Institute of Molecular Biology

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Eric Johnson

Eric Johnson

Professor, Biology
Member, IMB

Ph.D., University of Iowa
B.A., Grinnell College

Office: Streisinger Hall Room 312
Office Phone: 541-346-5183
Lab: Streisinger Hall Room 315
Lab Phone: 541-346-5994

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Research Interests


We develop new molecular and computational methods to harness the rapidly-increasing power of next-generation sequencing. Our lab developed Restriction-site Associated DNA (RAD) sequencing, which is being used for trait mapping, creation of genetic maps, phylogeography, association and population structure studies. A variant called RAD paired-end contig sequencing is used to create high-quality genome assemblies by partitioning the sequence reads into manageable groups. We have also developed new methods for rapidly screening populations for mutations, an update to TILLING, and genome-wide methods for assaying enhancer activity.

johnson research RAD paired-end contigs are assembled from the randomly sheared fragment ends that sample the region around a restriction site. Sequences sharing a restriction site sequence are assembled into a contig that forgoes many of the problems of whole-genome assembly.

Gene regulation

The response to low oxygen, or hypoxia, involves the regulation of many cellular pathways that shut down low priority cellular activity and increase stress responses. We carry out genome-wide studies to identify genetic targets of hypoxic regulation and how the regulatory network is organized. Using the fruit fly Drosophila as a model system, we have shown that HIF-1, the key transcription factor regulating the response to low oxygen, has connections to many other key signaling pathways in the cell that allow it to orchestrate the cellular response. Hypoxia is an important aspect of the pathology of heart attack and stroke, so understanding the regulatory network gives insight into potential therapeutic targets.

johnson research Drosophila tissue culture cells carrying a fluorescent reporter driven by a HIF-1 enhancer from the Heat shock factor gene is turned on by low oxygen stress and requires HIF-1.

Recent publications

(pulled from pubmed)

Recent publications

(pulled from pubmed)

Massively parallel characterization of restriction endonucleases.
Kamps-Hughes N, Quimby A, Zhu Z, Johnson EA
Nucleic acids research 2013
Sgt1 acts via an LKB1/AMPK pathway to establish cortical polarity in larval neuroblasts.
Andersen RO, Turnbull DW, Johnson EA, Doe CQ
Developmental biology 2012
SNP discovery and genotyping for evolutionary genetics using RAD sequencing.
Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA
Methods in molecular biology (Clifton, N.J.) 2011
Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing.
O'Rourke SM, Yochem J, Connolly AA, Price MH, Carter L, Lowry JB, Turnbull DW, Kamps-Hughes N, Stiffler N, Miller MR, Johnson EA, Bowerman B
Genetics 2011
HIF takes it up a notch.
Johnson EA
Science signaling 2011
Local de novo assembly of RAD paired-end contigs using short sequencing reads.
Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA
PloS one 2011
A survey of new temperature-sensitive, embryonic-lethal mutations in C. elegans: 24 alleles of thirteen genes.
O'Rourke SM, Carter C, Carter L, Christensen SN, Jones MP, Nash B, Price MH, Turnbull DW, Garner AR, Hamill DR, Osterberg VR, Lyczak R, Madison EE, Nguyen MH, Sandberg NA, Sedghi N, Willis JH, Yochem J, Johnson EA, Bowerman B
PloS one 2011
Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.
Pfender WF, Saha MC, Johnson EA, Slabaugh MB
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 2011
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM
BMC genomics 2011
Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.
Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA
PLoS genetics 2010
Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation.
Yokoi H, Yan YL, Miller MR, BreMiller RA, Catchen JM, Johnson EA, Postlethwait JH
Developmental biology 2009
Recent advances in crustacean genomics.
Stillman JH, Colbourne JK, Lee CE, Patel NH, Phillips MR, Towle DW, Eads BD, Gelembuik GW, Henry RP, Johnson EA, Pfrender ME, Terwilliger NB
Integrative and comparative biology 2008
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA
PloS one 2008
High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora.
Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU
Genetics 2007
RAD marker microarrays enable rapid mapping of zebrafish mutations.
Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, Postlethwait JH, Johnson EA
Genome biology 2007