Inverse statistical problems: from the inverse Ising problem to data science

HC Nguyen, R Zecchina, J Berg - Advances in Physics, 2017 - Taylor & Francis
Inverse problems in statistical physics are motivated by the challenges of 'big data'in
different fields, in particular high-throughput experiments in biology. In inverse problems, the …

Predicting evolution

M Lässig, V Mustonen, AM Walczak - Nature ecology & evolution, 2017 - nature.com
The face of evolutionary biology is changing: from reconstructing and analysing the past to
predicting future evolutionary processes. Recent developments include prediction of …

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

M Łuksza, N Riaz, V Makarov, VP Balachandran… - Nature, 2017 - nature.com
Checkpoint blockade immunotherapies enable the host immune system to recognize and
destroy tumour cells. Their clinical activity has been correlated with activated T-cell …

Evolutionary determinants of cancer

M Greaves - Cancer discovery, 2015 - aacrjournals.org
Our understanding of cancer is being transformed by exploring clonal diversity, drug
resistance, and causation within an evolutionary framework. The therapeutic resilience of …

Towards multidrug adaptive therapy

J West, L You, J Zhang, RA Gatenby, JS Brown… - Cancer …, 2020 - aacrjournals.org
A new ecologically inspired paradigm in cancer treatment known as “adaptive therapy”
capitalizes on competitive interactions between drug-sensitive and drug-resistant subclones …

Computational approaches to modelling and optimizing cancer treatment

TO McDonald, YC Cheng, C Graser, PB Nicol… - Nature Reviews …, 2023 - nature.com
Computational models can be applied to optimize treatment schedules and model treatment
responses in cancer therapy. In this Review, we provide an overview of such computational …

Steering and controlling evolution—from bioengineering to fighting pathogens

M Lässig, V Mustonen, A Nourmohammad - Nature Reviews Genetics, 2023 - nature.com
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells
towards a desired outcome. Applications range from engineering biomolecules and …

Multidrug cancer therapy in metastatic castrate-resistant prostate cancer: an evolution-based strategy

JB West, MN Dinh, JS Brown, J Zhang… - Clinical Cancer …, 2019 - aacrjournals.org
Purpose: Integration of evolutionary dynamics into systemic therapy for metastatic cancers
can prolong tumor control compared with standard maximum tolerated dose (MTD) …

Pervasive and diverse collateral sensitivity profiles inform optimal strategies to limit antibiotic resistance

J Maltas, KB Wood - PLoS biology, 2019 - journals.plos.org
Evolved resistance to one antibiotic may be associated with" collateral" sensitivity to other
drugs. Here, we provide an extensive quantitative characterization of collateral effects in …

Deep reinforcement learning for the control of microbial co-cultures in bioreactors

NJ Treloar, AJH Fedorec, B Ingalls… - PLoS computational …, 2020 - journals.plos.org
Multi-species microbial communities are widespread in natural ecosystems. When
employed for biomanufacturing, engineered synthetic communities have shown increased …