1.6k citations · 3.5k across the 9 of their papers we have counts for
9 papers
Inference of cell dynamics on perturbation data using adjoint sensitivity
Weiqi Ji, Bo Yuan, Ciyue Shen +3
Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable mode…
Quantification of the effect of mutations using a global probability model of natural sequence variation
Thomas A. Hopf, John B. Ingraham, Frank J. Poelwijk +3
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information…
3D RNA and functional interactions from evolutionary couplings
Caleb Weinreb, Adam J. Riesselman, John B. Ingraham +3
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence…
Graph Curvature and the Robustness of Cancer Networks
Allen Tannenbaum, Chris Sander, Liangjia Zhu +5
The importance of studying properties of networks is manifest in diverse fields ranging from biology, engineering, physics, chemistry, neuroscience, and medicine. The functionality…
Sequence co-evolution gives 3D contacts and structures of protein complexes
Thomas A. Hopf, Charlotta P. I. Schärfe, João P. G. L. M. Rodrigues +4
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provide…
Perturbation Biology: inferring signaling networks in cellular systems
Evan J. Molinelli, Anil Korkut, Weiqing Wang +13
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combi…