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CONTACT INFORMATION

EDUCATION

  1. PhD Biological Sciences, 2016. Auburn University, Auburn, Alabama, USA.

  2. M.S. Forestry, 2006. Clemson University, Clemson, South Carolina, USA.

  3. B.S. Environmental and Natural Resources (concentration: Conservation Biology), 2003. Clemson University, Clemson, South Carolina, USA.

BIOINFORMATIC WORKSHOPS

  1. Bioinformatics Bootcamp (Auburn University; June 12, 2016)

EMPLOYMENT

  1. Postdoctoral Fellow in Computational Biology. 2016-present. Auburn University, USA.

  2. Research Scientist. October 2006-November 2008. Southeastern Natural Sciences Academy. Augusta, Georgia, USA.

  3. Research Technician. December 2003- August 2004. Warnell School of Forestry, University of Georgia. Athens, Georgia, USA.

SKILLS

Programming languages (listed in order of experience)

  1. R - 10 yrs
  2. Shell - 7 yrs
  3. Python - 9 months
  4. Perl - 9 months

Data Analysis

Statistical Experience

  1. Linear modeling

    • regression (OLS)
    • ANOVAs
    • robust statistics
    • mixed effects models
    • etc.

  2. Multivariate

    • PCA
    • PCoA
    • RDA
    • NMDS
    • etc.

  3. Machine Learning

    • classification and regression trees
    • cluster analysis
    • discriminant analysis
    • partial least squares
    • logistic regression
    • etc.

  4. Resampling based methods

    • boostrap
    • permutation

Computational Skills

  1. High Performance Computing

  2. Next Generation Sequencing Data Analysis

  3. SQL/Database design and use

  4. GIS analysis with Grass GIS/QGIS

  5. Other open source data analysis software

General Computer

  1. Significant linux command line experience.

  2. Server administration experience (2009-present); Ubuntu and Redhat Enterprise Linux.

  3. Platforms: (Linux, Macintosh, and Microsoft Windows).

SOFTWARE

R packages

  1. Sefick, S.A. 2008. StreamMetabolism. Stream Metabolism-A package for calculating single station metabolism from diurnal Oxygen curves. A package for R statistical software. http://cran.r-project.org/.

  2. Sefick, S.A. In Prep. CrossOveRs. A package for analyzing recombination from genotyping data.

Github Repositories

  1. https://github.com/ssefick/

  2. https://github.com/ssefick/StreamMetabolism

  3. https://github.com/ssefick/UsefulBioinformaticScripts

PUBLICATIONS

Google Scholar:

Peer Reviewed Publications

Published, In Press, and Accepted

  1. M.H. Paller, B.A. Prusha, D.E. Fletcher, E. Kosnicki, S.A. Sefick, M.S. Jarrell, S.C. Sterrett, A.M. Grosse, T.D. Tuberville, and J.W. Feminella. Accepted. Factors Influencing Stream Fish Species Composition and Functional Properties at Multiple Spatial Scales in the Sand Hills of the Southeastern United States. Transactions of the American Fisheries Society.

  2. Balenger, S.L., C. Bonneaud, S.A. Sefick, S.V. Edwards, G.E. Hill. 2015. Plumage color and pathogen-induced gene expression in a wild songbird. Behavioral Ecology. DOI: 10.1093/beheco/arv055.

  3. Sefick, S.A., L. Kalin, E. Kosnicki, B.P. Schneid, M.S. Jarrell, C.J. Anderson, M.H. Paller, and J.W. Feminella. 2015. Empirical Estimation of Stream Discharge Using Channel Geometry in Low-Gradient, Sand-Bed Streams of the Southeastern Plains. Journal of the American Water Resources Association (JAWRA) 51:1060-1071.

  4. Kosnicki, E., S.A. Sefick, M.H. Paller, M.S. Jarrell, B.A. Prusha, S.C. Sterrett, T.D. Tuberville, and J.W. Feminella. 2014. Defining the reference condition for wadeable streams in the Sand Hills subdivision of the Southeastern Plains ecoregion, USA. Environmental Management 54:494-504.

  5. Oliver, J. E., S. A. Sefick, J. K. Parker, T. Arnold, P. A. Cobine, and L. De La Fuente. 2014. Ionome changes in Xylella fastidiosa-infected Nicotiana tabacum correlate with the virulence and discriminate between subspecies of bacterial isolates. Molecular Plant-Microbe Interactions 27:1048-1058.

In Review

  1. Stevison, L., S. Sefick, C. Rushton, and R. Graze. Recombination rate plasticity: revealing mechanisms by design. Philosophical Transactions of the Royal Society B.
  2. Sefick, S.A., E. Kosnicki, M.H. Paller, and J.W. Feminella. Hydrogeomorphic reference condition and its relationship with macroinvertebrate assemblages in Southeastern US Sand Hills streams. Freshwater Science.

In Preparation

  1. Sefick, S.A., E. Kosnicki, M.H. Paller, and J.W. Feminella. In Prep. Direct and indirect effects of landcover on macroinvertebrate assemblage structure in Southeastern Plains, USA, streams. (Target: Ecological Applications).

  2. Sefick, S.A., N.E. Norieka, and J.W. Feminella. In Prep. Deterministic species sorting in response to simulated hydrologic disturbance in Southeastern Plains streams. (Target: Ecology).

  3. Sefick, S.A.. StreamMetabolism: An R package for calculating single station metabolism from diurnal Oxygen curves. (Target: The R Journal).

Non-Refereed Publications

Proceedings Manuscripts (* presenter)

  1. Moak, J.W.*, B.S. Metts, S.A. Sefick, G.W. Eidson, and O.P. Filte. 2010. Results of an intensive water quality study of the middle and lower Savannah River Basin. Proceedings of the 2010 South Carolina Water Resources Conference, held October 13-14, 2010, at the Columbia Metropolitan Convention Center. (published proceedings manuscript)

  2. Paller, M.*, J.W. Feminella, E. Kosnicki, S.A. Sefick, M. Jarrell, D. Fletcher,T. Tuberville, S. Sterrett, A. Grosse, B. Prusha. 2010. Ecological Reference Models for Blackwater Streams: a Prerequisite for Successful Ecosystem Recovery and Management. Proceedings of the 2010 South Carolina Water Resources Conference, held October 13-14, 2010, at the Columbia Metropolitan Convention Center. (published proceedings manuscript)

  3. Flite, O.*, G. Eidson, J. Moak, B. Metts, S.A. Sefick. 2008 .Overview of stable Isotopes results from a comprehensive Savannah River study. Proceedings of the 2008 South Carolina Water Resources Conference, held October 14-15, 2008, at the Charleston Area Event Center. (published proceedings manuscript)

  4. Flite, O.*, G. Eidson, J. Moak, B. Metts, and S.A. Sefick. 2007. PRELIMINARY DATA FROM A COMPREHENSIVE SAVANNAH RIVER STUDY: THE FIRST 6 MONTHS. 2007. Proceedings of the 2007 Georgia Water Resources Conference. (published proceedings manuscript)

Reports

  1. Michael Paller, Jack Feminella, Ely Kosnicki, Stephen Sefick, Miller Jarrell, Tracey Tuberville, Dean Fletcher, Andrew Grosse, Bess Harris, Sean Sterrett, Blair Prusha. 2014. DEVELOPMENT OF ECOLOGICAL REFERENCE MODELS AND AN ASSESSMENT FRAMEWORK FOR STREAMS ON THE ATLANTIC COASTAL PLAIN. SERDP Project RC-1694.

  2. Southeastern Natural Sciences Academy. 2008. Savannah River at Risk Annual Report February 2006 -- January 2008. Section 104(b) CP964507-06. Annual Report to the EPA.

PROFESSIONAL ORAL PRESENTATIONS (* presenter)

  1. Sefick, S.A.*, N. Noreika, and J.W. Feminalla. 2016. DISTURBANCE MODIFIES THE IMPORTANCE OF DETERMINISTIC AND STOCHASTIC ASSEMBLY MECHANISMS IN STREAM MACROINVERTEBRATE COMMUNITIES.* *2016 Annual Meeting of the Society for Freshwater Sciences. Sacramento, CA.

  2. Sefick, S.*; Kosnicki, E.; Paller, M.; Feminella, J. 2015. IS THE LANDCOVER CASCADE SYSTEM-SPECIFIC? A CASE STUDY IN SAND-BED STREAMS OF THE SOUTHEASTERN US SANDHILLS ECOREGION. 2015 Annual Meeting of the Society for Freshwater Sciences. Milwaukee, WI.

  3. Helms, B.*; Sefick, S.; Reithel, S.; Kosnicki, E.; Werneke, D.; Schneid, B.; Zink, J.; Feminella, J.; Jennings, G. 2014. GEOMORPHIC ASSESSMENTS AND INSTREAM ECOLOGICAL ENDPOINTS: INTEGRATION FOR RESTORATION AND MANAGEMENT . Joint Aquatic Sciences Meeting, 2014.

  4. Oliver, J.E.*, Sefick, S.A., Parker, J.K., Cobine, P.A., and De La Fuente, L. Understanding Xylella fastidiosa's interactions with plant hosts through the study of its effects on the host ionome. Annual Meeting of the Southeastern Branch of the American Society for Microbiology. 7th-9th November 2013. Auburn University, Auburn, Alabama, USA.

  5. Sefick, S.A.*, M.S. Jarrell, E. Kosnicki^1^, M.H. Paller^2^, and J.W. Feminella. 2013. CHANNEL MORPHOLOGY-BENTHIC MACROINVERTEBRATE TRAIT RELATIONSHIPS IN SOUTHEASTERN COASTAL PLAINS STREAMS. 2013 Annual Meeting of the Society for Freshwater Sciences. Jacksonville, Fl.

  6. Kosnicki, E*.; Sefick, S.; Jarrell, M.; Grosse, A.; Sterrett, S.; Tuberville, T.; Paller, M.; Feminella, J. DEVELOPMENT OF A MACROINVERTEBRATE O/E MODEL FRAMEWORK FOR ASSESSING STREAM BIOLOGICAL INTEGRITY IN THE SAND HILLS OF THE SOUTHEASTERN COASTAL PLAINS USA. * *2013 Annual Meeting of the Society for Freshwater Sciences. Jacksonville, Fl.

  7. Paller, M.*; Prusha, B.; Kosnicki, E.; Sefick, S.; Jarrell, M.; Feminella, J.; Fletcher, D.; Tuberville, T.; Grosse, A.; Sterrett, S. FISH ASSEMBLAGE STRUCTURE IN MINIMALLY DISTURBED STREAMS ON THE UPPER SOUTHEASTERN COASTAL PLAIN. 2013 Annual Meeting of the Society for Freshwater Sciences. Jacksonville, Fl.

  8. Sefick, S.A.*, W.R. English, J.W. Pike, K.M. Young, and G.D. Jennings.2006. Macroinvertebrate community response to priority II stream restoration.Annual Meeting of the North American Benthological Society.

  9. Pike, J.W.*, W.R. English, S.A. Sefick, C.R. Smeal, M.A. Goddard, J.D.Riley, and D.M. Rankin. 2006. Salvelinus fontinalis (brook trout) restoration in the Southeast United States: The impact of Fintrol (antimycin) on macroinvertebrate drift. Annual Meeting of the North American Benthological Society.

PROFESSIONAL POSTER PRESENTATIONS (* presenter)

  1. Jonathan E. Oliver, Stephen Sefick, Paul A. Cobine* and Leonardo De La Fuente (2013) "Ionomic fingerprinting of plant disease caused by Xylella fastidiosa" GRC: Cell Biology of Metals, Salve Regina University, Rhode Island, July 28-August 2.

  2. Sefick, S. A.*; Jarrell, M. S.; Kosnicki, E.; Schneid, B. P.; Paller, M. H.; Feminella, J. W.; IS THE HYDROGEOMORPHIC REFERENCE CONDITION RELATED TO BENTHIC MACROINVERTEBRATE ASSEMBLAGES IN COASTAL PLAINS STREAMS? 2012. Annual Meeting of the Society for Freshwater Sciences.

  3. Sefick, S. A.*; Jarrell, M. S.; Kosnicki, E.; Paller, M. H.; Feminella, J. W.; PRELIMINARY HYDROGEOMORPHIC CLASSIFICATION OF STREAM REFERENCE CONDITION FOR THE ATLANTIC COASTAL PLAIN AND SANDHILLS ECOREGIONS. 2011. Annual Meeting of the North American Benthological Society.

  4. Kosnicki, E.*; Prusha, B. A.; Sterrett, S. C.; Grosse, A. M., Sefick; S.A., Jerrell, M. S.; Tuberville, T. D.; Paller, M. H.; Feminella, J. W. 2011. PRELIMINARY FISH OBSERVED TO EXPECTED (O/E) MODELS FOR THE SAND HILLS SUBECOREGION OF THE SOUTHEASTERN UNITED STATES. Annual Meeting of the North American Benthological Society.

  5. Jarrell, M. S.*; Kosnicki, E.; Prusha, B. A.; Sefick, S. A.; Feminella, J. A.; Paller, M. H. 2011. RIPARIAN-AQUATIC RESPONSE TO TIMBER HARVEST IN A COASTAL PLAINS STREAM FOOD WEB. Annual Meeting of the North American Benthological Society.

UNDERGRADUATE MENTORING

  1. Yiwen
  2. Emma Diemert
  3. Nina E. Noreika

UNDERGRADUATE POSTER PRESENTATIONS (* presenter)

  1. Noreika, N.E.*, S.A. Sefick, J.W. Feminella. Does Disturbance Intensity Affect Macroinvertebrates in Southeastern Plains Streams? Auburn University Research Week.

GRANTS

  1. Auburn Graduate Travel Fellowship

Field/Lab (Abridged)

Field

  1. I have been exposed to a wide variety of field and lab techniques related to limnological analysis of lake, large river, and stream systems.

Lab

  1. Aquatic insect identification (with a special interest in the Chironomidae).

TEACHING EXPERIENCE

  1. Instructor of Record. Introductory Biology (1000). Spring 2016. Department of Biological Sciences, Auburn University. Auburn, Alabama, USA.

  2. Graduate Teaching Assistant. Spring Semester 2012; Fall 2013-2015. Department of Biological Sciences, Auburn University. Auburn, Alabama, USA.

  3. Adjunct Instructor (Instructor of Record). January 2009-May 2009. Science Department, Tricounty Technical College. Clemson, South Carolina, USA.

  • Courses Taught:
    • Introductory biology (4hrs. 2 sections) and introductory biology lab (1hr. 1 section).

GUEST LECTURES

  1. Advanced R Graphics -- Bioinformatics, Auburn University
  2. R Graphics with ggplot 2 -- Biocomputing, Auburn University
  3. Advanced Shell Scripting -- Bioinformatics, Auburn University

OUTREACH

  1. Developed a one day hypothesis driven 8^th^ grade lesson plan investigating anthropogenic watershed disturbance on in-stream water quality. This was a collaborative effort with Lynette Sefick (8^th^ grade earth science teacher Pickens County, SC), and Cathy Marion (Research Scientist at South Carolina Department of Natural Resources)).

  2. AU Explore at the Auburn University Museum of Natural History. Children learned about Alabama and Global biodiversity through guided collections exploration.

  3. AU Explore Stream/Pond study Science Olympiad.

  4. Boosting Engineering, Science, and Technology Judge

    • Student Notebooks
    • Student Presentations

AWARDS

  1. Xi Sigma Pi National Forestry Honor Society

PROFESSIONAL AFFILIATIONS

  1. Society for Freshwater Sciences

  2. American Society for the Advancement of Science

DEPARTMENTAL SERVICE

Auburn University

  1. Bioinformatics Search Committee (Graduate Student Representative 2013-2014)

  2. Departmental office manager (2011-2016)

  3. Space Committee (2011-2016)

  4. Hosted the Southeastern Ecology and Evolution Conference (Major responsibilities: website design/webmaster).

PROFESSIONAL SERVICE

Reviewed articles for:

  1. Journal of the American Water Resources Association (JAWRA)

  2. Freshwater Science

  3. Ecohydrology

Meeting Session Moderator

  1. 2015 annual Society for Freshwater Sciences Meeting

Alabama Biological Condition Gradient Workshop

  1. Sandhills Ecoregion; April 21-23, 2015