🙋🏼About Me

Hello! I am Pinglu Zhang (张平路), Phd at the    Institute of Fundamental and Frontier Sciences (IFFS), University of Electronic Science and Technology of China (UESTC) (电子科技大学，基础与前沿研究院), majoring in Computer Science and Technology.

I am also part of a joint training program (联合培养) at the    Zhongguancun Academy(北京中关村学院).

I am conducting research on Sequence Alignment at the Malab laboratory under the supervision of Prof. Quan Zou (邹权教授). My work focuses on developing multiple sequence alignment for large-scale data, mulitiple genome alignment, centromere region alignment, and related topics .

Researchers interested in collaboration are welcome to contact me at pingluzhang@outlook.com.

🔥 News

• 2025.12.11:  🎉🎉 NSFC Young Student Basic Research Grant （国自然博士生项目）！
• 2025.11.30:  🎉🎉 New article has been accepted by Genome Biology!
• 2025.02.07:  🎉🎉 New article has been accepted by Genome Research!
• 2024.12.30:  🎉🎉 I have been offered a joint PhD position at UESTC and Zhongguancun Academy.
• 2024.09.08:  🎉🎉 New Homepage was released!

💰 Fundings

• 国家自然科学基金青年学生基础研究项目（博士研究生） 面向全基因组的大规模多物种基因组比对研究

📝 Publications

Selected Publication

Genome Biology 2025

HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes

Pinglu Zhang^†, Tong Zhou^†, Yanming Wei, Qinzhong Tian, Yixiao Zhai, Yizheng Wang, Quan Zou, Furong Tang*, Ximei Luo*

Genome Biology, 2025, 中科院1区, IF2025=9.4

Paper   Code   

• HAlign-G is a fast and memory-efficient solution for large-scale multiple genome alignment, integrating BWT-FM-LIS indexing, an optimized K-band algorithm, and a star-alignment strategy.

• It includes HAlign-G1 for intra-species multiple sequence alignment and HAlign-G2 for cross-species multiple genome alignment, each optimized for distinct evolutionary signals.

• Benchmarks indicate that HAlign-G achieves higher accuracy, lower memory usage, and significantly faster performance than existing methods across both short- and long-genome datasets.

Genome Research 2025

Fast sequence alignment for centromere with RaMA

Pinglu Zhang, Yanming Wei, Qinzhong Tian, Quan Zou, Yansu Wang*

Genome Research, 2025, 中科院1区, nature index journal, IF2024=6.24.

Paper  Code  

• RaMA is a novel sequence alignment tool designed for centromeric regions, leveraging rare matches as anchors and a 2-piece affine gap cost to capture genetic evolution accurately.
• RaMA utilizes parallel computing and the wavefront algorithm, achieving up to 13.66 times faster processing and using only 11% of UniAligner’s memory.
• Additionally, RaMA introduces two innovative methods for defining reliable alignment regions, which further refine the accuracy of centromeric alignment statistics and provide more robust insights into genetic variations.
• Downstream analysis of simulated data and HOR arrays demonstrates RaMA’s superior accuracy in capturing true HOR structures and defining reliable alignment regions.

Bioinformatics 2024

FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets

Pinglu Zhang, Huan Liu, Yanming Wei, Yixiao Zhai, Qinzhong Tian, Quan Zou*

Bioinformatics, 2024, 中科院3区, CCF-B, IF2024=4.4.

Paper  Code  

• FMAlign2 is an improved MSA method that uses a suffix array and vertical division strategy to align ultralong sequences in parallel.
• FMAlign2 reduces processing time while maintaining accuracy, handling sequences up to billions in length efficiently.

Other Publications

• PS-mixer: A polar-vector and strength-vector mixer model for multimodal sentiment analysis, H Lin^†, P Zhang^†, J Ling, Z Yang*, LK Lee, W Liu. Information Processing & Management, 2023, 中科院1区, CCF-B, IF2023=8.6.  Paper  Code  

• Chimera: Ultrafast and Memory-efficient Database Construction for High-Accuracy Taxonomic Classification in the Age of Expanding Genomic Data, Q Tian^†, P Zhang^†, Y Wei, Q Zou, Y Wang*, X Luo*. bioRxiv, 2025.  Paper  Code  

• HAlign-4: A New Strategy for Rapidly Aligning Millions of Sequences, T Zhou, P Zhang, Q Zou*, W Han*. Bioinformatics, 2024, 中科院3区, CCF-B, IF2024=4.4.  Paper  Code  

• TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments, Y Zhai, J Chao, Y Wang, P Zhang, F Tang*, Q Zou*. PLOS Computational Biology, 2024, 中科院2区, CCF-B, IF2024=3.8.  Paper  Code  

• ReAlign-P: A vertical iterative realignment method for protein multiple sequence alignment, Y Zhai, P Zhang, Q Zou, X Luo*. Bioinformatics, 2025, 中科院3区, CCF-B, IF2025=5.4.  Paper  Code  

• Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data, Q Tian, P Zhang, Y Zhai, Y Wang*, Q Zou*. Genome Biology and Evolution, 2024, 中科院2区, IF2024=3.2.  Paper  Code  

• ReAlign-Star: An Optimized Realignment Method for Multiple Sequence Alignment, Targeting Star Algorithm Tools, Y Zhai, P Zhang, Y Liu, Q Zou*. International Conference on Intelligent Computing, 2025, CCF-C.  Paper  Code  

• TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine, Xin Zhang, Feiran Zhou, Pinglu Zhang, Quan Zou* and Ying Zhang*. Current Bioinformatics, 2024, 中科院3区, IF2024=2.4.  Paper  

🎖 Awards

• 2023.09 The First Prize (Ranked 1st Overall) in the CBC Data Challenge (CBC数据挑战赛全国一等奖).
• 2025.03 电子科技大学优秀研究生和学术青苗.

📖 Educations

• 2023.09 - (now): Phd, Institute of Fundamental and Frontier Sciences (IFFS), University of Electronic Science and Technology of China (UESTC) (电子科技大学，基础与前沿研究院).   

• 2025.03 - (now): Phd (Joint Program), Zhongguancun Academy(北京中关村学院). 

• 2024.06 - 2025.03: Master (Joint Program), Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China (UESTC) (电子科技大学，长三角研究院).   

• 2019.09 - 2023.06: Bachelor, School of Computer Science, Guangdong University of Technology (GDUT) (广东工业大学，计算机学院).