Publications

*: equal contribution

Selected publications

Full List

Please visit my Google scholar page for my detailed list of publications.

  1. Chen, Nae-Chyun, Luis F Paulin, Fritz J Sedlazeck, Sergey Koren, Adam M Phillippy, Ben Langmead. "Improved sequence mapping using a complete reference genome and lift-over." bioRxiv (2022).
  2. Nurk, Sergey*, Sergey Koren*, Arang Rhie*, Mikko Rautiainen*, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick GS Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian FA Smit, Daniela C Soto, Ivan Sović, Jessica M Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan MD Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O’Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, Adam M Phillippy. "The complete sequence of a human genome." Science (2022).
  3. Chen, Nae-Chyun, Alexey Kolesnikov, Sidharth Goel, Taedong Yun, Pi-Chuan Chang*, Andrew Carroll*. "Improving variant calling using population data and deep learning." bioRxiv (2021).
  4. Mun, Taher*, Nae-Chyun Chen*, Ben Langmead. "LevioSAM: fast lift-over of variant-aware reference alignments." Bioinformatics (2021).
  5. Lin, Mao-Jan*, Yu-Chun Lin*, Nae-Chyun Chen*, Allen Chilun Luo, Sheng-Kai Lai, Chia-Lang Hsu, Jacob Shjui Hsu, Chien-Yu Chen, Wei-Shiung Yang, Pei-Lung Chen. "Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite. bioRxiv (2021).
  6. Chen, Nae-Chyun, Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead. "Reference flow: reducing reference bias using multiple population genomes." Genome biology (2021).
  7. Pritt, Jacob, Nae-Chyun Chen, Ben Langmead. "FORGe: prioritizing variants for graph genomes." Genome biology (2018).
  8. Liao, Yi-Lun, Yu-Cheng Li, Nae-Chyun Chen, Yi-Chang Lu. "Adaptively Banded Smith-Waterman Algorithm for Long Reads and Its Hardware Accelerator." 2018 IEEE 29th International Conference on Application-specific Systems, Architectures and Processors (ASAP). IEEE, 2018.
  9. Chen, Nae-Chyun, Yu-Cheng Li, Yi-Chang Lu. "A Memory-Efficient FM-Index Constructor for Next-Generation Sequencing Applications on FPGAs." 2018 IEEE International Symposium on Circuits and Systems (ISCAS). IEEE, 2018. (This paper was accepted by 2018 IEEE ISCAS, but later removed because the co-author presented on-behalf of us hadn't fulfilled the presentation requirement. We posted the manuscript to arXiv with the agreement from IEEE.)
  10. Lin, Mao-Jan, Chih-Yu Chang, Yu-Cheng Li, Nae-Chyun Chen, Yi-Chang Lu. "A Hybrid Flow for Multiple Sequence Alignment with a BLASTn Based Pairwise Alignment Processor." 2018 IEEE International Symposium on Circuits and Systems (ISCAS). IEEE, 2018.
  11. Chang, Chih-Yu, Yu-Cheng Li, Nae-Chyun Chen, Xiao-Xuan Huang, Yi-Chang Lu. "A special processor design for nucleotide basic local alignment search tool with a new banded two-hit method." 2016 IEEE Nordic Circuits and Systems Conference (NORCAS). IEEE, 2016.
  12. Liu, Chun-Shen, Nae-Chyun Chen, Yu-Cheng Li, Yi-Chang Lu. "An FPGA-based quality filter for de novo sequence assembly pipeline." 2016 IEEE Asia Pacific Conference on Circuits and Systems (APCCAS). IEEE, 2016.
  13. Huang, Xiao-Xuan, Chun-Hsien Ho, Yu-Cheng Li, Nae-Chyun Chen, Yi-Chang Lu. "Step shift: A fast image segmentation algorithm and its hardware implementation for next-generation sequencing fluorescence data." 2016 IEEE Asia Pacific Conference on Circuits and Systems (APCCAS). IEEE, 2016.
  14. Chen, Yi-Hsiang, Nae-Chyun Chen, Yu-Hsiang Kao, Yu-Cheng Li, Yi-Chang Lu. "Queue-based segmentation algorithm for refining depth maps in light field camera applications." 2016 IEEE 5th Global Conference on Consumer Electronics. IEEE, 2016.
  15. Chen, Nae-Chyun, Tai-Yin Chiu, Yu-Cheng Li, Yu-Chun Chien, Yi-Chang Lu. "Power efficient special processor design for burrows-wheeler-transform-based short read sequence alignment." 2015 IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 2015