Reposted by Abdullah Al Nahid
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
📢OUT TODAY @natgenet.nature.com
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
📰Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk.
By @zeyunlu.bsky.social, @nmancuso.bsky.social and colleagues.
⬇️
www.nature.com/articles/s41...
Improved multiancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk - Nature Genetics
SuShiE is a multiancestry fine-mapping method for molecular quantitative trait loci that leverages linkage disequilibrium heterogeneity to improve resolution, infer cross-ancestry effect size correlat...
www.nature.com
July 21, 2025 at 6:54 PM
Super excited to see this out. What started as some math in a grant in 2020, to a student deciding to take this on in 2022, to published in 2025.
These things can take time and patience is key!
These things can take time and patience is key!
Reposted by Abdullah Al Nahid
People often intuitively interpret genetic ancestry PCA plots as simple genetic distances, but this is not always the case. Below are random pairs of individuals that are far apart in PCA space (lines) but actually have fewer total variant differences (numbers).
July 19, 2025 at 7:12 PM
People often intuitively interpret genetic ancestry PCA plots as simple genetic distances, but this is not always the case. Below are random pairs of individuals that are far apart in PCA space (lines) but actually have fewer total variant differences (numbers).
Reposted by Abdullah Al Nahid
I'm become quite partial to cell-type-biased (population-biased) terminology rather than cell-type-specific (population-specific) when it comes to QTLs, because it reflects better that these are a result of power, rather than biological differences.
July 8, 2025 at 4:59 PM
I'm become quite partial to cell-type-biased (population-biased) terminology rather than cell-type-specific (population-specific) when it comes to QTLs, because it reflects better that these are a result of power, rather than biological differences.
Reposted by Abdullah Al Nahid
Congrats on the first PhD work!! Very nicely done! @alnahid.bsky.social
traceax: a JAX-based framework for stochastic trace estimation https://www.biorxiv.org/content/10.1101/2025.07.14.662216v1
July 18, 2025 at 11:15 PM
Congrats on the first PhD work!! Very nicely done! @alnahid.bsky.social
Reposted by Abdullah Al Nahid
traceax: a JAX-based framework for stochastic trace estimation https://www.biorxiv.org/content/10.1101/2025.07.14.662216v1
July 18, 2025 at 3:51 PM
traceax: a JAX-based framework for stochastic trace estimation https://www.biorxiv.org/content/10.1101/2025.07.14.662216v1
Reposted by Abdullah Al Nahid
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
June 10, 2025 at 4:27 PM
Excited to announce our first interactive article on sandbox.bio, about genomic ranges: sandbox.bio/concepts/gen...
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Move & resize the ranges to see how that affects bedtools operations like merge and intersect in real time!
Reposted by Abdullah Al Nahid
5 papers all computational biologists should read 🧵
1. A Quick Guide to Organizing Computational Biology Projects
journals.plos.org/ploscompbio...
1. A Quick Guide to Organizing Computational Biology Projects
journals.plos.org/ploscompbio...
July 12, 2025 at 1:15 PM
5 papers all computational biologists should read 🧵
1. A Quick Guide to Organizing Computational Biology Projects
journals.plos.org/ploscompbio...
1. A Quick Guide to Organizing Computational Biology Projects
journals.plos.org/ploscompbio...
Reposted by Abdullah Al Nahid
Weekly Recap (June 2025, part 2): Interactive visualization of tabular data, shared foundations of gene expression and chromatin structure, fast protein structure searching with graph embeddings, visualizing cis-regulatory rules 🧬🖥️🧪 doi.org/10.59350/wrg...
June 27, 2025 at 8:56 PM
Weekly Recap (June 2025, part 2): Interactive visualization of tabular data, shared foundations of gene expression and chromatin structure, fast protein structure searching with graph embeddings, visualizing cis-regulatory rules 🧬🖥️🧪 doi.org/10.59350/wrg...
Reposted by Abdullah Al Nahid
This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
Excited to launch our AlphaGenome API goo.gle/3ZPUeFX along with the preprint goo.gle/45AkUyc describing and evaluating our latest DNA sequence model powering the API. Looking forward to seeing how scientists use it! @googledeepmind
June 25, 2025 at 4:18 PM
This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
Reposted by Abdullah Al Nahid
Awesome first night of the Galaxy and Bioconductor community conference at CSHL. The GBCC Live demo was the star showing off how to connect the communities through a detailed spatial omics tumor analysis. #GBCC2025 @galaxyproject.bsky.social @bioconductor.bsky.social @cshlmeetings.bsky.social
June 24, 2025 at 4:31 AM
Awesome first night of the Galaxy and Bioconductor community conference at CSHL. The GBCC Live demo was the star showing off how to connect the communities through a detailed spatial omics tumor analysis. #GBCC2025 @galaxyproject.bsky.social @bioconductor.bsky.social @cshlmeetings.bsky.social
Reposted by Abdullah Al Nahid
The first Galaxy / Bioconductor joint conference #GBCC2025 starts next week at CSHL! If anyone wants to connect feel free to reach out here.
Lightning talks signup form coming soon...
Lightning talks signup form coming soon...
June 19, 2025 at 1:03 PM
The first Galaxy / Bioconductor joint conference #GBCC2025 starts next week at CSHL! If anyone wants to connect feel free to reach out here.
Lightning talks signup form coming soon...
Lightning talks signup form coming soon...
Reposted by Abdullah Al Nahid
Excited to share that my PhD defense is coming up! I’ll be presenting on "statistical and computational approaches to characterize functional architectures for human diseases and complex traits".
📅 June 9 (Monday) at 2-4pm PST
zoom link: usc.zoom.us/j/93369681715
📅 June 9 (Monday) at 2-4pm PST
zoom link: usc.zoom.us/j/93369681715
June 4, 2025 at 6:40 PM
Excited to share that my PhD defense is coming up! I’ll be presenting on "statistical and computational approaches to characterize functional architectures for human diseases and complex traits".
📅 June 9 (Monday) at 2-4pm PST
zoom link: usc.zoom.us/j/93369681715
📅 June 9 (Monday) at 2-4pm PST
zoom link: usc.zoom.us/j/93369681715
Reposted by Abdullah Al Nahid
The work people wind up building on is the one with easy-to-use code and fast run-time. If you have a cool method but people aren't using it, try making it faster or more accessible! Sometimes that's all it is
May 23, 2025 at 3:02 PM
The work people wind up building on is the one with easy-to-use code and fast run-time. If you have a cool method but people aren't using it, try making it faster or more accessible! Sometimes that's all it is
Reposted by Abdullah Al Nahid
All NIH and NSF grants for my entire team--and for all of Harvard, I guess?--have been terminated.
As provocative as that sounds, the practical effect is probably not much. Everything was already frozen. 🤷♂️
On the upside, it makes tracking terminated grants easier. No more guesswork at Harvard!
As provocative as that sounds, the practical effect is probably not much. Everything was already frozen. 🤷♂️
On the upside, it makes tracking terminated grants easier. No more guesswork at Harvard!
May 15, 2025 at 8:11 PM
All NIH and NSF grants for my entire team--and for all of Harvard, I guess?--have been terminated.
As provocative as that sounds, the practical effect is probably not much. Everything was already frozen. 🤷♂️
On the upside, it makes tracking terminated grants easier. No more guesswork at Harvard!
As provocative as that sounds, the practical effect is probably not much. Everything was already frozen. 🤷♂️
On the upside, it makes tracking terminated grants easier. No more guesswork at Harvard!
Reposted by Abdullah Al Nahid
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping
Population-scale single-cell transcriptomic technologies (scRNA-seq) enable characterizing variant effects on gene regulation at the cellular level (e.g., single-cell eQTLs; sc-eQTLs). However, existi...
www.medrxiv.org
January 27, 2025 at 6:29 PM
Excited to present our work on developing jaxQTL, a fast single-cell eQTL mapping tool that improves power and robustness in identifying sc-eQTLs using count-based models. See details in threads 🧵
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Abdullah Al Nahid
Academia friends, this week I’m discussing scientific conference talks and posters with my graduate student course.
What are your top tips for how to give a good conference talk or a good poster presentation, how to design your slides or poster, or what not to do? 🧪
What are your top tips for how to give a good conference talk or a good poster presentation, how to design your slides or poster, or what not to do? 🧪
May 18, 2024 at 8:11 PM
Academia friends, this week I’m discussing scientific conference talks and posters with my graduate student course.
What are your top tips for how to give a good conference talk or a good poster presentation, how to design your slides or poster, or what not to do? 🧪
What are your top tips for how to give a good conference talk or a good poster presentation, how to design your slides or poster, or what not to do? 🧪
In my pursuit of learning R, contributing to tidyomics ecosystem, and advancing my education, Professor @mikelove.bsky.social has consistently guided me and shown kindness, support, and guidance.
Thank you so much Professor.
It is an incredible honor for me.
Thank you so much Professor.
It is an incredible honor for me.
Congrats to @abdnahid.bsky.social, headed to USC to start a PhD and already starting to teach students about software development, and R/Bioconductor packages!
🙌
🙌
May 13, 2024 at 1:02 PM
In my pursuit of learning R, contributing to tidyomics ecosystem, and advancing my education, Professor @mikelove.bsky.social has consistently guided me and shown kindness, support, and guidance.
Thank you so much Professor.
It is an incredible honor for me.
Thank you so much Professor.
It is an incredible honor for me.
Recently co-authored the preprint on the #tidyomics ecosystem.
Give it a read, check out the R packages, and explore omic data with tidyverse!
doi.org/10.1101/2023...
Give it a read, check out the R packages, and explore omic data with tidyverse!
doi.org/10.1101/2023...
September 25, 2023 at 12:03 AM
Recently co-authored the preprint on the #tidyomics ecosystem.
Give it a read, check out the R packages, and explore omic data with tidyverse!
doi.org/10.1101/2023...
Give it a read, check out the R packages, and explore omic data with tidyverse!
doi.org/10.1101/2023...
I developed an open-source app + REST API that lets you follow multiple handles at once in bsky.
app: bsky-app.vercel.app
api: github.com/nahid18/bsky...
app: bsky-app.vercel.app
api: github.com/nahid18/bsky...
September 12, 2023 at 10:47 AM
I developed an open-source app + REST API that lets you follow multiple handles at once in bsky.
app: bsky-app.vercel.app
api: github.com/nahid18/bsky...
app: bsky-app.vercel.app
api: github.com/nahid18/bsky...
I have deployed my personal website:
abdnahid.vercel.app
abdnahid.vercel.app
Abdullah Al-Nahid
Personal Website of Abdullah Al Nahid
abdnahid.vercel.app
September 4, 2023 at 7:31 PM
I have deployed my personal website:
abdnahid.vercel.app
abdnahid.vercel.app