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Items: 16

1.

DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

Mitra S, Biswas A, Narlikar L.

PLoS Comput Biol. 2018 Apr 23;14(4):e1006090. doi: 10.1371/journal.pcbi.1006090. eCollection 2018 Apr.

2.

THiCweed: fast, sensitive detection of sequence features by clustering big datasets.

Agrawal A, Sambare SV, Narlikar L, Siddharthan R.

Nucleic Acids Res. 2018 Mar 16;46(5):e29. doi: 10.1093/nar/gkx1251.

3.

No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites.

Mitra S, Narlikar L.

Bioinformatics. 2016 Mar 1;32(5):779-81. doi: 10.1093/bioinformatics/btv645. Epub 2015 Nov 2.

4.

Identification and computational analysis of gene regulatory elements.

Taher L, Narlikar L, Ovcharenko I.

Cold Spring Harb Protoc. 2015 Jan 5;2015(1):pdb.top083642. doi: 10.1101/pdb.top083642. Review.

5.

Multiple novel promoter-architectures revealed by decoding the hidden heterogeneity within the genome.

Narlikar L.

Nucleic Acids Res. 2014 Nov 10;42(20):12388-403. doi: 10.1093/nar/gku924. Epub 2014 Oct 17.

6.

One size does not fit all: on how Markov model order dictates performance of genomic sequence analyses.

Narlikar L, Mehta N, Galande S, Arjunwadkar M.

Nucleic Acids Res. 2013 Feb 1;41(3):1416-24. doi: 10.1093/nar/gks1285. Epub 2012 Dec 24.

7.

MuMoD: a Bayesian approach to detect multiple modes of protein-DNA binding from genome-wide ChIP data.

Narlikar L.

Nucleic Acids Res. 2013 Jan 7;41(1):21-32. doi: 10.1093/nar/gks950. Epub 2012 Oct 22.

8.

CLARE: Cracking the LAnguage of Regulatory Elements.

Taher L, Narlikar L, Ovcharenko I.

Bioinformatics. 2012 Feb 15;28(4):581-3. doi: 10.1093/bioinformatics/btr704. Epub 2011 Dec 22.

9.

ChIP-Seq data analysis: identification of protein-DNA binding sites with SISSRs peak-finder.

Narlikar L, Jothi R.

Methods Mol Biol. 2012;802:305-22. doi: 10.1007/978-1-61779-400-1_20.

10.

Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types.

Wei G, Abraham BJ, Yagi R, Jothi R, Cui K, Sharma S, Narlikar L, Northrup DL, Tang Q, Paul WE, Zhu J, Zhao K.

Immunity. 2011 Aug 26;35(2):299-311. doi: 10.1016/j.immuni.2011.08.007.

11.

Genome-wide discovery of human heart enhancers.

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.

Genome Res. 2010 Mar;20(3):381-92. doi: 10.1101/gr.098657.109. Epub 2010 Jan 14.

12.

Finding regulatory DNA motifs using alignment-free evolutionary conservation information.

Gordân R, Narlikar L, Hartemink AJ.

Nucleic Acids Res. 2010 Apr;38(6):e90. doi: 10.1093/nar/gkp1166. Epub 2010 Jan 4.

13.

Identifying regulatory elements in eukaryotic genomes.

Narlikar L, Ovcharenko I.

Brief Funct Genomic Proteomic. 2009 Jul;8(4):215-30. doi: 10.1093/bfgp/elp014. Epub 2009 Jun 4. Review.

14.

A nucleosome-guided map of transcription factor binding sites in yeast.

Narlikar L, Gordân R, Hartemink AJ.

PLoS Comput Biol. 2007 Nov;3(11):e215. Epub 2007 Sep 24.

15.

Informative priors based on transcription factor structural class improve de novo motif discovery.

Narlikar L, Gordân R, Ohler U, Hartemink AJ.

Bioinformatics. 2006 Jul 15;22(14):e384-92.

PMID:
16873497
16.

Sequence features of DNA binding sites reveal structural class of associated transcription factor.

Narlikar L, Hartemink AJ.

Bioinformatics. 2006 Jan 15;22(2):157-63. Epub 2005 Nov 2.

PMID:
16267080

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