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Harley H. McAdams - Publications

Affiliations: 
Developmental Biology Stanford University, Palo Alto, CA 
Area:
bacterial genetic regulation
Website:
http://med.stanford.edu/profiles/Harley_McAdams/

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Schrader JM, Li GW, Childers WS, Perez AM, Weissman JS, Shapiro L, McAdams HH. Dynamic translation regulation in Caulobacter cell cycle control. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791168 DOI: 10.1073/pnas.1614795113  1
2016 Ricci DP, Melfi MD, Lasker K, Dill DL, McAdams HH, Shapiro L. Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition. Proceedings of the National Academy of Sciences of the United States of America. PMID 27647925 DOI: 10.1073/pnas.1612579113  1
2015 Lasker K, Schrader JM, Men Y, Marshik T, Dill DL, McAdams HH, Shapiro L. CauloBrowser: A systems biology resource for Caulobacter crescentus. Nucleic Acids Research. PMID 26476443 DOI: 10.1093/nar/gkv1050  1
2015 Zhou B, Schrader JM, Kalogeraki VS, Abeliuk E, Dinh CB, Pham JQ, Cui ZZ, Dill DL, McAdams HH, Shapiro L. The global regulatory architecture of transcription during the Caulobacter cell cycle. Plos Genetics. 11: e1004831. PMID 25569173 DOI: 10.1371/journal.pgen.1004831  1
2014 Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, Williams B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L. The coding and noncoding architecture of the Caulobacter crescentus genome. Plos Genetics. 10: e1004463. PMID 25078267 DOI: 10.1371/journal.pgen.1004463  1
2014 Gonzalez D, Kozdon JB, McAdams HH, Shapiro L, Collier J. The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach. Nucleic Acids Research. 42: 3720-35. PMID 24398711 DOI: 10.1093/nar/gkt1352  1
2013 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. Global methylation state at base-pair resolution of the Caulobacter genome throughout the cell cycle. Proceedings of the National Academy of Sciences of the United States of America. 110: E4658-67. PMID 24218615 DOI: 10.1073/pnas.1319315110  1
2013 Hong SH, Toro E, Mortensen KI, de la Rosa MA, Doniach S, Shapiro L, Spakowitz AJ, McAdams HH. Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement. Proceedings of the National Academy of Sciences of the United States of America. 110: 1674-9. PMID 23319648 DOI: 10.1073/pnas.1220824110  1
2013 Alquraishi M, Mcadams HH. Three enhancements to the inference of statistical protein-DNA potentials Proteins: Structure, Function and Bioinformatics. 81: 426-442. PMID 23042633 DOI: 10.1002/prot.24201  1
2011 Hong SH, McAdams HH. Compaction and transport properties of newly replicated Caulobacter crescentus DNA Molecular Microbiology. 82: 1349-1358. PMID 22085253 DOI: 10.1111/j.1365-2958.2011.07899.x  1
2011 Umbarger MA, Toro E, Wright MA, Porreca GJ, Baù D, Hong SH, Fero MJ, Zhu LJ, Marti-Renom MA, McAdams HH, Shapiro L, Dekker J, Church GM. The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Molecular Cell. 44: 252-64. PMID 22017872 DOI: 10.1016/j.molcel.2011.09.010  1
2011 Christen B, Abeliuk E, Collier JM, Kalogeraki VS, Passarelli B, Coller JA, Fero MJ, McAdams HH, Shapiro L. The essential genome of a bacterium Molecular Systems Biology. 7. PMID 21878915 DOI: 10.1038/msb.2011.58  1
2011 AlQuraishi M, McAdams HH. Direct inference of protein-DNA interactions using compressed sensing methods Proceedings of the National Academy of Sciences of the United States of America. 108: 14819-14824. PMID 21825146 DOI: 10.1073/pnas.1106460108  1
2011 Kirschner MW, Shapiro L, McAdams H, Almouzni G, Sharp PA, Young RA, Alon U. Fifty years after Jacob and Monod: what are the unanswered questions in molecular biology? Molecular Cell. 42: 403-4. PMID 21748867  1
2011 Goley ED, Yeh YC, Hong SH, Fero MJ, Abeliuk E, Mcadams HH, Shapiro L. Assembly of the Caulobacter cell division machine Molecular Microbiology. 80: 1680-1698. PMID 21542856 DOI: 10.1111/j.1365-2958.2011.07677.x  1
2011 Britos L, Abeliuk E, Taverner T, Lipton M, McAdams H, Shapiro L. Regulatory response to carbon starvation in caulobacter crescentus Plos One. 6. PMID 21494595 DOI: 10.1371/journal.pone.0018179  1
2011 McAdams HH, Shapiro L. The architecture and conservation pattern of whole-cell control circuitry Journal of Molecular Biology. 409: 28-35. PMID 21371478 DOI: 10.1016/j.jmb.2011.02.041  1
2010 Tan HM, Kozdon JB, Shen X, Shapiro L, McAdams HH. An essential transcription factor, SciP, enhances robustness of Caulobacter cell cycle regulation Proceedings of the National Academy of Sciences of the United States of America. 107: 18985-18990. PMID 20956288 DOI: 10.1073/pnas.1014395107  1
2010 Yeh YC, Comolli LR, Downing KH, Shapiro L, McAdams HH. The caulobacter Tol-Pal complex is essential for outer membrane integrity and the positioning of a polar localization factor. Journal of Bacteriology. 192: 4847-58. PMID 20693330 DOI: 10.1128/JB.00607-10  1
2010 Christen B, Fero MJ, Hillson NJ, Bowman G, Hong SH, Shapiro L, McAdams HH. High-throughput identification of protein localization dependency networks Proceedings of the National Academy of Sciences of the United States of America. 107: 4681-4686. PMID 20176934 DOI: 10.1073/pnas.1000846107  1
2010 Bowman GR, Comolli LR, Gaietta GM, Fero M, Hong SH, Jones Y, Lee JH, Downing KH, Ellisman MH, McAdams HH, Shapiro L. Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function. Molecular Microbiology. 76: 173-89. PMID 20149103 DOI: 10.1111/j.1365-2958.2010.07088.x  1
2010 Yeh YC, Comolli LR, Downing KH, Shapiro L, McAdams HH. The Caulobacter Tol-Pal complex is essential for outer membrane integrity and the positioning of a polar localization factor Journal of Bacteriology. 192: 4847-4858. DOI: 10.1128/JB.00607-10  1
2009 Shapiro L, McAdams HH, Losick R. Why and how bacteria localize proteins Science. 326: 1225-1228. PMID 19965466 DOI: 10.1126/science.1175685  1
2009 McAdams HH, Shapiro L. System-level design of bacterial cell cycle control Febs Letters. 583: 3984-3991. PMID 19766635 DOI: 10.1016/j.febslet.2009.09.030  1
2009 Goley ED, Toro E, McAdams HH, Shapiro L. Dynamic chromosome organization and protein localization coordinate the regulatory circuitry that drives the bacterial cell cycle Cold Spring Harbor Symposia On Quantitative Biology. 74: 55-64. PMID 19687139 DOI: 10.1101/sqb.2009.74.005  1
2008 Toro E, Hong SH, McAdams HH, Shapiro L. Caulobacter requires a dedicated mechanism to initiate chromosome segregation Proceedings of the National Academy of Sciences of the United States of America. 105: 15435-15440. PMID 18824683 DOI: 10.1073/pnas.0807448105  1
2008 Shen X, Collier J, Dill D, Shapiro L, Horowitz M, McAdams HH. Architecture and inherent robustness of a bacterial cell-cycle control system Proceedings of the National Academy of Sciences of the United States of America. 105: 11340-11345. PMID 18685108 DOI: 10.1073/pnas.0805258105  1
2008 Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L. Small non-coding RNAs in Caulobacter crescentus Molecular Microbiology. 68: 600-614. PMID 18373523 DOI: 10.1111/j.1365-2958.2008.06172.x  1
2007 Laub MT, Shapiro L, McAdams HH. Systems biology of caulobacter Annual Review of Genetics. 41: 429-441. PMID 18076330 DOI: 10.1146/annurev.genet.41.110306.130346  1
2007 Collier J, McAdams HH, Shapiro L. A DNA methylation ratchet governs progression through a bacterial cell cycle Proceedings of the National Academy of Sciences of the United States of America. 104: 17111-17116. PMID 17942674 DOI: 10.1073/pnas.0708112104  1
2007 McGrath PT, Lee H, Zhang L, Iniesta AA, Hottes AK, Tan MH, Hillson NJ, Hu P, Shapiro L, McAdams HH. High-throughput identification of transcription start sites, conserved promoter motifs and predicted regulons. Nature Biotechnology. 25: 584-92. PMID 17401361 DOI: 10.1038/nbt1294  1
2006 Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Research. 16: 1169-81. PMID 16899655 DOI: 10.1101/gr.5235706  1
2006 McAdams HH. Bacterial stalks are nutrient-scavenging antennas. Proceedings of the National Academy of Sciences of the United States of America. 103: 11435-6. PMID 16868078 DOI: 10.1073/pnas.0605027103  1
2006 Iniesta AA, McGrath PT, Reisenauer A, McAdams HH, Shapiro L. A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression. Proceedings of the National Academy of Sciences of the United States of America. 103: 10935-40. PMID 16829582 DOI: 10.1073/pnas.0604554103  1
2006 McGrath PT, Iniesta AA, Ryan KR, Shapiro L, McAdams HH. A dynamically localized protease complex and a polar specificity factor control a cell cycle master regulator. Cell. 124: 535-47. PMID 16469700 DOI: 10.1016/j.cell.2005.12.033  1
2006 Chen JC, Hottes AK, McAdams HH, McGrath PT, Viollier PH, Shapiro L. Cytokinesis signals truncation of the PodJ polarity factor by a cell cycle-regulated protease. The Embo Journal. 25: 377-86. PMID 16395329 DOI: 10.1038/sj.emboj.7600935  1
2006 Srinivasan BS, Novak AF, Flannick JA, Batzoglou S, McAdams HH. Integrated protein interaction networks for 11 microbes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 1-14.  1
2005 Hu P, Brodie EL, Suzuki Y, McAdams HH, Andersen GL. Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. Journal of Bacteriology. 187: 8437-49. PMID 16321948 DOI: 10.1128/JB.187.24.8437-8449.2005  1
2005 Hottes AK, Shapiro L, McAdams HH. DnaA coordinates replication initiation and cell cycle transcription in Caulobacter crescentus. Molecular Microbiology. 58: 1340-53. PMID 16313620 DOI: 10.1111/j.1365-2958.2005.04912.x  1
2005 Judd EM, Comolli LR, Chen JC, Downing KH, Moerner WE, McAdams HH. Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes. Journal of Bacteriology. 187: 6874-82. PMID 16199556 DOI: 10.1128/JB.187.20.6874-6882.2005  1
2005 Crosson S, McGrath PT, Stephens C, McAdams HH, Shapiro L. Conserved modular design of an oxygen sensory/signaling network with species-specific output. Proceedings of the National Academy of Sciences of the United States of America. 102: 8018-23. PMID 15911751 DOI: 10.1073/pnas.0503022102  1
2004 Deich J, Judd EM, McAdams HH, Moerner WE. Visualization of the movement of single histidine kinase molecules in live Caulobacter cells. Proceedings of the National Academy of Sciences of the United States of America. 101: 15921-6. PMID 15522969 DOI: 10.1073/pnas.0404200101  1
2004 Crosson S, McAdams H, Shapiro L. A genetic oscillator and the regulation of cell cycle progression in Caulobacter crescentus. Cell Cycle (Georgetown, Tex.). 3: 1252-4. PMID 15467452  1
2004 Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L. Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proceedings of the National Academy of Sciences of the United States of America. 101: 9257-62. PMID 15178755 DOI: 10.1073/pnas.0402606101  1
2004 Holtzendorff J, Hung D, Brende P, Reisenauer A, Viollier PH, McAdams HH, Shapiro L. Oscillating global regulators control the genetic circuit driving a bacterial cell cycle. Science (New York, N.Y.). 304: 983-7. PMID 15087506 DOI: 10.1126/science.1095191  1
2004 McGrath PT, Viollier P, McAdams HH. Setting the pace: mechanisms tying Caulobacter cell-cycle progression to macroscopic cellular events. Current Opinion in Microbiology. 7: 192-7. PMID 15063858 DOI: 10.1016/j.mib.2004.02.012  1
2004 Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH. Codon usage between genomes is constrained by genome-wide mutational processes. Proceedings of the National Academy of Sciences of the United States of America. 101: 3480-5. PMID 14990797 DOI: 10.1073/pnas.0307827100  1
2004 Hottes AK, Meewan M, Yang D, Arana N, Romero P, McAdams HH, Stephens C. Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media. Journal of Bacteriology. 186: 1448-61. PMID 14973021 DOI: 10.1128/JB.186.5.1448-1461.2004  1
2004 McAdams HH, Srinivasan B, Arkin AP. The evolution of genetic regulatory systems in bacteria. Nature Reviews. Genetics. 5: 169-78. PMID 14970819 DOI: 10.1038/nrg1292  1
2003 McAdams HH, Shapiro L. A bacterial cell-cycle regulatory network operating in time and space. Science (New York, N.Y.). 301: 1874-7. PMID 14512618 DOI: 10.1126/science.1087694  1
2003 Judd EM, Ryan KR, Moerner WE, Shapiro L, McAdams HH. Fluorescence bleaching reveals asymmetric compartment formation prior to cell division in Caulobacter. Proceedings of the National Academy of Sciences of the United States of America. 100: 8235-40. PMID 12824468 DOI: 10.1073/pnas.1433105100  1
2002 Shapiro L, McAdams HH, Losick R. Generating and exploiting polarity in bacteria. Science (New York, N.Y.). 298: 1942-6. PMID 12471245 DOI: 10.1126/science.1072163  1
2002 Laub MT, Chen SL, Shapiro L, McAdams HH. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle Proceedings of the National Academy of Sciences of the United States of America. 99: 4632-4637. PMID 11930012 DOI: 10.1073/pnas.062065699  1
2000 Laub MT, McAdams HH, Feldblyum T, Fraser CM, Shapiro L. Global analysis of the genetic network controlling a bacterial cell cycle Science. 290: 2144-2148. PMID 11118148 DOI: 10.1126/science.290.5499.2144  1
2000 Judd EM, Laub MT, McAdams HH. Toggles and oscillators: New genetic circuit designs Bioessays. 22: 507-509. PMID 10842304 DOI: 10.1002/(SICI)1521-1878(200006)22:6<507::AID-BIES3>3.0.CO;2-0  1
2000 McAdams HH, Arkin A. Towards a circuit engineering discipline. Current Biology : Cb. 10: R318-20. PMID 10801411 DOI: 10.1016/S0960-9822(00)00440-1  1
1999 McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics : Tig. 15: 65-9. PMID 10098409 DOI: 10.1016/S0168-9525(98)01659-X  1
1998 Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 149: 1633-48. PMID 9691025  1
1998 McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annual Review of Biophysics and Biomolecular Structure. 27: 199-224. PMID 9646867 DOI: 10.1146/annurev.biophys.27.1.199  1
1997 McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proceedings of the National Academy of Sciences of the United States of America. 94: 814-9. PMID 9023339 DOI: 10.1073/pnas.94.3.814  1
1995 McAdams HH, Shapiro L. Circuit simulation of genetic networks. Science (New York, N.Y.). 269: 650-6. PMID 7624793  1
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