Published in Genome Research, 2026
The impute-first framework builds a personalized reference through imputation before aligning the full read set, reducing reference bias in downstream variant calling.
Recommended citation: Vaddadi, Kavya, Mao-Jan Lin, Sina Majidian, Taher Mun, and Ben Langmead. "Minimizing reference bias with an imputed personalized reference." Genome Research (2026).
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Published in Cell Reports Methods, 2025
Lymphoblastoid cell lines (LCLs) contain a mixture of germline and somatically recombined haplotypes in the immunoglobulin (IG) gene regions, making them hard to profile and assemble. IGLoo is a toolkit to profile the IG heavy chain (IGH) locus in LCLs with HiFi reads. It can also improve the assembly quality in the IGH locus.
Recommended citation: Lin, Mao-Jan, Ben Langmead, and Yana Safonova. "IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads." Cell Reports Methods 5(5) (2025): 101033.
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Published in Genome Biology, 2024
Recent alignment methods aim to reduce reference bias, where reads with non-reference alleles fail to align correctly. However, there is a lack of methods for analyzing reference bias. We present biastools, which measures and categorizes reference bias.
Recommended citation: Lin, Mao-Jan, et al. "Measuring, visualizing, and diagnosing reference bias with biastools." Genome Biology 25.1 (2024): 101.
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Published in Frontiers in Immunology, 2022
gAIRR-Suite is a new toolkit profiling genes encoding the Adaptive Immune Receptor Repertoire (AIRR). We combined experimental and computational methods to genotype both documented and novel V, D, J genes in the human germline genome.
Recommended citation: Lin, Mao-Jan, et al. "Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite." Frontiers in Immunology 13 (2022): 922513.
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Preprint on bioRxiv, 2026
ImpuT2T uses a panel of T2T or near-T2T assemblies to scaffold and patch gaps in assemblies generated from HiFi reads.
Recommended citation: Lin, Mao-Jan, Vikram S. Shivakumar, Ben Langmead, and Human Pangenome Reference Consortium. "ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies." bioRxiv (2026).
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Published in 2019 IEEE Biomedical Circuits and Systems Conference (BioCAS), 2019
We propose an ASIC design for dynamic programming sequence alignment with affine-gap traceback. The architecture reduce memory usage for traceback by 25%. The design speed up pairwise alignment by 570x
Recommended citation: Lin, Mao-Jan, Yu-Cheng Li, and Yi-Chang Lu. "Hardware accelerator design for dynamic-programming-based protein sequence alignment with affine gap tracebacks." 2019 IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 2019.
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Published in 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE), 2019
Recommended citation: Chen, Ming-Hung, Mao-Jan Lin, Yu-Cheng Li, and Yi-Chang Lu. "Banded Pair-HMM Algorithm for DNA Variant Calling and Its Hardware Accelerator Design." 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) (2019).
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