Modelling the molecular mechanisms of aging

MT Mc Auley, AM Guimera, D Hodgson… - Bioscience …, 2017 - portlandpress.com
The aging process is driven at the cellular level by random molecular damage that slowly
accumulates with age. Although cells possess mechanisms to repair or remove damage …

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling

V Touré, Å Flobak, A Niarakis… - Briefings in …, 2021 - academic.oup.com
Causal molecular interactions represent key building blocks used in computational
modeling, where they facilitate the assembly of regulatory networks. Logical regulatory …

Problems, challenges and promises: perspectives on precision medicine

DJ Duffy - Briefings in bioinformatics, 2016 - academic.oup.com
The 'precision medicine (systems medicine)'concept promises to achieve a shift to future
healthcare systems with a more proactive and predictive approach to medicine, where the …

Sea turtle fibropapilloma tumors share genomic drivers and therapeutic vulnerabilities with human cancers

DJ Duffy, C Schnitzler, L Karpinski, R Thomas… - Communications …, 2018 - nature.com
Wildlife populations are under intense anthropogenic pressures, with the geographic range
of many species shrinking, dramatic reductions in population numbers and undisturbed …

Precision wildlife medicine: applications of the human‐centred precision medicine revolution to species conservation

J Whilde, MQ Martindale, DJ Duffy - Global Change Biology, 2017 - Wiley Online Library
The current species extinction crisis is being exacerbated by an increased rate of
emergence of epizootic disease. Human‐induced factors including habitat degradation, loss …

Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance

DJ Duffy, A Krstic, M Halasz, T Schwarzl, A Konietzny… - Genome medicine, 2017 - Springer
Background Retinoid therapy is widely employed in clinical oncology to differentiate
malignant cells into their more benign counterparts. However, certain high-risk cohorts, such …

PCA-based synthetic sensitivity coefficients for chemical reaction network in cancer

G Biddau, G Caviglia, M Piana, S Sommariva - Scientific Reports, 2024 - nature.com
Chemical reaction networks are powerful tools for modeling cell signaling and its disruptions
in diseases like cancer. Realistic chemical reaction networks involve hundreds of proteins …

[HTML][HTML] Wnt signalling is a bi-directional vulnerability of cancer cells

DJ Duffy, A Krstic, T Schwarzl, M Halasz, K Iljin, D Fey… - Oncotarget, 2016 - ncbi.nlm.nih.gov
Wnt signalling is involved in the formation, metastasis and relapse of a wide array of
cancers. However, there is ongoing debate as to whether activation or inhibition of the …

Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells

S Sommariva, G Caviglia, S Ravera, F Frassoni… - Scientific reports, 2021 - nature.com
Colorectal cancer (CRC) is one of the most deadly and commonly diagnosed tumors
worldwide. Several genes are involved in its development and progression. The most …

A fast and convergent combined Newton and gradient descent method for computing steady states of chemical reaction networks

S Berra, A La Torraca, F Benvenuto… - arXiv preprint arXiv …, 2022 - arxiv.org
In this work we present a fast, globally convergent, iterative algorithm for computing the
asymptotically stable states of nonlinear large--scale systems of quadratic autonomous …