Portfolio item number 1
Short description of portfolio item number 1
Posts by Collection
portfolio
Portfolio item number 2
Short description of portfolio item number 2
publications
Hardware Accelerator Design for Dynamic-Programming-Based Protein Sequence Alignment with Affine Gap Tracebacks
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.
Download Paper
Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite
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.
Download Paper
Measuring, visualizing, and diagnosing reference bias with biastools
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.
Download Paper
IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads
Published in bioRxiv, 2024
The Lymphoblastoid Cell Lines (LCLs) is 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: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads." bioRxiv (2024).
Download Paper
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown file that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
This is a description of a teaching experience. You can use markdown like any other post.
Teaching experience 2
Workshop, University 1, Department, 2015
This is a description of a teaching experience. You can use markdown like any other post.