Untitled-1Steven R. Eichten

steven.eichten@anu.edu.au
Ph.D. University of Minnesota – Plant Biological Sciences
B.S. Biology – Augsburg College
HFSP PostDoctoral Fellow (2014-2015)
ARC DECRA Fellow (2015-Present)
CV (Updated Oct, 2016)
GitHub repos


Biography:

I joined the Borevitz lab in December 2013 after being a Postdoctoral fellow and PhD student under Nathan Springer at the University of Minnesota. My research has primarily focussed on identifying and classifying DNA methylation variation within Zea mays. I now have largely moved to working with the model monocot Brachypodium distachyon to study how natural variation and adaptation are influenced (or influence) chromatin states in the genome.

Outside of science, I spend my time playing guitar, fishing, hiking, and playing old video games.


Current projects:

IMG_20151216_103903

ARC DECRA 2015:
IMG_20140811_133357
Adaptation and the Extended Genotype of Brachypodium distachyon

I collaborate with many researchers at the new ARC Centre of Excellence in Plant Energy Biology to add an additional dimension to our understanding of the relationship between genotype, phenotype and the environment through analysis of genome wide associations in chromatin markers. The pilot study investigating genetically diverse B. distachyon has recently been published:


Eichten SR
, Stuart T, Srivastava A, Lister R, Borevitz JO. DNA methylation profiles of diverse Brachypodium distachyon aligns with underlying genetic diversity. Genome Res. 2016 Sep 9. pii: gr.205468.116. PubMed PMID: 27613611.

Local, long-read sequencing using the MinION platform20160830_080324

As the technology has improved, I am interested in the possible applications of the Oxford Nanopore MinION sequencer to natural variation studies. I am working with a variety of people in the lab to identify methods of DNA extraction and quality isolation for field-based genomic applications. To go from sample to sequence in a matter of minutes would be a powerful change in how we can approach genomic sample identification.


Teaching:

ANU BIOL3161 Genomics and its Applications


Past projects with associated publications:

Chromatin Profiling & Epigenetic Analyses:

Eichten SR*, Swanson-Wagner RA*, Schnable J, Waters A, Hermanson P, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable P, Vaughn M, Springer NM. 2011 Heritable epigenetic variation among maize inbreds. PLoS Genet 7(11) *Authors contributed equally to this publication

Eichten SR, Vaughn M, Hermanson P, Springer NM. 2012. Variation In DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues. Plant Genome 10.3835/plantgenome2012.06.0009

Eichten SR, Ellis NA, Makarevitch I, Yeh C, Gent J, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM. 2012. Spreading of Heterochromatin is Limited to Specific Families of Maize Retrotransposons. PLoS Genet 8(12).

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. 2013. Epigenetic and genetic influences on DNA methylation variation in maize populations. The Plant Cell 25 (8).

Li Q, Eichten SR, Hermanson PJ, Springer NM. 2013. Inheritance Patterns and Stability of DNA Methylation Variation in Maize Near-Isogenic Lines. Genetics 113.158980

 

Genomic Analysis of Structural Variation:

Springer NM, Eichten S, Smith A, Papa CM, Steinway S, Kaeppler SM. 2009. Characterization of a novel maize retrotransposon family SPRITE that shows high levels of variability among maize inbred lines. Maydica 54: 417-428.

Swanson-Wagner RA*, Eichten SR*, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM. 2010. Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor.  Genome Research 20(12):1689-99.

Eichten SR, Foerster J, de Leon N, Kai Y, Yeh C, Liu S, Jeddeloh J, Schnable P, Kaeppler S, Springer N. 2011. Genetic architecture of maize B73-Mo17 near isogenic lines (NILs). Plant Physiology. 156 (4):1679-1690

Munoz-Amatriain, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer K, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N. 2013. Distribution, functional impact and origin mechanisms of copy number variation in the barley genome. Genome Biology 14(58).

 

Histone Modifications & Genetic Imprinting:

Waters AJ, Billinski P, Eichten SR, Vaughn MV, Ross-Ibarra J, Gehring M, Springer NM. 2013. Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species. PNAS 110 (48).

Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM. 2013. Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27. Plant Cell 25 (1).

Waters AJ*, Makarevitch I*, Eichten SR*, Swanson-Wagner RA, Yeh C, Xu W, Schnable P, Vaughn M, Gehring M, Springer NM. 2011. Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm. Plant Cell 7(1) 4221-4233.