Jonathan E. Allen

Bioinformatics Scientist
Lawrence Livermore National Laboratory
Livermore, CA

contact: sifting at cs.jhu.edu

Research


My work focuses on the development and application of new software tools to address various genome sequence analysis problems. Problem areas of interest include prediction of genetic virulence markers in viruses, detecting genetic engineering in bacteria and eukaryotic gene prediction.

Education

Ph.D. (2006), M.S.E. (2001), Computer Science, Johns Hopkins University
Dissertation Title: Predicting gene structure in eukaryotic genomes
Advisor: Steven L. Salzberg

B.A. (1996), Computer Science, University of California, Santa Cruz
Minor in History

Selected Publications


Allen JE, Gardner SN, Vitalis EA, Slezak TR. Conserved amino acid markers from past pandemic influenza strains. BMC Microbiology. 2009 9:77.

A discussion of the work in Nature Medicine News (subscription required).

Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, the nGASP Consortium, Stein LD. nGASP the nematode genome annotation assessment project. BMC Bioinformatics. 2008 9:549

Allen JE, Gardner SN, Slezak TR. DNA Signatures for detecting genetic engineering in bacteria. Genome Biology. 2008 9:R56.

A discussion of this work in a Wired.com commentary.

Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, Orvis J, White O, Buell CR, Wortman JR. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology. 2008 9:R7.

Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, et al. Draft Genome of the Filarial Nematode Parasite Brugia malayi. Science. 2007 317(5845):1756-1760

Allen JE, Salzberg SL. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms for Molecular Biology. 2006, 1:14.

Allen JE, Majoros WH, Pertea M, Salzberg SL. JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions. Genome Biology. 2006 7(Suppl 1):S9.

Allen JE, Salzberg SL. JIGSAW: integration of multiple sources of evidence for gene prediction Bioinformatics. 2005 21(18):3596-603.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, et al. The transcriptional landscape of the mammalian genome. Science. 2005 309(5740):1559-63

Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Res. 2004 Jan;14(1):142-8.

Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002 Oct 3;419(6906):512-9.



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