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Jonathan Allen - Publications

Affiliations: 
2006 Computer Science Johns Hopkins University, Baltimore, MD 
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25 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends in Microbiology. PMID 33455849 DOI: 10.1016/j.tim.2020.12.002  0.395
2020 Pincus NB, Ozer EA, Allen JP, Nguyen M, Davis JJ, Winter DR, Chuang CH, Chiu CH, Zamorano L, Oliver A, Hauser AR. A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates. Mbio. 11. PMID 32843552 DOI: 10.1128/Mbio.01527-20  0.416
2020 Allen JP, Ozer EA, Minasov G, Shuvalova L, Kiryukhina O, Satchell KJF, Hauser AR. A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant. Proceedings of the National Academy of Sciences of the United States of America. PMID 32156726 DOI: 10.1073/Pnas.1919198117  0.338
2019 Sichtig H, Minogue T, Yan Y, Stefan C, Hall A, Tallon L, Sadzewicz L, Nadendla S, Klimke W, Hatcher E, Shumway M, Aldea DL, Allen J, Koehler J, Slezak T, et al. FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nature Communications. 10: 3313. PMID 31346170 DOI: 10.1038/S41467-019-11306-6  0.469
2017 Venkateswaran K, Checinska Sielaff A, Ratnayake S, Pope RK, Blank TE, Stepanov VG, Fox GE, van Tongeren SP, Torres C, Allen J, Jaing C, Pierson D, Perry J, Koren S, Phillippy A, et al. Draft Genome Sequences from a Novel Clade of Bacillus cereus Sensu Lato Strains, Isolated from the International Space Station. Genome Announcements. 5. PMID 28798168 DOI: 10.1128/Genomea.00680-17  0.68
2016 Checinska Sielaff A, Singh NK, Allen JE, Thissen J, Jaing C, Venkateswaran K. Draft Genome Sequences of Biosafety Level 2 Opportunistic Pathogens Isolated from the Environmental Surfaces of the International Space Station. Genome Announcements. 4. PMID 28034853 DOI: 10.1128/genomeA.01263-16  0.402
2016 Gardner SN, McLoughlin K, Be NA, Allen J, Weaver SC, Forrester N, Guerbois M, Jaing C. Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses. Plos One. 11: e0152604. PMID 27054586 DOI: 10.1371/Journal.Pone.0152604  0.516
2015 Gardner SN, Frey KG, Redden CL, Thissen JB, Allen JE, Allred AF, Dyer MD, Mokashi VP, Slezak TR. Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing. Bmc Research Notes. 8: 682. PMID 26572552 DOI: 10.1186/s13104-015-1530-0  0.332
2015 Ames SK, Gardner SN, Marti JM, Slezak TR, Gokhale MB, Allen JE. Using populations of human and microbial genomes for organism detection in metagenomes. Genome Research. 25: 1056-67. PMID 25926546 DOI: 10.1101/Gr.184879.114  0.356
2014 Ozer EA, Allen JP, Hauser AR. Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt. Bmc Genomics. 15: 737. PMID 25168460 DOI: 10.1186/1471-2164-15-737  0.419
2014 Devault AM, McLoughlin K, Jaing C, Gardner S, Porter TM, Enk JM, Thissen J, Allen J, Borucki M, DeWitte SN, Dhody AN, Poinar HN. Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Scientific Reports. 4: 4245. PMID 24603850 DOI: 10.1038/Srep04245  0.401
2013 Borucki MK, Allen JE, Chen-Harris H, Zemla A, Vanier G, Mabery S, Torres C, Hullinger P, Slezak T. The role of viral population diversity in adaptation of bovine coronavirus to new host environments. Plos One. 8: e52752. PMID 23308119 DOI: 10.1371/journal.pone.0052752  0.351
2012 Ozer EA, Allen JP, Hauser AR. Draft genome sequence of the Pseudomonas aeruginosa bloodstream isolate PABL056. Journal of Bacteriology. 194: 5999. PMID 23045505 DOI: 10.1128/Jb.01421-12  0.409
2008 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. 9: R7. PMID 18190707 DOI: 10.1186/Gb-2008-9-1-R7  0.721
2007 Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, Crabtree J, Allen JE, Delcher AL, Guiliano DB, Miranda-Saavedra D, Angiuoli SV, Creasy T, Amedeo P, Haas B, El-Sayed NM, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science (New York, N.Y.). 317: 1756-60. PMID 17885136 DOI: 10.1126/Science.1145406  0.782
2006 Allen JE, Salzberg SL. A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons. Algorithms For Molecular Biology : Amb. 1: 14. PMID 16934144 DOI: 10.1186/1748-7188-1-14  0.512
2006 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. 7. PMID 16925843 DOI: 10.1186/Gb-2006-7-S1-S9  0.706
2005 Allen JE, Salzberg SL. JIGSAW: Integration of multiple sources of evidence for gene prediction Bioinformatics. 21: 3596-3603. PMID 16076884 DOI: 10.1093/bioinformatics/bti609  0.591
2005 Gardner MJ, Bishop R, Shah T, de Villiers EP, Carlton JM, Hall N, Ren Q, Paulsen IT, Pain A, Berriman M, Wilson RJ, Sato S, Ralph SA, Mann DJ, Xiong Z, ... ... Allen J, et al. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (New York, N.Y.). 309: 134-7. PMID 15994558 DOI: 10.1126/Science.1110439  0.777
2005 Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, et al. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (New York, N.Y.). 307: 1321-4. PMID 15653466 DOI: 10.1126/Science.1103773  0.771
2004 Allen JE, Pertea M, Salzberg SL. Computational gene prediction using multiple sources of evidence. Genome Research. 14: 142-8. PMID 14707176 DOI: 10.1101/Gr.1562804  0.737
2002 Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, ... ... Allen J, et al. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature. 419: 531-4. PMID 12368868 DOI: 10.1038/nature01094  0.757
2002 Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 419: 512-9. PMID 12368865 DOI: 10.1038/Nature01099  0.784
2002 Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, ... ... Allen J, et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 419: 498-511. PMID 12368864 DOI: 10.1038/Nature01097  0.791
1989 Allen JE, Stephens RS. Identification by sequence analysis of two-site posttranslational processing of the cysteine-rich outer membrane protein 2 of Chlamydia trachomatis serovar L2 Journal of Bacteriology. 171: 285-291. PMID 2914847 DOI: 10.1128/Jb.171.1.285-291.1989  0.3
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