Jonathan E. Allen

Center for Bioinformatics and Computational Biology
3115 Biomolecular Sciences Building #296, Room 3120A
University of Maryland, College Park, MD 20742
Email: jeallen

umiacs.umd.edu

I recently defended my Ph.D. thesis in Computer Science at Johns Hopkins University. My thesis advisor was Steven L. Salzberg. I am currently working in the CBCB.

CV: pdf

Research Interests

My broad research interest is in the area of designing algorithms to extract biological meaning from genomic sequence. I am currently working on new methods to integrate gene expression evidence with gene finders to accurately identify precise protein coding gene structures in DNA. I am also working on a project to characterize alternative splicing in pre-mRNA using hidden Markov models.

Software

JIGSAW - Automated gene annotation system
ExAlt! - Alternative exon isoform prediction
Documentation for a basic C++ bioinformatics library

Selected Publications

J. E. Allen and S. L. Salzberg. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms for Molecular Biology, 1:14, 2006.

J. E. Allen, W. H. Majoros, M. Pertea, and S. L. Salzberg. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biology, 7(S1):S9, 2006.

J. E. Allen and S. L. Salzberg. JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics, 21(18): 3596-3603, 2005.

The FANTOM Consortium. The transcriptional landscape of the mammalian genome. Science 309(5740):1559-63, 2005.

Loftus BJ, Fung E, Roncaglia P, et al., The genome of the basidiomycetous yeast and human pathogen cryptococcus neoformans. Science, 307(5713), 2005.

J. E. Allen, M. Pertea, and S. L. Salzberg. Computational gene prediction using multiple sources of evidence. Genome Research, 14(1), 2004.

Carlton JM, Angiuoli SV, Suh BB, et al., Genome sequence and comparative analysis of the model rodent malaria parasite plasmodium yoelii yoelii. Nature, 419(6906), 2002.

Gardner MJ, Hall N, Fung E, et al., Genome sequence of the human malaria parasite plasmodium falciparum. Nature, 419(6906), 2002.

Miscellaneous

Here's a slightly less recent picture of me.