Writings

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)