My name is Yilei Fu (付译磊), a postdoctoral fellow at Baylor College of Medicine, Human Genome Sequencing Center. My research interests include cancer genomics, long-read genome-scale algorithms, epigenetic signal analysis and metagenomics.

I graduated from Habin Institute of Technology in 2019, with a B.S. in Computer Science and Technology. Under the supervision of Dr. Todd Treangen and Dr. Fritz Sedlazeck, I graduated from Rice University, Computer Science Department in November 2023.

At the time I am writing this post, I am sitting at my small apartment in Houston Texas, waiting my father and my cousin’s visit tomorrow for my Ph.D. commencement ceremony.

Selected Publications

Fu, Y., Aganezov, S., Mahmoud, M., Beaulaurier, J., Juul, S., Treangen, T. J., & Sedlazeck, F. J. (2023). MethPhaser: methylation-based haplotype phasing of human genomes. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.05.12.540573

Fu, Y., Mahmoud, M., Muraliraman, V. V., Sedlazeck, F. J., & Treangen, T. J. (2021). Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. In GigaScience (Vol. 10, Issue 9). Oxford University Press (OUP). https://doi.org/10.1093/gigascience/giab063

Lou, E. G., Fu, Y., Wang, Q., Treangen, T. J., & Stadler, L. B. (2023). Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2023.08.08.23293828

Experience

Bioinformatics Intern | 2022.5-2022.8 | Oxford Nanopore Technology, Inc.

  • Developed a methylation-based long read phasing method.

Teaching and Research Assistant | 2019.8 - 2023.11 | Rice University

  • Research assistant at Treangen Lab. Conducted research related to SARS-COV-2, long-read alignment and metagenomes.
  • 2-year TA experience on a graduate level course “Introduction to computer graphics”.

Research Scientist | 2018.1 - 2019.6 | The Center of Bioinformatics at HIT

  • Conducted research on Structural Variants detection in human genomes and read alignment.

Data Analyst | 2015.1 | Institute of Extreme Environmental Nutrition and Protection at HIT

  • Statistical analysis of experimental data of the paper Acanthopanax senticosus reduces brain injury in mice exposed to low linear energy transfer radiation.

Talks

Other Publications

  • CRISPR/Cas9 editing induces unintended large gene modifications in HSPCs from patients with sickle cell disease. Science Advances 2022.
  • KOMB: K-core based de novo characterization of copy number variation in microbiomes. Computational and Structural Biotechnology Journal, 2022
  • The World Ahead: The impact of long-read sequencing on metagenomics. Accepted by Nature Method
  • Olivar: fully automated and variant aware primer design for multiplex tiled amplicon sequencing of pathogen genomes. In prep.
  • The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Research, 2022
  • Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine. F1000Research, 2020
  • SpliVert: a protein multiple sequence alignment refinement method based on splitting-splicing vertically. Protein and Peptide Letters, 2020.
  • deGSM: memory scalable construction of large scale de Bruijn Graph. IEEE/ACM transactions on computational biology and bioinformatics, 2019.
  • Fast variation-aware read alignment with deBGA-VARA. In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018
  • Acanthopanax senticosus reduces brain injury in mice exposed to low linear energy transfer radiation. Biomedicine & Pharmacotherapy, 2018