Publications

Lab members are bold.

† denotes equal contribution * denotes co-corresponding authors.

used Xin Maizie Zhou (X. M. Zhou) for publications after 2022.

Preprints/Under Review

• Enhancing variant detection in complex genomes: leveraging linked reads for robust SNP, Indel, and structural variant analysis.
  C. Luo†, Y. H. Liu†, H. Liu, Z. Zhang, L. Zhang, B. A. Peters*, X. M. Zhou*.
  (2025)

• CSsingle: a unified tool for robust decomposition of bulk and spatial transcriptomic data across diverse single-cell references.
  W. Shen*, C. Liu, Y. Hu, Y. Lei, H.-S. Wong, S. Wu*, X. M. Zhou*.
  bioRxiv (2025)

• scLongTree: an accurate computational tool to infer the longitudinal tree for single-cell DNA sequencing data.
  R. Khan, X. M. Zhou*, X. Mallory*.
  (2025)

• MaskGraphene: an advanced framework for interpretable joint representation for multi-slice, multi-condition spatial transcriptomics.
  Y. Hu, Z. Lin, M. Xie, W. Yuan, Y. Li, M. Rao, Y. H. Liu, W. Shen, L. Zhang*, X. M. Zhou*.
  bioRxiv (2025)

• SCGclust: single cell graph clustering using graph autoencoders integrating SNVs and CNAs.
  T. Potu†, Y. Hu†, R. Khan, S. Dharani, J. Ni, L. Zhang*, X. M. Zhou*, X. Mallory*.
  bioRxiv (2025)

• stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images.
  K. Xu, X. M. Zhou*, L. Zhang*.
  bioRxiv (2025)

• FocalSV: target region-based structural variant assembly and refinement using single-molecule long read sequencing data.
  C. Luo†, Z. J. Zhou†, X. M. Zhou.
  bioRxiv (2024)

• Brain structure and activity predicting cognitive maturation in adolescence.
  J. Zhu, C. M. Garin, X.-L. Qi, A. Machado, Z. Wang, S. B. Hamed, T. R. Stanford, E. Salinas, C. T. Whitlow, A. W. Anderson, X. M. Zhou, F. Calabro, B. Luna, C. Constantinidis.
  bioRxiv (2024)

• CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data.
  W. Yuan†, C. Luo†, Y. Hu, L. Zhang, Z.-H. Wen, Y. H. Liu, X. Mallory*, X. M. Zhou*.
  bioRxiv (2024)

Peer-reviewed Publications

2025

• Large indel detection in region-based phased diploid assemblies from linked-reads.
  C. Luo, B. A. Peters, X. M. Zhou.
  BMC Genomics (2025) 26:263. DOI

• stDyer enables spatial domain clustering with dynamic graph embedding.
  K. Xu, Y. Xu, Z. Wang, X. M. Zhou*, L. Zhang*.
  Genome Biology (2025) 26:34. DOI

2024

• VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing.
  C. Luo†, Y. H. Liu†, X. M. Zhou.
  Nature Communications (2024) 15:6956. DOI

• Benchmarking clustering, alignment, and integration methods for spatial transcriptomics.
  Y. Hu, M. Xie, Y. Li, M. Rao, W. Shen, C. Luo, H. Qin, J. Baek, X. M. Zhou.
  Genome Biology (2024) 25:212. DOI

• SCCNAInfer: A robust and accurate tool to infer the absolute copy number on scDNA-seq data.
  L. Zhang, X. M. Zhou, X. Mallory.
  Bioinformatics (2024) 40(7), btae454. DOI

• Parallel signatures of cognitive maturation in primate antisaccade performance and prefrontal activity.
  J. Zhu, X. M. Zhou, C. Constantinidis, E. Salinas, T. R. Stanford.
  iScience (2024) 27(8):110488. DOI

• Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data.
  Y. H. Liu†, C. Luo†, S. G. Golding, J. B. Ioffe, X. M. Zhou.
  Nature Communications (2024) 15:2447. DOI

2023

• Laminar pattern of adolescent development changes in working memory neuronal activity.
  J. Zhu, B. Hammond, X. M. Zhou, C. Constantinidis.
  Journal of Neurophysiology (2023) 130(4):980-989. DOI

• Editorial: predicting high-risk individuals for common diseases using multi-omics and epidemiological data, volume II.
  W. P. Veldsman, X. M. Zhou, Y. Zhang, B. Li, L. Zhang.
  Front. Genet. (2023) 14:1280648. DOI

• ADEPT: Autoencoder with differentially expressed genes and imputation for robust spatial transcriptomics clustering.
  Y. Hu†, Y. Zhao†, C. T. Schunk, Y. Ma, T. Derr*, X. M. Zhou*.
  iScience (2023) 26(6):106792. DOI

• Haplotyping-assisted diploid assembly and variant detection with linked-reads.
  Y. Hu†, C. Yang†, L. Zhang*, X. Zhou*.
  Methods in Molecular Biology (2023) 2590:161-182. DOI

2022

• Haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model.
  C. Luo, P. A. Datar, Y. H. Liu, X. Zhou.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM), (2022) pp. 2326-2333. DOI

• A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants.
  C. Wang, J. Zhang, X. Zhou, L. Zhang.
  Briefings in Bioinformatics (2022) bbac552. DOI

• Automated filtering of genome-wide large deletions through an ensemble deep learning framework.
  Y. Hu, S. Mangal, L. Zhang, X. Zhou.
  Methods (2022) 206, 77-86. DOI

• Graphing cell relations in spatial transcriptomics.
  X. Zhou.
  Nature Computational Science (2022) 2, 354-355. DOI

• Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA reveals novel spatial biology.
  W. Zhang, I. Li, N. E. Reticker-Flynn, Z. Good, S. Chang, N. Samusik, S. Saumyaa, Y. Li, X. Zhou, et al.
  Nature Methods (2022) 9, 759–769. DOI

• Strong gamma frequency oscillations in the adolescent prefrontal cortex.
  Z. Wang, B. Singh, X. Zhou*, C. Constantinidis*.
  Journal of Neuroscience (2022) 42 (14) 2917-2929. DOI

• Benchmarking challenging small variants with linked and long reads.
  J. Wagner, N. D. Olson…, X. Zhou,…, J. Zook.
  Cell Genomics (2022) 2(5), 100128. DOI

• Neural mechanisms of working memory accuracy revealed by recurrent neural networks.
  Y. Xie, Y. H. Liu, C. Constantinidis, X. Zhou.
  Front. Syst. Neurosci. (2022) 16:760864. DOI

• A Bayesian factorization method to recover single-cell RNA sequencing data.
  Z.-H. Wen, J. L. Langsam, L. Zhang, W. Shen*, X. Zhou*.
  Cell Reports Methods (2022) 2, 100133. DOI

2021

• An ensemble deep learning framework to refine large deletions in linked-reads.
  Y. Hu, S. V. Mangal, L. Zhang, X. Zhou.
  IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2021) pp. 288-295. DOI

• The epithelial and stromal immune microenvironment in gastric cancer: a comprehensive analysis reveals prognostic factors with digital cytometry.
  W. Shen, G. Wang, G. R. Cooper, Y. Jiang, X. Zhou.
  Cancers (Basel) (2021) 13(21):5382. DOI

• Emergence of prefrontal neuron maturation properties by training recurrent neural networks in cognitive tasks.
  Y. H. Liu, J. Zhu, C. Constantinidis, X. Zhou.
  iScience (2021) 24(10):103178. DOI

• Editorial: predicting high-risk individuals for common diseases using multi-omics and epidemiological data.
  D. Chowdhury, X. Zhou, B. Li, Y. Zhang, W. K. Cheung, A. Lyu, L. Zhang.
  Front. Genet. (2021) 12:737598. DOI

• DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-Seq Data.
  J. Chen, C. Cheong, L. Lan, X. Zhou, J. Liu, A. Lyu, W. K. Cheung, L. Zhang.
  Briefings in Bioinformatics (2021) 22(6):bbab325. DOI

• Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes.
  S. Li†, Z. Guo†, J. B. Ioffe, Y. Hu, Y. Zhen*, X. Zhou*.
  Scientific Reports (2021) 11(1):15269. DOI

• Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads.
  Y. H. Liu, G. L. Grubbs, L. Zhang, X. Fang, D. L. Dill, A. Sidow, X. Zhou.
  Bioinformatics Advances (2021) 1, vbab007. DOI

2020 and earlier

• Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked-reads.
  X. Zhou*, L. Zhang, Z. Weng, D. L. Dill, A. Sidow*.
  Nature Communications (2021) 12:1077.

• A comprehensive investigation of metagenome assembly by linked-read sequencing.
  L. Zhang, X. Fang, H. Liao, Z. Zhang, X. Zhou, L. Han, Y. Chen, Q. Qiu, S. C. Li.
  Microbiome (2020) 8(1), 1-11.

• A diploid assembly-based benchmark for variants in the major histocompatibility complex.
  C. Chin, J. Wagner,…, X. Zhou,…, J. Zook.
  Nature Communications (2020) 11:4794.

• De novo diploid genome assembly for genome-wide structural variant detection.
  L. Zhang†, X. Zhou†, Z. Weng, A. Sidow.
  NAR Genomics and Bioinformatics (2020) 2(1), 1-10.

• Plasticity of persistent activity and its constraints.
  S. Li, X. Zhou, C. Constantinidis, X.-L. Qi.
  Frontiers in Neural Circuits (2020) 14:15.

• Assessment of human diploid genome assembly with 10x Linked-Reads data.
  L. Zhang†, X. Zhou†, Z. Weng, A. Sidow.
  GigaScience (2019) 8:1-11.

• Assessment of network module identification across complex diseases.
  S. Choobdar et al.
  Nature Methods (2019) 16:843-852.

• HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.
  X. Zhou, S. Batzoglou, A. Sidow, L. Zhang.
  BMC Genomics (2018) 19(1), 467.

• Anterior-posterior gradient of plasticity in primate prefrontal cortex.
  M. Riley, X.-L. Qi, X. Zhou, C. Constantinidis.
  Nature Communications (2018) 9(1):3790.

• Fixation target representation in prefrontal cortex during the anti-saccade task.
  X. Zhou, C. Constantinidis.
  J. Neurophysiology (2017) 117:2152-2162.

• Neural correlates of working memory development in adolescent primates.
  X. Zhou, D. Zhu, X.-L. Qi, S. H. Li, S. G. King, E. Salinas, T. R. Stanford, C. Constantinidis.
  Nature Communications (2016) 7:13423.

• Behavioral response inhibition and maturation of goal representation in prefrontal cortex after puberty.
  X. Zhou, D. Zhu, S. G. King, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis.
  Proc. Natl. Acad. Sci. USA (2016) 113(12):3353-3358.

• Distinct roles of the prefrontal and posterior parietal cortices in response inhibition.
  X. Zhou, X.-L. Qi, C. Constantinidis.
  Cell Reports (2016) 14(12):2765-2773.

• An evolutionary strategy for resilient cyber defense.
  E. W. Fulp, H. D. Gage, D. J. John, M. McNiece, W. H. Turkett, X. Zhou. [alphabetical]
  Proceedings of the IEEE Global Communications Conference (GLOBECOM) (2015).

• Age-dependent changes in prefrontal intrinsic connectivity.
  X. Zhou, D. Zhu, F. Katsuki, X.-L. Qi, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis.
  Proc. Natl. Acad. Sci. USA (2014) 111(10):3853-3858.

• Working memory performance and neural activity in the prefrontal cortex of peri-pubertal monkeys.
  X. Zhou, D. Zhu, X.-L. Qi, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis.
  J. Neurophysiology (2013) 110:2648-2660.

• Neurons with inverted tuning during the delay periods of working memory tasks in the dorsal prefrontal and posterior parietal cortex.
  X. Zhou, F. Katsuki, X.-L. Qi, C. Constantinidis.
  J. Neurophysiology (2012) 108:31-38.

• Cholinergic modulation of working memory activity in primate prefrontal cortex.
  X. Zhou, X.-L. Qi, K. Douglas, K. Palaninathan, H. S. Kang, J. J. Buccafusco, D. T. Blake, C. Constantinidis.
  J. Neurophysiology (2011) 106:2180-2188.

• Comparison of neural activity related to working memory in primate dorsolateral prefrontal and posterior parietal cortex.
  X.-L. Qi, F. Katsuki, T. Meyer, J. B. Rawley, X. Zhou, K. Douglas, C. Constantinidis.
  Front. Syst. Neurosci. (2010) 4:12.

Book Chapters

• Dynamic interactions in prefrontal functional connectivity during adolescence.
  X. Zhou, E. Salinas, T. R. Stanford, C. Constantinidis.
  In: Advances in Cognitive Neurodynamics (V) (2016) R. Wang and X. Pan, Editors. Springer. pp. 193-197

• Neurophysiological mechanisms of working memory: cortical specialization & plasticity.
  X.-L. Qi, X. Zhou, C. Constantinidis.
  In: Attention and Performance XXV (2015). Jolicoeur P., Lefebvre C. and Martinez-Trujillo J., Editors. Academic Press. pp. 171-186