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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. During his 10 years at IGS, he has directed the implementation, optimization, and operation of 15 high-throughput sequencing platforms, including multiple generations of Illumina, Roche/454, Applied Biosystems, Pacific Biosciences, and Oxford Nanopore technologies. Luke provides scientific guidance to researchers on the application of each sequencing platform and analysis of resulting data. Over the past 20 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 800 sequencing projects generating more than 200 trillion basepairs of data from more than 35,000 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
Price, E. P. et al. Whole-Genome Sequences of Burkholderia pseudomallei Isolates Exhibiting Decreased Meropenem Susceptibility. Genome Announc 5, doi:10.1128/genomeA.00053-17, 2017.
Lin, M. et al. Analysis of complete genome sequence and major surface antigens of Neorickettsia helminthoeca, causative agent of salmon poisoning disease. Microb Biotechnol, doi:10.1111/1751-7915.12731, 2017.
Silva, J. C. et al. Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Sci Rep 6, 35284, doi:10.1038/srep35284, 2016.
Kumar, N. et al. Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples. Sci Rep 6, 34850, doi:10.1038/srep34850, 2016.
Hooven, T. A. et al. The essential genome of Streptococcus agalactiae. BMC genomics 17, 406, doi:10.1186/s12864-016-2741-z, 2016.
Blanchette, K. A. et al. Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization. Infection and immunity 84, 2922-2932, doi:10.1128/IAI.00277-16, 2016.
Simpson, H. M. et al. Concurrent Mutations in ATM and Genes Associated with Common gamma Chain Signaling in Peripheral T Cell Lymphoma. PLoS One 10, e0141906, doi:10.1371/journal.pone.0141906, 2015.
Chancey, S. T. et al. Transcriptional Attenuation Controls Macrolide Inducible Efflux and Resistance in Streptococcus pneumoniae and in Other Gram-Positive Bacteria Containing mef/mel(msr(D)) Elements. PLoS One 10, e0116254, doi:10.1371/journal.pone.0116254, 2015.
Castillo, J. C. et al. Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq. BMC genomics 16, 519, doi:10.1186/s12864-015-1690-2, 2015.
Wang, W. et al. Cassava genome from a wild ancestor to cultivated varieties. Nat Commun 5, 5110, doi:10.1038/ncomms6110, 2014.
Tallon, L. J. et al. Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. BMC genomics 15, 788, doi:10.1186/1471-2164-15-788, 2014.
Sanjar, F. et al. Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States. Genome Announc 2, doi:10.1128/genomeA.01120-13, 2014.
Klasson, L. et al. Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae. BMC genomics 15, 1097, doi:10.1186/1471-2164-15-1097, 2014.
Ioannidis, P. et al. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC genomics 15, 738, doi:10.1186/1471-2164-15-738, 2014.
Dugan, V. G. et al. Standardized metadata for human pathogen/vector genomic sequences. PLoS One 9, e99979, doi:10.1371/journal.pone.0099979, 2014.
Zapata, J. C. et al. Genetic variation in vitro and in vivo of an attenuated Lassa vaccine candidate. J Virol, doi:10.1128/JVI.03035-13, 2013.
Veluchamy, A. et al. Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nat Commun 4, 2091, doi:10.1038/ncomms3091, 2013.
Sambuughin, N. et al. Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia. J Hum Genet, doi:http://www.nature.com/jhg/journal/vaop/ncurrent/suppinfo/jhg2012156s1.html, 2013.
Magoc, T. et al. GAGE-B: An Evaluation of Genome Assemblers for Bacterial Organisms. Bioinformatics, doi:10.1093/bioinformatics/btt273, 2013.
Liu, X. et al. Serum Antibody Repertoire Profiling Using In Silico Antigen Screen. PLoS ONE 8, e67181, doi:10.1371/journal.pone.0067181, 2013.
Kimaro Mlacha, S. Z. et al. Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells. BMC genomics 14, 383, doi:10.1186/1471-2164-14-383, 2013.
Khurana, E. et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 342, 1235587, doi:10.1126/science.1235587, 2013.
Ioannidis, P. et al. Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. BMC genomics 14, 639, doi:10.1186/1471-2164-14-639, 2013.
Eppinger, M. et al. Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome Announc 1, e0013412, doi:10.1128/genomeA.00134-12, 2013.
Chen, Y. P. et al. Genome sequencing and comparative genomics of honey bee microsporidia, Nosema Apis reveal novel insights into host-parasite interactions. BMC genomics 14, 451, doi:10.1186/1471-2164-14-451, 2013.
Tettelin, H. et al. Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense. Journal of Bacteriology 194, 5450, doi:10.1128/jb.01200-12, 2012.
Kumar, N. et al. Efficient subtraction of insect rRNA prior to transcriptome analysis of Wolbachia-Drosophila lateral gene transfer. BMC Research Notes 5, 230, 2012.
Hasan, N. A. et al. Genomic diversity of 2010 Haitian cholera outbreak strains. Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1207359109, 2012.
Genomes Project, C. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65, doi:10.1038/nature11632, 2012.
Dorsey, S. G. 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.
Cole, J. W. et al. Rare Variants in Ischemic Stroke: An Exome Pilot Study. PLoS ONE 7, e35591, doi:10.1371/journal.pone.0035591, 2012.