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Articles published in
PLoS Comput Biol
    November 2026
  1. WEN H, Shen Q, Zhang S
    SpatioCAD: Context-aware graph diffusion model for pinpointing spatially variable genes in heterogeneous tissues.
    PLoS Comput Biol. 2026;22:e1014923.
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    October 2026
  2. RIUDAVETS PUIG R, O'Mahony DG, Brorson IS, Sokolova K, et al
    HiFIseek: Gene-specific enrichment of high-impact mutations in associated genomic regions.
    PLoS Comput Biol. 2026;22:e1014842.
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    September 2026
  3. HUANG ZH, Xu Z, Hu P
    Spatially guided translation from histology images to transcriptomic profiles using foundation model-driven contrastive learning.
    PLoS Comput Biol. 2026;22:e1014762.
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  4. YANG C, Liao Y, Sheng Y, Jiao F, et al
    Integrating zero-inflation correction and transcriptional kinetics for single-cell transcriptomic analysis.
    PLoS Comput Biol. 2026;22:e1014779.
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    July 2026
  5. STANCIU A, Gombos A, Agostinetto E, Vincent D, et al
    ALFAssay: A feed?forward neural network for quantitative fragmentomics?based ctDNA profiling in breast cancer.
    PLoS Comput Biol. 2026;22:e1014505.
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    May 2026
  6. LEYVA A, Akbar AR, Niazi MKK
    Predicting protein cascade expression from H&E images.
    PLoS Comput Biol. 2026;22:e1014262.
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    March 2026
  7. VEITH T, Beck RJ, Brown JS, Andor N, et al
    Inverse game theory characterizes frequency-dependent selection driven by karyotypic diversity in triple negative breast cancer.
    PLoS Comput Biol. 2026;22:e1013897.
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  8. HUO X, Duan X, Huang X, Xue L, et al
    An integrative analysis reveals the mechanism of plastic stabilizers inducing breast cancer.
    PLoS Comput Biol. 2026;22:e1014025.
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  9. SU JC, Lee CL, Yang FW, Chen YC, et al
    Network-based exploration of 4-(phenylsulfonyl)morpholine molecules for metastatic triple-negative breast cancer suppression.
    PLoS Comput Biol. 2026;22:e1014132.
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  10. DAVYDZENKA K, Caravagna G, Sanguinetti G
    Extending differential gene expression testing to handle genome aneuploidy in cancer.
    PLoS Comput Biol. 2026;22:e1014134.
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    February 2026
  11. WANG Y, Zang C, Li Z, Guo CC, et al
    A comparative study of statistical methods for identifying differentially expressed genes in spatial transcriptomics.
    PLoS Comput Biol. 2026;22:e1013956.
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    January 2026
  12. JI T, Yang B, Wang M, Ji H, et al
    AugGCL: Multimodal graph learning for spatial transcriptomics analysis with enhanced gene and morphological data.
    PLoS Comput Biol. 2026;22:e1013912.
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    December 2025
  13. HAN C, Song Z, Xu Z, Chen J, et al
    MAGNET: Multi-view graph autoencoder with cell-gene attention for cell interaction network reconstruction from spatial transcriptomics.
    PLoS Comput Biol. 2025;21:e1013810.
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    November 2025
  14. FAHMI NA, Cheng S, Overstreet J, Song Q, et al
    IPScan: Detecting novel intronic PolyAdenylation events with RNA-seq data.
    PLoS Comput Biol. 2025;21:e1013668.
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    October 2025
  15. MATACHE A, Lima-Junior JR, Kuznetsov M, Urbaniak K, et al
    Ligand discrimination in immune cells: Signal processing insights into immune dysfunction in ER+ breast cancer.
    PLoS Comput Biol. 2025;21:e1013615.
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    September 2025
  16. NOUIRA A, Azencott CA
    Sparse multitask group Lasso for genome-wide association studies.
    PLoS Comput Biol. 2025;21:e1012734.
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    August 2025
  17. YAVUZ BR, Sahin U, Jang H, Nussinov R, et al
    Mutations in tumor signaling, metastases, and synthetic lethality establish distinct patterns.
    PLoS Comput Biol. 2025;21:e1013351.
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    May 2025
  18. HOPFL S, Ozverin M, Nowack H, Tamas R, et al
    Integrated mathematical and experimental modeling uncovers enhanced EMT plasticity upon loss of the DLC1 tumor suppressor.
    PLoS Comput Biol. 2025;21:e1013076.
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    April 2025
  19. NOURBAKHSH M, Zheng Y, Noor H, Chen H, et al
    Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight.
    PLoS Comput Biol. 2025;21:e1012999.
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    February 2025
  20. SAKAI SA, Nomura R, Nagasawa S, Chi S, et al
    SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data.
    PLoS Comput Biol. 2025;21:e1012854.
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  21. ZHAN X, Xu Q, Zheng Y, Lu G, et al
    Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction.
    PLoS Comput Biol. 2025;21:e1012803.
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    January 2025
  22. SHI X, Wang X, Jin L, Halakivi-Clarke L, et al
    Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data.
    PLoS Comput Biol. 2025;21:e1012750.
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    November 2024
  23. HUANG HY, Zhang FW, Yu J, Xiao YH, et al
    A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers.
    PLoS Comput Biol. 2024;20:e1012284.
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    October 2024
  24. CHEN L, Huang ZH, Sun Y, Domaratzki M, et al
    Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer.
    PLoS Comput Biol. 2024;20:e1012490.
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    June 2024
  25. XIE X, Sinha S
    Quantitative estimates of the regulatory influence of long non-coding RNAs on global gene expression variation using TCGA breast cancer transcriptomic data.
    PLoS Comput Biol. 2024;20:e1012103.
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  26. VANDERDOES J, Marceaux C, Yokote K, Asselin-Labat ML, et al
    Using random forests to uncover the predictive power of distance-varying cell interactions in tumor microenvironments.
    PLoS Comput Biol. 2024;20:e1011361.
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  27. DIMITRIOU NM, Flores-Torres S, Kyriakidou M, Kinsella JM, et al
    Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites.
    PLoS Comput Biol. 2024;20:e1012112.
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  28. PERRONE MC, Lerner MG, Dunworth M, Ewald AJ, et al
    Prioritizing drug targets by perturbing biological network response functions.
    PLoS Comput Biol. 2024;20:e1012195.
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    May 2024
  29. BENZEKRY S, Mastri M, Nicolo C, Ebos JML, et al
    Machine-learning and mechanistic modeling of metastatic breast cancer after neoadjuvant treatment.
    PLoS Comput Biol. 2024;20:e1012088.
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