2000-9

 

2009:

  1. • Using DNA mechanics to predict in vitro nucleosome positions and formation energies.  Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED.  Nucleic Acids Res. 37(14):4707-22. PDF

  2. • Forced periodic expression of G1 cyclins phase-locks the budding yeast cell cycle.  Charvin G, Cross FR, Siggia ED.  Proc Natl Acad Sci U S A. 106(16):6632-7. PDF  Suppl.pdf

  3. • Analysis of combinatorial cis-regulation in synthetic and genomic promoters Gertz J, Siggia ED, Cohen BA.  Nature. 457(7226):215-8. PDF

  4. •Scaling of BMP gradients in xenopus embryos. Francois P, Vonica A, Brivanlou AH, Siggia ED. Nature. 2009 Sep 3;461(7260). PDF

  5. •Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. Nucleic Acids Res. 2009 Aug;37(14):4707-22 PDF

2008:

  1. • Developmental regulatory bits  Siggia ED. Mol Syst Biol. 4:226. PDF 

  2. • Positive feedback of G1 cyclins ensures coherent cell cycle entry. Skotheim JM, Di Talia S, Siggia ED, Cross FR. Nature. 2008 Jul 17;454(7202):291-6. PDF

  3. • A case study of evolutionary computation of biochemical adaptation. François P, Siggia ED. Phys Biol. 2008 Jun 24;5(2):26009. PDF

  4. • Sequence context affects the rate of short insertions and deletions in flies and primates. Tanay A, Siggia ED. Genome Biol. 2008;9(2):R37. PDF

  5. • A microfluidic device for temporally controlled gene expression and long-term fluorescent imaging in unperturbed dividing yeast cells. Charvin G, Cross FR, Siggia ED. PLoS One. 2008 Jan 23;3(1):e1468. PDF  Suppl.pdf

2007:

  1. • Deriving structure from evolution: metazoan segmentation. François P, Hakim V, Siggia ED. Mol Syst Biol. 2007;3:154. PDF

  2. • The effects of molecular noise and size control on variability in the budding yeast cell cycle. Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR. Nature. 2007 Aug 23;448(7156):947-51. Erratum in: Nature. 2007 Dec 20;450(7173):1272. PDF

  3. • Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Mwangi MM, Wu SW, Zhou Y, Sieradzki K, de Lencastre H, Richardson P, Bruce D, Rubin E, Myers E, Siggia ED, Tomasz A. Proc Natl Acad Sci U S A. 2007 May 29;104(22):9451-6. PDF  Suppl.pdf

  4. • Connecting protein structure with predictions of regulatory sites. Morozov AV, Siggia ED. Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7068-73. PDF  Suppl6.pdf

2006:

  1. • Stubb: a program for discovery and analysis of cis-regulatory modules., Sinha S, Liang Y, Siggia E. Nucleic Acids Res. 34 W555-9, 2006. PDF

  2. • Gene expression from random libraries of yeast promoters. Ligr M, Siddharthan R, Cross FR, Siggia ED. Genetics. 2006 Apr;172(4):2113-22. PDF

  3. • Coherence and timing of cell cycle start examined at single-cell resolution. Bean JM, Siggia ED, Cross FR. Mol Cell. 2006 Jan 6;21(1):3-14. PDF

2005:

  1. • PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. Siddharthan R, Siggia ED, van Nimwegen E. PLoS Comput Biol. 2005 Dec;1(7):e67. PDF

  2. • Protein-DNA binding specificity predictions with structural models. Morozov AV, Havranek JJ, Baker D, Siggia ED. Nucleic Acids Res. 2005 Oct 24;33(18):5781-98. PDF

  3. • Mode locking the cell cycle. Cross FR, Siggia ED. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Aug;72(2 Pt 1):021910. PDF

  4. • Shake it, don't break it: positive feedback and the evolution of oscillator design. Cross FR, Siggia ED. Dev Cell. 2005 Sep;9(3):309-10. PDF

  5. • 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. Bean JM, Siggia ED, Cross FR. Genetics. 2005 Sep;171(1):49-61. PDF

  6. • Cross-species comparison of Drosophila male accessory gland protein genes. Mueller JL, Ravi Ram K, McGraw LA, Bloch Qazi MC, Siggia ED, Clark AG, Aquadro CF, Wolfner MF. Genetics. 2005 Sep;171(1):131-43. PDF

  7. • Computational methods for transcriptional regulation. Siggia ED. Curr Opin Genet Dev. 2005 Apr;15(2):214-21. PDF

  8. • Sequence turnover and tandem repeats in cis-regulatory modules in drosophila. Sinha S, Siggia ED. Mol Biol Evol. 2005 Apr;22(4):874-85. PDF

  9. • PhyloGibbs: A Gibbs sampler incorporating phylogenetic information.,  Rahul Siddhartan, Erik van Nimwegen, Eric D. Siggia, Eskin E, Workman C (eds), RECOMB 2004 Satellite Workshop on Regulatory Genomics, Lecture Notes in Computer Science vol. 3318, p30-41 (Springer-Verlag Berlin Heidelberg 2005). PDF

2004:

  1. • Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. Sinha S, Schroeder MD, Unnerstall U, Gaul U, Siggia ED. BMC Bioinformatics. 2004 Sep 9;5:129. PDF

  2. •Transcriptional control in the segmentation gene network of Drosophila. Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, Rajewsky N, Siggia ED, Gaul U. PLoS Biol. 2004 Sep;2(9):E271. PDF

2003:

  1. • Conservation of regulatory elements between two species of Drosophila. Emberly E, Rajewsky N, Siggia ED. BMC Bioinformatics. 2003 Nov 20;4:57. PDF

  2. • A probabilistic method to detect regulatory modules. Sinha S, van Nimwegen E, Siggia ED. Bioinformatics. 2003;19 Suppl 1:i292-301. PDF

  3. • Genome wide identification of regulatory motifs in Bacillus subtilis. Mwangi MM, Siggia ED. BMC Bioinformatics. 2003 May 16;4:18. PDF

2002:

  1. • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. Rajewsky N, Vergassola M, Gaul U, Siggia ED. BMC Bioinformatics. 2002 Oct 24;3:30. PDF

  2. • Intrinsic and extrinsic contributions to stochasticity in gene expression. Swain PS, Elowitz MB, Siggia ED. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12795-800. PDF  Suppl.pdf

  3. • “Some Physical Problems in Bioinformatics" in "Physics of Bio-Molecules and Cells"., H. Flyvbjerg, F. Jlicher, P. Ormos, F. David (Eds.) Les Houches Session LXXV, 2-27 July 2001, Springer (NY) 2002. PDF

  4. • Stochastic gene expression in a single cell. Elowitz MB, Levine AJ, Siggia ED, Swain PS. Science. 2002 Aug 16;297(5584):1183-6. PDF

  5. • Identification of the binding sites of regulatory proteins in bacterial genomes. Li H, Rhodius V, Gross C, Siggia ED. Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11772-7. PDF

  6. • Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED. Proc Natl Acad Sci U S A. 2002 May 28;99(11):7323-8. PDF   Suppl.pdf

  7. • The role of proofreading in signal transduction specificity. Swain PS, Siggia ED. Biophys J. 2002 Jun;82(6):2928-33. PDF

  8. • Dissection of COPI and Arf1 dynamics in vivo and role in Golgi membrane transport. Presley JF, Ward TH, Pfeifer AC, Siggia ED, Phair RD, Lippincott-Schwartz J. Nature. 2002 May 9;417(6885):187-93. PDF

  9. • The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Rajewsky N, Socci ND, Zapotocky M, Siggia ED. Genome Res. 2002 Feb;12(2):298-308. PDF

2001:

  1. • Regulatory element detection using correlation with expression. Bussemaker HJ, Li H, Siggia ED. Nat Genet. 2001 Feb;27(2):167-71. PDF

2000:

  1. • Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery. Siggia ED, Lippincott-Schwartz J, Bekiranov S. Biophys J. 2000 Oct;79(4):1761-70. PDF

  2. • Regulatory element detection using a probabilistic segmentation model. Bussemaker HJ, Li H, Siggia ED. Proc Int Conf Intell Syst Mol Biol. 2000;8:67-74. PDF

  3. • Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Bussemaker HJ, Li H, Siggia ED. Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):10096-100. PDF

  4. • Scalar turbulence Shraiman BI, Siggia ED. Nature. 2000 Jun 8;405(6787):639-46. PDF

  5. • Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme. Isambert H, Siggia ED. Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6515-20. PDF

  6. • Dynamics and retention of misfolded proteins in native ER membranes.", S. Nehls, E.L.Snapp, N. B. Cole, K.J.M. Zaal, A.K. Kenworthy,T. H. Roberts, J. Ellenberg, J.F. Presley, E.D. Siggia, J. Lippincott-Schwartz, Nature Cell Biology 2000. PDF