Bioinformatics by date:

  1. 1."Building a Dictionary for Genomes: Identification of Presumptive Regulatory Sites by Statistical Analysis", H. Bussemaker, H. Li, and and E.D. Siggia, PNAS 97 10096-10100 (2000).

  2. 2."Regulatory Element Detection Using Correlation with Genome-wide mRNA expression data ", H.J. Bussemaker, H. Li, and E.D. Siggia, Nature Genetics 27, 167-174 (2001).

  3. 3."Regulatory Element detection using a Probabilistic Segmentation Model", H.J. Bussemaker, H. Li, E.D. Siggia, Proceedings of the 8th International Conference on IntelligentSystems for Molecular Biology, La Jolla Aug 2000 R. Altman et al (eds)AAAI press Melno Park.

  4. 4."The Evolution of DNA Regulatory Regions for Proteo-gamma Bacteria by Interspecies Comparisons", N. Rajewsky, N. Socci, M. Zapotocky and E.D. Siggia, Genome Research 12 298-308 (2002).

  5. 5."Probabalistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics", E. van Nimwegen, M. Zavolan, N. Rajewsky, E.D. Siggia, PNAS 99 7323-8 (2002).  + Suppl

  6. 6."Identification of the binding sites of Regulatory Proteins in Bacterial Genomes", H. Li, V. Rhodius, C. Gross, and E.D. Siggia, Proc Natl Acad Sci (US) 99 11772-7 2002.

  7. 7."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.

  8. 8."Computational detection of genomic cis-regulatory modules, applied to body patterning in the early Drosophila embryo", N. Rajewsky, M. Vergassola, U. Gaul and E.D. Siggia, BMC Bioinformatics. 3 30, 2002.

  9. 9."Genome wide identification of regulatory motifs in Bacillus subtilis", M.M. Mwangi, E.D. Siggia, BMC Bioinformatics May 16;4(1):18, 2003.

  10. 10."A probabilistic method to detect regulatory modules", S. Sinha, E. Van Nimwegen, E.D. Siggia, Bioinformatics. Jul;19 Suppl 1:I292-I301 2003.

  11. 11."Conservation of Regulatory Elements between two species of Drosophila", E. Emberly, N. Rajewsky, and E. Siggia BMC Bioinformatics, 4 57, 2003.

  12. 12."Transcriptional Control in the Segmentation Gene Network of Drosophila", Mark D. Schroeder, Michael Pearce, John Fak, HongQing Fan , Ulrich Unnerstall, Eldon Emberly , Nikolaus Rajewsky, Eric D. Siggia, and Ulrike Gaul, PLoS 2 E 271, 2004.

  13. 13."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).

  14. 14."Cross-species comparisons significantly improves genome-wide prediction of cis-regulatory modules in Drosophila", Saurabh Sinha, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul, and Eric D. Siggia, BMC Bioinformatics, 5 129, 2004.

  15. 15."Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila", Saurabh Sinha and Eric D. Siggia, Mol Bio Evol 22 874-85, 2005.

  16. 16."Computational Methods for Transcriptional Regulation", E.D. Siggia, Currrent Opinion in Genetics and Development 15 214-221, 2005.

  17. 17."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 171 131-43, 2005.

  18. 18."Protein-DNA binding specificity predictions with structural model", Morozov AV, Havranek JJ, Baker D, Siggia ED, Nucleic Acids Res 33 5781-98, 2005.

  19. 19."PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny", Siddharthan R, Siggia ED, van Nimwegen E. PLoS Comput Bio 1 e67 , 2005.

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

  21. 21."Connecting protein structure with predictions of regulatory sites", Morozov AV, Siggia ED. PNAS 104 7068-73, 2007.

  22. 22."Sequence Contexts affect the mutability of short insertions and deletions in flies and primates", Tanay, A, Siggia, ED Genome Research , 2007.

  23. 23.   for later papers check pubmed

Algorithms (and protein structure):

  1. 1."Building a Dictionary for Genomes: Identification of Presumptive Regulatory Sites by Statistical Analysis", H. Bussemaker, H. Li, and and E.D. Siggia, PNAS 97 10096-10100 (2000).

  2. 2."Regulatory Element Detection Using Correlation with Genome-wide mRNA expression data ", H.J. Bussemaker, H. Li, and E.D. Siggia, Nature Genetics 27, 167-174 (2001).

  3. 3."Regulatory Element detection using a Probabilistic Segmentation Model", H.J. Bussemaker, H. Li, E.D. Siggia, Proceedings of the 8th International Conference on IntelligentSystems for Molecular Biology, La Jolla Aug 2000 R. Altman et al (eds)AAAI press Melno Park.

  4. 4."Probabalistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics", E. van Nimwegen, M. Zavolan, N. Rajewsky, E.D. Siggia, PNAS 99 7323-8 (2002).  + Suppl

  5. 5."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.

  6. 6."Computational detection of genomic cis-regulatory modules, applied to body patterning in the early Drosophila embryo", N. Rajewsky, M. Vergassola, U. Gaul and E.D. Siggia, BMC Bioinformatics. 3 30, 2002.

  7. 7."A probabilistic method to detect regulatory modules", S. Sinha, E. Van Nimwegen, E.D. Siggia, Bioinformatics. Jul;19 Suppl 1:I292-I301 2003.

  8. 8."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).

  9. 9."Computational Methods for Transcriptional Regulation", E.D. Siggia, Currrent Opinion in Genetics and Development 15 214-221, 2005.

  10. 10."Protein-DNA binding specificity predictions with structural model", Morozov AV, Havranek JJ, Baker D, Siggia ED, Nucleic Acids Res 33 5781-98, 2005.

  11. 11."PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny", Siddharthan R, Siggia ED, van Nimwegen E. PLoS Comput Bio 1 e67 , 2005.

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

  13. 13."Connecting protein structure with predictions of regulatory sites", Morozov AV, Siggia ED. PNAS 104 7068-73, 2007.

Molecular Evolution:

  1. 1. “Conservation of Regulatory Elements between two species of Drosophila", E. Emberly, N. Rajewsky, and E. Siggia BMC Bioinformatics, 4 57, 2003.

  2. 2."Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila", Saurabh Sinha and Eric D. Siggia, Mol Bio Evol 22 874-85, 2005

  3. 3."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 171 131-43, 2005.

  4. 4."Sequence Contexts affect the mutability of short insertions and deletions in flies and primates", Tanay, A, Siggia, ED Genome Research , 2007.

Applications (bacteria):

  1. 1."The Evolution of DNA Regulatory Regions for Proteo-gamma Bacteria by Interspecies Comparisons", N. Rajewsky, N. Socci, M. Zapotocky and E.D. Siggia, Genome Research 12 298-308 (2002).

  2. 2."Identification of the binding sites of Regulatory Proteins in Bacterial Genomes", H. Li, V. Rhodius, C. Gross, and E.D. Siggia, Proc Natl Acad Sci (US) 99 11772-7 2002.

  3. 3."Genome wide identification of regulatory motifs in Bacillus subtilis", M.M. Mwangi, E.D. Siggia, BMC Bioinformatics May 16;4(1):18, 2003.


Applications (fly blastoderm):

  1. 1."Transcriptional Control in the Segmentation Gene Network of Drosophila", Mark D. Schroeder, Michael Pearce, John Fak, HongQing Fan , Ulrich Unnerstall, Eldon Emberly , Nikolaus Rajewsky, Eric D. Siggia, and Ulrike Gaul, PLoS 2 E 271, 2004.

  2. 2."Cross-species comparisons significantly improves genome-wide prediction of cis-regulatory modules in Drosophila", Saurabh Sinha, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul, and Eric D. Siggia, BMC Bioinformatics, 5 129, 2004.

  3. 3.Evolution of transcription control in the segmentation gene network of Drosophila Saurabh Sinha, Michael Pearce, Ulrich Unnerstall, John Fak, Monica Dandapani, Mark D. Schroeder, Eric D. Siggia and Ulrike Gaul Preprint.

Papers grouped by subtopic with a chronological list of everything at the end