(Bugbears Publications page)

[research papers and reviews / book chapters indexed in Pubmed; *corresponding author(s)]

Chandraprakash D, Seshasayee AS*. Inhibition of factor-dependent transcription termination in Escherichia coli might relieve xenogene silencing by abrogating H-NS-DNA interactions in-vivo. Journal of Biosciences. 2014. 39: 53-61.

Kingsley RA*, Whitehead S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee AS, Harris S, Thomson NR, Gardner P, Rabsch W, Wigley P, Humphrey T, Parkhill J, Dougan G. Genome and transcriptome adaptation accompanying emergence of the DT2 host-restricted Salmonella Typhimurium pathovar. MBio. 2013. 4: e00565-13.

Sasidharan V, Lu Y, Bansal D, Dasari D, Poduval D, Seshasayee AS, Resch AM, Graveley BR*, Palakodeti D*. Identification of neoblast- and regeneration-specific miRNAs in the planerian Schmidtea mediterranea. RNA. 2013. 19: 1394-1404.

Srinivasan R, Chandraprakash D, Krishnamurthi R, Singh P, Scolari V, Krishna S, Seshasayee AS*. Genomic analysis reveals a bilayered epistatic control of “expensive” genes in Escherichia coli: implications for gene silencing. Molecular Biosystems. 2013. 9: 2021-33.

Prabhakara S, Khedkar S, Shambat S, Basu A, Norby-Teglund A, Seshasayee AS*, Arakere GA*. Genome sequencing reveals a novel sea enterotoxin-carrying PVL phage in Staphylococcus aureus ST772 from India. PLoS ONE. 2013. 8: e60013.

Khedkar S, Prabhakara S, Loganathan RM, S C, Gowda M, Arakere G*, Seshasayee AS*. Draft genome sequence of Staphylococcus aureus ST672, an emerging disease clone from India. J Bacteriol. 2012 Dec;194(24):6946-7.

Seshasayee AS*, Singh P, Krishna S. Context-dependent conservation of DNA methyltransferases in bacteria. Nucleic Acids Res. 2012 Aug;40(15):7066-73.

Prabhakara S, Khedkar S, Loganathan RM, Chandana S, Gowda M, Arakere G*, Seshasayee AS*. Draft genome sequence of Staphylococcus aureus 118 (ST772), a major disease clone from India. J Bacteriol. 2012 Jul;194(14):3727-8.

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM*, Seshasayee AS*. Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Nat Commun. 2012 Jun 6;3:886.

Martincorena I, Seshasayee AS, Luscombe NM*. Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature. 2012 May 3;485(7396):95-8.

Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee AS*, Luscombe NM*. Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res. 2012 Apr;40(8):3524-37.

Seshasayee AS*, Luscombe NM*. Comparative genomics suggests differential deployment of linear and branched signaling across bacteria. Mol Biosyst. 2011 Nov;7(11):3042-9.

Kahramanoglou C, Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM*, Luscombe NM*. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res. 2011 Mar;39(6):2073-91.

Seshasayee AS, Sivaraman K, Luscombe NM*. An overview of prokaryotic transcription factors : a summary of function and occurrence in bacterial genomes. Subcell Biochem. 2011;52:7-23 [review].

Seshasayee AS*, Fraser GM, Luscombe NM*. Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity. Nucleic Acids Res. 2010 Oct;38(18):5970-81.

Seshasayee AS*, Fraser GM, Babu MM*, Luscombe NM*. Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res. 2009 Jan;19(1):79-91.

Pearson MM, Sebaihia M, Churcher C, Quail MA, Seshasayee AS, Luscombe NM, Abdellah Z, Arrosmith C, Atkin B, Chillingworth T, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Walker D, Whithead S, Thomson NR, Rather PN, Parkhill J, Mobley HL*. Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol. 2008 Jun;190(11):4027-37.

Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P*. Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Mol Genet Genomics. 2008 May;279(5):523-34.

Sivaraman K, Seshasayee A, Tarwater PM, Cole AM*. Codon choice in genes depends on flanking sequence information - implications for theoretical reverse translation. Nucleic Acids Res. 2008 Feb;36(3):e16.

James JJ, Lakshmi BS, Seshasayee AS, Gautam P*. Activation of Candida rugosa lipase at alkane-aqueous interfaces: a molecular dynamics study. FEBS Lett. 2007 Sep 18;581(23):4377-83.

Seshasayee AS*. An assessment of the role of DNA adenine methyltransferase on gene expression regulation in E coli. PLoS One. 2007 Mar 7;2(3):e273.

Seshasayee AS, Bertone P, Fraser GM, Luscombe NM*. Transcriptional regulatory networks in bacteria: from input signals to output responses. Curr Opin Microbiol. 2006 Oct;9(5):511-9 [review].

Seshasayee AS*. Social behavior of the yeast protein-protein interaction network. In Silico Biol. 2006;6(1-2):127-30.

Seshasayee AS, Raghunathan K, Sivaraman K, Pennathur G*. Role of hydrophobic interactions and salt-bridges in beta-hairpin folding. J Mol Model. 2006 Jan;12(2):197-204.

Cherukuvada SL, Seshasayee AS, Raghunathan K, Anishetty S, Pennathur G*. Evidence of a double-lid movement in Pseudomonas aeruginosa lipase: insights from molecular dynamics simulations. PLoS Comput Biol. 2005 Aug;1(3):e28.

Sivaraman K, Seshasayee AS, Swaminathan K, Muthukumaran G, Pennathur G*. Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome. Theor Biol Med Model. 2005 May 31;2:20.

Seshasayee AS*. High-temperature unfolding of a trp-cage mini-protein: a molecular dynamics simulation study. Theor Biol Med Model. 2005 Mar 11;2:7.

[reviews / book chapters not indexed in Pubmed]

Lal A*, Seshasayee ASN*. The impact of next-generatoin sequencing technologies on bacterial genomics. Systems and Synthetic Biology. Springer-Verlag (2014). Ed. Vishwesh Kulkarni. In Press. [review]

Seshasayee ASN*, Madan Babu M*. Unanticipated intra- and inter-kingdom crosstalk involving small-molecules. Environmental Microbiology Reports (Crystal Ball Feature; 2011) 3: 1-26. [review]

Seshasayee ASN, Aravind L, Madan Babu M*. Gene expression studies in Arabidopsis thaliana: a network perspective. Floriculture, Ornamental and Plant Biotechnology. Global Science Press (2006). Ed. Jaime A. Teixeira da Silva. [review]

Seshasayee ASN, Madan Babu M*. Contextual inference of protein function. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley and Sons (2005). Ed. Shankar Subramanian. [review]