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Articles published in
PLoS Comput Biol
    May 2024
  1. 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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    April 2024
  2. LIU C, Xiao K, Yu C, Lei Y, et al
    A probabilistic knowledge graph for target identification.
    PLoS Comput Biol. 2024;20:e1011945.
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    March 2024
  3. VALEGA-MACKENZIE W, Rodriguez Messan M, Yogurtcu ON, Nukala U, et al
    Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine.
    PLoS Comput Biol. 2024;20:e1011247.
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    January 2024
  4. SUDO M, Fujimoto K
    Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation.
    PLoS Comput Biol. 2024;20:e1011693.
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  5. ZOU J, Shah O, Chiu YC, Ma T, et al
    Systems approach for congruence and selection of cancer models towards precision medicine.
    PLoS Comput Biol. 2024;20:e1011754.
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    November 2023
  6. ROMERO-ARIAS JR, Gonzalez-Castro CA, Ramirez-Santiago G
    A multiscale model of the role of microenvironmental factors in cell segregation and heterogeneity in breast cancer development.
    PLoS Comput Biol. 2023;19:e1011673.
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    August 2023
  7. MURILLO OD, Petrosyan V, LaPlante EL, Dobrolecki LE, et al
    Deconvolution of cancer cell states by the XDec-SM method.
    PLoS Comput Biol. 2023;19:e1011365.
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    May 2023
  8. WANG S, Lee D
    Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions.
    PLoS Comput Biol. 2023;19:e1011197.
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  9. FEDERICO A, Kern J, Varelas X, Monti S, et al
    Structure learning for gene regulatory networks.
    PLoS Comput Biol. 2023;19:e1011118.
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    April 2023
  10. GHANNOUM S, Fantini D, Zahoor M, Reiterer V, et al
    A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.
    PLoS Comput Biol. 2023;19:e1010995.
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  11. GUTTA C, Morhard C, Rehm M
    Applying a GAN-based classifier to improve transcriptome-based prognostication in breast cancer.
    PLoS Comput Biol. 2023;19:e1011035.
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    March 2023
  12. SUN L, Qiu Y, Ching WK, Zhao P, et al
    PCB: A pseudotemporal causality-based Bayesian approach to identify EMT-associated regulatory relationships of AS events and RBPs during breast cancer progression.
    PLoS Comput Biol. 2023;19:e1010939.
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  13. ARIAS-CALLUARI K, Colin T, Latty T, Myerscough M, et al
    Modelling daily weight variation in honey bee hives.
    PLoS Comput Biol. 2023;19:e1010880.
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  14. BENKIRANE H, Pradat Y, Michiels S, Cournede PH, et al
    CustOmics: A versatile deep-learning based strategy for multi-omics integration.
    PLoS Comput Biol. 2023;19:e1010921.
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    October 2022
  15. LALANI Z, Chu G, Hsu S, Kagawa S, et al
    CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data.
    PLoS Comput Biol. 2022;18:e1010614.
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    September 2022
  16. TERNES L, Lin JR, Chen YA, Gray JW, et al
    Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays.
    PLoS Comput Biol. 2022;18:e1010505.
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  17. MASSI MC, Dominoni L, Ieva F, Fiorito G, et al
    A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis.
    PLoS Comput Biol. 2022;18:e1009959.
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  18. SHMAROV F, Smith GR, Weatherhead SC, Reynolds NJ, et al
    Individualised computational modelling of immune mediated disease onset, flare and clearance in psoriasis.
    PLoS Comput Biol. 2022;18:e1010267.
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    June 2022
  19. JANSEN JE, Aschenbrenner D, Uhlig HH, Coles MC, et al
    A method for the inference of cytokine interaction networks.
    PLoS Comput Biol. 2022;18:e1010112.
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    April 2022
  20. LEE D, Wang D, Yang XR, Shi J, et al
    SUITOR: Selecting the number of mutational signatures through cross-validation.
    PLoS Comput Biol. 2022;18:e1009309.
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    March 2022
  21. HOWARD GR, Jost TA, Yankeelov TE, Brock A, et al
    Quantification of long-term doxorubicin response dynamics in breast cancer cell lines to direct treatment schedules.
    PLoS Comput Biol. 2022;18:e1009104.
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  22. JEUKEN GS, Tobin NP, Kall L
    Survival analysis of pathway activity as a prognostic determinant in breast cancer.
    PLoS Comput Biol. 2022;18:e1010020.
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  23. MOHAMMAD MIRZAEI N, Changizi N, Asadpoure A, Su S, et al
    Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model.
    PLoS Comput Biol. 2022;18:e1009953.
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  24. YAO K, Schaafsma E, Zhang B, Cheng C, et al
    Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer.
    PLoS Comput Biol. 2022;18:e1009495.
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    February 2022
  25. DI FILIPPO M, Pescini D, Galuzzi BG, Bonanomi M, et al
    INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation.
    PLoS Comput Biol. 2022;18:e1009337.
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    November 2021
  26. LIMA EABF, Faghihi D, Philley R, Yang J, et al
    Bayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth.
    PLoS Comput Biol. 2021;17:e1008845.
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  27. MADSSEN TS, Giskeodegard GF, Smilde AK, Westerhuis JA, et al
    Repeated measures ASCA+ for analysis of longitudinal intervention studies with multivariate outcome data.
    PLoS Comput Biol. 2021;17:e1009585.
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    September 2021
  28. LEE HG, Lee KJ
    Neighbor-enhanced diffusivity in dense, cohesive cell populations.
    PLoS Comput Biol. 2021;17:e1009447.
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  29. TRINCADO JL, Reixachs-Sole M, Perez-Granado J, Fugmann T, et al
    ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer.
    PLoS Comput Biol. 2021;17:e1009411.
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  30. GRANDE GUTIERREZ N, Alber M, Kahn AM, Burns JC, et al
    Computational modeling of blood component transport related to coronary artery thrombosis in Kawasaki disease.
    PLoS Comput Biol. 2021;17:e1009331.
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    July 2021
  31. ROZOVA VS, Anwer AG, Guller AE, Es HA, et al
    Machine learning reveals mesenchymal breast carcinoma cell adaptation in response to matrix stiffness.
    PLoS Comput Biol. 2021;17:e1009193.
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  32. ZHU K, Cai L, Cui C, de Los Toyos JR, et al
    Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts.
    PLoS Comput Biol. 2021;17:e1009228.
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    June 2021
  33. ERDEM C, Lee AV, Taylor DL, Lezon TR, et al
    Inhibition of RPS6K reveals context-dependent Akt activity in luminal breast cancer cells.
    PLoS Comput Biol. 2021;17:e1009125.
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  34. TRENTHAM-DIETZ A, Alagoz O, Chapman C, Huang X, et al
    Reflecting on 20 years of breast cancer modeling in CISNET: Recommendations for future cancer systems modeling efforts.
    PLoS Comput Biol. 2021;17:e1009020.
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  35. HELLSTERN M, Ma J, Yue K, Shojaie A, et al
    netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis.
    PLoS Comput Biol. 2021;17:e1008979.
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  36. LAL A, Liu K, Tibshirani R, Sidow A, et al
    De novo mutational signature discovery in tumor genomes using SparseSignatures.
    PLoS Comput Biol. 2021;17:e1009119.
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  37. DEUTSCH A, Nava-Sedeno JM, Syga S, Hatzikirou H, et al
    BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration.
    PLoS Comput Biol. 2021;17:e1009066.
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