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O'Shea Lab > Publications

Papers can also be reqested by sending your inquiry to the O'Shea Lab's Administrator Peter Arvidson.

J. Choi, A. Rajagopal, Y-F Xu, J. Rabinowitz and E. K. O’Shea, A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae, PLoS One, accepted for publication (2017).

X. Zheng and E. K. O’Shea, Cyanobacteria maintain constant protein concentration despite genome copy number variation, Cell Reports, accepted for publication (2017).

A. Puszynska and E. K. O’Shea, Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway, eLife, 2017;6:e23210 (2017). Article

X. Zhou, A. Blocker, E. Airoldi, and E. K. O’Shea, A computational approach to map nucleosome positions and alternative chromatin states with base pair resolution, eLife, 2016;10.7554/eLife.16970 (2016). Article

C. Chidley, S. A. Trauger, K. Birsoy, and E. K. O’Shea, The anticancer natural product ophiobolin A induces cytotoxicity by covalent modification of phosphatidylethanolamine, eLife, 2016:5:e14601 (2016). Article

A. S. Hansen and E. K. O’Shea, Encoding four gene expression programs in the activation dynamics of a single transcription factor, Current Biology, 26(7): R269-271 (2016). Article

A. S. Hansen and E. K. O’Shea, cis Determinants of Promoter Threshold and Activation Timescale, Cell Reports, 12(6):1226-1233 (2015). Article

A. S. Hansen and E. K. O’Shea, Limits on Information Transduction through Amplitude and Frequency Regulation of Transcription Factor Activity, eLife, 2015;10.7554/eLife.06559 (2015). Article

A. S. Hansen, N. Hao, E. K. O’Shea, High-throughput microfluidics to control and measure signaling dynamics in single yeast cells Nature Protocols,10(8):1181-1197 (2015). Article Cover

A. R. Subramaniam, B. Zid, E. K. O’Shea, An integrated approach reveals regulatory controls on bacterial translation elongation. Cell, 159(5):1200–1211 (2014). Article / Harvard Users

B. Zid and E.K. O'Shea, Promoter sequences influence cytoplasmic localization and translation of mRNAs during nutrient limitation. Nature, 514(7520):117-121 (2014). Article / Harvard Users

S. Mukherji and E.K. O'Shea, Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance. eLife, 2014;3:e02678 (2014). Article

A. R. Subramaniam, A. DeLoughery, N. Bradshaw, Y. Chen, E. K. O’Shea, R. Losick, Y. Chai. A serine sensor for multicellularity in a bacterium, eLife, 2013;2:e01501 (2013). Article

J.S. Markson*, J.R. Piechura*, A.M. Puszynska and E.K. O'Shea, Circadian control of global gene expression by the cyanobacterial master regulator RpaA, Cell, 155:6, pages 1396-1408 (2013). (* equal contribution) PubMed

A.S. Hansen and E.K. O'Shea, Promoter Decoding of Transcription Factor Dynamics Involves a Trade-Off between Noise and Control of Gene Expression, Molecular Systems Biology, 9:704 (2013). PubMed News & Views

S.W. Teng, S. Mukherji, J.R. Moffitt, S. de Buyl and E.K. O'Shea, Robust circadian oscillations in growing cyanobacteria require transcriptional feedback, Science, 340(6133) , pp. 737-740 (2013). PubMed

A. Gutu and and E.K. O'Shea, Two antagonistic clock-regulated histidine kinases time the activation of circadian gene expression, Molecular Cell, 50(2), pp. 288-294 (2013). PubMed

V. Vijayan and and E.K. O'Shea, Sequence determinants of circadian gene expression in cyanobacteria, Journal of Bacteriology, 195(4), pp. 665-671 (2013). PubMed

N. Hao, B.A. Budnik, J. Gunawardena and E.K. O'Shea, Tunable signal processing through modular control of transcription factor translocation, Science 339(460), pp. 460-464 (2013). PubMed

I. Carter-O'Connell, M.T. Peel, D.D. Wykoff, and E.K. O'Shea, Genome-Wide Characterization of the Phosphate Starvation Response in Schizosaccharomyces Pombe, BMC Genomics, 13: 697 (2012). PubMed

C. L. Grimes, L. De Zoysa Ariyanada, J. Melnyk and E.K. O'Shea, The innate immune protein Nod2 binds directly to MDP, a bacterial cell wall fragment, Journal of the American Chemical Society, 134(33) , pp. 13535-13537 (2012). PubMed

I. Jain, V. Vijayan and E.K. O'Shea, Spatial ordering of chromosomes enhances the fidelity of chromosome partitioning in cyanobacteria, Proc. Natl. Acad. Sci USA, 109(34) , 13638-43 (2012). PubMed

K. Cook and E.K. O'Shea, Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae,G3: Genes, Genomes, Genomics, 2(9) , pp. 1129-36.(2012). PubMed

N. Hao and E.K. O'Shea, Signal-dependent dynamics of transcription factor translocation controls gene expression, Nature Structural and Molecular Biology, 19(1):31-39 (2012). pdf

X. Zhou and E.K. O'Shea, Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4, Molecular Cell, 42(6):826-36 (2011). PubMed

V. Vijayan, I. H. Jain, E. K. O'Shea, A high resolution map of a cyanobacterial transcriptome, Genome Biology, 12:R47 (2011). PubMed

M. J. Rust, S. S. Golden, E. K. O'Shea. Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian clock, Science, 331 (614), 214-217 (2011). PubMed

C. L. Grimes, D. K. Poldolsky, E.K. O'Shea, Synthesis of Biologically Active Biotinylated Muramyl Dipeptides, Bioorganic & Medicinal Chemistry Letters, 20 (20), 6061-6063 (2010). PubMed

V. Vijayan, R. Zuzow, E.K. O'Shea, Oscillations in supercoiling drive circadian gene expression in cyanobacteria, PNAS,106 (52), 22564-22568 (2009).PubMed

J.S. Markson and E.K. O'Shea. The Molecular Clockwork of a Protein-based Circadian Oscillator, FEBS Letters, 583 (24), 3938-3947 (2009). PubMed

H.D. Kim*, T. Shay*, E.K. O’Shea, & A. Regev, Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets, Science, 325(5939), 429-432 (2009). (*equal contribution). PubMed

H.D. Kim and E.K. O’Shea, A quantitative model of transcription factor activated gene expression, Nature Structural Molecular Biology, 15(11), 1192-1198 (2008). PubMed

A.P. Capaldi, T. Kaplan, Y. Liu, N. Habib, A. Regev, N. Friedman, and E.K. O’Shea, Structure and Function of a Transcriptional Network Activated by the MAPK Hog1, Nature Genetics, 40(11), 1300-06 (2008). PubMed

F.H. Lam, D.J. Steger, & E.K. O'Shea, Chromatin Decouples Promoter Threshold from Dynamic Range, Nature, 453, 246-250 (2008). PubMed

Y.-S. Lee, K. Huang, F.A. Quiocho & E.K. O'Shea, Molecular Basis of Cyclin-CDK-CKI Regulation by Reversible Binding of an Inositol Pyrophosphate, Nature Chemical Biology, 4(1), 25-32 (2008). PubMed

K. Huang, I. Ferrin-O'Connell, W. Zhang, G. Leonard, E.K. O'Shea & F. A. Quiocho, Structure of the Pho85-Pho80 CDK-cyclin Complex of the Phosphate-responsive Signal Transduction Pathway, Molecular Cell, 28(4):614-23 (2007).PubMed

M.J. Rust*, J.S. Markson*, W.S. Lane, D.S. Fisher & E.K. O'Shea, Ordered Phosphorylation Governs Oscillation of a Three-Protein Circadian Clock, Science, 318, 809-812 (2007). (* equal contribution) Pub Med

D.Wykoff, A. Rizvi, J. Raser, B. Margolin and E. K. O'Shea, Positive feedback regulates switching of phosphate transporters in S. cerevisiae, Molecular Cell 27, 1005-1013 (2007). PubMed

Y-S. Lee, S. Mulugu, J. D. York, and E. K. O’Shea, Regulation of a Cyclin/CDK/CDK Inhibitor Complex by Inositol Pyrophosphates, Science, 316, 109-112 (2007). PubMed

N. Maheshri & E.K. O’Shea, Living with Noisy Genes: How Cells Function Reliably with Inherent Variability in Gene Expression, Annual Review of Biophysics and Biomolecular Structure, 36:413-34 (2007). pdf

A. Belle, E.K. O'Shea, et al, Quantification of protein half-lives in budding yeast proteome, Proc. Natl. Acad. Sci USA, 103, 13004-13009 (2006). PubMed

A. Bar-Even, J. Paulsson, N. Maheshri, M. Carmi, E. O'Shea, Y. Pilpel, & N. Barkai, Noise in protein expression scales with natural protein abundance, Nature Genetics, 38, 636-643 (2006). PubMed

N. J. Krogan et al., Global Landscape of Protein Complexes in the Yeast Saccharomyces cerevisiae, Nature, 440, 637-643 (2006). PubMed

N. Dephoure, R. Howson, J. Blethrow, K. M. Shokat & E.K. O'Shea, Combining Chemical Genetics and Proteomics to Identify Protein Kinase Substrates, Proc. Natl. Acad. Sci USA 102, 17940-17945 (2005). PubMed

J.M. Raser & E.K. O'Shea, Noise in Gene Expression: Origins, Consequences, and Control, Science 309, 2010-2013 (2005). PubMed

M.R. Thomas & E.K. O'Shea, An Intracellular Phosphate Buffer Filters Fluctuations in Extracellular Phosphate Levels, Proc. Natl. Acad. Sci USA 102, 9565-9570 (2005). PubMed

R. Howson, W.-K. Huh, S. Ghaemmaghami, J.V. Falvo, K. Bower, A. Belle, N. Dephoure, D.D. Wykoff, J.S. Weissman & E.K. O'Shea, Construction, Verification, and Experimental Use of Two Epitope-Tagged Collections of Budding Yeast Strains, Comp. Funct. Genomics 6, 2-16 (2005). PubMed

S. Huang & E.K. O'Shea, A Systematic High-Throughput Screen of a Yeast Deletion Collection for Mutants Defective in PHO5 Regulation, Genetics 169, 1859-1871 (2005). PubMed

D.D. Wykoff & E.K. O'Shea, Identification of Sumoylated Proteins by Systematic Immunoprecipitation of the Budding Yeast Proteome, Mol. Cell. Proteomics 4, 73-83 (2005). PubMed

J.S. Weissman & E.K. O'Shea, 2004 Irving Sigal Young Investigator Award, Protein Sci. 13, 3333-3335 (2004). PubMed

R.M. Marion, A. Regev, E. Segal, Y. Barash, D. Koller, N. Friedman & E.K. O'Shea, Sfp1 is a Stress- and Nutrient-Sensitive Regulator of Ribosomal Protein Gene Expression, Proc. Natl. Acad. Sci USA 101, 14315-14322 (2004). PubMed

J.M. Raser & E.K. O'Shea, Control of Stochasticity in Eukaryotic Gene Expression, Science, 304, 1811-1814 (2004). PubMed

D.J. Steger & E.K. O'Shea, Genetic Analysis of Chromatin Remodeling Using Budding Yeast as a Model, Methods Enzymol., 377, 55-60 (2004). PubMed

M. Byrne, N. Miller, M. Springer & E.K. O'Shea, A Distal, High-affinity Binding Site on the Cyclin-CDK Substrate Pho4 Is Important for Its Phosphorylation and Regulation, J. Mol. Biol., 335, 57-70 (2004). PubMed

M. Springer*, D.D. Wykoff*, N. Miller & E.K. O'Shea, Partially Phosphorylated Pho4 Activates Transcription of a Subset of Phosphate-Responsive Genes, PLoS Biol., 1, 261-270 (2003). PubMed

W.-K. Huh*, J.V. Falvo*, L.C. Gerke, A.S. Carroll, R.W. Howson, J.S. Weissman & E.K. O'Shea, Global Analysis of Protein Localization in Budding Yeast, Nature, 425, 686-691 (2003). PubMed

S. Ghaemmaghami, W.-K. Huh, K. Bower, R.W. Howson, A. Belle, N. Dephoure, E.K. O'Shea & J.S. Weissman, Global Analysis of Protein Expression in Yeast, Nature, 425, 737-741 (2003). PubMed

D.J. Steger, E.S. Haswell, A. Miller, S. Wente & E.K. O'Shea, Regulation of Chromatin Remodeling by Inositol Polyphosphates, Science, 299, 114-116 (2003). PubMed

A.S. Carroll & E.K. O’Shea, Pho85 and Signaling Environmental Stress, Trends Biochem. Sci., 27, 87-93 (2002). PubMed

S.M. O'Rourke, I. Herskowitz & E.K. O'Shea, Yeast Go Whole HOG for the Hyperosmotic Response, Trends in Genetics, 18, 405-412 (2002). PubMed

D.D. Wykoff & E.K. O'Shea, Phosphate transport and sensing in
Saccharomyces cerevisiae, Genetics, 159, 1491-1499 (2002). PubMed

A.S. Carroll, A.C. Bishop, J.L. DeRisi, K. Shokat & E.K. O’Shea, Chemical Inhibition of the Pho85 Cyclin-Dependent Kinase Reveals an Expanded Role in the Environmental Stress Response, Proc. Natl. Acad. Sci. USA 98,12578-12583 (2001). PubMed

A. Komeili & E.K. O'Shea, New Perspectives on Nuclear Transport, Ann. Rev. Genetics, 35, 341-364 (2001). PubMed

S. Huang, D. Jeffery, M. Anthony & E.K. O'Shea, Functional Analysis of the Cyclin-Dependent Kinase Inhibitor Pho81 Identifies a Novel Inhibitory Domain, Mol. Cell. Biol.21, 6695-6705 (2001). PubMed

D.A. Jeffery, M. Springer, D. King & E.K. O'Shea, Multi-Site Phosphorylation of Pho4 by the Cyclin-CDK Complex Pho80-Pho85 is Semi-Processive with Site Preference, J Mol. Biol. 306, 997-1010 (2001). PubMed

M.E. Lenburg & E.K. O'Shea, Genetic Evidence for a Morphogenetic Function of the Saccharomyces cerevisiae Pho85 Cyclin-Dependent Kinase, Genetics 157, 39-51 (2001). PubMed

E.K. O'Shea & I. Herskowitz, The Ins and Outs of Cell Polarity, Nature Cell Biol. 2, E39-E41 (2000). PubMed

W.-T. Lau, R.W. Howson, P. Malkus, R. Schekman & E.K. O'Shea, Pho86p, an ER Resident Protein in Saccharomyces cerevisiae, is Required for ER Exit of the High Affinity Phosphate Transporter Pho84p, Proc. Natl. Acad. Sci. USA 97, 1107-1112 (2000). PubMed

A. Komeili & E.K. O'Shea, Nuclear Transport and Transcription, Curr. Opin. Cell Biology 12, 355-360 (2000). PubMed

A. Komeili, K.P. Wedaman, E.K. O'Shea & T. Powers, Mechanism of Metabolic Control: TOR Signaling Links Nitrogen Quality to the Activity of the Rtg1p and Rtg3p Transcription Factors, J.Cell Biology 151, 863-878 (2000). PubMed

E.S. Haswell & E.K. O’Shea, An In Vitro System Recapitulates Chromatin Remodeling at the S. cerevisiae PHO5 Promoter, Mol. Cell. Biol.19, 2817-2827 (1999). PubMed

A. Komeili & E.K. O'Shea, Roles of Phosphorylation Sites in Regulating Activity of the Transcription Factor Pho4, Science 284, 977-980 (1999). PubMed

A. Kaffman & E.K. O'Shea, Regulation of Nuclear Localization: A Key to a Door, Ann. Rev. Cell Biol. 15, 291-339 (1999). PubMed

A. Kaffman, N.M. Rank & E.K. O’Shea, Phosphorylation regulates association of the transcription factor Pho4 with its import receptor Pse1/Kap121, Genes & Dev., 12, 2673-2683 (1998). PubMed

A. Kaffman, N.M. Rank, E.M. O’Neill, L. Huang & E.K. O’Shea, The Receptor Msn5 Exports the Phosphorylated Transcription Factor Pho4 Out of the Nucleus, Nature 396, 482-486 (1998). PubMed

W.-T. Lau, K.R. Schneider & E.K. O’Shea, A genetic study of signaling processes for repression of PHO5 transcription in S. cerevisiae, Genetics 150, 1349-1359 (1998). PubMed

E.S. Haswell & E.K. O’Shea, Specificity and Targeting of ATP-Dependent Chromatin Remodeling Machines in Yeast", Cold Spring Harbor Symposium on Quantitative Biology 63, 563-567 (1998). PubMed

E.M. O'Neill, A. Kaffman, E.R. Jolly & E.K. O'Shea, Regulation of PHO4 Nuclear Localization by the PHO80-PHO85 Cyclin-CDK Complex, Science, 271, 209-212 (1996). PubMed

M.E. Lenburg & E.K. O'Shea, Signaling Phosphate Starvation, TIBS 10, 383-387(1996). PubMed

E.M. O'Neill & E.K. O'Shea, Cyclins in initiation, Nature 374, 121-122 (1995). PubMed

A. Kaffman, I. Herskowitz, R. Tjian & E.K. O'Shea, Phosphorylation of the Transcription Factor PHO4 by a Cyclin-CDK Complex, PHO80-PHO85, Science 263, 1153-1156 (1994). PubMed

K.R. Schneider, R.L. Smith & E.K. O'Shea, Phosphate-Regulated Inactivation of the PHO80-PHO85 Kinase by the CDK Inhibitor PHO81, Science 266, 122-126 (1994). PubMed

E.K. O'Shea, K.J. Lumb & P.S. Kim, Peptide Velcro: Design of a Heterodimeric Coiled Coil, Current Biology 3, 658-667 (1993). PubMed

E.K. O'Shea, R. Rutkowski & P.S. Kim, Mechanism of Specificity in the Fos/Jun Oncoprotein Heterodimer, Cell 68, 699-708 (1992). PubMed

R. Rasmussen, D. Benvegnu, E.K. O'Shea, P.S. Kim & T. Alber, X-ray Scattering Indicates that the Leucine Zipper is a Parallel Coiled Coil, Proc. Natl. Acad. Sci. USA 88, 561-564 (1991). PubMed

E.K. O'Shea, J.D. Klemm, P.S. Kim & T. Alber, X-ray Structure of the GCN4 Leucine Zipper, A Two-Stranded, Parallel Coiled Coil, Science 254, 539-544 (1991). PubMed

T.G. Oas, L.P. McIntosh, E.K. O'Shea, F.W. Dahlquist & P.S. Kim, Secondary Structure of a Leucine Zipper Determined by Nuclear Magnetic Resonance Spectroscopy, Biochemistry 29, 2891-2894 (1990). PubMed

J.H. Hu, E.K. O'Shea, P.S. Kim & R.T. Sauer, Sequence Requirements for Coiled-Coils: Analysis With Lambda Repressor-GCN4 Leucine Zipper Fusions, Science 250, 1400-1403 (1990). PubMed

E.K. O'Shea, R. Rutkowski & P.S. Kim, Evidence that the Leucine Zipper is a Coiled Coil, Science 243, 538-542 (1989). PubMed

E.K. O'Shea, R. Rutkowski, W.F. Stafford, III & P.S. Kim, Preferential Heterodimer Formation by Isolated Leucine Zippers from Fos and Jun, Science 245, 646-648 (1989). PubMed



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