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Jump to: Quantum Computing · Machine Learning and Network Inference · Single-Cell Biology · Software Development · Population Genetics · Molecular Evolution · Microbial Genomics · Disease and Aging · Cancer · Metabolism and Nutrition · Neuroscience · Development and Regeneration · Other Collaborations

Quantum Computing 4

  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, Chapkin RS, Cai JJ. QuantumXCT: Learning Interaction-Induced State Transformation in Cell-Cell Communication via Quantum Entanglement and Generative Modeling. arXiv [Preprint]. 2026/04/02;(2604.02203). doi:10.48550/arXiv.2604.02203.
  3. 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.
  4. 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.

Machine Learning and Network Inference 12

  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.
  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. Chang H, Cai JJ, Zhou Q. Order-based structure learning without score equivalence. Biometrika. 2024/05/13;111(2)551-572. doi:10.1093/biomet/asad052.
  5. Yang Y, Lin YT, Li G, Zhong Y, Xu Q, Cai JJ. Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet. Brief Bioinform. 2023 Sep 22;24(6):bbad342. doi: 10.1093/bib/bbad342. PMID: 37798250.
  6. 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.
  7. 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.
  8. Zhou F, He K, Cai JJ, Davidson LA, Chapkin RS, Ni Y. A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization. Stat Biosci. 2023 Dec;15(3):669-691. doi: 10.1007/s12561-022-09350-w. PMID: 38179127.
  9. 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.
  10. Xu Q, Li G, Osorio D, Zhong Y, Yang Y, Lin YT, Zhang X, Cai JJ. scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation. Genes (Basel). 2022 Feb 18;13(2):371. doi: 10.3390/genes13020371. PMID: 35205415.
  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. Huang G, Yuan M, Chen M, Li L, You W, Li H, Cai JJ, Ji G. Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets. Analyst. 2017 Oct 7;142(19):3588-3597. doi: 10.1039/c7an00944e. PMID: 28853484.

Single-Cell Biology 15

  1. Romero S, Gupta S, Salinas ML, Mullens DA, Goldsby J, Fan YY, Davidson LA, Rivera-Rodriguez J, Wright GA, Safe SH, Cai JJ, Chapkin RS. Single-cell gene regulatory networks characterize colonic stem and immune cell homeostasis in Nr4a1 knockout mice. iScience. 2026 Sep 9;29(10):117466. doi: 10.1016/j.isci.2026.117466. PMID: 42756602.
  2. Xu L, Ortiz-Morea FA, Kim SI, Ferrari C, Yan Y, Liu D, Osorio Hurtado D, Cai JJ, Vandepoele K, Shan L, He P. Longitudinal zone- and cell type-specific pattern-triggered immune responses in Arabidopsis roots. Dev Cell. 2026 Jul 24:S1534-5807(26)00271-6. doi: 10.1016/j.devcel.2026.07.002. PMID: 42497852.
  3. Ahmad I, Gupta S, Thomas M, Cai JJ, Heaps CL, Newell-Fugate AE. Exercise decreases the number and modifies the transcriptome of M1 macrophages and CD8+ T cells in non-occluded epicardial adipose tissue of female pigs. Am J Physiol Cell Physiol. 2025 Oct 13. doi: 10.1152/ajpcell.00135.2025. PMID: 41083194.
  4. Salinas ML, Mulakala BK, Davidson LA, Cai JJ, Donovan SM, Chapkin RS, Yeruva L. Single-cell transcriptomics reveals that human milk feeding shapes neonatal immune cell interleukin signaling pathways in a nonrandomized clinical trial. Am J Clin Nutr. 2025 Jul;122(1):196-207. doi: 10.1016/j.ajcnut.2025.04.024. PMID: 40294751.
  5. 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.
  6. Moeng S, Chamorro-Parejo AD, Jeon MS, Cai JJ, Ramos KS. Single-Cell RNA Sequencing Reveals Extensive Heterogeneity and Unique Gene Trajectories in Non-Transformed and Transformed Human Lung Epithelial Cells: Insights into the Role of LncRNAs in Tumor Heterogeneity. Int J Mol Sci. 2025 Feb 16;26(4):1690. doi: 10.3390/ijms26041690. PMID: 40004153.
  7. 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.
  8. Xu Q, Yang Y, Gupta S, Chen BJ, Li G, Chamberlain M, Cai JJ. Role of RSPO3 in Estrogen-mediated Sex Differences in Body Fat Distribution: A Single-cell Data-driven Study. bioRxiv [Preprint]. 2025/01/04; 2025.01.03.631121-. doi:10.1101/2025.01.03.631121.
  9. 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.
  10. Ahmad I, Gupta S, Faulkner P, Mullens D, Thomas M, Sytha SP, Ivanov I, Cai JJ, Heaps CL, Newell-Fugate AE. Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells. Cell Commun Signal. 2024 Apr 26;22(1):243. doi: 10.1186/s12964-024-01587-w. PMID: 38671495.
  11. Xu Q, Yang Y, Zhang X, Cai JJ. Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis. Immunoinformatics (Amst). 2022 Jun;6:100013. doi: 10.1016/j.immuno.2022.100013. PMID: 35434695.
  12. Yang Y, Osorio D, Davidson LA, Han H, Mullens DA, Jayaraman A, Safe S, Ivanov I, Cai JJ, Chapkin RS. Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon. Cancer Prev Res (Phila). 2022 Jan;15(1):17-28. doi: 10.1158/1940-6207.CAPR-21-0378. PMID: 34815312.
  13. Osorio D, Cai JJ. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. Bioinformatics. 2021 May 17;37(7):963-967. doi: 10.1093/bioinformatics/btaa751. PMID: 32840568.
  14. 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.
  15. Osorio D, Yu X, Yu P, Serpedin E, Cai JJ. Single-cell RNA sequencing of a European and an African lymphoblastoid cell line. Sci Data. 2019 Jul 4;6(1):112. doi: 10.1038/s41597-019-0116-4. PMID: 31273215.

Software Development 8

  1. Zhong Y, Osorio D, Li G, Xu Q, Yang Y, Huang JZ, Cai JJ. scTenifoldNet and scTenifoldKnk: A package suite for single-cell gene regulatory network construction, comparison, and perturbation analysis. Statistical Theory and Related Fields. 2025/09/29;9(4)357-366. doi:10.1080/24754269.2025.2557719.
  2. Osorio D, Kuijjer ML, Cai JJ. rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. Bioinformatics. 2022 Jan 3;38(2):580-582. doi: 10.1093/bioinformatics/btab549. PMID: 34320637.
  3. 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.
  4. Guan J, Chen M, Ye C, Cai JJ, Ji G. AEGS: identifying aberrantly expressed gene sets for differential variability analysis. Bioinformatics. 2018 Mar 1;34(5):881-883. doi: 10.1093/bioinformatics/btx646. PMID: 29040376.
  5. Konganti K, Wang G, Yang E, Cai JJ. SBEToolbox: A Matlab Toolbox for Biological Network Analysis. Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. PMID: 24027418.
  6. Cai JJ. PGEToolbox: A Matlab toolbox for population genetics and evolution. J Hered. 2008 Jul-Aug;99(4):438-40. doi: 10.1093/jhered/esm127. PMID: 18310616.
  7. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox 2.0: an enhanced version of a MATLAB toolbox for molecular biology and evolution. Evol Bioinform Online. 2007 Feb 6;2:179-82. PMID: 19455210.
  8. Cai JJ, Smith DK, Xia X, Yuen KY. MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution. BMC Bioinformatics. 2005 Mar 22;6:64. doi: 10.1186/1471-2105-6-64. PMID: 15780146.

Population Genetics 14

  1. Eldridge R, Osorio D, Amstalden K, Edwards C, Young CR, Cai JJ, Konganti K, Hillhouse A, Threadgill DW, Welsh CJ, Brinkmeyer-Langford C. Antecedent presentation of neurological phenotypes in the Collaborative Cross reveals four classes with complex sex-dependencies. Sci Rep. 2020 May 13;10(1):7918. doi: 10.1038/s41598-020-64862-z. PMID: 32404926.
  2. Al Kawam A, Alshawaqfeh M, Cai JJ, Serpedin E, Datta A. Simulating variance heterogeneity in quantitative genome wide association studies. BMC Bioinformatics. 2018 Mar 21;19(Suppl 3):72. doi: 10.1186/s12859-018-2061-1. PMID: 29589560.
  3. Yang E, Wang G, Yang J, Zhou B, Tian Y, Cai JJ. Epistasis and destabilizing mutations shape gene expression variability in humans via distinct modes of action. Hum Mol Genet. 2016 Nov 15;25(22):4911-4919. doi: 10.1093/hmg/ddw314. PMID: 28171656.
  4. Brinkmeyer-Langford C, Balog-Alvarez C, Cai JJ, Davis BW, Kornegay JN. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy. BMC Genomics. 2016 Aug 22;17(1):665. doi: 10.1186/s12864-016-2948-z. PMID: 27549615.
  5. Stafuzza NB, Naressi BC, Yang E, Cai JJ, Amaral-Trusty ME. A framework radiation hybrid map of buffalo chromosome 1 ordering scaffolds from buffalo genome sequence assembly. Genet Mol Res. 2015 Oct 27;14(4):13096-104. doi: 10.4238/2015.October.26.5. PMID: 26535622.
  6. 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.
  7. Chang CL, Cai JJ, Huang SY, Cheng PJ, Chueh HY, Hsu SY. Adaptive human CDKAL1 variants underlie hormonal response variations at the enteroinsular axis. PLoS One. 2014 Sep 15;9(9):e105410. doi: 10.1371/journal.pone.0105410. PMID: 25222615.
  8. Wang G, Yang E, Mandhan I, Brinkmeyer-Langford CL, Cai JJ. Population-level expression variability of mitochondrial DNA-encoded genes in humans. Eur J Hum Genet. 2014 Sep;22(9):1093-9. doi: 10.1038/ejhg.2013.293. PMID: 24398800.
  9. 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.
  10. 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.
  11. Brinkmeyer-Langford CL, Cai JJ, Gill CA, Skow LC. Microsatellite variation in the equine MHC. Anim Genet. 2013 Jun;44(3):267-75. doi: 10.1111/age.12003. PMID: 23051181.
  12. Lu ZX, Jiang P, Cai JJ, Xing Y. Context-dependent robustness to 5' splice site polymorphisms in human populations. Hum Mol Genet. 2011 Mar 15;20(6):1084-96. doi: 10.1093/hmg/ddq553. PMID: 21224255.
  13. Chang CL, Cai JJ, Lo C, Amigo J, Park JI, Hsu SY. Adaptive selection of an incretin gene in Eurasian populations. Genome Res. 2011 Jan;21(1):21-32. doi: 10.1101/gr.110593.110. PMID: 20978139.
  14. Cai JJ, Macpherson JM, Sella G, Petrov DA. Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet. 2009 Jan;5(1):e1000336. doi: 10.1371/journal.pgen.1000336. PMID: 19148272.

Molecular Evolution 9

  1. Willis SC, Saenz DE, Wang G, Hollenbeck CM, Portnoy DS, Cai JJ, Winemiller KO. Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions. Conservation Genet Resour. 2022/12;14(4)391-401. doi:10.1007/s12686-022-01284-1.
  2. Chang CL, Semyonov J, Cheng PJ, Huang SY, Park JI, Tsai HJ, Lin CY, Grützner F, Soong YK, Cai JJ, Hsu SY. Widespread divergence of the CEACAM/PSG genes in vertebrates and humans suggests sensitivity to selection. PLoS One. 2013 Apr 16;8(4):e61701. doi: 10.1371/journal.pone.0061701. PMID: 23613906.
  3. Yang E, Hulse AM, Cai JJ. Evolutionary Analysis of Sequence Divergence and Diversity of Duplicate Genes in Aspergillus fumigatus. Evol Bioinform Online. 2012;8:623-44. doi: 10.4137/EBO.S10372. PMID: 23225993.
  4. Shen S, Lin L, Cai JJ, Jiang P, Kenkel EJ, Stroik MR, Sato S, Davidson BL, Xing Y. Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2837-42. doi: 10.1073/pnas.1012834108. PMID: 21282640.
  5. Tse H, Cai JJ, Tsoi HW, Lam EP, Yuen KY. Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes. BMC Genomics. 2010 Sep 9;11:491. doi: 10.1186/1471-2164-11-491. PMID: 20828396.
  6. Cai JJ, Petrov DA. Relaxed purifying selection and possibly high rate of adaptation in primate lineage-specific genes. Genome Biol Evol. 2010 Jul 12;2:393-409. doi: 10.1093/gbe/evq019. PMID: 20624743.
  7. Cai JJ, Borenstein E, Chen R, Petrov DA. Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biol Evol. 2009 May 27;1:131-44. doi: 10.1093/gbe/evp013. PMID: 20333184.
  8. Lin L, Shen S, Tye A, Cai JJ, Jiang P, Davidson BL, Xing Y. Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet. 2008 Oct 17;4(10):e1000225. doi: 10.1371/journal.pgen.1000225. PMID: 18841251.
  9. Cai JJ, Woo PC, Lau SK, Smith DK, Yuen KY. Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota. J Mol Evol. 2006 Jul;63(1):1-11. doi: 10.1007/s00239-004-0372-5. PMID: 16755356.

Microbial Genomics 17

  1. Hu X, Zhang Y, Wang J, Du M, Yang Y, Cai JJ, Yang E. Functional diversification of the MADS-box gene family in fine-tuning the dimorphic transition of Talaromyces marneffei. mSystems. 2025 Jun 3:e0046425. doi: 10.1128/msystems.00464-25. PMID: 40459274.
  2. Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, Sacchettini J, Cai JJ, Subashchandrabose S. Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli. J Bacteriol. 2024 Jul 25;206(7):e0011224. doi: 10.1128/jb.00112-24. PMID: 38856220.
  3. Chen B-J, Lin C-H, Wu H-Y, Cai JJ, Chao D-Y. Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer. Microbiol Spectr. 2024 Apr 2;12(4):e0395423. doi: 10.1128/spectrum.03954-23. PMID: 38483513.
  4. Rogovskyy AS, Bailey LK, Blazier JC, Cai JJ, Landis M, Lidbury JA, Pavlova E, Wu J. The Brief Case: Corynebacterium amycolatum in a Relapsing Urinary Tract Infection of a Feline Patient. J Clin Microbiol. 2022 Feb 16;60(2):e0045321. doi: 10.1128/JCM.00453-21. PMID: 35170983.
  5. Kumar V, Ivens A, Goodall Z, Meehan J, Doharey PK, Hillhouse A, Hurtado DO, Cai JJ, Zhang X, Schnaufer A, Cruz-Reyes J. Site-specific and substrate-specific control of accurate mRNA editing by a helicase complex in trypanosomes. RNA. 2020 Dec;26(12):1862-1881. doi: 10.1261/rna.076513.120. PMID: 32873716.
  6. Lau SKP, Lo GCS, Chow FWN, Fan RYY, Cai JJ, Yuen KY, Woo PCY. Novel Partitivirus Enhances Virulence of and Causes Aberrant Gene Expression in Talaromyces marneffei. mBio. 2018 Jun 12;9(3):e00947-18. doi: 10.1128/mBio.00947-18. PMID: 29895639.
  7. Chacko N, Zhao Y, Yang E, Wang L, Cai JJ, Lin X. The lncRNA RZE1 Controls Cryptococcal Morphological Transition. PLoS Genet. 2015 Nov 20;11(11):e1005692. doi: 10.1371/journal.pgen.1005692. PMID: 26588844.
  8. Yang E, Chow WN, Wang G, Woo PC, Lau SK, Yuen KY, Lin X, Cai JJ. Signature gene expression reveals novel clues to the molecular mechanisms of dimorphic transition in Penicillium marneffei. PLoS Genet. 2014 Oct 16;10(10):e1004662. doi: 10.1371/journal.pgen.1004662. PMID: 25330172.
  9. Wang L, Tian X, Gyawali R, Upadhyay S, Foyle D, Wang G, Cai JJ, Lin X. Morphotype transition and sexual reproduction are genetically associated in a ubiquitous environmental pathogen. PLoS Pathog. 2014 Jun 5;10(6):e1004185. doi: 10.1371/journal.ppat.1004185. PMID: 24901238.
  10. Yang E, Wang G, Woo PC, Lau SK, Chow WN, Chong KT, Tse H, Kao RY, Chan CM, Che X, Yuen KY, Cai JJ. Unraveling the molecular basis of temperature-dependent genetic regulation in Penicillium marneffei. Eukaryot Cell. 2013 Sep;12(9):1214-24. doi: 10.1128/EC.00159-13. PMID: 23851338.
  11. Woo PC, Lau SK, Liu B, Cai JJ, Chong KT, Tse H, Kao RY, Chan CM, Chow WN, Yuen KY. Draft genome sequence of Penicillium marneffei strain PM1. Eukaryot Cell. 2011 Dec;10(12):1740-1. doi: 10.1128/EC.05255-11. PMID: 22131218.
  12. Woo PC, Tam EW, Chong KT, Cai JJ, Tung ET, Ngan AH, Lau SK, Yuen KY. High diversity of polyketide synthase genes and the melanin biosynthesis gene cluster in Penicillium marneffei. FEBS J. 2010 Sep;277(18):3750-8. doi: 10.1111/j.1742-4658.2010.07776.x. PMID: 20718860.
  13. Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, Yuen KY. The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats. PLoS Genet. 2009 Mar;5(3):e1000416. doi: 10.1371/journal.pgen.1000416. PMID: 19283063.
  14. Woo PC, Chong KT, Tse H, Cai JJ, Lau CC, Zhou AC, Lau SK, Yuen KY. Genomic and experimental evidence for a potential sexual cycle in the pathogenic thermal dimorphic fungus Penicillium marneffei. FEBS Lett. 2006 Jun 12;580(14):3409-16. doi: 10.1016/j.febslet.2006.05.014. PMID: 16714021.
  15. Woo PC, Lau SK, Chu CM, Chan KH, Tsoi HW, Huang Y, Wong BH, Poon RW, Cai JJ, Luk WK, Poon LL, Wong SS, Guan Y, Peiris JS, Yuen KY. Characterization and complete genome sequence of a novel coronavirus, coronavirus HKU1, from patients with pneumonia. J Virol. 2005 Jan;79(2):884-95. doi: 10.1128/JVI.79.2.884-895.2005. PMID: 15613317.
  16. Woo PC, Zhen H, Cai JJ, Yu J, Lau SK, Wang J, Teng JL, Wong SS, Tse RH, Chen R, Yang H, Liu B, Yuen KY. The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts. FEBS Lett. 2003 Dec 18;555(3):469-77. doi: 10.1016/s0014-5793(03)01307-3. PMID: 14675758.
  17. Yuen KY, Pascal G, Wong SS, Glaser P, Woo PC, Kunst F, Cai JJ, Cheung EY, Médigue C, Danchin A. Exploring the Penicillium marneffei genome. Arch Microbiol. 2003 May;179(5):339-53. doi: 10.1007/s00203-003-0533-8. PMID: 12640520.

Disease and Aging 10

  1. Kluaiphanngam S, Saravanan IP, Kolla VSV, Krothapalli S, Azzi S, Miller E, Mohr O, Arosh JA, Lamon TK, Cai J, Allon M, Banu SK. Mechanisms of Hexavalent Chromium-Induced Reproductive Toxicity: A Focus on the Ovary and Placenta. Biol Reprod. 2026 Sep 10:ioag199. doi: 10.1093/biolre/ioag199. PMID: 42720308.
  2. Yang W, Kim DM, Jiang W, Ai W, Pan Q, Rahman S, Cai JJ, Brashear WA, Sun Y, Guo S. Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging. Aging Cell. 2023 Oct;22(10):e13968. doi: 10.1111/acel.13968. PMID: 37602516.
  3. Chen J, Tang S, Ke S, Cai JJ, Osorio D, Golovko A, Morpurgo B, Guo S, Sun Y, Winkle M, Calin GA, Tian Y. Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice. Redox Biol. 2022 Aug;54:102377. doi: 10.1016/j.redox.2022.102377. PMID: 35763934.
  4. Huang G, Osorio D, Guan J, Ji G, Cai JJ. Overdispersed gene expression in schizophrenia. NPJ Schizophr. 2020 Apr 3;6(1):9. doi: 10.1038/s41537-020-0097-5. PMID: 32245959.
  5. Guan J, Cai JJ, Ji G, Sham PC. Commonality in dysregulated expression of gene sets in cortical brains of individuals with autism, schizophrenia, and bipolar disorder. Transl Psychiatry. 2019 May 24;9(1):152. doi: 10.1038/s41398-019-0488-4. PMID: 31127088.
  6. Brinkmeyer-Langford C, Chu C, Balog-Alvarez C, Yu X, Cai JJ, Nabity M, Kornegay JN. Expression profiling of disease progression in canine model of Duchenne muscular dystrophy. PLoS One. 2018 Mar 19;13(3):e0194485. doi: 10.1371/journal.pone.0194485. PMID: 29554127.
  7. Brinkmeyer-Langford CL, Guan J, Ji G, Cai JJ. Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. Front Aging Neurosci. 2016 Aug 3;8:183. doi: 10.3389/fnagi.2016.00183. PMID: 27536236.
  8. Guan J, Yang E, Yang J, Zeng Y, Ji G, Cai JJ. Exploiting aberrant mRNA expression in autism for gene discovery and diagnosis. Hum Genet. 2016 Jul;135(7):797-811. doi: 10.1007/s00439-016-1673-7. PMID: 27131873.
  9. Wang G, Yang E, Smith KJ, Zeng Y, Ji G, Connon R, Fangue NA, Cai JJ. Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension. Front Genet. 2014 Sep 11;5:312. doi: 10.3389/fgene.2014.00312. PMID: 25309574.
  10. Cai JJ, Borenstein E, Petrov DA. Broker genes in human disease. Genome Biol Evol. 2010;2:815-25. doi: 10.1093/gbe/evq064. PMID: 20937604.

Cancer 7

  1. Carter K, Ogunlusi O, Sarkar M, Akanbi S, Nguyen C, Nekkanti M, Agarwal A, Fails D, Nawaratna GI, Klemashevich C, Cai J, Boland DJ, Sarkar TR. A stromal metabolic program suppresses NK-cell immunity to drive tumor progression in HER2-low breast cancer. bioRxiv [Preprint]. 2026/09/14; 2026.09.07.749862-. doi:10.64898/2026.09.07.749862.
  2. Das JK, Qin QM, Singh S, James Thomas C, Gupta S, Chatterjee A, Sunnagatta Nagaraja S, Guo F, Delgado K, Kumar A, Ryu E, Flannagan B, Agca C, Agca Y, Powell N, Barry E, Kahl-McDonagh MM, Chaki SP, Mendes Ribeiro Correa A, Niyakan S, Han SI, Cai JJ, Qian X, Kobayashi KS, Han A, Jayaraman A, Ficht TA, Adams LG, Alaniz RC, Yee C, Song J, de Figueiredo P. A Synthetic Microbial Therapy Rewires Antitumor Immunity Across Multiple Cancer Types. bioRxiv [Preprint]. 2026 Jul 22:2026. doi: 10.64898/2026.07.19.735925. PMID: 42539212.
  3. Safe S, Cai JJ, Chapkin RS. A Commentary on Dual Orphan Nuclear Receptor 4A1 (NR4A1) and NR4A2 Ligands. J Cell Immunol. 2026;8(1):30-36. doi: 10.33696/immunology.8.251. PMID: 42358741.
  4. Ogunlusi O, Sarkar M, Carter K, Chakrabarti A, Boland DJ, Nguyen T, Sampson J, Nguyen C, Fails D, Jones-Hall Y, Fu L, Wright G, Kim DM, Cai JJ, Mallick B, Keene AC, Jones JR, Roy Sarkar T. LILRB4 regulates circadian disruption-induced mammary tumorigenesis via non-canonical WNT signaling pathway. Oncogene. 2025 Oct 16. doi: 10.1038/s41388-025-03597-5. PMID: 41102383.
  5. Zhang L, Gatlin V, Gupta S, Salinas ML, Romero S, Cai JJ, Chapkin RS, Safe S. Expression of Prooncogenic Nuclear Receptor 4A (NR4A)-Regulated Genes β1-Integrin and G9a Inhibited by Dual NR4A1/2 Ligands. Int J Mol Sci. 2025 Apr 21;26(8):3909. doi: 10.3390/ijms26083909. PMID: 40332813.
  6. Safe S, Han H, Jayaraman A, Davidson LA, Allred CD, Ivanov I, Yang Y, Cai JJ, Chapkin RS. Aryl Hydrocarbon Receptor (AhR) Signaling in Colonic Cells and Tumors. Receptors (Basel). 2023 Mar;2(1):93-99. doi: 10.3390/receptors2010005. PMID: 38651159.
  7. Ni N, Fang X, Mullens DA, Cai JJ, Ivanov I, Bartholin L, Li Q. Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model. Cancers (Basel). 2022 Apr 27;14(9):2184. doi: 10.3390/cancers14092184. PMID: 35565312.

Metabolism and Nutrition 10

  1. Salinas ML, Fuentes NR, Wang X, Alexander Morris ER, Fan YY, Edwards ME, Yan X, Callaway ES, Landrock KK, Cai JJ, Chapkin RS. High-fat diet remodels plasma membrane rigidity to potentiate colonocyte stemness in mice. Cell Mol Gastroenterol Hepatol. 2026 Sep 3:101878. doi: 10.1016/j.jcmgh.2026.101878. PMID: 42692358.
  2. Mulakala BK, Salinas ML, Davidson LA, Romero S, Read QD, Fox R, LeRoith T, Cai JJ, Chapkin RS, Donovan SM, Yeruva L. Bifidobacteria infantis and human milk oligosaccharides have independent and synergistic effects on immune response and amino acid metabolism in germ-free mouse models. mSystems. 2026 Jun 15:e0039226. doi: 10.1128/msystems.00392-26. PMID: 42294916.
  3. Hailemariam A, Upadhyay S, Oany AR, Tsui WNT, Srivastava V, Sivaram G, Churion K, Chapkin RS, Davidson LA, Eitan S, Cai JJ, Norton R, Safe S. Brewed Coffee and Its Components Act Through Orphan Nuclear Receptor 4A1 (NR4A1). Nutrients. 2026 Mar 10;18(6):877. doi: 10.3390/nu18060877. PMID: 41901052.
  4. Fan YY, Salinas ML, Mullens DA, Davidson LA, Goldsby JS, Ivanov IV, Jayaraman A, Cai JJ, Levy L, Hullar MA, Navarro SL, Lampe JW, Chapkin RS. Pesco-vegetarian food components promote colonocyte ferroptosis in preclinical mouse models and a randomized crossover trial in healthy human adults. J Nutr. 2025 Dec 27:101287. doi: 10.1016/j.tjnut.2025.101287. PMID: 41461276.
  5. Guo X, Li H, Zhu B, Wang X, Xu Q, Aquino E, Koo M, Li Q, Cai J, Glaser S, Wu C. HFD feeding for seven months abolishes STING disruption-driven but not female sex-based protection against hepatic steatosis and inflammation in mice. J Nutr Biochem. 2025 Jan;135:109770. doi: 10.1016/j.jnutbio.2024.109770. PMID: 39284534.
  6. Li H, Zheng J, Xu Q, Yang Y, Zhou J, Guo X, Cai Y, Cai JJ, Xie L, Awika J, Han X, Li Q, Kennedy L, Francis H, Glaser S, Huo Y, Alpini G, Wu C. Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation. Gastroenterology. 2023 Jan;164(1):134-146. doi: 10.1053/j.gastro.2022.09.027. PMID: 36181835.
  7. Xu H, Zhu B, Li H, Jiang B, Wang Y, Yin Q, Cai J, Glaser S, Francis H, Alpini G, Wu C. Adipocyte inducible 6-phosphofructo-2-kinase suppresses adipose tissue inflammation and promotes macrophage anti-inflammatory activation. J Nutr Biochem. 2021 Sep;95:108764. doi: 10.1016/j.jnutbio.2021.108764. PMID: 33964465.
  8. Zhu B, Guo X, Xu H, Jiang B, Li H, Wang Y, Yin Q, Zhou T, Cai JJ, Glaser S, Meng F, Francis H, Alpini G, Wu C. Adipose tissue inflammation and systemic insulin resistance in mice with diet-induced obesity is possibly associated with disruption of PFKFB3 in hematopoietic cells. Lab Invest. 2021 Mar;101(3):328-340. doi: 10.1038/s41374-020-00523-z. PMID: 33462362.
  9. Chen J, Ke S, Zhong L, Wu J, Tseng A, Morpurgo B, Golovko A, Wang G, Cai JJ, Ma X, Li D, Tian Y. Long noncoding RNA MALAT1 regulates generation of reactive oxygen species and the insulin responses in male mice. Biochem Pharmacol. 2018 Jun;152:94-103. doi: 10.1016/j.bcp.2018.03.019. PMID: 29577871.
  10. Chang CL, Cai JJ, Cheng PJ, Chueh HY, Hsu SY. Identification of metabolic modifiers that underlie phenotypic variations in energy-balance regulation. Diabetes. 2011 Mar;60(3):726-34. doi: 10.2337/db10-1331. PMID: 21300845.

Neuroscience 9

  1. Chennakesavan K, Samikkannu M, Gupta S, Tayo OI, Acharya A, Cai JJ, Byrareddy SN, Samikkannu T. Molecular Signatures of HIV-Induced Neuroinflammation and Neurodegeneration in Human Cerebral Organoids: Identification of Therapeutic Targets for NeuroHIV. Adv Sci (Weinh). 2026 Oct 18:e77954. doi: 10.1002/advs.77954. PMID: 42893406.
  2. Mohan N, Ramakrishnan S, Sun X, Sun Y, Connors T, Chai V, Piermarini E, Baas PW, Cai J, Liu M, Qiang L. Modeling spastic paraplegia 4 with corticospinal motor neuron-enriched cortical organoids reveals genotype-phenotype and HDAC6-targetable pathology. Cell Rep. 2026 Feb 24;45(3):117036. doi: 10.1016/j.celrep.2026.117036. PMID: 41739645.
  3. Madhu LN, Kodali M, Rao S, Attaluri S, Upadhya R, Shankar G, Shuai B, Somayaji Y, Ganesh SV, Kumar VS, James JE, Shetty PA, LeMaire A, Rao X, Cai JJ, Shetty AK. Intranasal Human NSC-Derived EVs Therapy Can Restrain Inflammatory Microglial Transcriptome, and NLRP3 and cGAS-STING Signalling, in Aged Hippocampus. J Extracell Vesicles. 2026 Feb;15(2):e70232. doi: 10.1002/jev2.70232. PMID: 41656949.
  4. Chennakesavan K, Samikkannu M, Gupta S, Tayo OI, Acharya A, Cai JJ, Byrareddy SN, Samikkannu T. STAT1-Mediated Regulation of IL-17A/CEBPB/NF-κB Axis in HIV-1 Infected Human Cerebral Organoids Reveals Therapeutic Targets for Neuroprotection. bioRxiv [Preprint]. 2025/12/31; 2025.12.30.697044-. doi:10.64898/2025.12.30.697044.
  5. Rao S, Madhu LN, Babu RS, Shankar G, Kotian S, Nagarajan A, Upadhya R, Narvekar E, Cai JJ, Shetty AK. Extracellular vesicles from hiPSC-derived NSCs protect human neurons against Aβ-42 oligomers induced neurodegeneration, mitochondrial dysfunction and tau phosphorylation. Stem Cell Res Ther. 2025 Apr 18;16(1):191. doi: 10.1186/s13287-025-04324-3. PMID: 40251643.
  6. Madhu LN, Kodali M, Upadhya R, Rao S, Somayaji Y, Attaluri S, Shuai B, Kirmani M, Gupta S, Maness N, Rao X, Cai JJ, Shetty AK. Extracellular vesicles from human-induced pluripotent stem cell-derived neural stem cells alleviate proinflammatory cascades within disease-associated microglia in Alzheimer's disease. J Extracell Vesicles. 2024 Nov;13(11):e12519. doi: 10.1002/jev2.12519. PMID: 39499013.
  7. Bazan HA, Bhattacharjee S, Reid MM, Jun B, Polk C, Strain M, St Pierre LA, Desai N, Daly PW, Cucinello-Ragland JA, Edwards S, Recio J, Alvarez-Builla J, Cai JJ, Bazan NG. Transcriptomic signature, bioactivity and safety of a non-hepatotoxic analgesic generating AM404 in the midbrain PAG region. Sci Rep. 2024 May 15;14(1):11103. doi: 10.1038/s41598-024-61791-z. PMID: 38750093.
  8. Doke M, McLaughlin JP, Cai JJ, Pendyala G, Kashanchi F, Khan MA, Samikkannu T. HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis. Mol Ther Nucleic Acids. 2022 Jul 6;29:243-258. doi: 10.1016/j.omtn.2022.07.001. PMID: 35892093.
  9. Pinson MR, Chung DD, Mahnke AH, Salem NA, Osorio D, Nair V, Payne EA, Del Real JJ, Cai JJ, Miranda RC. Gag-like proteins: Novel mediators of prenatal alcohol exposure in neural development. Alcohol Clin Exp Res. 2022 Apr;46(4):556-569. doi: 10.1111/acer.14796. PMID: 35187673.

Development and Regeneration 7

  1. Yu L, Yan M, Scaturro KZ, Qureshi O, Lin YL, Bartelle BB, Smith CA, Hurtado DO, Cai JJ, Dawson LA, Brunauer R, Suva LJ, Han M, Dolan CP, Muneoka K. Digit regeneration in mice is stimulated by sequential treatment with FGF2 and BMP2. Nat Commun. 2026 Apr 17. doi: 10.1038/s41467-026-72066-8. PMID: 41997949.
  2. Yu L, Yan M, Wolff SM, Knue JD, Smith HM, Dolan CP, Muneoka K, Romero S, Cai JJ, Yun C, Boland DJ, Brunauer R, Dawson LA. FGF8 induces bone and joint regeneration at digit amputation wounds in neonate mice. Bone. 2025 Oct 2:117663. doi: 10.1016/j.bone.2025.117663. PMID: 41046114.
  3. Wang X, Dong C, Lamichhane B, Thapa S, Zhang Y, Gupta S, Cai JJ. Din Oversees Mesenchymal Stem Cell Homeostasis in Mouse Incisors. Res Sq [Preprint]. 2025 May 14:rs. doi: 10.21203/rs.3.rs-6568233/v1. PMID: 40470223.
  4. Tanaka J, Kondo Y, Sakurai M, Sawada A, Hwang Y, Miura A, Shimamura Y, Shimizu D, Hu Y, Sarmah H, Ninish Z, Cai J, Wu J, Mori M. Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells. bioRxiv [Preprint]. 2024 Jun 3:2024. doi: 10.1101/2024.06.02.597057. PMID: 38895424.
  5. Ferrer P, Upadhyay S, Cai JJ, Clement TM. Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis. bioRxiv [Preprint]. 2024 Feb 29:2024. doi: 10.1101/2024.02.29.582797. PMID: 38464253.
  6. Shimamura Y, Tanaka J, Kakiuchi M, Sarmah H, Miura A, Hwang Y, Sawada A, Ninish Z, Yamada K, Cai JJ, Mori M. A developmental program that regulates mammalian organ size offsets evolutionary distance. bioRxiv [Preprint]. 2022/10/21; 2022.10.19.512107-. doi:10.1101/2022.10.19.512107.
  7. Yu L, Lin YL, Yan M, Li T, Wu EY, Zimmel K, Qureshi O, Falck A, Sherman KM, Huggins SS, Hurtado DO, Suva LJ, Gaddy D, Cai J, Brunauer R, Dawson LA, Muneoka K. Hyaline cartilage differentiation of fibroblasts in regeneration and regenerative medicine. Development. 2022 Jan 15;149(2):dev200249. doi: 10.1242/dev.200249. PMID: 35005773.

Other Collaborations 2

  1. Salem GM, Chen FC, Cai JJ, Chao DY. Factors determining the outcomes of immune imprinting after repeated orthoflavivirus infections. Front Immunol. 2025 Jul 16;16:1560851. doi: 10.3389/fimmu.2025.1560851. PMID: 40740782.
  2. Yan X, Li C, Liu K, Zhang T, Xu Q, Li X, Zhu J, Wang Z, Yusuf A, Cao S, Peng X, Cai JJ, Zhang X. Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis. Nat Plants. 2024 Jul;10(7):1126-1143. doi: 10.1038/s41477-024-01725-9. PMID: 38918606.

Book Chapters

  • Cai JJ* (2011) Evolutionary bioinformatics with a scientific computing environment. Systems and Computational Biology - Bioinformatics and Computational Modeling Ning-Sun Yang (Ed.), 51-74, ISBN 978-953-307-875-5, InTech. [PDF][Link] [DOI]
  • Cai JJ*, Osorio D (2021) Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. Lecture Notes in Bioinformatics (LNBI): Computational Advances in Bio and Medical Sciences. Chapter 9, DOI: 10.1007/978-3-030-79290-9_8, Springer Nature Switzerland AG. [PDF][Link]