my profile

About Me

My name is Chengze Shen (CV) and I am a third-year PhD student @ UIUC Computer Science program. My advisor is Tandy Warnow.

I expect to graduate in Summer/Spring 2024 and I am looking for a job in the bioinformatics industry!

My Research

I am a computer scientist with strong programming skills and a broad background in bioinformatics.
I want to develop scalable solutions and software for challenging problems with ultra-large data in biology where advanced computer science is needed.

My research interests include


  1. [April 2023] Currently collaborating with Kelly P. Williams from Sandia National Lab on developing alignment methods that deal with missing clade in input data.

Teaching Assistantship

External Links

Github Page


  1. Chengze Shen, Paul Zaharias, and Tandy Warnow, MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences, Bioinformatics, Volume 38, Issue 4, 15 February 2022, Pages 918-924. (Link) (pdf)
  2. Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, and Tandy Warnow. UPP2: Fast and Accurate Alignment Estimation of Datasets with Fragmentary Sequences. bioRxiv, March 1, 2022. (Link)
  3. Chengze Shen, Minhyuk Park, and Tandy Warnow. WITCH: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden Markov Model Alignment. Journal of Computational Biology, May 17, 2022. (Link) (pdf)
  4. Chengze Shen, Baqiao Liu, and Tandy Warnow. SALMA: Scalable ALignment using MAFFT-Add. bioRxiv, Aug 12, 2022. (Link) (pdf)
  5. Mihir Mongia*, Chengze Shen*, Arash Gholami Davoodi, Guillaume Marcais, and Hosein Mohimani. Large Scale Sequence Alignment via Efficient Inference in Generative Models. Under revision at Nature Scientific Report.
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