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.

QUAL: PASSED
PRELIM: PASSED
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

• Bioinformatics
• Multiple sequence alignment
• Microbiome analysis
• Metagenomics
• GPU computing

News

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

• Fall 2020: CS125 (An Introduction to Computer Science)
• Spring 2021: CS125

External Links

Github Page

Publications

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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