April Wei

Method works from simple and complex scenarios in jointly estimating epoch time, population size, migration rate (symmetric or asymmetric), growth rate, and admixture proportion. Software integrated with msprime, demes, tsinfer/tsdate, relate, and singer. github.com/aprilweilab/...

08.10.2025 14:48 — 👍 4    🔁 4    💬 0    📌 0

Inference of complex demographic history using composite likelihood based on whole-genome genealogies Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

08.10.2025 14:48 — 👍 45    🔁 23    💬 1    📌 0

Fast Phenotype Simulation for Genotype Representation Graphs Motivation The Genotype Representation Graph (GRG) [[DeHaas et al., 2025][1]] is a graph representation of whole genome polymorphisms, designed to encode the variant hard-call information in phased wh...

Very proud of this manuscript with two talented undergraduate students, Aditya Syam and Chris Adonizio. We are continuing to push towards more scalable statistical genetics with Genotype Representation Graphs, and this is the start. www.biorxiv.org/content/10.1...

25.08.2025 14:26 — 👍 11    🔁 6    💬 0    📌 0

IGD: A simple, efficient genotype data format Motivation While there are a variety of file formats for storing reference-sequence-aligned genotype data, many are complex or inefficient. Programming language support for such formats is often limit...

Our work (by Drew DeHaas) on an extremely simple yet efficient binary genotype format - designed to facilitate scalable bioinformatics tool development. www.biorxiv.org/content/10.1...

12.02.2025 01:03 — 👍 10    🔁 10    💬 0    📌 0

Biologically inspired graphs to explore massive genetic datasets - Nature Computational Science A recent study proposes a data structure that addresses crucial challenges related to storage and computation of large genome databases.

📢In a recent News & Views, @ryanlayer.bsky.social discusses a data structure introduced by @aprilwei.bsky.social and colleagues for reducing storage and computational costs for phased whole-genome polymorphisms. www.nature.com/articles/s43...

🔓https://rdcu.be/d8ay3

31.01.2025 13:56 — 👍 6    🔁 2    💬 0    📌 1

Enabling efficient analysis of biobank-scale data with genotype representation graphs Nature Computational Science - The genotype representation graph (GRG) is a compact data structure that encodes 200,000 human genomes in just 5–26 gigabytes per chromosome. Computation...

Link to pdf. www.nature.com/articles/s43...

05.12.2024 17:10 — 👍 2    🔁 2    💬 0    📌 0

Wei Lab Web site created using create-react-app

My lab (aprilweilab.github.io) continues to develop GRG and ARG related methods & more. We are looking for a postdoc to join us.

05.12.2024 17:09 — 👍 4    🔁 5    💬 1    📌 0

Our work w/ two co-first authors Drew DeHaas and Ziqing Pan is now published. GRG allows large amounts of WGS polymorphism data to be analyzed in RAM via graph traversal & algebra operations & has some intrinsic connection w/ popgen data generating process & is different from ARG

05.12.2024 17:09 — 👍 21    🔁 11    💬 1    📌 0

Thanks, Alison. (that's me logging in 6mo later😂

19.11.2024 22:22 — 👍 1    🔁 0    💬 0    📌 0

Genotype Representation Graphs: Enabling Efficient Analysis of Biobank-Scale Data bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

We introduced an ARG-inspired data structure, Genotype Representation Graph (GRG), to enable lossless data compression and efficient computation through graph traversal. Developed a fast inference method. Cost ~80 GBP to convert 350TB VCF (200,000 UKBiobank WGS) into 160 GB GRG.
t.co/0badfCYz47

29.04.2024 18:20 — 👍 4    🔁 0    💬 1    📌 0