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Haky Im

@hakyim.bsky.social
1.4K followers 2.2K following 29 posts

Statistician doing genomic data science, faculty the University of Chicago, Korean, Argentinean, American. Love kimchi, math, science, books with beautiful prose.

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Haky Im @hakyim.bsky.social · 26/03/2026
We're Hiring! Computational Biologist / Genomic Data Scientist. Join our lab to use cutting-edge data & AI/ML to advance human health. - Genetics & Genomics analysis - AI/ML in biology - Solving real-world genomic problems 📄 Full details: docs.google.com/document/d/1...
docs.google.com
Job-computational-biologist-2025.docx
Genomic Data Scientist / Computational Biologist We are looking to hire a lifelong learner interested in developing statistical and computational tools to sift through large amounts of data to make di...
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Haky Im @hakyim.bsky.social · 12/09/2025
I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.
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Haky Im @hakyim.bsky.social · 14/05/2025
Check out our scPrediXcan paper www.cell.com/cell-genomic... Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6 and me, with thanks to many contributors. scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
cell.com
scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework
Zhou et al. introduce scPrediXcan, a novel transcriptome-wide association study framework that integrates the deep learning-based model ctPred for cell-type-specific expression prediction. Applied to ...
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Haky Im @hakyim.bsky.social · 14/02/2025
Need a break from doomscrolling? Do you study the genetics of disease subtypes? Have you ever wondered how to efficiently run gene-based associations with multicategorical outcomes? Join us for the IGES Journal Club on Wednesday, February 26, 2025! 11AM ET.
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Haky Im @hakyim.bsky.social · 11/02/2025
Ughhh, suffering the plos system now. My collaborators won’t let me submit future papers to PLoS
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Jonathan Pritchard @jkpritch.bsky.social · 26/01/2025
Modern GWAS can identify 1000s of significant hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? I'm very excited to present our new work combining associations and Perturb-seq to build interpretable causal graphs! A 🧵
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Michael Hoffman @michaelhoffman.bsky.social · 11/06/2024
1/At the #HoffmanLab lab meeting, we often have tech talks describing useful tools for other lab members. Since they might also prove useful for others, we've been posting almost every #HoffmanLabTechTalk for years. 🧪🧬💻
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Haky Im @hakyim.bsky.social · 15/11/2024
with invaluable contributions from @temicrates Lisha Zhu @ssalazar_02 Sarah Sumner Hyunki Kim Saideep Gona @Festus_nyasimi Rohit Kulkarni @drjosephpowell @madduri @boxiangliu
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Haky Im @hakyim.bsky.social · 15/11/2024
check out our new preprint led by Charles Zhou and supervised by Mengjie Chen and me doi.org/10.1101/2024... where we present scPrediXcan which integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework
doi.org
scPrediXcan integrates advances in deep learning and single-cell data into a powerful cell-type–specific transcriptome-wide association study framework
Transcriptome-wide association studies (TWAS) help identify disease causing genes, but often fail to pinpoint disease mechanisms at the cellular level because of the limited sample sizes and sparsity ...
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Haky Im @hakyim.bsky.social · 13/11/2024
Consistency is key
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Haky Im @hakyim.bsky.social · 13/11/2024
I’m at UChicago, develop methods to understand the biology of complex trait and diseases, aspire to help real people with my research. Currently very optimistic about predicting molecular traits from DNA sequences using m/billions of parameters
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🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · 11/11/2024
🆕 Blog: Genomics scientists from and in Mexico community building lcolladotor.github.io/2024/11/11/g... I want our voices🇲🇽 to be heard from the scientific community. But to be heard, we have to be a part of it #LCG-UNAM #LCG-EJ-UNAM @cdsbmexico.bsky.social #NNB-UNAM #RMB youtu.be/OVMw0k6AydA?...
youtu.be
[2024-10-30] LCG(EJ)-UNAM community building highlights for "Aplicaciones de la Genómica 2024"
YouTube video by Leonardo Collado Torres
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Dr Abeba Birhane @abeba.blacksky.app · 16/07/2024
Peter Buxtun, the whistleblower who revealed that the U.S. government allowed hundreds of Black men in rural Alabama to go untreated for syphilis in what became known as the Tuskegee study, has died. He was 86. apnews.com/article/buxt...
apnews.com
Tuskegee syphilis study whistleblower Peter Buxtun has died at age 86
The whistleblower who exposed the Tuskegee syphilis study that left hundreds of Black men untreated has died at age 86.
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Haky Im @hakyim.bsky.social · 18/04/2024
IGES (international genetic epidemiology society) journal club recording "The All of Us Research Program: Data Resources and Access"; by Dr. Anji Musick is available here: drive.google.com/file/d/1bty6...
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Anne Carpenter @drannecarpenter.bsky.social · 05/11/2023
Also worth noting: the US NIH offers financial support for those from ANY underrepresented group at ANY career stage to join an NIH funded lab! Find a professor whose research you’re interested in and see if they are willing to host you! grants.nih.gov/grants/guide...
grants.nih.gov
PA-23-189: Research Supplements to Promote Diversity in Health-Related Research (Admin Supp Clinical...
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Research Supplements to Promote Diversity in Health-Related Research (Admin Supp Clinical Trial Not Allowed) PA-23-189....
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Haky Im @hakyim.bsky.social · 23/10/2023
TWAS (transcriptome wide association study) is a statistical method that prioritizes genes that are more likely to cause a disease. It uses GWAS (genome wide association study) data, which is a method that identifies genomic loci associated with diseases
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Haky Im @hakyim.bsky.social · 21/10/2023
Preprint is up now www.biorxiv.org/content/10.1...
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Haky Im @hakyim.bsky.social · 18/10/2023
Preprint should be up shortly
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Haky Im @hakyim.bsky.social · 18/10/2023
4) LD is not necessary for the inflation to occur (our simulations were done using independent SNPs) 5) The inflation can be corrected by using the noncentral χ2 distribution with noncentrality parameter N h2δ Φ, where the factor Φ can be pre-calculated independent of the GWAS
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Haky Im @hakyim.bsky.social · 18/10/2023
2) Uncertainty in the prediction of the mediator does not cause inflation 3) Uncertainty in the prediction of the mediator reduces the power of the test
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Haky Im @hakyim.bsky.social · 18/10/2023
In summary 1) Polygenicity of the target trait induces inflation in the test statistics regardless of the genetic architecture of the mediating trait
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Haky Im @hakyim.bsky.social · 18/10/2023
Does this inflation affect other mediator-based *WAS? Yes What if we use PRS of GWAS traits to correlate with target traits? Is this going to be inflated? Yes. You need to estimate Φ and use the noncentral χ2 distribution
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Haky Im @hakyim.bsky.social · 18/10/2023
Back to the effect of precision Precision of prediction improves power, or equivalently prediction error reduces power but doesn’t increase inflation under the null
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Haky Im @hakyim.bsky.social · 18/10/2023
How well does your formula work under the alternative with finite N? Pretty well
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Haky Im @hakyim.bsky.social · 18/10/2023
What happens under the alternative? See figure for formula under the alternative τ2 is the precision of the prediction
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Haky Im @hakyim.bsky.social · 18/10/2023
Can you estimate Φ? Yes See figure: most of the Φ are around 10e-5
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Haky Im @hakyim.bsky.social · 18/10/2023
Can you fix it? Yes, just use the noncentral chi2 to compute the p-value instead of the standard chi2 pchisq(chi2, ncp=N*h2Y*phi, df=1, lower.tail=FALSE) where phi=Φ is the gene specific factor
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Haky Im @hakyim.bsky.social · 18/10/2023
Does it matter for TWAS in practice? Yes See inflation in figure when using UK Biobank genotype data and null traits Y. It will continue growing as N grows.
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Haky Im @hakyim.bsky.social · 18/10/2023
How we does your formula match with finite N? Quite well
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Haky Im @hakyim.bsky.social · 18/10/2023
Does prediction error drive inflation? No, it’s not the prediction error See figure Eχ2 does not depend on the precision consistent with established error in variable literature It’s the polygenicity of Y since Eχ2 = 1 + N h2 Φ. The inflation is 0 when the polygenic component of Y = 0
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Haky Im @hakyim.bsky.social · 18/10/2023
Does this matter? Yes See example in figure 1, pink area is much larger than the negligible blue area in this example
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Haky Im @hakyim.bsky.social · 18/10/2023
Under the null, the Eχ2 should be 1, but it’s larger than 1 when Y is polygenic
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Haky Im @hakyim.bsky.social · 18/10/2023
Yes TWAS yields inflated p-values when the target trait is polygenic
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Haky Im @hakyim.bsky.social · 18/10/2023
On the problem of inflation in TWAS Does TWAS yield inflated p-values?
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Steven Weisberg @stevenmweisberg.bsky.social · 26/09/2023
**Job Alert** Our department at UF is hiring a TT assistant professor in Quantitative Methods (open area). See job ad here, and please retweet: psych.ufl.edu/news/2023/as... #PsychSciSky #neurskyence #academicjobs #academia
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Carl T. Bergstrom @carlbergstrom.com · 26/09/2023
Covid testing is a good way to help keep family and friends safe. US residents can now receive 4 free tests in the mail by filling out the short form below.
covid.gov
COVID.gov - Free at-home COVID-19 tests
Every U.S. household is eligible to order 4 free at-home COVID-19 tests.
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