Research graph
References from Spatially resolved reaction–diffusion modeling reveals effects of intracellular spatial heterogeneity on yeast galactose network dynamics. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
2015 · External reference
Visualizing intracellular organelle and cytoskeletal interactions at nanoscale resolution on millisecond timescales
2018 · External reference
Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells
10.1073/pnas.2406340121 · 2025 · External reference
Quantitative influence of macromolecular crowding on gene regulation kinetics
10.1093/nar/gkt907 · 2014 · External reference
Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion
10.1371/journal.pcbi.1005122 · 2016 · External reference
Organelles - understanding noise and heterogeneity in cell biology at an intermediate scale
10.1242/jcs.181024 · 2017 · External reference
Genome organization: balancing stability and plasticity
10.1016/j.bbamcr.2008.07.022 · 2008 · External reference
Eukaryotic gene regulation in three dimensions and its impact on genome evolution
10.1016/j.gde.2008.10.002 · 2008 · External reference
Using gene expression noise to understand gene regulation
10.1126/science.1216379 · 2012 · External reference
Noise contributions in an inducible genetic switch: a whole-cell simulation study
10.1371/journal.pcbi.1002010 · 2011 · External reference
Integrating cellular and molecular structures and dynamics into whole-cell models
10.1016/j.sbi.2022.102392 · 2022 · External reference
A comparison of computational models for eukaryotic cell shape and motility
10.1371/journal.pcbi.1002793 · 2012 · External reference
Fundamental behaviors emerge from simulations of a living minimal cell
10.1016/j.cell.2021.12.025 · 2022 · External reference
10.1101/2025.06.10.658899
10.1101/2025.06.10.658899 · External reference
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations
10.1021/acs.jpcb.7b00672 · 2017 · External reference
The principles of whole-cell modeling
10.1016/j.mib.2015.06.004 · 2015 · External reference
An in-silico human cell model reveals the influence of spatial organization on RNA splicing
10.1371/journal.pcbi.1007717 · 2020 · External reference
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast
10.1038/ng1869 · 2006 · External reference
The galactose regulon of Escherichia coli
10.1111/j.1365-2958.1993.tb01950.x · 1993 · External reference
Environmental and genetic regulation of Streptococcus pneumoniae galactose catabolic pathways
10.1038/s41467-024-49619-w · 2024 · External reference
Galactose metabolism by Streptococcus mutans
10.1128/aem.70.10.6047-6052.2004 · 2004 · External reference
Electron tomography of yeast cells
10.1016/s0076-6879(02)51842-5 · 2002 · External reference
X-ray tomography generates 3-D reconstructions of the yeast, saccharomyces cerevisiae, at 60-nm resolution
10.1091/mbc.e03-07-0522 · 2004 · External reference
A 3D analysis of yeast ER structure reveals how ER domains are organized by membrane curvature
10.1083/jcb.201011039 · 2011 · External reference
High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy
10.2144/000113850 · 2012 · External reference
Quantitative analysis of yeast internal architecture using soft X-ray tomography
10.1002/yea.1834 · 2011 · External reference
Whole-cell imaging of the budding yeast Saccharomyces cerevisiae by high-voltage scanning transmission electron tomography
10.1016/j.ultramic.2014.05.008 · 2014 · External reference
mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding
10.1016/j.cell.2018.05.042 · 2018 · External reference
In situ architecture of the ER-mitochondria encounter structure
10.1038/s41586-023-06050-3 · 2023 · External reference
In situ structural analysis reveals membrane shape transitions during autophagosome formation
10.1073/pnas.2209823119 · 2022 · External reference
Cryo-ET detects bundled triple helices but not ladders in meiotic budding yeast
2022 · External reference
Polysome collapse and RNA condensation fluidize the cytoplasm
2024 · External reference
10.64898/2025.12.22.696049
10.64898/2025.12.22.696049 · External reference
Enhancement of cellular memory by reducing stochastic transitions
10.1038/nature03524 · 2005 · External reference
Hybrid CME-ODE method for efficient simulation of the galactose switch in yeast
10.1049/iet-syb.2017.0070 · 2018 · External reference
Fluorescence based assay of GAL system in yeast Saccharomyces cerevisiae
10.1016/j.femsle.2005.01.041 · 2005 · External reference
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae
10.1091/mbc.e15-07-0499 · 2015 · External reference
Transcriptional regulation in the yeast GAL gene family: a complex genetic network
10.1096/fasebj.9.9.7601342 · 1995 · External reference
The yeast galactose genetic switch is mediated by the formation of a Gal4p-Gal80p-Gal3p complex
10.1093/emboj/17.14.4086 · 1998 · External reference
Yeast Gal4: a transcriptional paradigm revisited
10.1038/sj.embor.7400679 · 2006 · External reference
The yeast galactose network as a quantitative model for cellular memory
10.1039/c4mb00448e · 2015 · External reference
Variation in the modality of a yeast signaling pathway is mediated by a single regulator
10.7554/elife.69974 · 2021 · External reference
Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators
10.1534/genetics.111.127019 · 2011 · External reference
Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations
10.1016/j.parco.2014.03.009 · 2014 · External reference
Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation
10.1002/jcc.23130 · 2013 · External reference
The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations
10.1371/journal.pone.0011725 · 2010 · External reference
Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases
10.1049/sb:20045021 · 2004 · External reference
MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit
10.1093/bioinformatics/bts584 · 2012 · External reference
Approximate accelerated stochastic simulation of chemically reacting systems
10.1063/1.1378322 · 2001 · External reference
Efficient step size selection for the tau-leaping simulation method
10.1063/1.2159468 · 2006 · External reference
Exact stochastic simulation of coupled chemical reactions
10.1021/j100540a008 · 1977 · External reference
Mediator subunit Med15 dictates the conserved “fuzzy” binding mechanism of yeast transcription activators Gal4 and Gcn4
10.1038/s41467-021-22441-4 · 2021 · External reference
SciPy 1.0: fundamental algorithms for scientific computing in Python
10.1038/s41592-019-0686-2 · 2020 · External reference
A three-dimensional model of the yeast genome
10.1038/nature08973 · 2010 · External reference
Principles of chromosomal organization: lessons from yeast
10.1083/jcb.201010058 · 2011 · External reference
Centromere positioning orchestrates telomere bouquet formation and the initiation of meiotic differentiation
10.1038/s41467-025-56049-9 · 2025 · External reference
Telomeres, the nuclear lamina, and membrane remodeling: Orchestrating meiotic chromosome movements
10.1083/jcb.202412135 · 2025 · External reference
Multiscale visualization of nucleolar chromatin in yeast Saccharomyces cerevisiae
10.1016/j.jsb.2025.108228 · 2025 · External reference
High plasticity of ribosomal DNA organization in budding yeast
10.1016/j.celrep.2024.113742 · 2024 · External reference
Three-dimensional structure of the yeast ribosome
10.1093/nar/26.2.655 · 1998 · External reference
Structome of Saccharomyces cerevisiae determined by freeze-substitution and serial ultrathin-sectioning electron microscopy
10.1093/jmicro/dfr052 · 2011 · External reference
Quantitative three-dimensional structural analysis of Exophiala dermatitidis yeast cells by freeze-substitution and serial ultrathin sectioning
10.1093/jmicro/52.2.133 · 2003 · External reference
The economics of ribosome biosynthesis in yeast
10.1016/s0968-0004(99)01460-7 · 1999 · External reference
Structural diversity within the endoplasmic reticulum—From the microscale to the nanoscale
10.1101/cshperspect.a041259 · 2023 · External reference
Single particle trajectories reveal active endoplasmic reticulum luminal flow
10.1038/s41556-018-0192-2 · 2018 · External reference
Endoplasmic Reticulum–Plasma Membrane Associations: Structures and Functions
10.1146/annurev-cellbio-111315-125024 · 2016 · External reference
ER-to-plasma membrane tethering proteins regulate cell signaling and ER morphology
10.1016/j.devcel.2012.11.004 · 2012 · External reference
Rough sheets and smooth tubules
10.1016/j.cell.2006.07.019 · 2006 · External reference
Computer visualization of three-dimensional image data using IMOD
10.1006/jsbi.1996.0013 · 1996 · External reference
Convolutional networks for supervised mining of molecular patterns within cellular context
10.1038/s41592-022-01746-2 · 2023 · External reference
EMAN2: an extensible image processing suite for electron microscopy
10.1016/j.jsb.2006.05.009 · 2007 · External reference
A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
10.7554/elife.83724 · 2022 · External reference
UCSF ChimeraX: Tools for structure building and analysis
2023 · External reference
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
2024 · External reference
Unresolved reference
External reference
Blik: an extensible napari plugin for cryo-ET data visualisation, annotation and analysis
2023 · External reference
Unresolved reference
External reference
Unresolved reference
External reference
The MaxQuant computational platform for mass spectrometry-based shotgun proteomics
10.1038/nprot.2016.136 · 2016 · External reference
A “proteomic ruler” for protein copy number and concentration estimation without spike-in standards
10.1074/mcp.m113.037309 · 2014 · External reference
Unresolved reference
External reference
Single-molecule long-read sequencing reveals the chromatin basis of gene expression
10.1101/gr.251116.119 · 2019 · External reference
Saccharomyces Genome Database: the genomics resource of budding yeast
10.1093/nar/gkr1029 · 2012 · External reference
ACCESS: Advancing innovation: NSF’s advanced cyberinfrastructure coordination ecosystem: services & support.
10.1145/3569951.3597559 · 2023 · External reference
Transfer of proteins across membranes. I. Presence of proteolytically processed and unprocessed nascent immunoglobulin light chains on membrane-bound ribosomes of murine myeloma
10.1083/jcb.67.3.835 · 1975 · External reference
The Sec61 complex is essential for the insertion of proteins into the membrane of the endoplasmic reticulum
10.1016/0014-5793(95)00223-v · 1995 · External reference
GAL2 codes for a membrane-bound subunit of the galactose permease in Saccharomyces cerevisiae
10.1128/jb.166.1.313-318.1986 · 1986 · External reference
The galactokinase enzyme of yeast senses metabolic flux to stabilize galactose pathway regulation
10.1038/s42255-024-01181-x · 2025 · External reference
Reaction-diffusion master equation, diffusion-limited reactions, and singular potentials
10.1103/physreve.80.066106 · 2009 · External reference
A convergent reaction-diffusion master equation
10.1063/1.4816377 · 2013 · External reference
Reaction rates for mesoscopic reaction-diffusion kinetics
10.1103/physreve.91.023312 · 2015 · External reference
Validity conditions for stochastic chemical kinetics in diffusion-limited systems
10.1063/1.4863990 · 2014 · External reference
The influence of spatial variation in chromatin density determined by X-ray tomograms on the time to find DNA binding sites
10.1007/s11538-013-9883-9 · 2013 · External reference
Physics of chemoreception
10.1016/s0006-3495(77)85544-6 · 1977 · External reference
The narrow escape problem for diffusion in cellular microdomains
10.1073/pnas.0706599104 · 2007 · External reference
Percolation and Clustering
10.1007/978-1-4757-6355-3_9 · 2002 · External reference
Diffusion in cytoplasm: effects of excluded volume due to internal membranes and cytoskeletal structures
10.1016/j.bpj.2009.05.036 · 2009 · External reference
Endoplasmic reticulum network heterogeneity guides diffusive transport and kinetics
10.1016/j.bpj.2023.06.022 · 2023 · External reference
