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Results: 11

1.

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J.

Genome Biol. 2015 Jun 9;16:122. doi: 10.1186/s13059-015-0683-4.

2.

The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila.

Feltzin VL, Khaladkar M, Abe M, Parisi M, Hendriks GJ, Kim J, Bonini NM.

Aging Cell. 2015 Jun;14(3):443-52. doi: 10.1111/acel.12323. Epub 2015 Mar 6.

3.

Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution.

Francis C, Natarajan S, Lee MT, Khaladkar M, Buckley PT, Sul JY, Eberwine J, Kim J.

BMC Genomics. 2014 Oct 9;15:883. doi: 10.1186/1471-2164-15-883.

4.

Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis.

Buckley PT, Khaladkar M, Kim J, Eberwine J.

Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):223-30. doi: 10.1002/wrna.1203. Epub 2013 Nov 4. Review.

5.

Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons.

Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J.

PLoS One. 2013 Oct 3;8(10):e76194. doi: 10.1371/journal.pone.0076194. eCollection 2013.

6.

Functional divergence of gene duplicates - a domain-centric view.

Khaladkar M, Hannenhalli S.

BMC Evol Biol. 2012 Jul 27;12:126. doi: 10.1186/1471-2148-12-126.

7.

A method for discovering common patterns from two RNA secondary structures and its application to structural repeat detection.

Hua L, Wang JT, Ji X, Malhotra A, Khaladkar M, Shapiro BA, Zhang K.

J Bioinform Comput Biol. 2012 Aug;10(4):1250001. doi: 10.1142/S0219720012500011. Epub 2012 Jun 22.

PMID:
22809414
8.

Epigenomic and RNA structural correlates of polyadenylation.

Khaladkar M, Smyda M, Hannenhalli S.

RNA Biol. 2011 May-Jun;8(3):529-37. Epub 2011 May 1.

9.

Detecting conserved secondary structures in RNA molecules using constrained structural alignment.

Khaladkar M, Patel V, Bellofatto V, Wilusz J, Wang JT.

Comput Biol Chem. 2008 Aug;32(4):264-72. doi: 10.1016/j.compbiolchem.2008.03.013. Epub 2008 Apr 8.

PMID:
18472302
10.

Mining small RNA structure elements in untranslated regions of human and mouse mRNAs using structure-based alignment.

Khaladkar M, Liu J, Wen D, Wang JT, Tian B.

BMC Genomics. 2008 Apr 25;9:189. doi: 10.1186/1471-2164-9-189.

11.

RADAR: a web server for RNA data analysis and research.

Khaladkar M, Bellofatto V, Wang JT, Tian B, Shapiro BA.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W300-4. Epub 2007 May 21.

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