Rokhsar, Daniel S.

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature

Metal Extraction and BioleachingGenomics and Phylogenetic Studies

Cited by 2,417

The Draft Genome of Ciona intestinalis : Insights into Chordate and Vertebrate Origins

Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., Davidson, B., Di Gregorio, A., Gelpke, M., Goodstein, D. M., et al. (2002) · Science

Developmental Biology and Gene RegulationGenomics and Phylogenetic Studies

Cited by 1,641

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

Aparicio, S., Chapman, J., Stupka, E., Putnam, N., Chia, J.-M., Dehal, P., Christoffels, A., Rash, S., Hoon, S., Smit, A., et al. (2002) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,591

A chromosome-based draft sequence of the hexaploid bread wheat ( Triticum aestivum ) genome

The International Wheat Genome Sequencing Consortium (IWGSC), Mayer, K. F. X., Rogers, J., Doležel, J., Pozniak, C., Eversole, K., Feuillet, C., Gill, B., Friebe, B., Lukaszewski, A. J., et al. (2014) · Science

Wheat and Barley Genetics and PathologyChromosomal and Genetic Variations

Cited by 1,583

Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization

Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 1,555

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature

Marine Invertebrate Physiology and EcologyProtist diversity and phylogeny

Cited by 1,139

The Amphimedon queenslandica genome and the evolution of animal complexity

Srivastava, M., Simakov, O., Chapman, J., Fahey, B., Gauthier, M. E. A., Mitros, T., Richards, G. S., Conaco, C., Dacre, M., Hellsten, U., et al. (2010) · Nature

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 1,049

Genome evolution in the allotetraploid frog Xenopus laevis

Session, A. M., Uno, Y., Kwon, T., Chapman, J. A., Toyoda, A., Takahashi, S., Fukui, A., Hikosaka, A., Suzuki, A., Kondo, M., et al. (2016) · Nature

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 949

The Trichoplax genome and the nature of placozoans

Srivastava, M., Begovic, E., Chapman, J., Putnam, N. H., Hellsten, U., Kawashima, T., Kuo, A., Mitros, T., Salamov, A., Carpenter, M. L., et al. (2008) · Nature

Marine Invertebrate Physiology and EcologyGenomics and Phylogenetic Studies

Cited by 889

The dynamic genome of Hydra

Chapman, J. A., Kirkness, E. F., Simakov, O., Hampson, S. E., Mitros, T., Weinmaier, T., Rattei, T., Balasubramanian, P. G., Borman, J., Busam, D., et al. (2010) · Nature

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 810

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Putnam, N. H., O'Connell, B. L., Stites, J. C., Rice, B. J., Blanchette, M., Calef, R., Troll, C. J., Fields, A., Hartley, P. D., Sugnet, C. W., et al. (2016) · Genome Research

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 732

Insights into bilaterian evolution from three spiralian genomes

Simakov, O., Marletaz, F., Cho, S.-J., Edsinger-Gonzales, E., Havlak, P., Hellsten, U., Kuo, D.-H., Larsson, T., Lv, J., Arendt, D., et al. (2013) · Nature

Genomics and Phylogenetic StudiesMarine Invertebrate Physiology and Ecology

Cited by 656

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

Palenik, B., Grimwood, J., Aerts, A., Rouzé, P., Salamov, A., Putnam, N., Dupont, C., Jorgensen, R., Derelle, E., Rombauts, S., et al. (2007) · Proceedings of the National Academy of Sciences

Protist diversity and phylogenyChromosomal and Genetic Variations

Cited by 625

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

Holland, L. Z., Albalat, R., Azumi, K., Benito-Gutiérrez, È., Blow, M. J., Bronner-Fraser, M., Brunet, F., Butts, T., Candiani, S., Dishaw, L. J., et al. (2008) · Genome Research

Developmental Biology and Gene RegulationChromosomal and Genetic Variations

Cited by 512

Deeply conserved synteny resolves early events in vertebrate evolution

Simakov, O., Marlétaz, F., Yue, J.-X., O’Connell, B., Jenkins, J., Brandt, A., Calef, R., Tung, C.-H., Huang, T.-K., Schmutz, J., et al. (2020) · Nature Ecology & Evolution

Chromosomal and Genetic VariationsGenome Rearrangement Algorithms

Cited by 363

Ancient gene linkages support ctenophores as sister to other animals

Schultz, D. T., Haddock, S. H. D., Bredeson, J. V., Green, R. E., Simakov, O., & Rokhsar, D. S. (2023) · Nature

Marine Invertebrate Physiology and EcologyProtist diversity and phylogeny

Cited by 362

Suboptimization of developmental enhancers

Farley, E. K., Olson, K. M., Zhang, W., Brandt, A. J., Rokhsar, D. S., & Levine, M. S. (2015) · Science

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 319

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

Marlétaz, F., Peijnenburg, K. T. C. A., Goto, T., Satoh, N., & Rokhsar, D. S. (2019) · Current Biology

Invertebrate Taxonomy and EcologyMarine Invertebrate Physiology and Ecology

Cited by 268

Anatomy and development of the nervous system of Nematostella vectensis , an anthozoan cnidarian

Marlow, H. Q., Srivastava, M., Matus, D. Q., Rokhsar, D., & Martindale, M. Q. (2009) · Developmental Neurobiology

Marine Invertebrate Physiology and EcologyDevelopmental Biology and Gene Regulation

Cited by 247

Deeply conserved synteny and the evolution of metazoan chromosomes

Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D. T., O’Connell, B. L., Dear, P., Martinez, D. E., Steele, R. E., et al. (2022) · Science Advances

Chromosomal and Genetic VariationsGenome Rearrangement Algorithms

Cited by 197

The NK homeobox gene cluster predates the origin of Hox genes.

Larroux, C., Fahey, B., Degnan, S. M., Adamski, M., Rokhsar, D. S., & Degnan, B. M. (2007) · Current Biology

Developmental Biology and Gene RegulationMarine Invertebrate Physiology and Ecology

Cited by 173

Young inversion with multiple linked QTLs under selection in a hybrid zone

Lee, C.-R., Wang, B., Mojica, J. P., Mandáková, T., Prasad, K. V. S. K., Goicoechea, J. L., Perera, N., Hellsten, U., Hundley, H. N., Johnson, J., et al. (2017) · Nature Ecology & Evolution

Chromosomal and Genetic VariationsEvolution and Genetic Dynamics

Cited by 119

Plant pan-genomics comes of age

Lei, L., Goltsman, E., Goodstein, D., Wu, G. A., Rokhsar, D. S., & Vogel, J. P. (2021) · Annual Review of Plant Biology

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 102

The little skate genome and the evolutionary emergence of wing-like fins

Marlétaz, F., de la Calle-Mustienes, E., Acemel, R. D., Paliou, C., Naranjo, S., Martínez-García, P. M., Cases, I., Sleight, V. A., Hirschberger, C., Marcet-Houben, M., et al. (2023) · Nature

Developmental Biology and Gene RegulationGenomics and Chromatin Dynamics

Cited by 71