98 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Michigan State UniversityUS7 papers
- University of California San DiegoUS5 papers
- Salgomed (United States)US4 papers
- Arizona State UniversityUS2 papers
- Discovery InstituteUS2 papers
- Rice UniversityUS2 papers
- University of HoustonUS2 papers
- Australian National UniversityAU1 paper
- Ben-Gurion University of the NegevIL1 paper
- Boğaziçi UniversityTR1 paper
- Brandenburg University of Technology Cottbus-SenftenbergDE1 paper
- Brown UniversityUS1 paper
11 papers
Humanity's Last Exam
Long Phan, Alice Gatti, Ziwen Han +1168
Benchmarks are important tools for tracking the rapid advancements in large language model (LLM) capabilities. However, benchmarks are not keeping pace in difficulty: LLMs now achi…
Ultra-Sharp Nanowire Arrays Natively Permeate, Record, and Stimulate Intracellular Activity in Neuronal and Cardiac Networks
Ren Liu, Jihwan Lee, Youngbin Tchoe +16
Intracellular access with high spatiotemporal resolution can enhance our understanding of how neurons or cardiomyocytes regulate and orchestrate network activity, and how this acti…
Determining the atomic charge of calcium ion requires the information of its coordination geometry in an EF-hand motif
Pengzhi Zhang, Jaebeom Han, Piotr Cieplak +1
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding a…
Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
Anthony Szedlak, Spencer Sims, Nicholas Smith +2
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmace…
Evolutionary and topological properties of gene modules and driver mutations in a leukemia gene regulatory network
Anthony Szedlak, Nicholas Smith, Li Liu +2
The diverse, specialized genes in today's lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is co…
Control of asymmetric Hopfield networks and application to cancer attractors
Anthony Szedlak, Giovanni Paternostro, Carlo Piermarocchi
The asymmetric Hopfield model is used to simulate signaling dynamics in gene/transcription factor networks. The model allows for a direct mapping of a gene expression pattern into…
Prediction of kinase inhibitor response using activity profiling, in-vitro screening, and elastic net regression
Trish Tran, Edison Ong, Andrew P. Hodges +2
Many kinase inhibitors have been approved as cancer therapies. Recently, libraries of kinase inhibitors have been extensively profiled, thus providing a map of the strength of acti…
Biological control networks suggest the use of biomimetic sets for combinatorial therapies
Jacob D. Feala, Jorge Cortes, Phillip M. Duxbury +3
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly unde…
Systems approaches and algorithms for discovery of combinatorial therapies
Jacob D. Feala, Jorge Cortes, Phillip M. Duxbury +3
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as…
Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue
Laurence Coquin, Jacob D. Feala, Andrew D. McCulloch +1
The fruit fly D. melanogaster is increasingly used as a model organism for studying acute hypoxia tolerance and for studying aging, but the interactions between these two factors a…
Selective control of the apoptosis signaling network in heterogeneous cell populations
Diego Calzolari, Giovanni Paternostro, Patrick L. Harrington +2
Selective control in a population is the ability to control a member of the population while leaving the other members relatively unaffected. The concept of selective control is de…