Stanford School of Medicine

Chemical & Systems Biology


Featured Publications

Ahrends R, Ota A, Kovary KM, Kudo T, Park BO, Teruel MN. (2014) Controlling low rates of cell differentiation through noise and ultrahigh feedback. Science. 2014 Jun 20;344(6190):1384-9.[PubMed]

Cappell SD, Chung M, Jaimovich A, Spencer SL, Meyer T. (2016) Irreversible APC(Cdh1) Inactivation Underlies the Point of No Return for Cell-Cycle Entry. Cell. 2016 Jun 30;166(1):167-80. doi: 10.1016/j.cell.2016.05.077. [PubMed]

Chakrabortee S, Byers III JS, Jones SK, Garcia DM, Bhullar B,Chang A, Lee L, Fremin B,  Lindquist S, Jarosz DF. (2016)  Intrinsically disordered proteins drive heritable transformations of biological traits. Accepted at Cell.

Chang JB, Ferrell JE Jr. (2013) Mitotic trigger waves and the spatial coordination of the Xenopus cell cycle.Nature. 2013 Aug 29;500(7464):603-7.  [PubMed]

Chen CH, Cruz LA, Mochly-Rosen D. (2015) Pharmacological recruitment of aldehyde dehydrogenase 3A1 (ALDH3A1) to assist ALDH2 in acetaldehyde and ethanol metabolism in vivo. Proc Natl Acad Sci. 2015 Mar 10;112(10):30 [PubMed]

Devabhaktun,i A, Elias, JE (2016)  Application of de Novo Sequencing to Large-Scale Complex Proteomics Data Sets. J Proteome Res. 2016 Mar 4;15(3):732-42. doi: 10.1021/acs.jproteome.5b00861. [PubMed]

Ha SH, Ferrell JE Jr. (2016) Thresholds and ultrasensitivity from negative cooperativity. Science. 2016 May 20;352(6288):990-3. doi: 10.1126/science.aad5937. [PubMed]

Jarosz D. (2016) Hsp90: A Global Regulator of the Genotype-to-Phenotype Map in Cancers. Adv Cancer Res. 2016;129:225-47. doi: 10.1016/bs.acr.2015.11.001. [PubMed]

Kile AC, Chavez DA, Bacal J, Eldirany S, Korzhnev DM, Bezsonova I, Eichman BF, Cimprich KA. (2015) HLTF’s Ancient HIRAN Domain Binds 3′ DNA Ends to Drive Replication Fork Reversal. Mol Cell. 2015 Jun 18;58(6):1090-100. [PubMed]

Lichtman JS, Ferreyra JA, Ng KM, Smits SA, Sonnenburg JL, Elias JE. (2016) Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases. Cell Rep. 2016 Jan 27. pii: S2211-1247(16)00029-2. doi: 10.1016/j.celrep.2016.01.009. [PubMed]

Miyazaki Y, Chen LC, Chu BW, Swigut T, Wandless TJ. (2015) Distinct transcriptional responses elicited by unfolded nuclear or cytoplasmic protein in mammalian cells. Elife. 2015 Aug 28;4. [PubMed]

Miyazaki Y, Mizumoto K, Dey G, Kudo T, Perrino J, Chen LC, Meyer T, Wandless TJ.  (2016) A method to rapidly create protein aggregates in living cells. Nat Commun. 2016 May 27;7:11689. doi: 10.1038/ncomms11689. [PubMed]

Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. (2015) ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. Elife.  2015 Nov 2;4. pii: e10150. [PubMed]

Payumo AY, McQuade LE, Walker WJ, Yamazoe S, Chen JK (2016) Tbx16 regulates hox gene activation in mesodermal progenitor cells. Nat Chem Biol. 2016 Jul 4. doi: 10.1038/nchembio.2124. [PubMed]

Park BO, Ahrends R, Teruel MN. (2012) Consecutive positive feedback loops create a bistable switch that controls preadipocyte-to-adipocyte conversion.Cell Rep 2(4):976-90 [PubMed]

Prescott SL, Srinivasan R, Marchetto MC, Grishina I, Narvaiza I, Selleri L, Gage FH, Swigut T, Wysocka J. (2015) Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. Cell. Sep 24;163(1):68-83. [PubMed]

Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA. (2016) Cell. 2013 Feb 28;152(5):1173-83. doi: 10.1016/j.cell.2013.02.022. [PubMed]

Qvit N, Disatnik MH, Sho E, Mochly-Rosen D, (2016) Selective Phosphorylation Inhibitor of Delta Protein Kinase C-Pyruvate Dehydrogenase Kinase Protein-Protein Interactions: Application for Myocardial Injury in Vivo.J Am Chem Soc. 2016 Jun 22;138(24):7626-35. doi: 10.1021/jacs.6b02724. [PubMed]

Rack PG, Ni J, Payumo AY, Nguyen V, Crapster JA, Hovestadt V, Kool M, Jones DT, Mich JK, Firestone AJ, Pfister SM, Cho YJ,Chen JK. (2014)  Arhgap36-dependent activation of Gli transcription factors. Proc Natl Acad Sci U S A. 2014 Jul 29;111(30):11061-6. [PubMed]

Stork CT, Bocek M, Crossley MP, Sollier J, Sanz LA, Chédin F, Swigut T, Cimprich KA. (2016) Co-transcriptional R-loops are the main cause of estrogen-induced DNA damage. Elife. 2016 Aug 23;5. pii: e17548. doi: 10.7554/eLife.17548. [PubMed]

Yang HW, Collins SR, Meyer T. (2016) Locally excitable Cdc42 signals steer cells during chemotaxis. Nat Cell Biol. 2016 Feb;18(2):191-201. doi: 10.1038/ncb3292. [PubMed]

Zalatan JG, Lee ME, Gilbert LA, Almeida R, Tsai JC, Whitehead EH, Weissman JS, Dueber JE, Qi LS*, Lim WA*. (2015) Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell. 2015 Jan 15;160(1-2):339-50. [PubMed] (* Co-corresponding author)