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Free Subscription Articles published in PLoS Comput Biol Retrieve available abstracts of 41 articles: HTML format

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June 2024
1. 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.
   PubMed     Abstract available
   
   
   
2. 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.
   PubMed     Abstract available
   
   
   
3. 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.
   PubMed     Abstract available
   
   
   
4. 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.
   PubMed     Abstract available
   
   
   May 2024
5. 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.
   PubMed     Abstract available
   
   
   April 2024
6. LIU C, Xiao K, Yu C, Lei Y, et al
   A probabilistic knowledge graph for target identification.
   PLoS Comput Biol. 2024;20:e1011945.
   PubMed     Abstract available
   
   
   March 2024
7. 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.
   PubMed     Abstract available
   
   
   January 2024
8. SUDO M, Fujimoto K
   Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation.
   PLoS Comput Biol. 2024;20:e1011693.
   PubMed     Abstract available
   
   
   
9. 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.
   PubMed     Abstract available
   
   
   November 2023
10. 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.
    PubMed     Abstract available
    
    
    August 2023
11. 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.
    PubMed     Abstract available
    
    
    May 2023
12. WANG S, Lee D
    Identifying prognostic subgroups of luminal-A breast cancer using deep autoencoders and gene expressions.
    PLoS Comput Biol. 2023;19:e1011197.
    PubMed     Abstract available
    
    
    
13. FEDERICO A, Kern J, Varelas X, Monti S, et al
    Structure learning for gene regulatory networks.
    PLoS Comput Biol. 2023;19:e1011118.
    PubMed     Abstract available
    
    
    April 2023
14. 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.
    PubMed     Abstract available
    
    
    
15. 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.
    PubMed     Abstract available
    
    
    March 2023
16. 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.
    PubMed     Abstract available
    
    
    
17. 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.
    PubMed     Abstract available
    
    
    
18. 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.
    PubMed     Abstract available
    
    
    October 2022
19. 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.
    PubMed     Abstract available
    
    
    September 2022
20. 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.
    PubMed     Abstract available
    
    
    
21. 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.
    PubMed     Abstract available
    
    
    
22. 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.
    PubMed     Abstract available
    
    
    June 2022
23. 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.
    PubMed     Abstract available
    
    
    April 2022
24. 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.
    PubMed     Abstract available
    
    
    March 2022
25. 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.
    PubMed     Abstract available
    
    
    
26. JEUKEN GS, Tobin NP, Kall L
    Survival analysis of pathway activity as a prognostic determinant in breast cancer.
    PLoS Comput Biol. 2022;18:e1010020.
    PubMed     Abstract available
    
    
    
27. 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.
    PubMed     Abstract available
    
    
    
28. 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.
    PubMed     Abstract available
    
    
    February 2022
29. 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.
    PubMed     Abstract available
    
    
    November 2021
30. 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.
    PubMed     Abstract available
    
    
    
31. 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.
    PubMed     Abstract available
    
    
    September 2021
32. LEE HG, Lee KJ
    Neighbor-enhanced diffusivity in dense, cohesive cell populations.
    PLoS Comput Biol. 2021;17:e1009447.
    PubMed     Abstract available
    
    
    
33. 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.
    PubMed     Abstract available
    
    
    
34. 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.
    PubMed     Abstract available
    
    
    July 2021
35. 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.
    PubMed     Abstract available
    
    
    
36. 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.
    PubMed     Abstract available
    
    
    June 2021
37. 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.
    PubMed     Abstract available
    
    
    
38. 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.
    PubMed     Abstract available
    
    
    
39. 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.
    PubMed     Abstract available
    
    
    
40. 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.
    PubMed     Abstract available
    
    
    
41. 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.
    PubMed     Abstract available
    
    

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