Erica Sodergren, Ph.D.
Research Accomplishments & Interests
Dr. Erica Sodergren joined The Genome Institute in January 2008 as a Research Associate Professor in the Genetics Department. As Assistant Director of Microbial Genomics, she is responsible for managing The Genome Institute's efforts on the Human Microbiome and related projects. She entered the field of genomics in the mid-1990s, when she joined the Weinstock lab to help analyze the genome of Treponema pallidum, the causative agent of syphilis. Shortly after this the lab began working with the Baylor College of Medicine Human Genome Sequencing Center (BCM-HGSC) to sequence the human genome. There, Dr. Sodergren led efforts to scale up sequencing and managed the front end of the sequencing pipeline.
Dr. Sodergren was also the leader of the sea urchin genome project, which posed particular challenges due to the lack of similarity to other sequenced genomes. She was involved in developing a microbial genomics program at the BCM-HGSC, where she focused on microbial sequencing and work on the Human Microbiome Project (HMP). At The Genome Institute she has continued to be active in developing and coordinating many of the new processes needed for the HMP including acquisition of strains to sequence, quality control of strains before they enter the sequencing pipeline, data collection and analysis from next generation sequencing platforms, sequence assembly and annotation, and software development for tracking and analysis of the HMP data.
Other Biographical Information
Dr. Sodergren began her research career as a technician with Dr. Salvador Luria in 1970. She received her Ph.D. in Microbiology from the Massachusetts Institute of Technology, following this with postdoctoral work at Stanford University School of Medicine. She was a research scientist at the NCI-Frederick Cancer Research Facility. In 1984 she joined the Biochemistry Department at the University of Texas - Houston Medical School moving to the Microbiology Department as a Research Assistant Professor.
Selected Publications
Holtz LR, Wylie KM, Sodergren E, Jiang Y, Franz CJ, Weinstock GM, Storch GA, Wang…
Astrovirus MLB2 Viremia in Febrile Child.
Emerg Infect Dis. 2011 Nov;17(11):2050-2. PubMed | View Abstract
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst…
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. PubMed | View Abstract
Monier A, Welsh RM, Gentemann C, Weinstock G, Sodergren E, Armbrust EV, Eisen JA, Worden…
Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges.
Environ Microbiol. 2011 Sep 14. doi: 10.1111/j.1462-2920.2011.02576.x. [Epub ahead of print] PubMed | View Abstract
Arias CA, Panesso D, McGrath DM, Qin X, Mojica MF, Miller C, Diaz L, Tran…
Genetic Basis for In Vivo Daptomycin Resistance in Enterococci
N Engl J Med. 2011 Sep 8;365(10):892-900. PubMed | View Abstract
Bowne SJ, Humphries MM, Sullivan LS, Kenna PF, Tam LC, Kiang AS, Campbell M, Weinstock…
A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement.
Eur J Hum Genet. 2011 Jun 8. doi: 10.1038/ejhg.2011.86. [Epub ahead of print] PubMed | View Abstract
Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi…
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications.
Nat Biotechnol. 2011 May 6;29(5):415-420. [Epub ahead of print] PubMed | View Abstract
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa…
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Genome Res. 2011 Mar;21(3):494-504. Epub 2011 Jan 6. PubMed | View Abstract
Mikalová L, Strouhal M, Čejková D, Zobaníková M, Pospíšilová P, Norris SJ, Sodergren E, Weinstock…
Genome analysis of Treponema pallidum subsp. pallidum and subsp. pertenue strains: most of the genetic differences are localized in six regions.
PLoS One. 2010 Dec 29;5(12):e15713. PubMed | View Abstract
Nelson DE, Van Der Pol B, Dong Q, Revanna KV, Fan B, Easwaran S, Sodergren…
Characteristic male urine microbiomes associate with asymptomatic sexually transmitted infection.
PLoS One. 2010 Nov 24;5(11):e14116. PubMed | View Abstract
Bowne SJ, Sullivan LS, Koboldt DC, Ding L, Fulton R, Abbott RM, Sodergren EJ, Birch…
Identification of Disease-Causing Mutations in Autosomal Dominant Retinitis Pigmentosa (adRP) Using Next-Generation DNA Sequencing.
Invest Ophthalmol Vis Sci. 2010 Sep 22. [Epub ahead of print] PubMed | View Abstract
Marri PR, Paniscus M, Weyand NJ, Rendón MA, Calton CM, Hernández DR, Higashi DL, Sodergren…
Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.
PLoS One. 2010 Jul 28;5(7):e11835. PubMed | View Abstract
The Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, Worley KC,…
A Catalog of Reference Genomes from the Human Microbiome.
Science. 2010 May 21;328(5981):994-999. PubMed | View Abstract
Salzman NH, Hung K, Haribhai D, Chu H, Karlsson-Sjöberg J, Amir E, Teggatz P, Barman…
Enteric defensins are essential regulators of intestinal microbial ecology.
Nat Immunol. 2010 Jan;11(1):76-83. Epub 2009 Oct 22. PubMed | View Abstract
Bovine Genome Sequencing and Analysis Consortium, Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny…
The genome sequence of taurine cattle: a window to ruminant biology and evolution.
Science. 2009 Apr 24;324(5926):522-8. PubMed | View Abstract
Liu Y, Qin X, Song XZ, Jiang H, Shen Y, Durbin KJ, Lien S, Kent…
Bos taurus genome assembly.
BMC Genomics. 2009 Apr 24;10(1):180. [Epub ahead of print] PubMed | View Abstract
