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Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types.

Published in PLoS computational biology

Protein kinases play a vital role in a wide range of cellular processes, and compounds that inhibit kinase activity emerging as a primary focus for targeted therapy development, especially in cancer. Consequently, efforts to characterize the behavior of kinases in response to inhibitor treatment, as well as downstream cellular responses, have been ...

Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms.

Published in PLoS computational biology

Epigenetic regulatory mechanisms allow multicellular organisms to develop distinct specialized cell identities despite having the same total genome. Cell-fate choices are based on gene expression programs and environmental cues that cells experience during embryonic development, and are usually maintained throughout the life of the organism despite...

Resonant learning in scale-free networks.

Published in PLoS computational biology

Large networks of interconnected components, such as genes or machines, can coordinate complex behavioral dynamics. One outstanding question has been to identify the design principles that allow such networks to learn new behaviors. Here, we use Boolean networks as prototypes to demonstrate how periodic activation of network hubs provides a network...

Genome-wide identification and characterization of DNA enhancers with a stacked multivariate fusion framework.

Published in PLoS computational biology

Enhancers are short non-coding DNA sequences outside of the target promoter regions that can be bound by specific proteins to increase a gene's transcriptional activity, which has a crucial role in the spatiotemporal and quantitative regulation of gene expression. However, enhancers do not have a specific sequence motifs or structures, and their sc...

Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene reg...

Published in PLoS computational biology

Quantitative stochastic models of gene regulatory networks are important tools for studying cellular regulation. Such models can be formulated at many different levels of fidelity. A practical challenge is to determine what model fidelity to use in order to get accurate and representative results. The choice is important, because models of successi...

Recalibrating probabilistic forecasts of epidemics.

Published in PLoS computational biology

Distributional forecasts are important for a wide variety of applications, including forecasting epidemics. Often, forecasts are miscalibrated, or unreliable in assigning uncertainty to future events. We present a recalibration method that can be applied to a black-box forecaster given retrospective forecasts and observations, as well as an extensi...

Ten simple rules and a template for creating workflows-as-applications.

Published in PLoS computational biology

Using smartphone-GPS data to quantify human activity in green spaces.

Published in PLoS computational biology

Cities are growing in density and coverage globally, increasing the value of green spaces for human health and well-being. Understanding the interactions between people and green spaces is also critical for biological conservation and sustainable development. However, quantifying green space use is particularly challenging. We used an activity inde...

Ten simple rules for launching an academic research career.

Published in PLoS computational biology

Ten simple rules for failing successfully in academia.

Published in PLoS computational biology

Failure is an integral part of life and by extension academia. At the same time, failure is often ignored, with potentially negative consequences both for the science and the scientists involved. This article provides several strategies for learning from and dealing with failure instead of ignoring it. Hopefully, our recommendations are widely appl...