Publications

2013

Johnson BR, Borowiec ML, Chiu JC, Lee EK, Atallah J, Ward PS. (2013) Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Current Biology 23(20):2058–2062.

Singh R, Ong-Abdullah M, Low ET, Manaf MAA, Rosli R, Nookiah R, Ooi CL, Ooi SW, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing R, Wilson RK, Fulton RS, Ordway JM, Martienssen RA and Sambanthamurthi R. (2013) Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature 500:335–339.

2012

Rosenfeld JA, Payne A, DeSalle R. (2012) Random roots and lineage sorting. Molecular Phylogenetics and Evolution 64(1):12-20.

Rosenfeld J, DeSalle R. (2012) E value cutoff and eukaryotic genome content phylogenetics. Molecular Phylogenetics and Evolution 63(2):342-350.

Pentony MM, Winters P, Penfold-Brown D, Drew K, Narechania A, DeSalle R, Bonneau R, Purugganan MD. (2012) The Plant Proteome Folding Project: structure and positive selection in plant protein families. Genome Biology and Evolution 4(3):360-371.

Narechania A, Baker RH, Sit R, Kolokotronis SO, DeSalle R, Planet PJ. (2012) Random Addition Concatenation Analysis: a novel approach to the exploration of phylogenomic signal Reveals strong agreement between core and shell genomic partitions in the Cyanobacteria. Genome Biology and Evolution 4(1):30-43.

2011

Lee EK*, Cibrian-Jaramillo A*, Kolokotronis SO*, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, DeSalle R. (2011) A functional phylogenomics view of the seed plants. PLoS Genetics 7(12):e1002411. *equal contribution {press release} {NYT} {NSF Science360} {Genome Technology}

2010

Cibrián-Jaramillo A, Daly AC, Brenner E, DeSalle R, Marler TE. (2010) When North and South don’t mix: genetic connectivity of a recently endangered oceanic cycad, Cycas micronesica, in Guam using EST-microsatellites. Molecular Ecology 19(12):2364–2379.

Cibrián-Jaramillo A, De la Torre-Barcena JE, Lee EK, Katari MS, Little DP, Stevenson DW, Martienssen R, Coruzzi GM, DeSalle R. (2010) Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biology and Evolution 2:225-239.

Schulz C, Little DP, Stevenson DW, Nowogrodzki A, Paquiot D. (2010) Growth and care instructions of a new model species–the lycophyte Selaginella apoda. American Fern Journal 100(3):167-171.

Schulz C, Little DP, Stevenson DW, Bauer D, Moloney C, Stutzel. (2010) An overview of the morphology, anatomy, and life cycle of a new model species: The lycophyte Selaginella apoda (L.) Spring. International Journal of Plant Sciences 171(7):693-712.

Knopf P, Schulz C, Little DP, Stutzel T, Stevenson DW. (2010) Relationships within Podocarpaceae based on DNA sequence, anatomical, morphological, and biogeographical data. Cladistics 28(3):271-299.

Nicolalde-Morejón F, Vergara-Silva F, González-Astorga J, Stevenson DW. (2010) Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales). Mitochondrial DNA 21(Suppl 1):51-59.

2009
de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R. (2009) The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data. PLoS ONE 4(6):e5764.

Cibrián-Jaramillo A, Martienssen RA & the New York Plant Genomics Consortium. (2009) Abominable mystery: The role of RNA interference in the evolution of flowering plants. Cold Spring Harbor Symposia on Quantitative Biology 74:267-273.

Brenner ED, Feinberg P, Runko S, Coruzzi GM. (2009) A mutation in the Proteosomal Regulatory Particle AAA-ATPase-3 in Arabidopsis impairs the light-specific hypocotyl elongation response elicited by a glutamate receptor agonist, BMAA. Plant Molecular Biology 70(5):523-533.

2008
Cibrián-Jaramillo A, Marler TE, DeSalle R, Brenner ED. (2008) Development of EST-microsatellites from the cycad Cycas rumphii, and their use in the recently endangered Cycas micronesica. Conservation Genetics 9:1051-1054.

Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R. (2008) Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phylogenomics. BMC Bioinformatics 9:103.

2007
Little DP, Moran RC, Brenner ED, Stevenson DW. (2007) Nuclear genome size in Selaginella. Genome 50(4):351-6.

2006
Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, Depamphilis C, DeSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS 10(2):231-237.

de la Torre JE, Egan MG, Katari M, Brenner ED, Stevenson DW, Coruzzi GM, DeSalle R. (2006) ESTimating plant phylogeny: lessons from partitioning. BMC Evolutionary Biology 6(1):48.

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R. (2006) OrthologID: automation of genome-scale ortholog identification within a parsimony framework. Bioinformatics 22(6):699-707.

2005
Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM. (2005) EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. BMC Genomics 6:143.

2003
Brenner ED, Stevenson DW, Twigg RW. (2003) Cycads: evolutionary innovations and the role of plant-derived neurotoxins. Trends in Plant Science 8(9):446-452.

Brenner ED, Stevenson DW, McCombie RW, Katari MS, Rudd SA, Mayer KF, Palenchar PM, Runko SJ, Twigg RW, Dai G, Martienssen RA, Benfey PN, Coruzzi GM. (2003) Expressed sequence tag analysis in Cycas, the most primitive living seed plant. Genome Biology 4:R78.

Books, Chapters, Conference Proceedings

Cibrián-Jaramillo A, Martienssen R. (2009) Darwin’s “abominable mystery”: the role of RNA interference in the evolution of flowering plants. Cold Spring Harbor Symposia on Quantitative Biology vol. 74, pp. 267-273.

Egan M, Lee EK, Chiu JC, Coruzzi G, DeSalle R. (2009) Gene orthology assessment with OrthologIDMethods in Molecular Biology. In: Bioinformatics for DNA Sequence Analysis. Posada D, editor. vol. 537, pp. 23-38. Humana Press.

Brenner ED, Stevenson DW, Katari MS, McCombie RW, Rudd SA, Runko SJ, Martienssen RA, Coruzzi GM. (2006) Genomic Studies in Cycas rumphii. In: Proceedings of Cycad 2005 – The 7th International Conference on Cycad Biology. Memoirs of The New York Botanical Garden, vol. 97. Vovides AP et al., editors. The New York Botanical Garden Press.

Brenner ED, Stevenson DW. (2006) Using genomics to study evolutionary origins of seeds. In: Landscapes, Genomics and Transgenic Conifers. Williams CG, editor. pp. 85-106. Springer.