14.3k citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Columbia UniversityUS16 papers
- Harvard UniversityUS13 papers
- Stanford UniversityUS12 papers
- Cornell UniversityUS11 papers
- National Institutes of HealthUS7 papers
- New York UniversityUS7 papers
- University of California, San FranciscoUS7 papers
- Emory UniversityUS6 papers
- Georgia Institute of TechnologyUS6 papers
- Hebrew University of JerusalemIL6 papers
- Imperial College LondonGB6 papers
- Mayo ClinicUS6 papers
8 papers · 1 filter
Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks
Arthur P. Goldberg, David R. Jefferson, John A. P. Sekar +1
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulati…
Large Collection of Diverse Gene Set Search Queries Recapitulate Known Protein-Protein Interactions and Gene-Gene Functional Associations
Avi Ma'ayan, Neil R. Clark
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual…
Dynamic Modeling of the Interaction Between Autophagy and Apoptosis in Mammalian Cells
I. Tavassoly, J. Parmar, A. N. Shajahan-Haq +3
Autophagy is a conserved biological stress response in mammalian cells that is responsible for clearing damaged proteins and organelles from the cytoplasm and recycling their conte…
Inferring the Sign of Kinase-Substrate Interactions by Combining Quantitative Phosphoproteomics with a Literature-Based Mammalian Kinome Network
Marylens Hernandez, Alexander Lachmann, Shan Zhao +2
Protein phosphorylation is a reversible post-translational modification commonly used by cell signaling networks to transmit information about the extracellular environment into in…
Functions of Bifans in Context of Multiple Regulatory Motifs in Signaling Networks
Azi Lipshtat, Sudarshan P. Purushothaman, Ravi Iyengar +1
Representation of intracellular signaling networks as directed graphs allows for the identification of regulatory motifs. Regulatory motifs are groups of nodes with the same connec…
Deterministic and Stochastic Simulations of Simple Genetic Circuits
Ofer Biham, Nathalie Q. Balaban, Adiel Loinger +2
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and th…
Stochastic Simulations of Genetic Switch Systems
Adiel Loinger, Azi Lipshtat, Nathalie Q. Balaban +1
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and…
Genetic Toggle Switch Without Cooperative Binding
Azi Lipshtat, Adiel Loinger, Nathalie Q. Balaban +1
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative…