The paper analyzes disease-associated tandem repeat loci across diverse populations using long-read data, revealing ancestry-specific variation and complex genotype-phenotype relationships.

Nature Communications · Aug 6, 2026Peer-reviewedGenetic & Genomic Medicine

A comprehensive tandem repeat catalog of the human genome

Readman Chiu, Indhu‐Shree Rajan‐Babu, Jan M Friedman, İnanç BİROL

The paper creates a comprehensive catalog of tandem repeat loci in the human genome using long-read sequencing data from 272 genomes.

Nature Communications · Jan 28, 2026Peer-reviewedGenetic & Genomic Medicine

Defining a tandem repeat catalog and variation clusters for genome-wide analyses

Ben Weisburd, Egor Dolzhenko, Mark F. Bennett, Matt Christopher Danzi, Isaac R. L. Xu, Hope A. Tanudisastro, Bida Gu, Adam C. English, Laurel Hiatt, Tom Mokveld, Guilherme De Sena Brandine, Readman Chiu, Nehir Edibe Kurtas, Helyaneh Ziaei Jam, Harrison Brand, , Heidi L. Rehm

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

bioRxiv · Oct 4, 2024 · PreprintGenomics

Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

Ka Ming Nip, Saber Hafezqorani, Kristina Gagalova, Readman Chiu, Chen Yang, René L. Warren, İnanç Birol

RNA-Bloom2 is a reference-free transcriptome assembler for long-read data, showing competitive performance with reference-based methods and lower resource usage.

Nature Communications · May 22, 2023Peer-reviewedBioinformatics

Genome-Wide Sequencing as a First-Tier Screening Test for Short Tandem Repeat Expansions

Indhu‐Shree Rajan‐Babu, Junran J. Peng, Readman Chiu, IMAGINE Study, Patricia H. Birch, Madeline Couse, Colleen Guimond, Anna Lehman, Jill C. Mwenifumbo, Clara van Karnebeek, Jan M. Friedman, CAUSES Study, Shelin Adam, Christèle du Souich, Alison M. Elliott, , İnanç Birol

The paper evaluates STR detection tools and develops a pipeline to identify pathogenic expansions in exome/genome data, finding 27 samples with STR mutations in 306 families.

Genome Medicine · Aug 9, 2021Peer-reviewedGenetics

RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

Ka Ming Nip, Readman Chiu, Chen Yang, Justin Chu, Hamid Mohamadi, René L. Warren, İnanç Birol

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

Genome Research · Aug 1, 2020Peer-reviewedBioinformatics

Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters

Justin Chu, Hamid Mohamadi, Emre Erhan, Jeffery Tse, Readman Chiu, Sarah K. Yeo, İnanç Birol

The paper introduces a multi-index Bloom filter for alignment-free sequence classification, showing improved sensitivity and efficiency over existing methods in read binning and taxonomic assignment.

bioRxiv · Oct 5, 2018 · PreprintBioinformatics

Pan-cancer analysis reveals complex tumor-specific alternative polyadenylation

Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila M. Reynolds, İnanç Birol

The paper analyzes APA patterns in 114 cancer-related genes across 33 cancer types to show complex 3 UTR cleavage changes in tumors.

BMC Genomics · Jul 13, 2018Peer-reviewedGenomics