#CV.md#

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title: CV
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CONTACT INFORMATION
===================

-   Department of Biological Sciences
-   Room 379 CASIC Building
-   559 Devall Drive
-   Auburn University, AL 36849 USA
-   Telephone: 864-985-2297
-   Email: ssefick@auburn.edu

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:
---------------

-   <https://scholar.google.com/citations?user=TWH2UnIAAAAJ&hl=en>

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 (April 21 -- April 23, 2015)
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