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Dynamic translation regulation in Caulobacter cell cycle control.

Schrader JM, Li GW, Childers WS, Perez AM, Weissman JS, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):E6859-E6867. Epub 2016 Oct 17.


Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition.

Ricci DP, Melfi MD, Lasker K, Dill DL, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):E5952-E5961. Epub 2016 Sep 19.


CauloBrowser: A systems biology resource for Caulobacter crescentus.

Lasker K, Schrader JM, Men Y, Marshik T, Dill DL, McAdams HH, Shapiro L.

Nucleic Acids Res. 2016 Jan 4;44(D1):D640-5. doi: 10.1093/nar/gkv1050. Epub 2015 Oct 17.


The global regulatory architecture of transcription during the Caulobacter cell cycle.

Zhou B, Schrader JM, Kalogeraki VS, Abeliuk E, Dinh CB, Pham JQ, Cui ZZ, Dill DL, McAdams HH, Shapiro L.

PLoS Genet. 2015 Jan 8;11(1):e1004831. doi: 10.1371/journal.pgen.1004831. eCollection 2015 Jan.


The coding and noncoding architecture of the Caulobacter crescentus genome.

Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L.

PLoS Genet. 2014 Jul 31;10(7):e1004463. doi: 10.1371/journal.pgen.1004463. eCollection 2014 Jul.


The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.

Gonzalez D, Kozdon JB, McAdams HH, Shapiro L, Collier J.

Nucleic Acids Res. 2014 Apr;42(6):3720-35. doi: 10.1093/nar/gkt1352. Epub 2014 Jan 7.


Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle.

Kozdon JB, Melfi MD, Luong K, Clark TA, Boitano M, Wang S, Zhou B, Gonzalez D, Collier J, Turner SW, Korlach J, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2013 Nov 26;110(48):E4658-67. doi: 10.1073/pnas.1319315110. Epub 2013 Nov 11.


Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement.

Hong SH, Toro E, Mortensen KI, de la Rosa MA, Doniach S, Shapiro L, Spakowitz AJ, McAdams HH.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1674-9. doi: 10.1073/pnas.1220824110. Epub 2013 Jan 14.


Three enhancements to the inference of statistical protein-DNA potentials.

AlQuraishi M, McAdams HH.

Proteins. 2013 Mar;81(3):426-42. doi: 10.1002/prot.24201. Epub 2012 Nov 12.


Compaction and transport properties of newly replicated Caulobacter crescentus DNA.

Hong SH, McAdams HH.

Mol Microbiol. 2011 Dec;82(6):1349-58. doi: 10.1111/j.1365-2958.2011.07899.x. Epub 2011 Nov 16.


The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.

Umbarger MA, Toro E, Wright MA, Porreca GJ, BaĆ¹ D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM.

Mol Cell. 2011 Oct 21;44(2):252-64. doi: 10.1016/j.molcel.2011.09.010.


The essential genome of a bacterium.

Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L.

Mol Syst Biol. 2011 Aug 30;7:528. doi: 10.1038/msb.2011.58.


Direct inference of protein-DNA interactions using compressed sensing methods.

AlQuraishi M, McAdams HH.

Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14819-24. doi: 10.1073/pnas.1106460108. Epub 2011 Aug 8.


Assembly of the Caulobacter cell division machine.

Goley ED, Yeh YC, Hong SH, Fero MJ, Abeliuk E, McAdams HH, Shapiro L.

Mol Microbiol. 2011 Jun;80(6):1680-98. doi: 10.1111/j.1365-2958.2011.07677.x. Epub 2011 May 17.


The architecture and conservation pattern of whole-cell control circuitry.

McAdams HH, Shapiro L.

J Mol Biol. 2011 May 27;409(1):28-35. doi: 10.1016/j.jmb.2011.02.041. Epub 2011 Mar 1.


An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation.

Tan MH, Kozdon JB, Shen X, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2010 Nov 2;107(44):18985-90. doi: 10.1073/pnas.1014395107. Epub 2010 Oct 18.


The caulobacter Tol-Pal complex is essential for outer membrane integrity and the positioning of a polar localization factor.

Yeh YC, Comolli LR, Downing KH, Shapiro L, McAdams HH.

J Bacteriol. 2010 Oct;192(19):4847-58. doi: 10.1128/JB.00607-10. Epub 2010 Aug 6.


High-throughput identification of protein localization dependency networks.

Christen B, Fero MJ, Hillson NJ, Bowman G, Hong SH, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2010 Mar 9;107(10):4681-6. doi: 10.1073/pnas.1000846107. Epub 2010 Feb 22.


Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function.

Bowman GR, Comolli LR, Gaietta GM, Fero M, Hong SH, Jones Y, Lee JH, Downing KH, Ellisman MH, McAdams HH, Shapiro L.

Mol Microbiol. 2010 Apr;76(1):173-89. doi: 10.1111/j.1365-2958.2010.07088.x. Epub 2010 Feb 10.


Why and how bacteria localize proteins.

Shapiro L, McAdams HH, Losick R.

Science. 2009 Nov 27;326(5957):1225-8. doi: 10.1126/science.1175685. Review.


System-level design of bacterial cell cycle control.

McAdams HH, Shapiro L.

FEBS Lett. 2009 Dec 17;583(24):3984-91. doi: 10.1016/j.febslet.2009.09.030. Review.


Dynamic chromosome organization and protein localization coordinate the regulatory circuitry that drives the bacterial cell cycle.

Goley ED, Toro E, McAdams HH, Shapiro L.

Cold Spring Harb Symp Quant Biol. 2009;74:55-64. doi: 10.1101/sqb.2009.74.005. Epub 2009 Aug 17. Review.


Caulobacter requires a dedicated mechanism to initiate chromosome segregation.

Toro E, Hong SH, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2008 Oct 7;105(40):15435-40. doi: 10.1073/pnas.0807448105. Epub 2008 Sep 29.


Architecture and inherent robustness of a bacterial cell-cycle control system.

Shen X, Collier J, Dill D, Shapiro L, Horowitz M, McAdams HH.

Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11340-5. doi: 10.1073/pnas.0805258105. Epub 2008 Aug 6.


Small non-coding RNAs in Caulobacter crescentus.

Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L.

Mol Microbiol. 2008 May;68(3):600-14. doi: 10.1111/j.1365-2958.2008.06172.x. Epub 2008 Mar 25.


Systems biology of Caulobacter.

Laub MT, Shapiro L, McAdams HH.

Annu Rev Genet. 2007;41:429-41. Review.


A DNA methylation ratchet governs progression through a bacterial cell cycle.

Collier J, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17111-6. Epub 2007 Oct 17.


High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons.

McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams HH.

Nat Biotechnol. 2007 May;25(5):584-92. Epub 2007 Apr 1.


Graemlin: general and robust alignment of multiple large interaction networks.

Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S.

Genome Res. 2006 Sep;16(9):1169-81. Epub 2006 Aug 9.


Bacterial stalks are nutrient-scavenging antennas.

McAdams HH.

Proc Natl Acad Sci U S A. 2006 Aug 1;103(31):11435-6. Epub 2006 Jul 25. No abstract available.


A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression.

Iniesta AA, McGrath PT, Reisenauer A, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10935-40. Epub 2006 Jul 7.


A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator.

McGrath PT, Iniesta AA, Ryan KR, Shapiro L, McAdams HH.

Cell. 2006 Feb 10;124(3):535-47.


Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease.

Chen JC, Hottes AK, McAdams HH, McGrath PT, Viollier PH, Shapiro L.

EMBO J. 2006 Jan 25;25(2):377-86. Epub 2006 Jan 5.


Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus.

Hu P, Brodie EL, Suzuki Y, McAdams HH, Andersen GL.

J Bacteriol. 2005 Dec;187(24):8437-49.


DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus.

Hottes AK, Shapiro L, McAdams HH.

Mol Microbiol. 2005 Dec;58(5):1340-53.


Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes.

Judd EM, Comolli LR, Chen JC, Downing KH, Moerner WE, McAdams HH.

J Bacteriol. 2005 Oct;187(20):6874-82.


Conserved modular design of an oxygen sensory/signaling network with species-specific output.

Crosson S, McGrath PT, Stephens C, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):8018-23. Epub 2005 May 23.


Visualization of the movement of single histidine kinase molecules in live Caulobacter cells.

Deich J, Judd EM, McAdams HH, Moerner WE.

Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15921-6. Epub 2004 Nov 2.


Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication.

Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L.

Proc Natl Acad Sci U S A. 2004 Jun 22;101(25):9257-62. Epub 2004 Jun 3.


Oscillating global regulators control the genetic circuit driving a bacterial cell cycle.

Holtzendorff J, Hung D, Brende P, Reisenauer A, Viollier PH, McAdams HH, Shapiro L.

Science. 2004 May 14;304(5673):983-7. Epub 2004 Apr 15.


Setting the pace: mechanisms tying Caulobacter cell-cycle progression to macroscopic cellular events.

McGrath PT, Viollier P, McAdams HH.

Curr Opin Microbiol. 2004 Apr;7(2):192-7. Review.


Codon usage between genomes is constrained by genome-wide mutational processes.

Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3480-5. Epub 2004 Feb 27.


Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media.

Hottes AK, Meewan M, Yang D, Arana N, Romero P, McAdams HH, Stephens C.

J Bacteriol. 2004 Mar;186(5):1448-61.


The evolution of genetic regulatory systems in bacteria.

McAdams HH, Srinivasan B, Arkin AP.

Nat Rev Genet. 2004 Mar;5(3):169-78. Review. No abstract available.


A bacterial cell-cycle regulatory network operating in time and space.

McAdams HH, Shapiro L.

Science. 2003 Sep 26;301(5641):1874-7. Review.


Fluorescence bleaching reveals asymmetric compartment formation prior to cell division in Caulobacter.

Judd EM, Ryan KR, Moerner WE, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8235-40. Epub 2003 Jun 24.


Generating and exploiting polarity in bacteria.

Shapiro L, McAdams HH, Losick R.

Science. 2002 Dec 6;298(5600):1942-6. Review.


Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle.

Laub MT, Chen SL, Shapiro L, McAdams HH.

Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4632-7.


Global analysis of the genetic network controlling a bacterial cell cycle.

Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L.

Science. 2000 Dec 15;290(5499):2144-8.


Toggles and oscillators: new genetic circuit designs.

Judd EM, Laub MT, McAdams HH.

Bioessays. 2000 Jun;22(6):507-9. Review.


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