Selected Publications

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Preprints 2

  1. Gupta S, Romero S, Cai JJ. Mapping Gene Impact on Single-cell Transcriptomic Networks via Perturbation Response Scanning. bioRxiv [Preprint]. 2025 Dec 17:2025.12.15.694358. doi: 10.64898/2025.12.15.694358. PMID: 41473321.
  2. Gupta S, Chaudhuri A, Raghuraman V, Ni Y, Cai JJ. CONSTRUCTING GENE REGULATORY NETWORK USING CHATTERJEE'S RANK CORRELATION WITH SINGLE-CELL TRANSCRIPTOMIC DATA. bioRxiv [Preprint]. 2025 Sep 23:2025.09.17.676530. doi: 10.1101/2025.09.17.676530. PMID: 41000795.

Journal Articles 16

  1. Romero S, Kumar VS, Chapkin RS, Cai JJ. Quantum generative modeling of single-cell transcriptomes: Capturing gene–gene and cell–cell interactions. APL Quantum. 2026/08/12;3(3)036106-. doi:10.1063/5.0317792.
  2. Romero S, Gupta S, Gatlin V, Chapkin RS, Cai JJ. Quantum annealing for enhanced feature selection in single-cell RNA sequencing data analysis. Quantum Mach Intell. 2025/12;7(2)114-. doi:10.1007/s42484-025-00312-1.
  3. Zhong Y, Hou Y, Yang Y, Zheng X, Cai JJ. scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation. Bioinformatics. 2025 Sep 1;41(9):btaf483. doi: 10.1093/bioinformatics/btaf483. PMID: 40889281.
  4. Gatlin V, Gupta S, Romero S, Chapkin RS, Cai JJ. Exploring cell-to-cell variability and functional insights through differentially variable gene analysis. NPJ Syst Biol Appl. 2025 Mar 20;11(1):29. doi: 10.1038/s41540-025-00507-z. PMID: 40113778.
  5. Gupta S, Cai JJ. Gene function revealed at the moment of stochastic gene silencing. Commun Biol. 2025 Jan 19;8(1):88. doi: 10.1038/s42003-025-07530-0. PMID: 39828795.
  6. Zhong Y, Cui S, Yang Y, Cai JJ. Controlled noise: evidence of epigenetic regulation of single-cell expression variability. Bioinformatics. 2024 Jul 1;40(7):btae457. doi: 10.1093/bioinformatics/btae457. PMID: 39018178.
  7. Roman-Vicharra C, Cai JJ. Quantum gene regulatory networks. npj Quantum Inf. 2023/07/13;9(1)67-. doi:10.1038/s41534-023-00740-6.
  8. Yang Y, Li G, Zhong Y, Xu Q, Chen BJ, Lin YT, Chapkin RS, Cai JJ. Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks. Nucleic Acids Res. 2023 Jul 21;51(13):6578-6592. doi: 10.1093/nar/gkad450. PMID: 37246643.
  9. Yang Y, Li G, Zhong Y, Xu Q, Lin YT, Roman-Vicharra C, Chapkin RS, Cai JJ. scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs. Cell Syst. 2023 Apr 19;14(4):302-311.e4. doi: 10.1016/j.cels.2023.01.004. PMID: 36787742.
  10. Osorio D, Zhong Y, Li G, Xu Q, Yang Y, Tian Y, Chapkin RS, Huang JZ, Cai JJ. scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. Patterns (N Y). 2022 Feb 1;3(3):100434. doi: 10.1016/j.patter.2022.100434. PMID: 35510185.
  11. Osorio D, Zhong Y, Li G, Huang JZ, Cai JJ. scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. Patterns (N Y). 2020 Nov 5;1(9):100139. doi: 10.1016/j.patter.2020.100139. PMID: 33336197.
  12. Osorio D, Yu X, Zhong Y, Li G, Yu P, Serpedin E, Huang JZ, Cai JJ. Single-Cell Expression Variability Implies Cell Function. Cells. 2019 Dec 19;9(1):14. doi: 10.3390/cells9010014. PMID: 31861624.
  13. Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019 Nov 7:btz830. doi: 10.1093/bioinformatics/btz830. PMID: 31697351.
  14. Zeng Y, Wang G, Yang E, Ji G, Brinkmeyer-Langford CL, Cai JJ. Aberrant gene expression in humans. PLoS Genet. 2015 Jan 24;11(1):e1004942. doi: 10.1371/journal.pgen.1004942. PMID: 25617623.
  15. Wang G, Yang E, Brinkmeyer-Langford CL, Cai JJ. Additive, epistatic, and environmental effects through the lens of expression variability QTL in a twin cohort. Genetics. 2014 Feb;196(2):413-25. doi: 10.1534/genetics.113.157503. PMID: 24298061.
  16. Hulse AM, Cai JJ. Genetic variants contribute to gene expression variability in humans. Genetics. 2013 Jan;193(1):95-108. doi: 10.1534/genetics.112.146779. PMID: 23150607.