Publications and Presentations

Funded by this fellowship:

 

  1. Mitra S, Biswas A, Narlikar L. DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP. PLoS Comput Biol. 2018 Apr 23;14(4):e1006090. 

  2. Agrawal A, Sambare SV, Narlikar L, Siddharthan R. THiCweed: fast, sensitive detection of sequence features by clustering big datasets. Nucleic Acids Res. 2018 Mar 16;46(5):e29.

  3. Mitra S and Narlikar L. No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites. Bioinformatics. 2016 March 1; 32(5):779-81.

  4. Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elementsCold Spring Harb Protoc2015 Jan 5;2015(1):pdb.top083642.

  5. Narlikar L. Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome. Nucleic Acids Res. 2014 Nov 10; 42(20):12388-403.

  6. Narlikar L. MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data. Nucleic Acids Res. 2013 Jan 7; 41(1):21-32.
     

Others:

 

  1. Narlikar L, Mehta N, Galande S, Arjunwadkar M. One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses. Nucleic Acids Res. 2013, 41:1416-1424.

  2. Taher L, Narlikar L, Ovcharenko I. CLARE: Cracking the LAnguage of Regulatory Elements. Bioinformatics. 2012 Feb 15;28(4):581-3.

  3. Narlikar L, Jothi R. ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder. Methods Mol Biol. 2012;802:305-22.

  4. Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K. Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity. 2011 Aug 26;35(2):299-311.

  5. Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I. Genome-wide discovery of human heart enhancers. Genome Res. 2010 Mar;20(3):381-92.

  6. Gordân R, Narlikar L, Hartemink AJ. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res. 2010 Apr;38(6):e90.

  7. Narlikar L, Ovcharenko I. Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic. 2009 Jul;8(4):215-30.

  8. Gordân R, Narlikar L, Hartemink AJ. A fast, alignment-free, conservation-based method for transcription factor binding site discovery. In RECOMB08, Lecture notes in Computer Science. 2008;4955:98--111.

  9. Narlikar L, Gordân R, Hartemink AJ. A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol. 2007 Nov;3(11):e215.

  10. Narlikar L, Gordân R, Hartemink AJ.  Nucleosome occupancy information improves de novo motif discovery. In RECOMB07, Lecture notes in Computer Science. 2007;4453:107--121.

  11. Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. In ISMB 2006, Bioinformatics. 2006 Jul 15;22(14):e384-92.

  12. Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics. 2006 Jan 15;22(2):157-63.