Data Management Lead
Welcome to the data management group for the BioSciences Division at Oak Ridge National Laboratory. We focus on utilizing cutting edge sensor and data management technologies to standardize and streamline the acquisition, management, and curation of data on scales ranging from individual genomes to entire ecosystems. Our strategy is to leverage the ongoing work of colleagues who are developing existing bioinformatics tools and pipelines and expand on these to accommodate larger and more diverse data types. We have a strong interest in developing packages to manage data streams from sensors mounted on both proximal and remote sensing platforms. These data streams can then be merged and curated to create holistic and FAIR data repositories that lend themselves to rapid and automated extraction of information for analysis, research, publications, and public dissemination. We utilize both specialized equipment (such as hyperspectral imagers mounted on UAV’s ) and commodity equipment (cell phone GPS and cameras) to rapidly acquire field and greenhouse image data that can be translated into phenology measurements of interest to researchers.
One significant focus for our group is managing the data streams coming from experiments associated with the Center for Bioenergy Innovation (CBI). These data streams derive from individual genotypes of Poplar and Switchgrass that have been sequenced and cultivated in common gardens and green house facilities across the United States. Data types from these experiments can include tissue assays, soil assays, microbial assays, and environmental assays. We collaborate with researchers to develop new methods and new tools to help with standardizing and homogenizing the data streams coming from the experiments. Data is curated, manipulated, and FAIRified on our internal data platforms before being released as production data sets.
Micro- and Nanotechnology Sensors, Systems, and Applications X, 1063916 (8 May 2018);
Martin, SL. Real-Time Analytics can help stop Ebola. Information Week HealthCare
October 29, 2014.
Wilson, CM. Rodriguez M.J., Johnson, CM. Martin, SL, Chu, TM, Wolfinger, RD, Hauser, LJ, Land ML,
Klingeman, DM, Syed, MH, Ragauskas, AJ, Tschaplinski, Tj, Mielenz, JR., Brown, SD. Global transcriptome
analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and
switchgrass. Biotechnol. Biofuels. 2013. Dec 2;6(1):179 doi: 10.1186/1754-6834-6-179.
Y. Liang, S. Pattathil, D. Basu, W-L Xu, A. Venetos, S.L. Martin, A. Faik, M.G. Hahn, A.M. Showalter.
Biochemical and physiological characterization of fut4 and fut6 mutants defective in arabinogalactan-protein
fucosylation in Arabidopsis. J. Exp. Bot. 2013 Dec;64(18):5537-51 doi:10.1093/jxb/ert321
Martin, SL, He, L. Meilleur, F. Guenther, RH, Sit, TL, Lommel, SA, Heller, WT. New insight into the structure of
RNA in red clover necrotic mosaic virus and the role of divalent cations revealed by small-angle neutron scattering.
Archives of Virology, 2013 Aug; 158(8):1661-1669
Miller, HD, Clark, BW., Hinton, D E., Whitehead, A., Martin, S, Kwok, KW., Kullman, SW. Anchoring
Ethinylestradiol Induced Gene Expression Changes with Testicular Morphology and Reproductive function in the
Medaka. PLoS One. December 26, 2012;7(12):e52479.
Brown, SD, Utturkar SM, Klingeman, DM, Johnson, CM, Martin, SL, Land, ML, Lu, Ty, Schadt CW, Doktycz MJ,
Pelletier, DA. Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse
bacteria isolated from the rhizosphere and endosphere of Populus deltoides.
J. Bacteriology. 2012 Nov; 194(21):5991-3.
Kalamorz F, Keis S, McMillan DG, Olsson K, Stanton JA, Stockwell P, Black MA, Klingeman DM, Land ML, Han
CS, Martin SL, Becher SA, Peddie CJ, Morgan HW, Matthies D, Preiss L, Meier T, Brown SD, Cook GM. Draft
genome sequence of the thermoalkaliphilic Caldalkalibacillus thermarum strain TA2.A1. J Bacteriol. 2011
Martin SL, Guenther RH, Sit TL, Swartz PD, Meilleur F, Lommel SA, Rose RB. Crystallization and preliminary X-
ray diffraction analysis of Red Clover Necrotic Mosaic Virus. Acta Crystallogr Sect F Struct Biol Cryst Commun.
2010 Nov 1;66(Pt 11):1458-62
Yang S, Land ML, Klingeman DM, Pelletier DA, Lu TY, Martin SL, Guo HB, Smith JC, Brown SD. Paradigm for
industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces
cerevisiae. ProcNatl Acad Sci U S A. 2010 Jun 8;107(23):10395-400
Learman DR, Yi H, Brown SD, Martin SL, Geesey GG, Stevens AM, Hochella MF Jr. Involvement of Shewanella
oneidensis MR-1 LuxS in biofilm development and sulfur metabolism. Appl Environ Microbiol. 2009
Yang S, Tschaplinski TJ, Engle NL, Carroll SL, Martin SL, Davison BH, Palumbo AV, Rodriguez M Jr, Brown SD.
Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC
Genomics. 2009 Jan 20;10:34.
Mudge J, Miller NA, Khrebtukova I, Lindquist IE, May GD, Huntley JJ, Luo S, Zhang L, van Velkinburgh JC,
Farmer AD, Lewis S, Beavis WD, Schilkey FD, Virk SM, Black CF, Myers MK, Mader LC, Langley RJ, Utsey JP,
Kim RW, Roberts RC, Khalsa SK, Garcia M, Ambriz-Griffith V, Harlan R, Czika W, Martin S, Wolfinger RD,
Perrone-Bizzozero NI, Schroth GP, Kingsmore SF. Genomic convergence analysis of schizophrenia: mRNA
sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One. 2008;3(11):e3625.
Kennerly E, Ballmann A, Martin S, Wolfinger R, Gregory S, Stoskopf M, Gibson G. A gene expression signature of
confinement in peripheral blood of red wolves (Canis rufus). Mol Ecol. 2008 Jun;17(11):2782-91.
Thon MR, Martin SL, Goff S, Wing RA, Dean RA. BAC end sequences and a physical map reveal transposable
element content and clustering patterns in the genome of Magnaporthe grisea. Fungal Genet Biol. 2004
Johnson, Arthur F., Martin, Stanton L, Baucom, Christie, Hubbard, Kristy M., Ulrich, Erin. R and Sederoff, Ronald
R. "CpG and TpA Suppression in the Woody Gymnosperm Pinus taeda L. (Loblolly Pine) Plant and Animal
Genomes XI Conference Jan. 11-15, 2003. P553
Martin, et. al. 2002: “MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC
end derived sequences for the rice blast fungus Magnaporthe grisea.” Nucleic Acids Research Vol 30. No.1 121-
M.K. Kukolich, L.L. Estabrooks, S.L. Martin. "Chromosome abnormalities due to maternal translocations not
detected with routine amniocentesis." Genetics in Medicine January/February, 1999.
M.K. Kukolich, S.L. Martin:"45,X/46,XY Mosaicism: Clinical management and Counseling Issues" Genetics in
Medicine January/February, 1999.