Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms
M AlQuraishi, PK Sorger - Nature methods, 2021 - nature.com
Deep learning using neural networks relies on a class of machine-learnable models
constructed using 'differentiable programs'. These programs can combine mathematical …
constructed using 'differentiable programs'. These programs can combine mathematical …
[HTML][HTML] Sphingolipid and glycosphingolipid metabolic pathways in the era of sphingolipidomics
AH Merrill Jr - Chemical reviews, 2011 - ACS Publications
Much has been made about JLW Thudichum's colorful, and one could say clairvoyant,
naming of sphingosine “in commemoration of the many enigmas which it presented to the …
naming of sphingosine “in commemoration of the many enigmas which it presented to the …
Scientific novelty beyond the experiment
Practical experiments drive important scientific discoveries in biology, but theory‐based
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …
research studies also contribute novel—sometimes paradigm‐changing—findings. Here, we …
Boolean modeling in systems biology: an overview of methodology and applications
Mathematical modeling of biological processes provides deep insights into complex cellular
systems. While quantitative and continuous models such as differential equations have been …
systems. While quantitative and continuous models such as differential equations have been …
Toxicity testing in the 21st century: a vision and a strategy
D Krewski, D Acosta Jr, M Andersen… - Journal of Toxicology …, 2010 - Taylor & Francis
With the release of the landmark report Toxicity Testing in the 21st Century: A Vision and a
Strategy, the US National Academy of Sciences, in 2007, precipitated a major change in the …
Strategy, the US National Academy of Sciences, in 2007, precipitated a major change in the …
[HTML][HTML] Engineering a model cell for rational tuning of GPCR signaling
WM Shaw, H Yamauchi, J Mead, GOF Gowers, DJ Bell… - Cell, 2019 - cell.com
G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to
respond to specific cues in their environment. However, the relationship between stimulus …
respond to specific cues in their environment. However, the relationship between stimulus …
[图书][B] Toxicity testing in the 21st century: a vision and a strategy
National Research Council, Division on Earth… - 2007 - books.google.com
Advances in molecular biology and toxicology are paving the way for major improvements in
the evaluation of the hazards posed by the large number of chemicals found at low levels in …
the evaluation of the hazards posed by the large number of chemicals found at low levels in …
[HTML][HTML] Universally sloppy parameter sensitivities in systems biology models
RN Gutenkunst, JJ Waterfall, FP Casey… - PLoS computational …, 2007 - journals.plos.org
Quantitative computational models play an increasingly important role in modern biology.
Such models typically involve many free parameters, and assigning their values is often a …
Such models typically involve many free parameters, and assigning their values is often a …
Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy
A Jiménez-Sánchez, P Cybulska, KLV Mager… - Nature Genetics, 2020 - nature.com
In metastatic cancer, the degree of heterogeneity of the tumor microenvironment (TME) and
its molecular underpinnings remain largely unstudied. To characterize the tumor–immune …
its molecular underpinnings remain largely unstudied. To characterize the tumor–immune …
Structure-based control of complex networks with nonlinear dynamics
What can we learn about controlling a system solely from its underlying network structure?
Here we adapt a recently developed framework for control of networks governed by a broad …
Here we adapt a recently developed framework for control of networks governed by a broad …