Publications
Publications
This list will be updated regularly
2020
Neumann J, DeSalle R, Narechania A, Schierwater B, and Tessler M. (2020) Morphological Characters Can Strongly Influence Early Animal Relationships Inferred from Phylogenomic Data Sets, Systematic Biology. syaa038, https://doi.org/10.1093/sysbio/syaa038 2020
2019
Díaz FP, Latorre C, Carrasco-Puga G, et al.(2019) Multiscale climate change impacts on plant diversity in the Atacama Desert. Global Change Biology. 2019 May;25(5):1733-1745. https://doi.org/10.1111/gcb.14583 2019
2018
Fernández-Gómez B, Maldonado J, Mandakovic D, Gaete A, Gutiérrez R,A., Maass A, Cambiazo V, González M. (2018) Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Scientific Reports, Nature Publisher Group. 9:1-12. https://doi.org/10.1038/s41598-018-37776-0 2018
Mandakovic D, Rojas C, Maldonado J, Latorre M, Travisany D, Delage E, Bihouée A, Jean G, Díaz FP, Fernández-Gómez B, Cabrera P, Gaete A, Latorre C, Gutiérrez R, Maass A, Cambiazo V, Navarrete S, Eveillard A and González M. (2018) Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci Rep 8, 5875 (2018). https://doi.org/10.1038/s41598-018-23931-0 2018
Wood JR, Díaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA. (2018) Plant pathogen responses to Late Pleistocene and Holocene climate change in the central Atacama Desert, Chile. Scientific reports, V8, P17208, https://doi.org/10.1038/s41598-018-35299-2 2018
2017
Chicote, Javier U., Rob DeSalle, and Antonio García-España.(2017) “Phosphotyrosine phosphatase R3 receptors: Origin, evolution and structural diversification.” PloS One 12, no. 3 (2017): https://doi.org/10.1371/journal.pone.0172887. 2017
Leung, Maxwell CK, Andrew C. Procter, Jared V. Goldstone, Jonathan Foox, Robert DeSalle, Carolyn J. Mattingly, Mark E. Siddall, and Alicia R. Timme-Laragy. (2017) “Applying evolutionary genetics to developmental toxicology and risk assessment.” Reproductive Toxicology 69 (2017): 174-186. https://doi.org/10.1016/j.reprotox.2017.03.003. 2017
Pastenes, L., Valdivieso, C., Di Genova, A. et al. (2017) Global gene expression analysis provides insight into local adaptation to geothermal streams in tadpoles of the Andean toad Rhinella spinulosa . Sci Rep 7, 1966 (2017). https://doi.org/10.1038/s41598-017-01982-z
2016
Baker RH, Narechania A, DeSalle R, Johns PM, Reinhardt JA and Wilkinson GS (2016) Spermatogenesis drives rapid gene creation and masculinization of the X chromosome in stalk-eyed flies (Diopsidae). Genome Biology and Evolution 8(3): 896-914. 10.1093/gbe/evw043 2016
Diaz F, Frugone M, Gutierrez RA and Latorre C (2016) Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet. Sci Reports 6, 2226. https://doi.org/10.1038/srep22226 2016
Rosenfeld J, Foox J and DeSalle R (2016) Data for constructing insect genome content matrices for phylogenetic analysis and functional annotation. Data Brief 6(3): 279-281.10.1016/j.dib.2015.12.015. 2016
Schierwater B, Holland PW, Miller DJ, Stadler PF, Wiegmann BM, Worheide G, Wray GA and DeSalle R (2016) Never ending analysis of a century old evolutionary debate: “unringing” the urmetazoon bell. Frontiers in Ecology and Evolution 4:5. https://doi.org/10.3389/fevo.2016.00005. 2016
2015
Mariana Obertello, Stuti Shrivastava, Manpreet S. Katari and Gloria M. Coruzzi. (2015) “Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice,” Plant Physiology, v.168, 2015, p. 1830. doi:10.1104
2014
Delaux P-M, Varala K, Edger PP, Coruzzi GM, Pires JC, Ane J-M. (2014) “Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution,” PLoS Genetics, v.10, 2014, p. e1004487. doi:10.1371/journal.pgen.1004487
Pierre-Marc Delaux, Kranthi Varala, Patrick P. Edger, Gloria M. Coruzzi, J. Chris Pires, and Jean-Michel Ané. (2014) “Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution,” PLOS Genetics, v.10, 2014, https://doi.org/10.1371/journal.pgen.1004487
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
Knopf, P; Schulz, C; Little, DP; Stutzel, T; Stevenson, DW. (2012) “Relationships within Podocarpaceae based on DNA sequence, anatomical, morphological, and biogeographical data,” CLADISTICS, v.28, 2012, p. 271. doi:10.1111/j.1096-0031.2011.00381.
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.
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.
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.
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 OrthologID. Methods 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.