Papers @ Stanford 2016-present

A Shariati, A Dominguez, M Wernig, LS Qi & JM Skotheim, “Reversible inhibition of specific transcription factor-DNA interactions using CRISPR” Manuscript available as a preprint from: to appear in Molecular Cell (2019).

BR Topacio, E Zatulovskiy, S Cristea, S Xie, CS Tambo, SM Rubin, J Sage, M Kõivomägi & JM Skotheim, “Cyclin D-Cdk4,6 drives cell cycle progression via the retinoblastoma protein’s C-terminal helix”, DOI: Molecular Cell (2019)

 JC Bell, D Jukam, NA Teran, VI Risca, OK Smith, WL Johnson, JM Skotheim, WJ Greenleaf & AF Straight, “Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts” eLife 7:e27024 (2018).

C Schwarz, A Johnson, M Koivomagi, E Zatulovskiy, C Kravitz, A Doncic & JM Skotheim, “A precise Cdk2 threshold determines passage through the restriction point” Molecular Cell, 69 (2), 253-264, e5 (2018).

D Chandler-Brown*, K Schmoller*, Y Winetraub & JM Skotheim, “The adder phenomenon emerges from independent control of pre- and post-Start phases of the budding yeast cell cycle”, Current Biology, Volume 27, Issue 18, 2774-2783.e3 (2017).

U Eser*, D Chandler-Brown*, F Ay, AF Straight, Z Duan, WS Noble, JM Skotheim, “Form and function of topologically associated domains in yeast” PNAS E3061–E3070, doi: 10.1073/pnas.1612256114 (2017).

O Atay & JM Skotheim, “Spatial and Temporal Signal Processing and Decision Making by MAPK Pathways”, DOI: 10.1083/jcb.201609124 Journal of Cell Biology (2017).

D Jukam, A Shariati & JM Skotheim, “Zygotic genome activation in vertebrates”, Developmental Cell 42, 316–332 (2017).

O Atay, A Doncic & JM Skotheim, “Switch-like transitions can modularize complex biological networks”, Cell Systems doi:10.1016/j.cels.2016.06.010 (2016).

B Treutlein, QY Lee, J Camp, M Mall, A Shariati, S Sim, N Neff, JM Skotheim, M Wernig, W Koh & S Quake, “Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq”, Nature, doi:10.1038/nature18323 (2016).

E Medina-Tovar, JJ Turner, JM Skotheim & NE Buchler, “Punctuated evolution of a complex ancestral cell cycle” eLife, DOI: 10.7554/eLife.09492.001 (2016).

J Ewald, A Kuehne, N Zamboni & JM Skotheim, “The yeast cyclin-dependent kinase routes carbon fluxes to fuel cell cycle progression” Molecular Cell 62, 532-45 (2016). 

Papers @ Stanford 2008-2015

A Doncic, O Atay, E Valk, A Grande, A Bush, G Vasen, A Colman-Lerner, M Loog & JM Skotheim, “Compartmentalization of a bistable switch enhances memory across a cellular transition” Cell 160, 1182-95 (2015).


E Zatulovskiy & JM Skotheim, 'Mitosis is swell' doi: 10.1083/jcb.201511007 JCB (2015) 

K Schmoller, JJ Turner, M Koivomagi & JM Skotheim, 'Dilution of the cell cycle inhibitor Whi5 controls budding yeast cell size' DOI: 10.1038/nature14908 Nature (2015).

AA Amodeo, D Jukam, AF Straight & JM Skotheim, 'Histone titration by DNA sets the threshold for the mid-blastula transition in Xenopus', PNAS 2015.

EA Peroza, JC Ewald, G Parakkal, JM Skotheim, N Zamboni, 'A genetically encoded FRET sensor reveals in vivo trehalose-6-phosphate dynamics' Analytical Biochemistry doi:10.1016/j.ab.2014.12.019 (2015).

O Atay & JM Skotheim, 'Modularity and predictability in cell signaling and decision-making' MBoC 25, 3445-50 (2014).

M Koivomagi and JM Skotheim, 'Docking interactions: the cell cycle and beyond' Current Biology 24, R647-9 (2014).

 CA Anderson, U Eser, T Korndorf, ME Borsuk, JM Skotheim, AS Gladfelter, 'Nuclear repulsion enables division autonomy in a single cytoplasm' Current Biology 23, 1999-2010 (2013).

A Johnson & JM Skotheim, 'Start and the Restriction Point', Current Opinion in Cell Biology25, 717-723 (2013).

C Bertoli, JM Skotheim & RA de Bruin, ‘Transcriptional control of the G1-to-S transition’, Nature Rev. Mol. Cell Bio. 14, 518-28 (2013).

F Caval-Holme, JL Payne & JM Skotheim, “Physiological and cell biological limits on protist offspring size”  Evolution DOI: 10.1111/evo.12210 (2013).

A Doncic & JM Skotheim, “Feed-forward regulation ensures stability and rapid reversibility of a cellular state”,  Mol. Cell. 50, 1-13 (2013).

A Doncic, U Eser, O Atay & JM Skotheim, “An algorithm to automate yeast segmentation and tracking” PLoS ONE 8(3): e57970 (2013).  

U Eser, Ph.D. Thesis 2013, "Spatio-temporal regulation of cell cycle transcription" click to download.

A Doncic & JM Skotheim, “Cell cycle control: single-cell analysis”, Encyclopedia for Systems Biology, Dubitzky, W.; Wolkenhauer, O.; Yokota, H.; Cho, K.-H. (Eds.) (2013).

JM Skotheim, 'Cell growth and cell cycle control', MBoC 24, 678 (2013).

JL Payne, AB Jost, SC Wang & JM Skotheim, “A shift in the long-term mode of foraminiferan size evolution caused by the end-Permian mass extinction” Evolution 67, 816-27 (2013).

JL Payne, JR Groves, AB Jost, T Nguyen, S Myhre, TM Hills & JM Skotheim, “Late Paleozoic fusulinoidean gigantism driven by atmospheric hyperoxia” Evolution 66, 2929-39 (2012).

J Turner, J Ewald & JM Skotheim, "Cell size control in yeast" Current Biology, 22, R350-9 (2012).

FR Cross, N Buchler & JM Skotheim, “Evolution of networks and sequences in eukaryotic cell cycle control” Phil. Trans. Roy. Soc. B 366, 3532-3544 (2011).

A Doncic, M Falleur-Fettig & JM Skotheim, “Distinct interactions select and maintain a specific cell fate” Mol. Cell 43, 528–539 (2011).  Featured in Mol. Cell preview; Selected for faculty of 1000. 

U Eser, M Falleur-Fettig, A Johnson & JM Skotheim, “Commitment to a cellular transition precedes genome-wide transcriptional change” Mol. Cell 43, 515–527 (2011).   Featured in Mol. Cell preview; Selected for faculty of 1000

S DiTalia, H Wang, JM Skotheim, A Rosebrock, B Futcher & FR Cross, “Daughter-specific transcription factors regulate cell size control in budding yeast” PLoS Biology 7(10): e1000221 (2009). See Nature Reviews Genetics research highlight.

JM Skotheim, “To divide or not to divide”, Science 324, 476-7 (2009).


Papers @ Rockefeller University 2005-8

JM Skotheim, S DiTalia, ED Siggia & FR Cross, "Positive feedback of G1 cyclins ensures coherent cell cycle entry", Nature 454, 291-296 (2008). See Nature News and Views; Mol. Cell preview; Cell Leading Edge; Selected for Faculty of 1000.

S DiTalia, JM Skotheim, JM Bean, ED Siggia & FR Cross, "The effects of molecular noise and size control on variability in the budding yeast cell cycle", Nature 448, 947-951 (2007). Selected for faculty of 1000.

M Argentina, JM Skotheim & L Mahadevan, “Settling and swimming of flexible fluid-lubricated foils,” Phys. Rev. Lett. 99, 224503 (2007).

JM Skotheim & TW Secomb, "Red blood cells and other non-spherical capsules in shear flow: oscillatory motion and the tank-treading-to-tumbling transition", Phys Rev. Lett. 98, 078301 (2007).

Papers @ University of Cambridge 2001-2005

JM Skotheim & L Mahadevan, “Soft elastohydrodynamic contacts”, Phys. Fluids, 17, 092101 (2005). Awarded the François Frenkiel Award by the American Physical Society for significant contributions to the field of fluid mechanics by a young scientist.

S Manley, JM Skotheim, L Mahadevan & DA Weitz, “Gravitational collapse of colloidal gels,” Phys. Rev. Lett., 94, 218302 (2005).

JM Skotheim & L Mahadevan “Physical limits and design principles for plant and fungal movements,” Science, 308, 1308-1310 (2005). Featured on the cover; Selected for Faculty of 1000.

Y Forterre, JM Skotheim, J Dumais & L Mahadevan, “How the Venus flytrap snaps,” Nature, 433, 421-425 (2005). Selected for Faculty of 1000.

JM Skotheim & L Mahadevan, “Soft lubrication,” Phys. Rev. Lett. 92, 245509 (2004).

JM Skotheim & L Mahadevan, “Dynamics of poroelastic filaments,” Proc. R. Soc. London Ser. A 460, 1995-2020 (2004).

JM Skotheim, U Thiele & B Scheid, “On the instability of a falling film due to localized heating,” J. Fluid Mech., 475, 1-19, (2003).

Papers @ MIT

JM Skotheim & JWM Bush, “Evaporatively driven convection in a draining soap film,” Phys. Fluids, S1, Sept. (2000). Featured on the Cover.