Genomics Resource Center - Luke J. Tallon

Luke J. Tallon, Scientific Director, is responsible for the scientific oversight of the Genomics Resource Center, including the high-throughput sequencing platforms, the LIMS, sequence data processing and analysis systems, and laboratory and informatics R&D projects. Luke provides scientific guidance to researchers on the application of each sequencing platform and analysis of resulting data. Over the past 14 years, he has developed expertise in high-throughput genome and transcriptome sequencing, assembly, finishing, variant detection, and analysis. Under Mr. Tallon's leadership since its inception in 2007, the GRC has conducted more than 450 sequencing projects generating more than 22 trillion basepairs of data from more than 7,000 biological samples. Prior to joining IGS in July 2007, Mr. Tallon served as co-director of the genome finishing group and manager of the production assembly and sequence data management team at TIGR/JCVI. He directed more than 70 genome projects and led the development and implementation of software pipelines for genome assembly and finishing, sequence analysis, and data management.

Recent Publications

1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65. (2012)

Tettelin H, Sampaio EP, Daugherty SC, Hine E, Riley DR, Sadzewicz L, Sengamalay N, Shefchek K, Su Q, Tallon LJ, Conville P, Olivier KN, Holland SM, Fraser CM, Zelazny AM. Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense. Journal of Bacteriology 194: 5450. (2012)

Kumar N, Creasy T, Sun Y, Flowers M, Tallon L, et al. Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer. BMC Research Notes 5: 230. (2012)

Hasan NA, Choi SY, Eppinger M, Clark PW, Chen A, Alam M, Haley BJ, Taviani E, Hine E, Su Q, Tallon LJ, Prosper JB, Furth K, Hoq MM, Li H, Fraser-Liggett CM, Cravioto A, Huq A, Ravel J, Cebula TA, Colwell RR. Genomic diversity of 2010 Haitian cholera outbreak strains. Proc Natl Acad Sci U S A 109(29):E2010-7

Cole JW, Stine OC, Liu X, Pratap A, Cheng Y, Tallon LJ, et al. (2012) Rare Variants in Ischemic Stroke: An Exome Pilot Study. PLoS ONE 7: e35591. (2012)

Dorsey, S. G., Lovering RM, Renn CL, Leitch CC, Liu X, Tallon LJ, et al. Genetic deletion of trkB.T1 increases neuromuscular function. American Journal of Physiology - Cell Physiology 302, C141-C153, doi:10.1152/ajpcell.00469.2010 (2012).

Grinblat-Huse V, Drabek EF, Creasy HH, Daugherty SC, Jones KM, Santana-Cruz I, Tallon LJ, Read TD, Hatch TP, Bavoil P, Myers GS. Genome sequences of the zoonotic pathogens Chlamydia psittaci 6BC and Cal10. J Bacteriol 193, 4039-4040 (2011).

Rathe, J. A., Liu, X., Tallon, L. J., Gern, J. E. & Liggett, S. B. Full-genome sequence and analysis of a novel human rhinovirus strain within a divergent HRV-A clade. Arch Virol 155, 83-87, doi:10.1007/s00705-009-0549-8 (2010).

Moriel, D. G., Bertoldi I., Spagnuolo A., Marchi S., Rosini R., Nesta B., Pastorello I., Corea V.A., Torricelli G., Cartocci E., Savino S., Scarselli M., Dobrindt U., Hacker J., Tettelin H., Tallon L.J., Sullivan S., Wieler L.H., Ewers C., Pickard D., Dougan G., Fontana M.R., Rappuoli R., Pizza M., Serino L. Identification of protective and broadly conserved vaccine antigens from the genome of extraintestinal pathogenic Escherichia coli. Proc Natl Acad Sci U S A 107, 9072-9077, doi:0915077107 [pii] 10.1073/pnas.0915077107 (2010).

Dongying Wu, Jason Raymond, Martin Wu, Sourav Chatterji, Qinghu Ren, Joel E. Graham, Donald A. Bryant, Frank Robb, Albert Colman, Luke J. Tallon, Jonathan H. Badger, Ramana Madupu, Naomi L. Ward, and Jonathan A. Eisen. Complete Genome Sequence of the Aerobic CO-Oxidizing Thermophile Thermomicrobium roseum. PLoS ONE. 2009; 4(1): e4207.

Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fadrosh DW, Fuester RW, Pedroni MJ, Haas BJ, Schatz MC, Jones KM, Crabtree J, Forberger H, Nene V. Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps. Genome Biology 2008, 9(12):R183

Coyne RS, Thiagarajan M, Jones KM, Wortman JR, Tallon LJ, Haas BJ, Cassidy-Hanley DM, Wiley EA, Smith JJ, Collins K, Lee SR, Couvillion MT, Liu Y, Garg J, Pearlman RE, Hamilton EP, Orias E, Eisen JA, Methé BA. Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure. BMC Genomics 2008, 9:562.

Nithya Raghavan, Hervé Tettelin, André Miller, Jessica Hostetler, Luke Tallon and Matty Knight. Nimbus (BgI): An active non-LTR retrotransposon of the Schistosoma mansoni snail host Biomphalaria glabrata. International Journal for Parasitology, Volume 37, Issue 12, Pages 1307-1318, 2007.

Desjardins CA, Gundersen-Rindal DE, Hostetler JB, Tallon LJ, Fuester RW, Schatz MC, Pedroni MJ, Fadrosh DW, Haas BJ, Toms BS, Chen D, Nene V. Structure and evolution of a proviral locus of Glyptapanteles indiensis bracovirus. BMC Microbiology 7:61, 2007.

Elodie Ghedin, Shiliang Wang, David Spiro, Elisabet Caler, Qi Zhao, Jonathan Crabtree, Jonathan E. Allen, Arthur L. Delcher, David B. Guiliano, Diego Miranda-Saavedra, Samuel V. Angiuoli, Todd Creasy, Paolo Amedeo, Brian Haas, Najib M. El-Sayed, Jennifer R. Wortman, Tamara Feldblyum, Luke Tallon, Michael Schatz, Martin Shumway, Hean Koo, Steven L. Salzberg, Seth Schobel, Mihaela Pertea, Mihai Pop, Owen White, Geoffrey J. Barton, Clotilde K. S. Carlow, Michael J. Crawford, Jennifer Daub, Matthew W. Dimmic, Chris F. Estes, Jeremy M. Foster, Mehul Ganatra, William F. Gregory, Nicholas M. Johnson, Jinming Jin, Richard Komuniecki, Ian Korf, Sanjay Kumar, Sandra Laney, Ben-Wen Li, Wen Li, Tim H. Lindblom, Sara Lustigman, Dong Ma, Claude V. Maina, David M. A. Martin, James P. McCarter, Larry McReynolds, Makedonka Mitreva, Thomas B. Nutman, John Parkinson, José M. Peregrín-Alvarez, Catherine Poole, Qinghu Ren, Lori Saunders, Ann E. Sluder, Katherine Smith, Mario Stanke, Thomas R. Unnasch, Jenna Ware, Aguan D. Wei, Gary Weil, Deryck J. Williams, Yinhua Zhang, Steven A. Williams, Claire Fraser, Barton Slatko, Mark L. Blaxter, and Alan L. Scott (2007) Draft Genome of the Filarial Nematode Parasite Brugia malayi. Science 317 (5845), 1756, 2007.

Donald A. Bryant, Amaya M. Garcia Costas, Julia A. Maresca, Aline Gomez Maqueo Chew, Christian G. Klatt, Mary M. Bateson, Luke J. Tallon, Jessica Hostetler, William C. Nelson, John F. Heidelberg, and David M. Ward. Candidatus Chloracidobacterium thermophilum: An Aerobic Phototrophic Acidobacterium. Science 317 (5837), 523, 2007.

Eisen, J.A., Coyne, R.S., Wu, M., Wu, D., Thiagarajan, M., Wortman, J.R., Badger, J.H., Ren, Q., Amedeo, P., Jones, K.M., Tallon, L.J., Delcher, A.L., Salzberg, S.L., Silva, J.C., Haas, B.J., Majoros, W.H., Farzad, M., Carlton, J.M., Smith, R.K., Garg, J., Pearlman, R.E., Karrer, K.M., Sun, L., Manning, G., Elde, N.C., Turkewitz, A.P., Asai, D.J., Wilkes, D.E., Wang, Y., Cai, H., Collins, K., Stewart, B.A., Lee, S.R., Wilamowska, K., Weinberg, Z., Ruzzo, W.L., Wloga, D., Gaertig, J., Frankel, J., Tsao, C.C., Gorovsky, M.A., Keeling, P.J., Waller, R.F., Patron, N.J., Cherry, J.M., Stover, N.A., Krieger, C.J., Del Toro, C., Ryder, H.F., Williamson, S.C., Barbeau, R.A., Hamilton, E.P., Orias, E. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLoS Biol 4 (9):e286, 2006.

Fouts, D.E., Rasko, D.A., Cer, R.Z., Jiang, L., Fedorova, N.B., Shvartsbeyn, A., Vamathevan, J.J., Tallon, L., Althoff, R., Arbogast, T.S., Fadrosh, D.W., Read, T.D., Gill, S.R. Sequencing Bacillus anthracis Typing Phages Gamma and Cherry Reveals a Common Ancestry. J Bacteriol 188 (9):3402-3408, 2006.

Goldberg, S.M., Johnson, J., Busam, D., Feldblyum, T., Ferriera, S., Friedman, R., Halpern, A., Khouri, H., Kravitz, S.A., Lauro, F.M., Li, K., Rogers, Y.H., Strausberg, R., Sutton, G., Tallon, L., Thomas, T., Venter, E., Frazier, M., Venter, J.C. A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103 (30):11240-11245, 2006.

Lee, S.B., Kaittanis, C., Jansen, R.K., Hostetler, J.B., Tallon, L.J., Town, C.D., Daniell, H. The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genomics 7 (1):61, 2006.

Ruhlman, T., Lee, S.B., Jansen, R.K., Hostetler, J.B., Tallon, L.J., Town, C.D., Daniell, H. Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7 (1):222, 2006.

Seshadri, R., Joseph, S.W., Chopra, A.K., Sha, J., Shaw, J., Graf, J., Haft, D., Wu, M., Ren, Q., Rosovitz, M.J., Madupu, R., Tallon, L., Kim, M., Jin, S., Vuong, H., Stine, C.O., Ali, A., Horneman, A.J., Heidelberg, J.F. Genome Sequence of Aeromonas hydrophila ATCC 7966T: The Jack of All Trades. J Bacteriol 186 (23):8272-82, 2006.

Town, C.D., Cheung, F., Maiti, R., Crabtree, J., Haas, B.J., Wortman, J.R., Hine, E.E., Althoff, R., Arbogast, T.S., Tallon, L.J., Vigouroux, M., Trick, M., Bancroft, I. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18 (6):1348-1359, 2006.

Wu, D., Daugherty, S.C., Aken, S.E., Pai, G.H., Watkins, K.L., Khouri, H., Tallon, L.J., Zaborsky, J.M., Dunbar, H.E., Tran, P.L., Moran, N.A., Eisen, J.A. Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters. PLoS Biol 4 (6):e188, 2006.