User profiles for Eric J. Deeds

Eric J. Deeds

Professor, UCLA
Verified email at ucla.edu
Cited by 2315

Curvature in metabolic scaling

T Kolokotrones, V Savage, EJ Deeds, W Fontana - Nature, 2010 - nature.com
For more than three-quarters of a century it has been assumed 1 that basal metabolic rate
increases as body mass raised to some power p. However, there is no broad consensus …

Machine learning classification can reduce false positives in structure-based virtual screening

…, EJ Deeds, J Karanicolas - Proceedings of the …, 2020 - National Acad Sciences
With the recent explosion in the size of libraries available for screening, virtual screening is
positioned to assume a more prominent role in early drug discovery’s search for active …

Robust protein–protein interactions in crowded cellular environments

EJ Deeds, O Ashenberg, J Gerardin… - Proceedings of the …, 2007 - National Acad Sciences
The capacity of proteins to interact specifically with one another underlies our conceptual
understanding of how living systems function. Systems-level study of specificity in protein–…

A novel metric reveals previously unrecognized distortion in dimensionality reduction of scRNA-Seq data

…, T Hamilton, SD Aragones, JCJ Ray, EJ Deeds - Biorxiv, 2019 - biorxiv.org
High-dimensional data are becoming increasingly common in nearly all areas of science.
Developing approaches to analyze these data and understand their meaning is a pressing …

[HTML][HTML] Sizing up allometric scaling theory

VM Savage, EJ Deeds, W Fontana - PLoS computational biology, 2008 - journals.plos.org
Metabolic rate, heart rate, lifespan, and many other physiological properties vary with body
mass in systematic and interrelated ways. Present empirical data suggest that these scaling …

Fundamental trade-offs between information flow in single cells and cellular populations

…, A Smith, PK Sorger, EJ Deeds - Proceedings of the …, 2017 - National Acad Sciences
Signal transduction networks allow eukaryotic cells to make decisions based on information
about intracellular state and the environment. Biochemical noise significantly diminishes the …

[PDF][PDF] Crosstalk and the evolution of specificity in two-component signaling

MA Rowland, EJ Deeds - Biophysical Journal, 2014 - cell.com
Two-component Signaling (TCS) serves as the dominant signaling modality in bacteria. A
typical pathway includes a sensor Histidine Kinase (HK) that phosphorylates a Response …

Intrinsic limits of information transmission in biochemical signalling motifs

R Suderman, EJ Deeds - Interface Focus, 2018 - royalsocietypublishing.org
All living things have evolved to sense changes in their environment in order to respond in
adaptive ways. At the cellular level, these sensing systems generally involve receptor …

A simple physical model for scaling in protein-protein interaction networks

EJ Deeds, O Ashenberg… - Proceedings of the …, 2006 - National Acad Sciences
It has recently been demonstrated that many biological networks exhibit a “scale-free” topology,
for which the probability of observing a node with a certain number of edges (k) follows a …

Docking-based long timescale simulation of cell-size protein systems at atomic resolution

…, PJ Kundrotas, EJ Deeds - Proceedings of the …, 2022 - National Acad Sciences
Computational methodologies are increasingly addressing modeling of the whole cell at the
molecular level. Proteins and their interactions are the key component of cellular processes. …