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A list of all the posts and pages found on the site. For you robots out there, there is an XML version available for digesting as well.
Pages
Posts
Future Blog Post
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Blog Post number 4
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 3
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 2
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
Blog Post number 1
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This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
portfolio
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Portfolio item number 2
Short description of portfolio item number 2
posters
dotears: Scalable, consistent DAG estimation using observational and interventional data
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I presented at the NIHGRI conference in both 2023 and 2024 about dotears, which learns causal gene regulatory networks from Perturb-seq data. The relevant paper is here. This was as part of the UCLA Genomic Analysis and Interpretation Training Grant (T-32).
keju: powerful and accurate inference in Massively Parallel Reporter Assays
Published:
I will be at Probgen 2026! Please say hi there.
publications
dotears: Scalable and consistent directed acyclic graph estimation using observational and interventional data
Published in iScience, 2025
We learned causal gene regulatory networks using Perturb-seq data.
Recommended citation: Albert Xue, Jingyou Rao, Sriram Sankararaman, and Harold Pimentel (2025). "dotears: Scalable and consistent directed acyclic graph estimation using observational and interventional data." iScience, Volume 28, Issue 2, 111673. doi.org/10.1016/j.isci.2024.111673.
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Multiplexed Perturbation Enables Scalable Pooled Screens
Published in biorxiv, 2025
We see how cells react to multiple CRISPR perturbations.
Recommended citation: Stefan Oberlin, Neil Tay, Albert Xue, Harold Pimentel, and Michael T McManus (2025). "Multiplexed Perturbation Enables Scalable Pooled Screens." biorxiv.
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A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic epistasis
Published in Nature Genetics, 2025
We learn marginal epistasis in the UK Biobank.
Recommended citation: Boyang Fu, Ali Pazokitoroudi, Zuozheng Shi, Asha Kar, Albert Xue, Akarsh Anand, Prateek Anand, Zhengtong Liu, Richard Border, Päivi Pajukanta, Noah Zaitlen, and Sriram Sankararaman (2025). "A biobank-scale test of marginal epistasis reveals genome-wide signals of polygenic epistasis." Nature Genetics.
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keju: powerful and accurate inference in Massively Parallel Reporter Assays
Published in biorxiv, 2026
We build a better statistical tool for MPRAs.
Recommended citation: Albert Xue, Adam M Zahm, Justin English, Sriram Sankararaman, and Harold Pimentel (2026). "keju: powerful and accurate inference in Massively Parallel Reporter Assays." biorxiv.
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talks
dotears: Causal structure learning using interventional data
Published:
I gave a talk at the Biological Data Science CSHL conference about dotears, which learns causal gene regulatory networks from Perturb-seq data. The relevant paper is here.
teaching
CM 121 - Introduction to Bioinformatics
Undergraduate course, UCLA, Computer Science, 2023
I TAed CM 121 - Introduction to Bioinformatics for Harold, along with two other TAs. Topics included ranged from basic statistics topics like Maximum Likelihood, to RNA-seq normalization, to pseudoalignment, to dimension reduction and PCA. My responsibilities included writing (1/3 of the) lecture notes for discussion, giving discussion, grading, and responding to Piazza posts. If you’re curious, you can view my discussion notes here, here, and here.