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Education

Columbia University, Graduate School of Arts and Sciences, New York, NY

Doctor of Philosophy, Biological Sciences, October 2010

Rice University, Houston, TX

Bachelor of Fine Arts, Photography, May 2000 Bachelor of Arts, double major: Art & Art History, Biology, May 1999

Experience

##California Digital Library, UC Office of the President, Oakland, CA, 2013 – present

CLIR/DLF postdoctoral fellowship in data curation for the sciences and social sciences

Supervisor: Dr. Carly Strasser

  • Comprehensively reviewed new and ongoing data publication initiatives; published the findings as an article in F1000Research.
  • Surveyed researcher practices and perceptions relating to data publication to inform initiatives at the California Digital Library and beyond.
  • Wrote blog posts for Data Pub and the Digital Library Federation.
  • Led a data publication session at the 2013 CLIR Fellows Winter Meeting. Presented review article to UC Berkeley Research IT reading group.
  • Served on the FORCE11 Data Citation Implementation Working Group.

San Diego Zoo Institute for Conservation Research, San Diego, CA

###Volunteer research, 2012 - 2013

Principal Investigator: Dr. Lance Miller

  • Contributed to database of natural history of species in the San Diego Zoo’s collection
  • Collected exhaustive data on behavioral and ecological metrics from the literature.

Department of Biological Sciences, Columbia University, New York, NY

###Graduate dissertation research, 2003 - 2010

Advisor: Dr. Martin Chalfie, Nobel Laureate Thesis Title: Prohibitin homology domain proteins in Caenorhabditis elegans.

  • Analyzed C. elegans prohibitin homology domain (PHB-d) protein sequences from public databases using bioinformatics tools and classified into subfamilies.
  • Devised confocal microscopy protocol for cell mapping. In collaboration with WormAtlas, fully characterized PHB-d protein family expression and subcellular localization.
  • Correlated sequence data and expression patterns to identify subfamily enriched in neurons.
  • Tested for functional roles and identified a gene needed for sensitive odor detection.
  • Established mammalian cell culture system for expression of C. elegans proteins.
  • Managed collaborations with Benzing and Hall labs.
  • Trained and supervised two undergraduate technicians.

###Graduate rotation research, Spring 2003

Principal Investigator: Dr. Darcy Kelley

  • Electrophysiology and immunohisotchemistry of Xenopus laevis larynx.

###Graduate rotation research, Summer 2003

Principal Investigator: Dr. Harmen Bussemaker

  • Implemented a computational method to use gene expression data to identify up or down regulated Gene Ontology categories.

###Teaching Assistant, Spring 2006

Bioinformatics of Gene Expression: Dr. Harmen Bussemaker

  • Wrote and edited on-line Perl tutorials and bioinformatics programming assignments.
  • Provided one-on-one guidance to students during lab sessions.

###Teaching Assistant, Fall 2005

Neurobiology I: Cellular and Molecular Biology: Dr. Jian Yang

  • Led weekly discussion of journal articles.
  • Organized exam review sessions; graded exams.

Department of Neuropathology, Johns Hopkins University, Baltimore, MD

###Senior Laboratory Technician, 2000 - 2002

Principal Investigator: Dr. Charles Eberhart

  • Studied role of Wnt signaling in medullobastoma, a pediatric brain tumor.
  • Characterized two transgenic mouse strains and managed mouse colony, including all genetics and genotyping.

Skills & Techniques

Computer Skills & Software

  • General Purpose: Microsoft Office, EndNote, Zotero, Adobe Illustrator, Evernote, Mendeley.
  • Data Analysis: IPython, NumPy, Pandas, SciPy, TextMate.
  • Image Acquisition & Analysis: Adobe Photoshop, ImageJ, AxioVision, FluoView.
  • Sequence Analysis: BLAST, ClustalW, JALView, Dendroscope, TreeviewX, EnzymeX, ApE.
  • Computer Language/Syntax: C/C++, LaTeX, Markdown, Python, XML.

###Bench Biology

  • Microscopy: Confocal, Transmission Electron, Epifluorescent, DIC.
  • Molecular Biology: Cloning, DNA Electrophoresis, Restriction Digest, PCR, RT-PCR.
  • Biochemistry: Immunohistochemistry, Western Blot, Blue Native Gel Electrophoresis, in situ Hybridization.
  • Genetics: Classical Genetics, Genotyping, RNAi, Behavioral Assays.
  • Model Systems: C. elegans, Mice, X. laevis, Mammalian Cell Culture

Courses & Certificates

##University of California San Diego Extension, San Diego, CA

  • C/C++ Programming Certificate, 2012

##Coursera

  • Introduction to Databases, Winter 2013
  • Computing for Data Analysis, Fall 2012
  • Writing in the Sciences, Fall 2012

##Columbia University, New York, NY

  • Structure and Function of Membrane Channels, Spring 2006
  • Signal Transduction, Fall 2005
  • Computational Genomics, Spring 2004

#Fellowships

CLIR/DLF Postdoctoral Fellowship in Data Curation, 2013 - 2015 Columbia University Presidential Fellowship, 2002 - 2010 National Institute of Health Training Grant, 2005 - 2007

#Publications

J. E. Kratz and C. Strasser, Data publication consensus and controversies. F1000Research 3:94 (2014) doi:10.12688/f1000research.4518

E. M. Schurek, J. Tax, L. A. Völker, T. Lamkemeyer, D. Ungrue, J. E. Kratz, Y. Tian, K. Kunzelmann, M. Chalfie, B. Schermer, T. Benzing, M. Höhne, A disease-causing mutation illuminates protein membrane topology of the kidney protein podocin. Journal of Biological Chemistry 289, 11262-71 (Apr 18, 2014). doi:10.1074/jbc.M113.521773

J. E. Kratz, What is the circadian clock? The Where, The What & The How: 75 Artists Illustrate the Wondrous Mysteries of the Universe. Ed. Julia Rothman. Chronicle Books, September 2012.

A. Bounoutas, J. E. Kratz, L. Emtage, C. Ma, K. Nguyen, M. Chalfie, Microtubule depolymerization in C. elegans touch receptor neurons reduces gene expression through a p38 MAPK pathway. Proceeding of the National Academy of Sciences 108, 3982-3987 (Mar 8, 2011). doi:10.1073/pnas.1101360108

C. G. Eberhart, J. Kratz, Y. Wang, K. Summers, D. Stearns, K. Cohen, C. V. Dang, P. C. Burger, Histopathological and molecular prognostic markers in medulloblastoma: c-myc, N-myc, TrkC, and anaplasia. Journal of Neuropathology & Experimental Neurology 63, 441-9 (May, 2004).

X. Fan, Y. Wang, J. E. Kratz, D. J. Brat, Y. Robitaille, A. Moghrabi, E. J. Perlman, C. V. Dang, P. C. Burger, C. G. Eberhart, hTERT gene amplification and increased mRNA expression in central nervous system embryonal tumors. American Journal of Pathology 162, 1763-1769 (June, 2003). doi:10.1016/S0002-9440(10)64311-8

J. E. Kratz, D. Stearns, D. L. Huso, H. H. Slunt, D. L. Price, D. R. Borchelt, C. G. Eberhart, Expression of stabilized beta-catenin in differentiated neurons of transgenic mice does not result in tumor formation. BMC Cancer 2, 33-42 (Dec 2, 2002). doi:10.1186/1471-2407-2-33

C. G. Eberhart, J. E. Kratz, A. Schuster, P. Goldthwaite, K. J. Cohen, E. J. Perlman, P. C. Burger, Comparative genomic hybridization detects an increased number of chromosomal alterations in large cell/anaplastic medulloblastomas. Brain Pathology 12, 36-44 (Jan, 2002). doi:10.1111/j.1750-3639.2002.tb00420.x

#Presentations

J. E. Kratz, G. Janee, J. Kunze, J. Starr, S. Abrams, C. Strasser, Metadata publication for datasets through EZID. Poster, presented at the 9th International Digital Curation Conference. San Francisco, California (February 24, 2014)

J. E. Kratz, M. Chalfie, The PHB-domain protein STO-1 is required for sensitive chemotaxis to diacetyl. Poster, presented at the 17th Biennial International C. elegans Conference. Los Angeles, California (June 24, 2009).

J. E. Kratz, S. Zhang, T. Benzing, M. Chalfie, Characterizing the C. elegans PHB domain proteins. Poster, presented at the 16th Biennial International C. elegans Conference. Los Angeles, California (June 27, 2007).

J. E. Kratz, M. Chalfie, A worm identikit for neuron identification. Poster, presented at the 15th Biennial International C. elegans Conference. Los Angeles, California (June 25, 2005).

C. G. Eberhart, J. E. Kratz, A. Schuster, E. Gabrielson, E. J. Perlman, P. C. Burger, Numerous chromosomal alterations and unique gene-expression profiles in large-cell/anaplastic medulloblastomas. Poster, presented at Mechanisms for Cell Growth and Differentiation. Houston, Texas (Oct 2, 2001).