Curriculum Vitae – Dan Spakowicz

Yale University and The Jackson Laboratory for Genomic Medicine

266 Whitney Ave, New Haven, CT 06511 (612) 807-6316 daniel.spakowicz@yale.edu

EMPLOYMENT

National Library of Medicine Postdoctoral Fellow in Medical Informatics 06/2015-05/2017

Postdoctoral Researcher 09/2014-06/2015

Instructor, Rainforest Expedition and Laboratory Course 01/2014-09/2014

Junior Researcher 2004-7

Instructor, Rainforest Expedition and Laboratory Course 01/2014-09/2014

Junior Researcher 2004-7

Student Researcher 2003

Laboratory Technician 2001-2


EDUCATION

M.S. Yale University, Biomedical Informatics 2015-17

Ph.D. Yale University, Molecular Biophysics & Biochemistry 2008-13

B.S. University of Minnesota, Minneapolis, MN 2000-4


HONORS AND AWARDS

Postdoctoral Fellowship in Medical Informatics 2015-17

Yale Excellence in Teaching Award 2011

Poster Awards


PUBLICATIONS

First author and co-first author

1. Spakowicz, D. J. and Strobel, S. A. “Biosynthesis of Hydrocarbons and Volatile Organic Compounds by Fungi: Bioengineering PotentialApplied microbiology and biotechnology 99, no. 12 (2015): 4943–4951.
2. Shaw, J. J.*, Spakowicz, D. J.*, Dalal, R. S., Davis, J. H., Lehr, N. A., Dunican, B. F., Orellana, E. A., Narváez-Trujillo, A., and Strobel, S. A. “Biosynthesis and Genomic Analysis of Medium-Chain Hydrocarbon Production by the Endophytic Fungal Isolate Nigrograna Mackinnonii E5202HApplied Microbiology and Biotechnology (2015): doi:10.1007/s00253-014-6206-5 * these authors contributed equally
3. Gianoulis, T. A.*, Griffin, M. A.*, Spakowicz, D. J.*, Dunican, B. F., Alpha, C. J., Sboner, A., Sismour, A. M., Kodira, C., Egholm, M., Church, G. M., Gerstein, M. B., and Strobel, S. A. “Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne SarcoidesPLoS Genet 8, no. 3 (2012): e1002558. doi:10.1371/journal.pgen.1002558 *these authors contributed equally

Other

Bibliography
1. Muir, P., Li, S., Lou, S., Wang, D., Spakowicz, D. J., Salichos, L., Zhang, J., Weinstock, G. M., Isaacs, F., Rozowsky, J., and Gerstein, M. “The Real Cost of Sequencing: Scaling Computation to Keep Pace with Data GenerationGenome Biology 17, (2016): doi:10.1186/s13059-016-0917-0, Available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806511/
2. Kolařík, M., Spakowicz, D. J., Gazis, R., Shaw, J., Kubátová, A., Nováková, A., Chudíčková, M., Forcina, G. C., Kang, K. W., Kelnarová, I., Skaltsas, D., Portero, C. E., Strobel, S. A., and Narváez-Trujillo, A. “Biatriospora (Ascomycota: Pleosporales) Is an Ecologically Diverse Genus Including Facultative Marine Fungi and Endophytes with Biotechnological PotentialPlant Systematics and Evolution (2016): 1–16. doi:10.1007/s00606-016-1350-2
3. Sena Filho, J. G. de, Quin, M. B., Spakowicz, D. J., Shaw, J. J., Kucera, K., Dunican, B., Strobel, S. A., and Schmidt-Dannert, C. “Genome of Diaporthe Sp. Provides Insights into the Potential Inter-Phylum Transfer of a Fungal Sesquiterpenoid Biosynthetic PathwayFungal Biology (2016): Available at http://www.sciencedirect.com/science/article/pii/S187861461630023X
4. Shaw, J. J., Berbasova, T., Sasaki, T., Jefferson-George, K., Spakowicz, D. J., Dunican, B. F., Portero, C. E., Narvaez-Trujillo, A., and Strobel, S. A. “Identification of a Fungal 1,8-Cineole Synthase from Hypoxylon Sp. with Common Specificity Determinants to the Plant SynthasesJournal of Biological Chemistry (2015): jbc.M114.636159. doi:10.1074/jbc.M114.636159
5. Rundell, S. M., Spakowicz, D. J., Narváez-Trujillo, A., and Strobel, S. A. “The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of EcuadorJournal of Fungi 1, no. 3 (2015): 384–396.
6. Patridge, E. V., Darnell, A., Kucera, K., Phillips, G. M., Bokesch, H. R., Gustafson, K. R., Spakowicz, D. J., Zhou, L., Hungerford, W. M., Plummer, M., and others. “Pyrrolocin A, a 3-Decalinoyltetramic Acid with Selective Biological Activity, Isolated from Amazonian Cultures of the Novel Endophyte Diaporthales Sp. E6927E.Natural product communications 10, no. 10 (2015): 1649–1654.
7. Forcina, G. C., Castro, A., Bokesch, H. R., Spakowicz, D. J., Legaspi, M. E., Kucera, K., Villota, S., Narváez-Trujillo, A., McMahon, J. B., Gustafson, K. R., and others. “Stelliosphaerols A and B, Sesquiterpene–Polyol Conjugates from an Ecuadorian Fungal EndophyteJournal of natural products (2015): Available at http://pubs.acs.org/doi/abs/10.1021/acs.jnatprod.5b00749
8. Tomsheck, A. R., Strobel, G. A., Booth, E., Geary, B., Spakowicz, D., Knighton, B., Floerchinger, C., Sears, J., Liarzi, O., and Ezra, D. “Hypoxylon Sp., an Endophyte of Persea Indica, Producing 1, 8-Cineole and Other Bioactive Volatiles with Fuel PotentialMicrobial ecology 60, no. 4 (2010): 903–914.
9. Strobel, G., Tomsheck, A., Geary, B., Spakowicz, D., Strobel, S., Mattner, S., and Mann, R. “Endophyte Strain NRRL 50072 Producing Volatile Organics Is a Species of AscocoryneMycology 1, no. 3 (2010): 187–194.
10. Griffin, M. A., Spakowicz, D. J., Gianoulis, T. A., and Strobel, S. A. “Volatile Organic Compound Production by Organisms in the Genus Ascocoryne and a Re-Evaluation of Myco-Diesel Production by NRRL 50072Microbiology 156, no. 12 (2010): 3814–3829.
11. Banerjee, D., Strobel, G. A., Booth, E., Geary, B., Sears, J., Spakowicz, D., and Busse, S. “An Endophytic Myrothecium Inundatum Producing Volatile Organic CompoundsMycosphere 1, no. 3 (2010): 229–240.
12. Strobel, G. A., Knighton, B., Kluck, K., Ren, Y., Livinghouse, T., Griffin, M., Spakowicz, D., and Sears, J. “The Production of Myco-Diesel Hydrocarbons and Their Derivatives by the Endophytic Fungus Gliocladium Roseum (NRRL 50072)Microbiology 154, no. 11 (2008): 3319–3328. doi:10.1099/mic.0.2008/022186-0
13. Prochniewicz, E., Spakowicz, D., and Thomas, D. D. “Changes in Actin Structural Transitions Associated with Oxidative Inhibition of Muscle Contraction†Biochemistry 47, no. 45 (2008): 11811–11817.
14. Prochniewicz, E., Lowe, D. A., Spakowicz, D. J., Higgins, L., O’Conor, K., Thompson, L. V., Ferrington, D. A., and Thomas, D. D. “Functional, Structural, and Chemical Changes in Myosin Associated with Hydrogen Peroxide Treatment of Skeletal Muscle FibersAmerican Journal of Physiology-Cell Physiology 294, no. 2 (2008): C613–C626.

TEACHING EXPERIENCE

Instructor, Rainforest Expedition and Laboratory Course 01/2014-09/2014

Yale University, New Haven, CT

Teaching Assistant, Rainforest Expedition and Laboratory Course 2008-11

Yale University, New Haven, CT


TALKS

Mycological Society of America Meeting, New Haven, CT 2012

Yale Molecular Biophysics and Biochemistry Department Retreat 2010

US Department of Defense National Security Fellows Conference, Washington D.C. 07/2009

Cell and Molecular Biology Training Grant Symposium, Yale University 02/2009


POSTERS

American Society for Microbiology 06/2015

Yale Molecular Biophysics and Biochemistry Department Retreat 10/2012

Gordon Research Conference: Natural Products 07/2012

Yale Climate and Energy Institute Conference 2011

Yale Climate and Energy Institute Conference 2010

Yale Molecular Biophysics and Biochemistry Department Retreat 2009

Yale Molecular Biophysics and Biochemistry Department Retreat 2008

Biophysical Society Meeting 2007

Biophysical Society Meeting 2006


FIELD WORK

Sarawak, Malaysia 11/2011

Amazon Basin, Ecuador 03/2008-10

Patagonia, Chile 12/2007

Monteverde, Costa Rica 02-06/2004


OTHER RELEVANT EXPERIENCE

Scientific Reviewing/Judging/Mentoring

Community Involvement/Outreach


PROFESSIONAL MEMBERSHIPS


GRADUATE COURSEWORK