Preprints
- scCausalVI disentangles single-cell perturbation responses with causality-aware generative model
An SK, Cho JW, Cao K, Xiong JK, Hemberg M*, Wan L* (2025)
bioRxiv, doi: 10.1101/2025.02.02.636136.
(An extended version of RECOMB 2025 paper)
- Integrate and generate single-cell proteomics from transcriptomics with cross-attention
Xiong JK, Zheng SQ, Gong FZ, Ma L*, Wan L* (2025)
bioRxiv, doi: 10.1101/2025.01.28.635217.
Papers
(† co-first authors; * corresponding or co-corresponding author)
- Causal disentanglement of treatment effects in single-cell RNA Sequencing through counterfactual inference
An SK, Cho JW, Cao K, Xiong JK, Hemberg M*, Wan L* (2025)
Proceedings of RECOMB 2025, in press.
- Dynamic Modeling, Optimization, and Deep Learning for High-Dimensional Complex Biological
Data (in Chinese)
Jiang Q, Wan L* (2025)
SCIENTIA SINICA Mathematica, in press.
- A physics-informed neural SDE network for learning cellular dynamics from time-series scRNA-seq data
Jiang Q, Wan L* (2024)
Bioinformatics, 40(Supplement_2):ii120-ii127; doi: 10.1093/bioinformatics/btae400.
(ECCB 2024)
- Graspot: A graph attention network for spatial transcriptomics data integration with optimal transport
Gao ZZ, Cao K*, Wan L* (2024)
Bioinformatics, 40(Supplement_2):ii137-ii145; doi: 10.1093/bioinformatics/btae394.
bioRxiv, doi: 10.1101/2024.02.01.578505.
(ECCB 2024)
- scVIC: Deep generative modeling of heterogeneity for scRNA-seq data
Xiong JK, Gong FZ, Ma L*, Wan L* (2024)
Bioinformatics Advances, 4(1):vbae086; doi: 10.1093/bioadv/vbae086.
- A multi-view graph contrastive learning framework for deciphering spatially resolved transcriptomics data
Zhang L, Liang S*, Wan L* (2024)
Briefings in Bioinformatics, 25(4):bbae255; doi: 10.1093/bib/bbae255.
- Joint inference of clonal structure using single-cell genome and transcriptome sequencing data
Bai XQ, Duren Z, Wan L*, Xia L* (2024)
NAR Genomics and Bioinformatics, 6(1):lqae017.
bioRxiv, doi: 10.1101/2020.02.04.934455.
- RobustTree: An adaptive, robust PCA algorithm for embedded tree structure recovery from single-cell sequencing data
Chen ZW, Zhang BW, Gong FZ, Wan L*, Ma L* (2023)
Frontiers in Genetics, 14:1110899; doi: 10.3389/fgene.2023.1110899.
- A unified computational framework for single-cell data integration with optimal transport
Cao K, Gong QY, Hong YG*, Wan L* (2022)
Nature Communications, 13:7419; doi: 10.1038/s41467-022-35094-8.
bioRxiv, doi: 10.1101/2022.02.14.480323.
- A New Context Tree Inference Algorithm for Variable Length Markov Chain Model with Applications to Biological Sequence Analyses
An SK, Ren J, Sun FZ, Wan L* (2022)
Journal of Computational Biology, 29(8):839-856; doi: 10.1089/cmb.2021.0604.
(Waterman Special Issue)
- BiTSC2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
Chen ZW, Gong FZ, Wan L*, Ma L* (2022)
Briefings in Bioinformatics, 23(3):bbac092; doi: 10.1093/bib/bbac092.
bioRxiv, doi: 10.1101/2020.11.30.380949.
(RECOMB-Seq 2021)
- Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data
Jiang Q, Zhang S, Wan L* (2022)
PLOS Computational Biology, 18(1): e1009821; doi: 10.1371/journal.pcbi.1009821.
- Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
Cao K, Hong YG, Wan L* (2022)
Bioinformatics, 38(1): 211-219; doi: 10.1093/bioinformatics/btab594.
bioRxiv, doi: 10.1101/2020.11.03.366146.
- D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell data
An SK, Huang JZ*, Wan L* (2020)
GigaScience, 9(11): giaa126; doi: 10.1093/gigascience/giaa126.
- Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration
Cao K, Bai XQ, Hong YG, Wan L* (2020)
Bioinformatics, 36(Supplement_1):i48-i56; doi: 10.1093/bioinformatics/btaa443.
bioRxiv, doi: 10.1101/2020.02.02.931394.
(ISMB 2020)
- RobustClone: A robust PCA method for tumor clone and evolution inference from single-cell sequencing data
Chen ZW, Gong FZ, Wan L*, Ma L* (2020)
Bioinformatics, 36(11):3299-3306; doi: 10.1093/bioinformatics/btaa172.
bioRxiv, doi: 10.1101/10.1101/666271.
- NeuralEE: a GPU-accelerated elastic embedding dimensionality reduction method for visualizing large-scale scRNA-seq data
Xiong JK, Gong FZ, Wan L*, Ma L* (2020)
Frontiers in Genetics, 11:786; doi: 10.3389/fgene.2020.00786.
- Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data
Wan L, Kang X, Ren J, Sun FZ* (2020)
Quantitative Biology, 8(2):143-154; doi: 10.1007/s40484-020-0200-y.
- International Workshop on Applications of Probability and Statistics to Biology, July 11-13, 2019
Deng MH, Feng JF, Qian H, Wan L, Sun FZ* (2020)
Quantitative Biology, 8(2):177-186; doi: 10.1007/s40484-019-0182-9.
- A Branch Point on Differentiation Trajectory is the Bifurcating Event Revealed by Dynamical Network Biomarker Analysis of Single-Cell Data
Chen ZW, Bai XQ, Ma L*, Wang XW, Liu XQ, Liu YT, Chen LN*, Wan L* (2020)
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(2): 366-375; doi: 10.1109/TCBB.2018.2847690.
- Statistical test of structured continuous trees based on discordance matrix
Bai XQ, Ma L*, Wan L* (2019)
Bioinformatics, 35(23):4962-4970; doi: 10.1093/bioinformatics/btz425.
- TSEE: an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data
An SK, Ma L*, Wan L* (2019)
BMC Genomics, 20(Suppl 2):224; doi: 10.1186/s12864-019-5477-8.
(Best Paper Award of APBC2019)
- DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data
Chen ZW, An SK, Bai XQ, Gong FZ, Ma L*, Wan L* (2019)
Bioinformatics, 35(15):2593-2601; doi: 10.1093/bioinformatics/bty1009.
bioRxiv, doi: 10.1101/276311.
- A remark on copy number variation detection methods
Li S, Dou X, Gao R, Ge X, Qian M*, Wan L* (2018)
PLoS ONE, 13(4): e0196226; doi: 10.1371/journal.pone.0196226.
- Statistical testing and power analysis for brain-wide association study
Gong WK, Wan L, Lu WL, Ma L, Cheng F, Cheng W, Gruenewald S, Feng JF (2018)
Medical Image Analysis, 47:15-30; doi: 10.1016/j.media.2018.03.014.
- Individual differences in schizophrenia
Rolls ET, Lu W, Wan L, Yan H, Wang C, Yang F, Tan Y, Li L, Chinese Schizophrenia Collaboration Group, Yu H, Liddle PF, Palaniyappan L, Zhang D, Yue W, Feng J (2017)
British Journal of Psychiatry Open, 3(6):265-273; doi: 10.1192/bjpo.bp.117.005058.
- Estimating Phred scores of Illumina base calls by logistic regression and sparse modeling
Zhang S, Wang B, Wan L, Li LM (2017)
BMC Bioinformatics, 18:335; doi: 10.1186/s12859-017-1743-4.
- An adaptive decorrelation method removes Illumina DNA base-calling errors caused by crosstalk between adjacent clusters
Wang B, Wan L, Wang AQ, Li LM (2017)
Scientific Reports, 7:41348; doi: 10.1038/srep41348.
- Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis
Cheng W, Rolls ET, Zhang J, Sheng W, Ma L, Wan L, Luo Q, Feng J (2017)
NeuroImage, 148:169-178; doi: 10.1016/j.neuroimage.2016.12.068.
- Achieving Accurate and Fast Base-calling by a Block Model of the Illumina Sequencing Data
Wang B, Wan L, Li LM (2015)
IFAC-PapersOnLine, 48(28):1462-1465; doi: 10.1016/j.ifacol.2015.12.339.
- Tracking the Evolving Spatial-Temporal Gene Networks
Gong WK, Wan L* (2015)
IFAC-PapersOnLine, 48(28):1365-1368; doi: 10.1016/j.ifacol.2015.12.322.
- Modeling RNA degradation for RNA-Seq with applications
Wan L,Yan XT, Chen T, Sun FZ (2012)
Biostatistics, 13(4):734-747; doi: 10.1093/biostatistics/kxs001.
- CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq
Wan L, Sun FZ (2012)
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5): 1281-1292; doi: 10.1109/TCBB.2012.83.
- Hybridization and amplification rate correction for affymetrix SNP arrays
Wang Q, Peng PC, Qian MP, Wan L*, Deng MH* (2012)
BMC Medical Genomics, 5:24; doi: 10.1186/1755-8794-5-24.
- A study of biases of DNA copy number estimation based on PICR model
Wang Q, Qu JH, Cheng XX, Kang YJ, Wan L, Qian MP, Deng MH (2011)
Frontiers of Mathematics in China, 6(6) 1203-1216; doi: 10.1007/s11464-011-0125-x.
- RseqFlow: Workflows for RNA-Seq data analysis
Wang Y, Mehta G, Mayani R, Lu J, Souaiaia T, Chen Y, Clark A, Yoon HJ, Wan L, Evgrafov OV, Knowles JA, Deelman E, Chen T (2011)
Bioinformatics, 27(18): 2598-2600; doi: 10.1093/bioinformatics/btr441.
- New powerful statistics for alignment-free sequence comparison under a pattern transfer model
Liu XM†, Wan L†, Li J, Reinert G, Waterman MS, Sun FZ (2011)
Journal of Theoretical Biology, 284(1): 106-116; doi: 10.1016/j.jtbi.2011.06.020.
- Alignment-free sequence comparison (II): Theoretical power of comparison statistics
Wan L, Reinert G, Sun FZ, Waterman MS (2010)
Journal of Computational Biology, 17(11): 1467-1490; doi: 10.1089/cmb.2010.0056.
- The biases of copy numbers from Affymetrix SNP arrays and their corrections
Wan L, Xiao Y, Deng MH, Qian MP (2010)
Communications in Information and Systems, 10(2):83-98.
- Hybridization modeling of oligonucleotide SNP arrays for accurate DNA copy number estimation
Wan L, Sun KL, Ding Q, Cui YH, Li M, Wen YL, Elston R, Qian MP, Fu WJ (2009)
Nucleic Acids Research, 37(17):e117; doi: 10.1093/nar/gkp559.
- Nonlinear cooperation of p53-ING1-induced bax expression and protein S-nitrosylation in GSNO-induced thymocyte apoptosis: a quantitative approach with cross-platform validation
Duan SJ†, Wan L†, Fu WJ, Pan H, Ding Q, Chen C, Han PW, Zhu XY, Du LY, Liu HX, Chen YX, Liu XM, Yan XT, Deng MH, Qian MP (2009)
Apoptosis, 14:236-245; doi: 10.1007/s10495-008-0288-4.
- Searching for bidirectional promoters in Arabidopsis thaliana
Wang Q, Wan L, Li DY, Zhu LH, Qian MP, Deng MH (2009)
BMC Bioinformatics, 10(Suppl 1):S29; doi: 10.1186/1471-2105-10-S1-S29.
(APBC2009)
- Conservation and implications of eukaryote transcriptional regulatory regions across multiple species
Wan L, Li DY, Zhang DL, Liu X, Fu WJ, Zhu Li, Deng MH, Sun FZ, Qian MP (2008)
BMC Genomics, 9:623; doi: 10.1186/1471-2164-9-623.
- Relaxation dynamics and glass transition in glassy materials
Wang CJ, Huang YN, Wan L,Yin HC, Wang YN, Riande E (2003)
Synthetic Metals, 135:495-496; doi: 10.1016/S0379-6779(02)00708-7.
Book Chapters
- An efficient algorithm for deciphering regulatory motifs
Feng XC, Wan L, Deng MH, Sun FZ, Qian MP (2007)
In Feng J, Jost J and Qian MP (eds), Networks: from Biology to Theory, Springer-Verlag London Ltd.