About Me
My name is Chengze Shen
(CV)
and I am a fifth-year (started 2020) PhD student
@ UIUC Computer Science program. My advisor is
Tandy Warnow.
QUAL: PASSED
PRELIM: PASSED
I expect to graduate by Jan/May 2025 and I am looking
for job opportunities in industry.
Seeking a role in software engineering/data science/algorithmic design
to apply extensive research and technical expertise in developing
high-performance, scalable solutions.
My Research
I am a computer scientist with strong programming skills
and a broad background in bioinformatics.
I 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
Talks and Presentations
- [November 11, 2024] PPoSS Meeting, Clusterings and Multiple Sequence Alignments.
- [September 4, 2023] ACM-BCB/WABI 2023, EMMA: accepted paper presentation.
Link
- [September 1, 2022] Sandia National Lab Presentation on Scalable Alignment and Tree Estimation.
Link
News
- [Decemeber 7, 2023] EMMA has been formally published
on Algorithms for Molecular Biology.
DOI link
- [November 19, 2023] "EMMA: A New Method for Computing
Multiple Sequence Alignments Given a Constraint
Subset Alignment" has been accepted for publication
in Algorithms for Molecular Biology!
- [September 3-6, 2023] Attended ACM-BCB/WABI 2023
for presentation and poster session for new multiple
sequence alignment research results - EMMA.
See Publications for the EMMA paper.
- [April 2023] Currently collaborating with
Kelly P. Williams
from Sandia National Lab on developing alignment methods
that deal with missing clade in input data.
Publications
-
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)
-
Minhyuk Park, Stefan Ivanovic, Gillian Chu, Chengze Shen, and Tandy Warnow. UPP2: Fast and Accurate Alignment of Datasets with Fragmentary Sequences.” Bioinformatics 39, no. 1 (January 1, 2023): btad007.
(Link)
-
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)
-
Chengze Shen, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. EMMA: A New Method for Computing Multiple Sequence Alignments Given a Constraint Subset Alignment. Accepted for publication in Algorithms for Molecular Biology.
(Link)
-
Mihir Mongia*, Chengze Shen*, Arash Gholami Davoodi, Guillaume Marcais, and Hosein Mohimani. Large Scale Sequence Alignment via Efficient Inference in Generative Models. Scientific Reports 13, no. 1 (May 4, 2023): 7285.
(Link)
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