Research

(Note: "source" indicates latex/revtex with eps figures, in .gz or .tar.gz format; "ps" indicates gzipped postscript; "arXiv" indicates the abstract page from the arXiv.org archive, from where also many of these can be downloaded.)

• Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model
  G Jayaraman and R Siddharthan, BMC Bioinformatics 11:464 (2010)

• Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix
  Siddharthan R. PLoS One 5(3):e9722 (2010).

• The complex spatio-temporal regulation of the Drosophila myoblast attractant gene duf/kirre
  Guruharsha KG, Ruiz-Gomez M, Ranganath HA, Siddharthan R, Vijayraghavan K. PLoS One 4(9):e6960 (2009)

• Rapid evolution of Cse4p-rich centromeric DNA sequences in closely related pathogenic yeasts, Candida albicans and Candida dubliniensis
  Padmanabhan S, Thakur J, Siddharthan R, Sanyal K. Proc Natl Acad Sci U S A. 105(50):19797-802 (2008)

• PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling
  Rahul Siddharthan, PLoS Comput Biol. Aug 29;4(8):e1000156 (2008).

• (Review article) Detecting regulatory sites using PhyloGibbs
  Rahul Siddharthan, Erik van Nimwegen, in "Comprehensive Genomics", Nicholas H. Bergman (Ed.), Methods in Molecular Biology vol 395, p 381-402 (2007). (pdf)

• Sigma: multiple alignment of weakly-conserved non-coding DNA sequences
  Rahul Siddharthan, BMC Bioinformatics 7:143 (2006)

• Gene Expression from Random Libraries of Yeast Promoters
  M Ligr, R Siddharthan, F Cross, E D Siggia, Genetics 172, 2113 (2006) (PDF)

• PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
  Rahul Siddharthan, Eric D. Siggia, Erik van Nimwegen, PLoS Comput Biol 1(7): e67 (2005).

• PhyloGibbs: A Gibbs sampler incorporating phylogenetic information
  Rahul Siddharthan, Erik van Nimwegen, Eric D. Siggia, in E Eskin, C Workman (eds), RECOMB 2004 Satellite Workshop on Regulatory Genomics, LNBI 3318, 30­41 (Springer-Verlag Berlin Heidelberg 2005).

• Dynamical Mean-Field Theory of Resonating Valence Bond Antiferromagnets
  Antoine Georges, Rahul Siddharthan, Serge Florens, Phys. Rev. Lett. 87, 277203 (2001) (source) (ps) (arXiv)

• The ``square kagome'' quantum antiferromagnet and the eight vertex model
  Rahul Siddharthan, Antoine Georges, Phys. Rev. B 65, 014417 (2002) (source) (ps) (arXiv)

• Ordering and partial ordering in holmium titanate and related systems
  Rahul Siddharthan, B Sriram Shastry, A P Ramirez, Phys. Rev. B 63, 184412 (2001) (source) (ps) (arXiv)

• Crystal-field interaction in the pyrochlore magnet Ho2Ti2O7
  S. Rosenkranz, A. P. Ramirez, A. Hayashi, R. J. Cava, R. Siddharthan, B. S. Shastry, J. Appl. Phys. 87(9), 5914 (2000)

• Exact ground state and kink-like excitations of a two-dimensional Heisenberg antiferromagnet
  Rahul Siddharthan, Phys. Rev. B 60, R9904 (Rapid Comm.) (1999) (source ) (ps) (arXiv)

• Ising pyrochlore magnets: Low temperature properties, ice rules and beyond
  R. Siddharthan, B. S. Shastry, A. P. Ramirez, A. Hayashi, R. J. Cava, S. Rosenkranz, Phys. Rev. Lett. 83, 1854 (1999) (source ) (ps) (arXiv)

• Zero point entropy in spin ice
  A. P. Ramirez, A. Hayashi, R. J. Cava, R. Siddharthan, B. S. Shastry, Nature 399, 333 (1999).

• Singularities in the Bethe solution of the XXX and XXZ Heisenberg spin chains
  Rahul Siddharthan, cond-mat/9804210 (source ) (ps) (arXiv)

• Quantizing the Toda lattice
  Rahul Siddharthan and B. Sriram Shastry, Phys. Rev. B 55, 12196 (1997) (source ) (ps) (arXiv)

• A study of harmonic overtones in Indian drums
  Rahul Siddharthan, Pinaki Chatterjee, Vikram Tripathi, Physics Education (India), Oct. 1994
  (pdf, 2 MB, scanned page images)

Opinion

• What we can learn from the inter-academy report
  Gautam I. Menon and Rahul Siddharthan, Current Science 99(8), 1011 (pdf)

• The case of the Padmanaban Committee
  Rahul Siddharthan, Current Science 93(2), 281 (2007) (pdf)

Educational

• Music, mathematics and Bach
  Rahul Siddharthan, Resonance, March and May 1999
  (source ) (ps)

• Exchange and sign-change: The Pauli exclusion principle
  Rahul Siddharthan, Resonance, April 1999
  (source ) (ps)

• The Uncertainty Principle for dummies
  Rahul Siddharthan, Resonance, February 1999
  (source ) (ps)