6MF60f
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Reposted by Sumaiya Nazeen
Tom Gauld @tomgauld.bsky.social · 27/06/2026
My latest cartoon for @newscientist.com
Title: "In shops now: Classic literature with added mathematics!"

Image: Four book covers.

The Prime Number of Miss Jean Brodie, by Muriel Spark.
Empire of the Sum, by JG Ballard.
Wuthering Heights × lengths × widths, by Emily Bronte.
The Remains Of the Data by Kazuo Ishiguro.
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Sumaiya Nazeen @snz20.bsky.social · 25/06/2026
HMS press release about our network-based statistical framework, NERINE, recently published in @cellpress.bsky.social
hms.harvard.edu
New Tool Helps Uncover Rare Genetic Mutations in Common Diseases, Including Parkinson’s
NERINE bridges model systems and human genetics, points to potential drug targets
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Sumaiya Nazeen @snz20.bsky.social · 25/06/2026
Our network-based rare variant association framework, NERINE, is out in Cell Genomics: www.cell.com/cell-genomic... #StatisticalGenetics #Parkinson's #ComplexDiseaseGenetics #alpha-synuclein #prolactin #rare_variant_association
cell.com
NERINE reveals rare variant associations in gene networks across phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson’s disease
In this article, Nazeen, Khurana, Sunyaev, and colleagues present NERINE, a statistical test that links rare genetic variation in gene networks to human diseases, identifying new disease associations ...
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Reposted by Sumaiya Nazeen
prathitha.bsky.social @prathitha.bsky.social · 23/06/2026
Excited to share our new preprint, "Inference of elevated mutation rates and variant effects using 700k exomes"! - www.biorxiv.org/content/10.6... Using gnomAD v4, we estimate per-variant missense selection coefficients, and find loss-of-function (LoF) mutations with enhanced mutation rates.
biorxiv.org
Inference of elevated mutation rates and variant effects using 700k exomes
Genomic sequencing is now widely accessible for genetic diagnostics and is emerging as a component of newborn screening. This technological development generates the need to characterize incoming muta...
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Reposted by Sumaiya Nazeen
Stephen Turner @stephenturner.us · 13/06/2026
www.anthropic.com/news/fable-m...
anthropic.com
Statement on the US government directive to suspend access to Fable 5 and Mythos 5
The US government has issued an export control directive to suspend all access to Fable 5 and Mythos 5 by any foreign national, whether inside or outside the United States.
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Sumaiya Nazeen @snz20.bsky.social · 11/06/2026
Check out the latest work from Prathitha Kar! Glad to be a part of it.
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Reposted by Sumaiya Nazeen
Simon Fisher @profsimonfisher.bsky.social · 23/05/2026
ICYMI
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Sumaiya Nazeen @snz20.bsky.social · 14/04/2026
My MPG primer talk from last week at the Broad Institute. Primers are weekly lectures on genetics topics related to human populations and disease. #RVAT #Stat #NERINE #Genetics #CAD #Parkinson's #StatGen Link to the talk: youtu.be/KO-6M5lXTlI?...
youtu.be
MPG Primer: Network-based rare variant association for complex diseases (2026)
YouTube video by Broad Institute
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Reposted by Sumaiya Nazeen
Steven Salzberg @stevensalzberg.bsky.social · 30/03/2026
In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...
stevensalzberg.substack.com
AI is starting to look like pseudoscience
Not all of it, but some scientists are too eager to believe their own hype
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Stephen Turner @stephenturner.us · 09/02/2026
Multiple protein structure alignment at scale with FoldMason www.science.org/doi/10.1126/... 🧬💻🧪
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Reposted by Sumaiya Nazeen
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026
Our take-aways are that GWAS can be broadly linked to eQTLs—just not in humans (yet). This is probably due to selection and population history. We expect that as we find human eQTLs under stronger selection, colocalizations will increase.
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Sumaiya Nazeen @snz20.bsky.social · 05/02/2026
Check out this exciting preprint from @noahconnally.bsky.social to see how studying other species may be useful for searching trait-associated eQTLs in humans.
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Reposted by Sumaiya Nazeen
Science Magazine @science.org · 03/02/2026
"… I realized that an environment where people would feel free to share their thoughts with me and think creatively, regardless of the power hierarchy, was exactly what I wanted in my lab." #ScienceWorkingLife scim.ag/4adQwdQ
An illustration of a woman talking to other people with a cloud of bright colored symbols behind her. The headline is: I needed a culture shift in my lab. I’m grateful one student spoke up
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Rob Patro @robp.bsky.social · 02/02/2026
I have to believe in the many worlds hypothesis because, somehow, we ended up in the worst of all possible worlds. I have to believe worlds that evaded this horrific fate must exist.
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Ingomar Gutmann @gutmann.bsky.social · 02/02/2026
European Scientists who said NO to Epstein-funding are the heroines of this hour🦸‍♀️ They show: It was your choice to SAY NO to Epstein's $ as scientist- you just had to have ethics & a spine Kudos to Physicist IVETTE FUENTES who said NO She was working at @quantumunivie.bsky.social @univie.ac.at
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Wendy Bickmore @wbickmor.bsky.social · 01/02/2026
At a time when the UK should be capitalising on its global reputation as a great place to do science, this is an enormous own goal. I am so sorry for all those who jobs are going to be impacted.
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Kaessmann Lab @kaessmannlab.bsky.social · 29/01/2026
We are thrilled that our study on the evolution of gene regulation in mammalian cerebellum development – led by @ioansarr.bsky.social, @marisepp.bsky.social and @tyamadat.bsky.social, in collaboration with @steinaerts.bsky.social – is now out in @ScienceMagazine! www.science.org/doi/10.1126/...
science.org
The evolution of gene regulation in mammalian cerebellum development
Gene regulatory changes are considered major drivers of evolutionary innovations, including the cerebellum’s expansion during human evolution, yet they remain largely unexplored. In this study, we com...
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Reposted by Sumaiya Nazeen
Itai Yanai @itaiyanai.bsky.social · 27/01/2026
With all the excitement about AI giving us answers, we often forget that the real trick is to figure out what is the question! Thank you Tim Ferriss for recommending "What is the question" on the Night Science creative process in your newsletter! link.springer.com/article/10.1...
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Ming Tommy Tang @tommytang.bsky.social · 21/01/2026
In a rapidly changing AI landscape, how do you stay relevant? Focus on timeless skills: 1. the ability to learn and have the curiosity to learn.
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Sumaiya Nazeen @snz20.bsky.social · 20/10/2025
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!
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Reposted by Sumaiya Nazeen
Yun S. Song @yun-s-song.bsky.social · 22/09/2025
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)
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Heng Li @lh3lh3.bsky.social · 30/09/2025
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
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University of Cambridge @cam.ac.uk · 01/10/2025
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...
youtube.com
Jane Goodall - Finding our way to a better future
YouTube video by Cambridge University
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Tuuli Lappalainen @tuuliel.bsky.social · 20/09/2025
Yup. This was me 10 years ago.
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Hannah Richter @hannah-richter.bsky.social · 19/09/2025
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...
science.org
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
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Arc Institute @arcinstitute.org · 17/09/2025
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.
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Shai Carmi @shaicarmi.bsky.social · 11/09/2025
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...
medrxiv.org
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...
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Rob Patro @robp.bsky.social · 09/09/2025
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 ....
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Reposted by Sumaiya Nazeen
Tom Albright @talbright.bsky.social · 06/09/2025
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
'MODERN-DAY DAY ORACLES or BULLSHIT MACHINES? How to thrive in a ChatGPT world Developed by Carl T Bergstrom and Jevin D. West Yet for all the good that AI systems will do, they will also saturate our information environment with bullshit at ata a scale never before encountered.'
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Pierre Peterlongo @pierrepeterlongo.bsky.social · 04/09/2025
❗ 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
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Jeremy Berg @jeremymberg.bsky.social · 24/08/2025
New York Times story with profiles of researchers whose grants were terminated. [Gift Link] www.nytimes.com/2025/08/24/o...
nytimes.com
Opinion | America First? Not When It Comes to Your Health.
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Electronic Frontier Foundation @eff.org · 19/08/2025
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.”
eff.org
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...
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Alexander Luckmann @aluckmann.bsky.social · 20/08/2025
Academia may not give you job security, flexibility, or wealth, but it will let you unexpectedly connect to eduroam in foreign cities
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Vincent Carchidi @vcarchidi.bsky.social · 13/08/2025
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
Intelligent Humans vs. Smart AI: The Ultimate Showdown
YouTube video by Machine Learning Street Talk
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Sina Majidian @sinamajidian.bsky.social · 11/08/2025
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
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Liana Lareau @lianafaye.bsky.social · 07/08/2025
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.
Scatterplot showing fitness effect of ~7000 synonymous mutations in yeast: read count at start vs log2 fold change. Most data points are not significant but 204 points are significant outliers, either advantageous or deleterious.
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The Onion @theonion.com · 05/08/2025
‘Seek Funding’ Step Added To Scientific Method
theonion.com
‘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...
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Sumaiya Nazeen @snz20.bsky.social · 20/07/2025
thought of this episode from Recess www.youtube.com/watch?v=1mLo...
youtube.com
Disney's Recess - Gus's Last Stand
YouTube video by iVideoXD
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Reposted by Sumaiya Nazeen
Claus Wilke @clauswilke.com · 12/07/2025
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
No, AlphaFold has not completely solved protein folding
Biology is hard. Yes, even for AI.
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George Takei @georgetakei.bsky.social · 11/07/2025
“There is a cult of ignorance in the United States and there always has been.” — Isaac Asimov.
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Adam Rogers @jetjocko.bsky.social · 01/07/2025
No you cannot determine which drugs are safe and effective with machine learning. You cannot. It will not work. People will die.
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Ida Momennejad @neuroai.bsky.social · 20/06/2025
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...
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Will Ratcliff @wcratcliff.bsky.social · 24/06/2025
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....
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Denis Wirtz @deniswirtz.bsky.social · 09/06/2025
The NIH has not issued a single new call for proposals since the end of January.
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Sumaiya Nazeen @snz20.bsky.social · 06/06/2025
Eid mubarak to all who are celebrating!
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Jake Yeston @jakeyeston.bsky.social · 05/06/2025
More from @holdenthorp.bsky.social in @science.org "A world where the United States is no longer leading the scientific enterprise will still benefit from science [...] The global enterprise will adapt to the lack of American leadership, but the steep loss for the country itself is unambiguous."
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Nikolai Slavov @slavov-n.bsky.social · 05/06/2025
A case study on the challenges of evaluating AI predictions in biology and the implications for published results. 1/2 rachel.fast.ai/posts/2025-0...
rachel.fast.ai
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
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Kathleen Bachynski @bachynski.bsky.social · 02/06/2025
“The group estimated that reducing the operating budget by $900 million, as the Trump administration wants to do, would require closing 350 of the 433 parks, monuments, historic sites and other locations overseen by the Park Service… we would be witnessing the dismantling of a century-old system”
nytimes.com
Opinion | Is This the Beginning of the End of America’s National Parks?
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American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 29/05/2025
HEY! The countdown is on—abstract submissions for #ASHG25 close in 11 days! 🔬 Share your research. 🤝 Build your network. ✨ Inspire your field. 🗓️ Submit now: www.ashg.org/meetings/202... #ASHG #HumanGenetics
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