Erin Osborne Nishimura



B. S. University of California, Santa Cruz
Ph.D. University of California, Berkeley

Previous Positions

Postdoctoral Fellow: University of North Carolina
Fellow: East Asian Pacific Island Summer Research Institute (NSF-JSPS) at the University of Osaka, Japan
Intern: Roche BioSciences
Technician: Santa Cruz Biotechnology, Inc.

Courses & Workshops

    2016, fall: Linux as a computational platform

    2016, fall: RNA-sequencing data analysis

    2015, summer: Next generation sequencing analysis workshop

Next generation sequencing analysis -- webpage
Next generation sequencing analysis -- github

    2015, summer: How to learn how to code

How to learn how to code -- large group
How to learn how to code -- shell scripting small group
How to learn how to code -- github, notes
How to learn how to code --github, project

    2015, summer: High throughput sequencing based techniques


Publications & Datasets


Professorship Research

see Publications


post-Postdoctoral Research

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism.
Saha S, Weber CA, Nousch M, Adame-Arana O, Hoege C, Hein MY, Osborne-Nishimura E, Mahamid J, Jahnel M, Jawerth L, Pozniakovski A, Eckmann CR, Jülicher F, Hyman AA.
Cell. 2016 Sep 8;166(6):1572-1584.e16.

Probing and rearranging the transcription factor network controlling the C. elegans endoderm
Wiesenfahrt T, Osborne Nishimura E, Berg JY, McGhee JD.
Worm Commentary. 2016 June 10; e1198869

Postdoctoral Research - Developmental genomics in C. elegans and other organisms

A Transcriptional Lineage of the Early C. elegans Embryo.
Tintori SC, Osborne Nishimura E, Golden P, Lieb JD, Goldstein B.
Dev Cell. 2016 Aug 22;38(4):430-44.

The function and regulation of the GATA factor ELT-2 in the C. elegans endoderm.
Wiesenfahrt T, Berg JY, Osborne Nishimura E, Robinson AG, Goszczynski B, Lieb JD, McGhee JD.
Development. 2016 Feb 1;143(3):483-91.

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.
Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Osborne Nishimura E, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B.
Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15976-81.

Asymmetric Transcript Discovery by RNA-seq in C. elegans Blastomeres Identifies neg-1, a Gene Important for Anterior Morphogenesis.
Osborne Nishimura  E, Zhang JC, Werts AD, Goldstein B, Lieb JD.
PLoS Genetics. Apr 13, 2015. 

RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.
Amin NM, Tandon P, Osborne-Nishimura E, Conlon FL.
Methods. 2013 Jun 20. 

Graduate Research - Transcriptional Silencing in S. cerevisiae

The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer.
Teytelman L, Osborne Nishimura EA, Özaydin B, Eisen MB, Rine J.
G3 (Bethesda). 2012 Dec;2(12):1555-62.

Symmetry, asymmetry, and kinetics of silencing establishment in Saccharomyces cerevisiae revealed by single-cell optical assays.
Osborne EA, Hiraoka Y, Rine J.
Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1209-16. 

The establishment of gene silencing at single-cell resolution.
Osborne EA, Dudoit S, Rine J.
Nat Genet. 2009 Jul;41(7):800-6. 

Technician Work - Plant Genetics in Arabidopsis and Zea mays

The Cellulose Synthase Superfamily
Youngs HL, Hamann T, Osborne E, Somerville C.
Springer; 2007. Chapter 3; p.35-48. Brown R, Saxena IM, editors. The University of Texas, Austin, TX.

Toward a systems approach to understanding plant cell walls.
Somerville C, Bauer S, Brininstool G, Facette M, Hamann T, Milne J, Osborne E, Paredez A, Persson S, Raab T, Vorwerk S, Youngs H.
Science. 2004 Dec 24;306(5705):2206-11. Review.

WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis.
Broun P, Poindexter P, Osborne E, Jiang CZ, Riechmann JL.
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4706-11. 

Maize mutants lacking chloroplast FtsY exhibit pleiotropic defects in the biogenesis of thylakoid membranes.
Asakura Y, Hirohashi T, Kikuchi S, Belcher S, Osborne E, Yano S, Terashima I, Barkan A, Nakai M.
Plant Cell. 2004 Jan;16(1):201-14. 

Tissue specific expression of CESA and CSL genes in Arabidopsis
Hamann T, Osborne E, Youngs HL, Misson J, Nussaume L, et al.
Cellulose. 2004; 11:279 - 286.

Microspore separation in the quartet 3 mutants of Arabidopsis is impaired by a defect in a developmentally regulated polygalacturonase required for pollen mother cell wall degradation.
Rhee SY, Osborne E, Poindexter PD, Somerville CR.
Plant Physiol. 2003 Nov;133(3):1170-80.

Group II intron splicing factors derived by diversification of an ancient RNA-binding domain.
Ostheimer GJ, Williams-Carrier R, Belcher S, Osborne E, Gierke J, Barkan A.
EMBO J. 2003 Aug 1;22(15):3919-29.