Interests

I am interested in understanding how the information in DNA creates the amazing variety of life on this planet. With a focus on human genomics, that means identifying all functional genomic elements, determining what they do, and understanding how they have evolved. Currently in John Rinn's lab, I'm focused on studying genomes through the largely unexplored and poorly understood world of long noncoding RNA genes. (Also, check out my citeulike tag cloud for a messier but neat view of my reading interests)

Publications

Transposable elements reveal a stem cell specific class of long noncoding RNA

Kelley DR, Rinn JL. Genome Biology 13:R107 (2012).

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Trapnell C et al. Nature Protocols 7:3 (2012).

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering

Kelley DR, Liu B, Delcher A, Pop M, Salzberg SL. Nucleic Acids Research 40:1 e9 (2012) [software]

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Earl D, et al. Genome Research 21:12 (2011)

Quake: quality-aware detection and correction of sequencing errors

Kelley DR, Schatz MC, Salzberg SL. Genome Biology 11:R116 (2010) [software]

Clustering metagenomic sequences with interpolated Markov models

Kelley DR, Salzberg SL. BMC Bioinformatics 11:544 (2010) [software]

Detection and correction of false segmental duplications caused by genome mis-assembly

Kelley DR, Salzberg SL. Genome Biology 11:R28 (2010)

Extracting between-pathway models from E-MAP interactions using expected graph compression

Kelley DR, Kingsford C. Journal of Computational Biology 18:3 (2011). [supplement]

Extracting between-pathway models from E-MAP interactions using expected graph compression

Kelley DR, Kingsford C. RECOMB (2010). [supplement]

A whole-genome assembly of the domestic cow, Bos taurus

Zimin AV, Delcher AL, Florea L, Kelley DR, et al, Genome Biology 10:R42 (2009)

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Salzberg SL et al. BMC Genomics 9:204 (2008)

Software

Glimmer-MG

Gene prediction on metagenomic sequences augmented by classification and clustering.

Quake

Detection and correction of substitution errors in whole-genome shotgun datasets with deep coverage.

Scimm + PhyScimm

Unsupervised clustering of metagenomic sequences using interpolated Markov models.

Contrail

Short read de novo assembly of large genomes using Hadoop.

Posters

Gene prediction in metagenomic sequences using Glimmer augmented by phylogenetic classification and clustering

Kelley DR, Liu B, Delcher A, Pop M, Salzberg SL. CSHL Biology of Genomes (2011).

Quality-aware error correction of sequencing reads

Kelley DR, Schatz MC, Salzberg SL. ISMB (2010).

Clustering metagenomic sequencing with interpolated Markov models

Kelley DR, Salzberg SL. RECOMB (2010).

De Novo Assembly of Large Genomes with Cloud Computing

Schatz MC, Sommer D, Kelley DR, Pop M. CSHL Biology of Genomes (2010).

Extracting between-pathway model from E-MAP interactions using expected graph compression

Kelley DR, Kingsford C. WABI (2009).

 
 

Research