User:Eric Lyons

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Contact Info

Eric Lyons (an artistic interpretation)

• Eric Lyons
• UC Berkeley
• Department of Plant and Microbial Biology
• 111 Koshland Hall
• Berkeley, CA 94720
• Email me through OpenWetWare

I work in the laboratory of Michael Freeling at UC Berkeley.

Education

• 2008, PhD, Plant biology, UC Berkeley
• 1999, MS, Microbial Biology, UC Berkeley
• 1997, BS, Molecular and Cell Biology (Immunology), UC Berkeley

Research interests

Comparison of syntenic regions from Arabidopsis (At), Grape (Vv), and Papaya (Cp). Note that At has had two sequential genomic duplication events subsequent to its divergence from the lineages of papaya and grape, while the latter two have had none. Graphics on the left is the output from GEvo. Each region has gene models above and below the dotted line, which delineates the top and bottom stands of DNA. Blast hits are represented as colored blocks with lines drawn connecting regions of sequence similarity between different genomic regions.

Comparative genomic and genome evolution, specifically in plant genome evolution I am the project manager and lead developed of the CoGe Comparative Genomics Platform.
This system is designed to:

• store multiple versions of multiple genomes from multiple organisms in a single system
• find an retrieve any genomic region from any set of organisms
• get information about those genomic regions
• compare those genomic regions using any sequence comparison algorithm (although only a half dozen or so have been implemented thus far)
• visualize genomic data and results of comparative analyses

CoGe allows researchers to quickly and efficiently start with a genomic feature of interest (e.g. gene accession, gene name, sequence, genomic location, organism), find syntenic regions within the same genome or among different organisms, and visualize the results in an intuitive and interactive system that permits the rapid identification and characterization of genomic patterns of evolution.

Currently, CoGe has genomes for over 6,000 organisms (in various states of completion and assembly) from all domains of life.

Some tools that CoGe contains are:

• SynMap -- compare any two genomes to identify syntenic regions and visualize the output as syntenic dot-plots. (Uses DagChainer to identify regions of synteny by finding collinear series of putatively homologous genes or sequences.)
• CoGeBlast -- CoGe's interface to blast that allows researchers to select any set of genomes in CoGe to search their sequence(s) against
• GEvo -- compare multiple genomic regions using a variety of sequence comparison algorithms. Sequences may be from CoGe's genomes database, NCBI, or added by a researcher
• GenomeView -- CoGe's genome browser based on GIS technology to have an interactive system much like Google-maps.
• FeatView -- search for genes and other genomic features by name, annotation, organisms, type, etc.

Syntenic comparison between two strains of E. coli using SynMap

Publications

1. Freeling M, Lyons E, Pedersen B, Alam M, Ming R, and Lisch D. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res. 2008 Dec;18(12):1924-37. DOI:10.1101/gr.081026.108 |
2. Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KL, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen C, Qian W, Shen J, Du P, Eustice M, Tong E, Tang H, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan P, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang J, Wang J, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei H, Irikura B, Paidi M, Jiang N, Zhang W, Presting G, Windsor A, Navajas-Pérez R, Torres MJ, Feltus FA, Porter B, Li Y, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang J, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, and Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 2008 Apr 24;452(7190):991-6. DOI:10.1038/nature06856 |
3. Lyons E and Freeling M. How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 2008 Feb;53(4):661-73. DOI:10.1111/j.1365-313X.2007.03326.x |
4. Freeling M, Rapaka L, Lyons E, Pedersen B, and Thomas BC. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell. 2007 May;19(5):1441-57. DOI:10.1105/tpc.107.050419 |
5. Thomas BC, Rapaka L, Lyons E, Pedersen B, and Freeling M. Arabidopsis intragenomic conserved noncoding sequence. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3348-53. DOI:10.1073/pnas.0611574104 |
6. Leung S, Holbrook A, King B, Lu HT, Evans V, Miyamoto N, Mallari C, Harvey S, Davey D, Ho E, Li WW, Parkinson J, Horuk R, Jaroch S, Berger M, Skuballa W, West C, Pulk R, Phillips G, Bryant J, Subramanyam B, Schaefer C, Salamon H, Lyons E, Schilling D, Seidel H, Kraetzschmar J, Snider M, and Perez D. Differential inhibition of inducible T cell cytokine secretion by potent iron chelators. J Biomol Screen. 2005 Mar;10(2):157-67. DOI:10.1177/1087057104272394 |
7. Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, and Pace NR. Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol. 2003 Jan;41(1):295-303. DOI:10.1128/JCM.41.1.295-303.2003 |
8. Washburn JO, Lyons EH, Haas-Stapleton EJ, and Volkman LE. Multiple nucleocapsid packaging of Autographa californica nucleopolyhedrovirus accelerates the onset of systemic infection in Trichoplusia ni. J Virol. 1999 Jan;73(1):411-6. DOI:10.1128/JVI.73.1.411-416.1999 |

Useful links

• CoGe: A new kind of Comparative Genomics