Eric D. Siggia - Publications

Affiliations: 
Rockefeller University, New York, NY, United States 

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2015 Kidd PB, Young MW, Siggia ED. Temperature compensation and temperature sensation in the circadian clock. Proceedings of the National Academy of Sciences of the United States of America. 112: E6284-92. PMID 26578788 DOI: 10.1073/pnas.1511215112  1
2014 Warmflash A, Zhang Q, Brivanlou AH, Siggia ED. Comment on "Controlling long-term signaling: receptor dynamics determine attenuation and refractory behavior of the TGF-β pathway"-Smad2/3 activity does not predict the dynamics of transcription. Science Signaling. 7: lc1. PMID 25249655 DOI: 10.1126/scisignal.2005562  1
2014 Warmflash A, Sorre B, Etoc F, Siggia ED, Brivanlou AH. A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods. 11: 847-54. PMID 24973948 DOI: 10.1038/nmeth.3016  1
2012 Warmflash A, Siggia ED, Brivanlou AH. Signaling dynamics and embryonic development. Cell Cycle (Georgetown, Tex.). 11: 3529-30. PMID 22935712 DOI: 10.4161/cc.21964  1
2012 Warmflash A, Francois P, Siggia ED. Pareto evolution of gene networks: an algorithm to optimize multiple fitness objectives. Physical Biology. 9: 056001. PMID 22874123 DOI: 10.1088/1478-3975/9/5/056001  1
2012 Warmflash A, Zhang Q, Sorre B, Vonica A, Siggia ED, Brivanlou AH. Dynamics of TGF-β signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4. Proceedings of the National Academy of Sciences of the United States of America. 109: E1947-56. PMID 22689943 DOI: 10.1073/pnas.1207607109  1
2010 Bai L, Charvin G, Siggia ED, Cross FR. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Developmental Cell. 18: 544-55. PMID 20412770 DOI: 10.1016/j.devcel.2010.02.007  1
2010 Charvin G, Oikonomou C, Siggia ED, Cross FR. Origin of irreversibility of cell cycle start in budding yeast. Plos Biology. 8: e1000284. PMID 20087409 DOI: 10.1371/journal.pbio.1000284  1
2009 Francois P, Vonica A, Brivanlou AH, Siggia ED. Scaling of BMP gradients in Xenopus embryos. Nature. 461: E1; discussion E2. PMID 19736667 DOI: 10.1038/nature08305  1
2009 Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Research. 37: 4707-22. PMID 19509309 DOI: 10.1093/nar/gkp475  1
2009 Gertz J, Siggia ED, Cohen BA. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature. 457: 215-8. PMID 19029883 DOI: 10.1038/nature07521  1
2008 Skotheim JM, Di Talia S, Siggia ED, Cross FR. Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature. 454: 291-6. PMID 18633409 DOI: 10.1038/nature07118  1
2008 Charvin G, Cross FR, Siggia ED. A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. Plos One. 3: e1468. PMID 18213377 DOI: 10.1371/journal.pone.0001468  1
2007 François P, Hakim V, Siggia ED. Deriving structure from evolution: metazoan segmentation. Molecular Systems Biology. 3: 154. PMID 18091725 DOI: 10.1038/msb4100192  1
2007 Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature. 448: 947-51. PMID 17713537 DOI: 10.1038/nature06072  1
2007 Mwangi MM, Wu SW, Zhou Y, Sieradzki K, de Lencastre H, Richardson P, Bruce D, Rubin E, Myers E, Siggia ED, Tomasz A. Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proceedings of the National Academy of Sciences of the United States of America. 104: 9451-6. PMID 17517606 DOI: 10.1073/pnas.0609839104  1
2007 Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 7068-73. PMID 17438293 DOI: 10.1073/pnas.0701356104  1
2006 Ligr M, Siddharthan R, Cross FR, Siggia ED. Gene expression from random libraries of yeast promoters. Genetics. 172: 2113-22. PMID 16415362 DOI: 10.1534/genetics.105.052688  1
2006 Bean JM, Siggia ED, Cross FR. Coherence and timing of cell cycle start examined at single-cell resolution. Molecular Cell. 21: 3-14. PMID 16387649 DOI: 10.1016/j.molcel.2005.10.035  1
2005 Siddharthan R, Siggia ED, van Nimwegen E. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. Plos Computational Biology. 1: e67. PMID 16477324 DOI: 10.1371/journal.pcbi.0010067  0.32
2005 Morozov AV, Havranek JJ, Baker D, Siggia ED. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Research. 33: 5781-98. PMID 16246914 DOI: 10.1093/nar/gki875  1
2005 Cross FR, Siggia ED. Mode locking the cell cycle. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 021910. PMID 16196607 DOI: 10.1103/PhysRevE.72.021910  1
2005 Cross FR, Siggia ED. Shake it, don't break it: positive feedback and the evolution of oscillator design. Developmental Cell. 9: 309-10. PMID 16139219 DOI: 10.1016/j.devcel.2005.08.006  1
2005 Bean JM, Siggia ED, Cross FR. High functional overlap between MluI cell-cycle box binding factor and Swi4/6 cell-cycle box binding factor in the G1/S transcriptional program in Saccharomyces cerevisiae. Genetics. 171: 49-61. PMID 15965243 DOI: 10.1534/genetics.105.044560  1
2005 Sinha S, Siggia ED. Sequence turnover and tandem repeats in cis-regulatory modules in drosophila. Molecular Biology and Evolution. 22: 874-85. PMID 15659554 DOI: 10.1093/molbev/msi090  0.32
2004 Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED. Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. Bmc Bioinformatics. 5: 129. PMID 15357878 DOI: 10.1186/1471-2105-5-129  1
2004 Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U. Transcriptional control in the segmentation gene network of Drosophila. Plos Biology. 2: E271. PMID 15340490 DOI: 10.1371/journal.pbio.0020271  1
2003 Sinha S, van Nimwegen E, Siggia ED. A probabilistic method to detect regulatory modules. Bioinformatics (Oxford, England). 19: i292-301. PMID 12855472  0.32
2002 Rajewsky N, Vergassola M, Gaul U, Siggia ED. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. Bmc Bioinformatics. 3: 30. PMID 12398796 DOI: 10.1186/1471-2105-3-30  1
2002 Swain PS, Elowitz MB, Siggia ED. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proceedings of the National Academy of Sciences of the United States of America. 99: 12795-800. PMID 12237400 DOI: 10.1073/pnas.162041399  1
2002 Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science (New York, N.Y.). 297: 1183-6. PMID 12183631 DOI: 10.1126/science.1070919  1
2002 van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED. Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proceedings of the National Academy of Sciences of the United States of America. 99: 7323-8. PMID 12032281 DOI: 10.1073/pnas.112690399  0.32
2002 Presley JF, Ward TH, Pfeifer AC, Siggia ED, Phair RD, Lippincott-Schwartz J. Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport. Nature. 417: 187-93. PMID 12000962 DOI: 10.1038/417187a  1
2002 Rajewsky N, Socci ND, Zapotocky M, Siggia ED. The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Research. 12: 298-308. PMID 11827949 DOI: 10.1101/gr.207502. Article published online before print in January 2002  1
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