691 citations · 1k across the 11 of their papers we have counts for
13 papers
Flash Invariant Point Attention
Andrew Liu, Axel Elaldi, Nicholas T Franklin +4
Invariant Point Attention (IPA) is a key algorithm for geometry-aware modeling in structural biology, central to many protein and RNA models. However, its quadratic complexity limi…
Physics Approaches to the Spatial Distribution of Immune Cells in Tumors
Clare C. Yu, Juliana C. Wortman, Ting-Fang He +12
The goal of immunotherapy is to enhance the ability of the immune system to kill cancer cells. Immunotherapy is more effective and, in general, the prognosis is better, when more i…
Learning quantitative sequence-function relationships from massively parallel experiments
Gurinder S. Atwal, Justin B. Kinney
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochem…
Equitability, mutual information, and the maximal information coefficient
Justin B. Kinney, Gurinder S. Atwal
Reshef et al. recently proposed a new statistical measure, the "maximal information coefficient" (MIC), for quantifying arbitrary dependencies between pairs of stochastic quantitie…
Kerfuffle: a web tool for multi-species gene colocalization analysis
Robert Aboukhalil, Bernard Fendler, Gurinder S. Atwal
The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally sim…
Utilizing RNA-Seq Data for Cancer Network Inference
Ying Cai, Bernard Fendler, Gurinder S. Atwal
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next g…