raganelė mark raganelė
Anchor papers

Publications and anchor papers

The composed body is anchored to peer-reviewed papers. Each entry below is a paper whose mathematical structure — equations, parameters, calibration anchors — is reproduced inside one of our subsystem modules. This is not a literature survey; it is the source list the model is built from.

Cardiovascular

  • O'Hara T, Virág L, Varró A, Rudy Y. Simulation of the undiseased human cardiac ventricular action potential. PLoS Comput Biol 2011;7:e1002061.
    Role · Cardiac electrophysiology (41-state action potential)
  • Dutta S, Chang KC, Beattie KA et al. Optimization of an in silico cardiac cell model for proarrhythmia risk assessment. Front Physiol 2017;8:616.
    Role · Drug-induced TdP screening
  • Roden DM. Drug-induced prolongation of the QT interval. NEJM 2004;350:1013–1022.
    Role · TdP risk framework
  • Guyton AC. Blood pressure control — special role of the kidneys and body fluids. Science 1991;252:1813–1816.
    Role · Long-term BP regulation, RAAS coupling
  • Cohen A, Myerscough MR, Thompson RS. Athero-protective effects of high density lipoproteins (HDL): an ODE model. Bull Math Biol 2014;76:1117–1142.
    Role · Atherosclerosis foam-cell dynamics
  • Snelder N, Heinig R et al. Population PK and exposure-response analyses of finerenone. Diabetes Obes Metab 2024;26.
    Role · Finerenone PK/PD; FIGARO-DKD / FIDELIO-DKD

Oncology

  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011;144:646–674.
    Role · 14-hallmark framework anchor
  • Hanahan D. Hallmarks of cancer: new dimensions. Cancer Discov 2022;12:31–46.
    Role · Emerging hallmarks — plasticity, senescence, microbiome, polyploidy
  • Ahn MJ, Cho BC, Felip E et al. Tarlatamab for previously treated SCLC. NEJM 2023;389:2063–2075.
    Role · DeLLphi-301 schedule replication
  • Folkman J. Tumor angiogenesis: therapeutic implications. NEJM 1971;285:1182–1186.
    Role · VEGF-driven angiogenesis substrate
  • Friberg LE, Henningsson A, Maas H et al. Model of chemotherapy-induced myelosuppression. J Clin Oncol 2002;20:4713–4721.
    Role · Marrow-toxicity constraint across all cytotoxic schedules

Bone, metabolic, endocrine

  • Lemaire V, Tobin FL, Greller LD et al. Modeling the interactions between osteoblast and osteoclast activities in bone remodeling. J Theor Biol 2004;229:293–309.
    Role · Bone-remodelling baseline
  • Pivonka P, Zimak J, Smith DW et al. Model structure and control of bone remodeling. Bone 2008;43:249–263.
    Role · TGF-β extension; RANKL/OPG balance
  • Graham JM, Ayati BP et al. The role of osteocytes in targeted bone remodeling. PLoS ONE 2013;8:e63884.
    Role · Wnt/sclerostin mechanical-load coupling

Immune / infectious

  • Mulangu S, Dodd LE, Davey RT et al. A randomized, controlled trial of Ebola virus disease therapeutics. NEJM 2019;381:2293–2303.
    Role · PALM trial — antibody therapy timing replication
  • Mertz GJ, Miedzinski L, Goade D et al. Placebo-controlled trial of IV ribavirin for hantavirus cardiopulmonary syndrome. Clin Infect Dis 2004;39:1307–1313.
    Role · HPS — late-treatment null
  • Safronetz D, Haddock E, Feldmann F et al. PNAS 2011;108:13166–13171.
    Role · HPS — early-treatment positive (Safronetz hamster study)
  • Bauer M, Reinhart K et al. Sepsis mathematical modeling literature 2006–2008.
    Role · Sepsis cascade kernel anchor
  • Moormann AM et al. Exposure to holoendemic malaria results in suppression of EBV-specific T-cell surveillance. J Infect Dis 2007;195:799–808.
    Role · Endemic Burkitt lymphoma — chronic-perturbation mechanism

CNS

  • van Dyck CH, Swanson CJ, Aisen P et al. Lecanemab in early Alzheimer's disease. NEJM 2023;388:9–21.
    Role · Clarity-AD primary endpoint reproduction
  • Sims JR, Zimmer JA, Evans CD et al. Donanemab in early symptomatic Alzheimer's disease. JAMA 2023;330:512–527.
    Role · TRAILBLAZER-ALZ-2 primary endpoint reproduction
  • Westerhout J, Smeets J, Danhof M, de Lange ECM. BBB PK modelling framework. J Pharmacokinet Pharmacodyn 2014.
    Role · Blood-brain-barrier drug transport

PK/PD framework

  • Allen RJ, Rieger TR, Musante CJ. Efficient generation and selection of virtual populations in QSP models. CPT Pharmacomet Syst Pharmacol 2016;5:140–146.
    Role · Virtual-cohort generation across every trial replication
  • Wilkinson GR. Drug metabolism and variability among patients in drug response. NEJM 2005;352:2211–2221.
    Role · CYP450 substrate-competition framework
  • Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics, 5th ed. LWW 2019.
    Role · Standard PK reference (absorption, distribution, clearance)
  • Bliss CI. The toxicity of poisons applied jointly. Ann Appl Biol 1939;26:585.
    Role · Combination null baseline (Bliss independence)
  • Segel IH. Enzyme Kinetics. Wiley 1975.
    Role · Competitive inhibition kinetics for DDI

We do not claim authorship of these papers. We reproduce their structure inside a composed body so the whole organism runs as one program. Where our extension introduces a new mechanism, equation, or calibration, that is documented in the corresponding case study.