PUBLICATIONS

Previous Publications (before 2015)

Publications from our lab

Phase diagram for cell replication (budding yeast)
Yeasts collectively extend the limits of habitable temperatures by secreting glutathione
Diederik S. Laman Trip, and Hyun Youk
Nature Microbiology ( Research Article - 5: 943-954) ( April 2020 )
   Research Article (.pdf)       Supp. Figs. + Math model (.pdf)       bioRxiv preprint (Aug. 2019)   
   News & Views on this work (.pdf)       TU Delft News on this work (.html)   
spiral wave created by cell in middle
Cellular dialogues: cell-cell communication through diffusible molecules yields dynamic spatial patterns
Yiteng Dang, Douwe A. J. Grundel, and Hyun Youk
Cell Systems ( Research Article - 10: 1-17 ) ( Jan. 2020 )
   Research Article (.pdf)       Supp. Figures (.pdf)       Supp. Text (.pdf)       Supp. Movies (.html)   
   Transparent Peer Review Record (.pdf)       TU Delft News on this work (.html)   
   Software for visualizing spatial-pattern formations (open-source software on GitHub) (.html)   
   bioRxiv preprint (July 2019)   
Dormancy spectrum
Modeling cell-cell communication for immune systems across space and time
Hirad Daneshpour and Hyun Youk
Current Opinion in Systems Biology ( Review - 18: 44-52 ) ( Dec. 2019 )
   Review (.pdf)   
Dormancy spectrum
Dormancy-to-death transition in yeast spores occurs due to gradual loss of gene-expressing ability
Théo Maire, Tim Allertz, Max A. Betjes, and Hyun Youk
bioRxiv ( Research Article (preprint) - doi:10.1101/747766v2) ( August 2020 (revised Aug. 2019 version) )
   Research Article - updated in Aug. 2020 (.pdf)   
Featured and published as outstanding peer review
Evaluation of Schink et al.: Having the gem shine through a fog
Diederik S. Laman Trip, Théo Maire, and Hyun Youk
Cell Systems ( Featured as Exemplary Peer Review - 9: 3-7 ) ( July 2019 )
   Featured as Exemplary Peer Review (.pdf)       pubmed   
Mapping cellular automaton to a drifting-diffusing particle
Statistical dynamics of spatial-order formation by communicating cells
Eduardo P. Olimpio*, Yiteng Dang*, and Hyun Youk
iScience ( Research article - 2: 27-40 ) (*co-first authors) ( April 2018 )
   research article + Supp. Inf. (.pdf)       arXiv: 1706.06481       pubmed   
   Reviewers' comments & our response (.pdf)   
   Research Features - Summary of this work (.pdf)   
Positive feedbacks and controlling signal-range
Progress towards design principles of multicellular systems
Eduardo P. Olimpio, Diego R. Gomez-Alvarez, and Hyun Youk
in Systems Biology, (Editors: J. Nielsen and S. Hohmann), Wiley-VCH
( Book chapter) ( March 2017 )
   book chapter (.pdf)       arXiv: 1602.08526   
Positive feedbacks and controlling signal-range
Autocrine signaling and quorum sensing: Extreme ends of a common spectrum
Berkalp A. Doganer, Lawrence K. Q. Yan, and Hyun Youk
Trends in Cell Biology ( Review - 26: 262-271 ) ( April 2016 )
   review (.pdf)       arXiv: 1602.06859       pubmed   
Molecular-level tuning of cellular autonomy controls the collective behaviors of cell populations
Théo Maire and Hyun Youk
Cell Systems ( Research Article - 1: 349-360) ( November 2015 )
   research article (.pdf)       article + supp. info. (.pdf)       arXiv: 1602.05558       pubmed   
   Preview by C. Ratzke & J. Gore: "Shaping the crowd: The social life of cells" (.pdf)       TU Delft News   
   Reviewers' comments & our response (.pdf)   
Positive feedbacks and controlling signal-range
A collective path toward regeneration
Théo Maire and Hyun Youk
Cell ( Preview - 161:195-196) ( April 2015 )
   preview (.pdf)       pubmed   
Positive feedbacks and controlling signal-range
IL-2 mediated multicellular bistability
Sending mixed messages for cell population control
Hyun Youk and Wendell A. Lim
Cell ( Preview - 158:973-975) ( August 2014 )
   preview (.pdf)       pubmed   
Secreting and sensing the same molecule allows cells to achieve versatile social behaviors
Hyun Youk and Wendell A. Lim
Science ( Research Article - 343:1242782) ( February 2014 )
   research article (.pdf)       supplementary material (.pdf)       pubmed   
   Perspective by Anna J. Lee & Lingchong You: "Cells listen to their inner voice" (.pdf)   
   Editor's choice in Science Signaling: "The message in the medium"   
   Synopsis by Faculty of 1000 (F1000 Prime)       Chemical & Engineering News: Highlight   
   SGD Blog: "Signaling in a crowd"   
Growth landscape formed by perception and import of glucose
bottom up hierarcy: secrete and sense
secrete and sense circuit
self vs neighbor communication
Altruistic defence
Hyun Youk and Alexander van Oudenaarden
Nature ( News & Views - 467:34-35 ) ( September 2010 )
   news & views (.pdf)       pubmed   
Imaging single mRNA molecules in yeast
Hyun Youk, Arjun Raj, and Alexander van Oudenaarden
Methods in Enzymology ( Book Chapter - 470:429 ) ( 2010 )
   book chapter (.pdf)       pubmed   
Phenomenological models in biological physics: Cell growth and pluripotency maintenance
Hyun Youk
Ph.D. Thesis in Physics, MIT ( June 2010 )
  Ph.D. Thesis (.pdf)      thesis @ MIT Libraries   
Growth landscape formed by perception and import of glucose in yeast
Hyun Youk and Alexander van Oudenaarden
Nature ( Research Article - 462:875-879 ) ( December 2009 )
  article (.pdf)      supplementary information (.pdf)      pubmed  
   Editor's summary of this work   
   Cell select: "How yeast knows when it is time to grow " (.pdf)  
E.coli
Hxt_strain_schematic
Single murine ESC - RNA FISH on Oct4
Optimal transporter equation
RNA FISH Probes - Schematic
Snowdrift game dynamics and facultative cheating in yeast
Jeff Gore, Hyun Youk, and Alexander van Oudenaarden
Nature ( Research Letter - 459:253-256 ) ( May 2009 )
cooperator vs cheater
  letter (.pdf)      supplementary information (.pdf)      pubmed  
  Editor's summary of this work  
Halfvortices in flat nanomagnets
Gia-Wei Chern, David Clarke, Hyun Youk, and Oleg Tchernyshyov
Quantum Magnetism ( Book chapter - pp35-48 ) ( 2008 )
  book chapter (.pdf)     arXiv: 1007.2158   
+1/2 vortex
-1/2 vortex
Composite domain walls in flat nanomagnets: The magnetostatic limit
Hyun Youk, Gia-Wei Chern, Kathleen Merit, Benjamin Oppenheimer, and Oleg Tchernyshyov
Journal of Applied Physics ( Research article - 99:08B101 ) ( 2006 )
  research article (.pdf)      arXiv: cond-mat/0508741   
vortices
smooth vortex
Topological defects in flat nanomagnets: The magnetostatic limit
Gia-Wei Chern, Hyun Youk, and Oleg Tchernyshyov
Journal of Applied Physics ( Research article - 99:08Q505 ) ( 2006 )
  research article (.pdf)      arXiv: cond-mat/0508740   
Condensation of magnons and spinons in a frustrated ladder
Jean-Baptiste Fouet, Frédéric Mila, David Clarke, Hyun Youk, Oleg Tchernyshyov, Paul Fendley, and R.M. Noack
Physical Review B ( Research article - 73:214405 ) ( 2006 )
  research article (.pdf)      arXiv: cond-mat/0603609   
frustrated ladder
The growth of ice crystals by molecular diffusion
Hyun Youk, Roland List, and Theophilus Ola
Journal of the Atmospheric Sciences ( Research article - 63:1650-1657 ) ( 2006 )
  research article (.pdf)      arXiv: physics/0404094   
finite element geometry
Numerical study of quadrupole magnetic traps for neutral atoms: Anti-Helmholtz coils and U-chip
Hyun Youk
Canadian Undergraduate Physics Journal ( Research article - 3: 13-18 ) ( 2005 )
  research article (.pdf)   
quadrupole field