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D. Rokhsar · SciRah

Researcher profile · Semantic Scholar

D. Rokhsar

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D. Rokhsar — researcher profile on SciRah

h-index: 95
Works: 275
Citations: 73K

Most-cited papers

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
K. Mayer, J. Rogers, J. El, Curtis J. Pozniak +92 more
2014Science1,600 citations Open access
Semantic Scholar
A reference genome for common bean and genome-wide analysis of dual domestications
J. Schmutz, P. McClean, S. Mamidi, G. A. Wu +37 more
2014Nature Genetics1,214 citations Open access
Semantic Scholar
Genome evolution in the allotetraploid frog Xenopus laevis
Adam M. Session, Yoshinobu Uno, T. Kwon, J. Chapman +70 more
2016Nature909 citations Open access
Semantic Scholar
The genome of Eucalyptus grandis
A. Myburg, D. Grattapaglia, G. Tuskan, U. Hellsten +76 more
2014Nature813 citations Open access
Semantic Scholar
Genomics of the origin and evolution of Citrus
G. Wu, J. Terol, Victoria Ibanez, A. López-García +14 more
2018Nature777 citations Open access
Semantic Scholar
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
N. Putnam, Brendan L. O’Connell, Jonathan Stites, Brandon J. Rice +9 more
2015Genome Research733 citations Open access
Semantic Scholar
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
G. A. Wu, S. Prochnik, J. Jenkins, J. Salse +51 more
2014Nature Biotechnology636 citations Open access
Semantic Scholar
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle
Wen Wang, G. Haberer, H. Gundlach, C. Gläßer +22 more
2014Nature Communications334 citations Open access
Semantic Scholar
Deeply conserved synteny resolves early events in vertebrate evolution
O. Simakov, Ferdinand Marlétaz, Jia-Xing Yue, Brendan L O'Connell +11 more
2020Nature Ecology & Evolution327 citations Open access
Semantic Scholar
Suboptimization of developmental enhancers
E. Farley, K. M. Olson, Wei Zhang, Alexander J. Brandt +2 more
2015Science307 citations Open access
Semantic Scholar
Ancient gene linkages support ctenophores as sister to other animals
Darrin T. Schultz, S. Haddock, J. Bredeson, R. Green +2 more
2023Nature297 citations Open access
Semantic Scholar
Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)
S. Brawley, N. Blouin, E. Ficko-Blean, G. Wheeler +46 more
2017Proceedings of the National Academy of Sciences of the United States of America259 citations Open access
Semantic Scholar
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome
J. Chapman, M. Mascher, Aydın Buluç, K. Barry +14 more
2015Genome Biology259 citations Open access
Semantic Scholar
Hemichordate genomes and deuterostome origins
O. Simakov, T. Kawashima, Ferdinand Marlétaz, J. Jenkins +57 more
2015Nature234 citations Open access
Semantic Scholar
A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans.
Ferdinand Marlétaz, K. T. C. A. Peijnenburg, T. Goto, N. Satoh +1 more
2019Current Biology230 citations Open access
Semantic Scholar
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass
J. Lovell, Alice H. MacQueen, S. Mamidi, J. Bonnette +62 more
2021Nature216 citations Open access
Semantic Scholar
Deeply conserved synteny and the evolution of metazoan chromosomes
O. Simakov, J. Bredeson, Kodiak C. Berkoff, Ferdinand Marlétaz +9 more
2022Science Advances186 citations Open access
Semantic Scholar
Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
E. Farley, K. M. Olson, Wei Zhang, D. Rokhsar +1 more
2016Proceedings of the National Academy of Sciences of the United States of America162 citations Open access
Semantic Scholar
Chordate evolution and the three-phylum system
N. Satoh, D. Rokhsar, T. Nishikawa
2014Proceedings of the Royal Society of London. Biological Sciences144 citations Open access
Semantic Scholar
The genomic landscape of molecular responses to natural drought stress in Panicum hallii
J. Lovell, J. Jenkins, D. Lowry, S. Mamidi +23 more
2018Nature Communications118 citations Open access
Semantic Scholar
Genome biology of the paleotetraploid perennial biomass crop Miscanthus
T. Mitros, Adam M. Session, Brandon T James, G. Wu +38 more
2020Nature Communications109 citations Open access
Semantic Scholar
Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing
A. Glazer, E. Killingbeck, T. Mitros, D. Rokhsar +1 more
2015G3: Genes, Genomes, Genetics107 citations Open access
Semantic Scholar
Young inversion with multiple linked QTLs under selection in a hybrid zone
Cheng-Ruei Lee, Bao-Sheng Wang, Julius P. Mojica, T. Mandáková +22 more
2017Nature Ecology &Evolution105 citations Open access
Semantic Scholar
A chromosome‐scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus
Ze Peng, J. Bredeson, G. Wu, S. Shu +8 more
2020The Plant Journal101 citations Open access
Semantic Scholar
Genome and transcriptome mechanisms driving cephalopod evolution
C. Albertin, Sofía Medina-Ruíz, T. Mitros, H. Schmidbaur +7 more
2022Nature Communications94 citations Open access
Semantic Scholar
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly
Evangelos Georganas, Aydın Buluç, J. Chapman, L. Oliker +2 more
2014International Conference for High Performance Computing, Networking, Storage and Analysis90 citations
Semantic Scholar
HipMer: an extreme-scale de novo genome assembler
Evangelos Georganas, Aydın Buluç, J. Chapman, S. Hofmeyr +5 more
2015International Conference for High Performance Computing, Networking, Storage and Analysis88 citations
Semantic Scholar
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors
Sean P. Gordon, B. Contreras-Moreira, Joshua J. Levy, Armin Djamei +29 more
2020Nature Communications82 citations Open access
Semantic Scholar
Supplementary Information Appendix for Symbiotic Organs Shaped by Distinct Modes of Genome Evolution in Cephalopods
M. Belcaid, G. Casaburi, Sarah J. McAnulty, H. Schmidbaur +18 more
201982 citations
Semantic Scholar
Plant Pan-Genomics Comes of Age.
L. Lei, E. Goltsman, D. Goodstein, G. Wu +2 more
2021Annual Review of Plant Biology81 citations
Semantic Scholar
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
J. Bredeson, J. Lyons, Ibukun O. Oniyinde, N. Okereke +29 more
2021Nature Communications80 citations Open access
Semantic Scholar
Terabase-scale metagenome coassembly with MetaHipMer
S. Hofmeyr, R. Egan, Evangelos Georganas, A. Copeland +9 more
2020Scientific Reports70 citations Open access
Semantic Scholar
The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii
D. Lowry, Kyle M. Hernandez, Samuel H. Taylor, E. Meyer +6 more
2014New Phytologist67 citations Open access
Semantic Scholar
A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis
Y. Matsuda, Yoshinobu Uno, M. Kondo, Michael J. Gilchrist +4 more
2015Cytogenetic and Genome Research66 citations Open access
Semantic Scholar
Diversification of mandarin citrus by hybrid speciation and apomixis
G. Wu, C. Sugimoto, H. Kinjo, Chika Azama +4 more
2021Nature Communications63 citations Open access
Semantic Scholar
QTL Mapping for Pest and Disease Resistance in Cassava and Coincidence of Some QTL with Introgression Regions Derived from Manihot glaziovii
I. Nzuki, M. Katari, J. Bredeson, E. Masumba +9 more
2017Frontiers in Plant Science62 citations Open access
Semantic Scholar
A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.
T. Mitros, J. Lyons, Adam M. Session, J. Jenkins +10 more
2019Developmental Biology60 citations Open access
Semantic Scholar
Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Bao-Sheng Wang, Julius P. Mojica, Nadeesha Perera, Cheng-Ruei Lee +8 more
2019Genome Biology54 citations Open access
Semantic Scholar
merAligner: A Fully Parallel Sequence Aligner
Evangelos Georganas, Aydın Buluç, J. Chapman, L. Oliker +2 more
2015IEEE International Parallel and Distributed Processing Symposium52 citations Open access
Semantic Scholar
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Austin B. Mudd, J. Bredeson, Rachel Baum, Dirk Hockemeyer +1 more
2020Communications Biology48 citations Open access
Semantic Scholar
CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production
Michael A. Gomez, Kodiak C. Berkoff, Baljeet K. Gill, A. Iavarone +11 more
2021bioRxiv47 citations Open access
Semantic Scholar
The hagfish genome and the evolution of vertebrates
Ferdinand Marlétaz, N. Timoshevskaya, Vladimir A. Timoshevskiy, O. Simakov +7 more
2023bioRxiv40 citations Open access
Semantic Scholar
Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs
J. Bredeson, Austin B. Mudd, Sofía Medina-Ruíz, T. Mitros +31 more
2021bioRxiv40 citations Open access
Semantic Scholar
Transposon signatures of allopolyploid genome evolution
Adam M. Session, D. Rokhsar
2023Nature Communications37 citations Open access
Semantic Scholar
BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper
Giulia Guidi, Marquita Ellis, D. Rokhsar, K. Yelick +1 more
2018bioRxiv34 citations Open access
Semantic Scholar
Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)
G. Sanchez, F. Fernández-Álvarez, Morag Taite, C. Sugimoto +5 more
2021Communications Biology32 citations Open access
Semantic Scholar
A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution
Daria Gavriouchkina, Yongkai Tan, F. Ziadi-Künzli, Yuko Hasegawa +6 more
2022bioRxiv31 citations Open access
Semantic Scholar
Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage
Regina Rillo-Bohn, Renzo S. Adilardi, T. Mitros, Barış Avşaroğlu +8 more
2019bioRxiv27 citations Open access
Semantic Scholar
Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity
Namrata Ahuja, Ernie Hwaun, J. Pungor, Ruhina Rafiq +16 more
2023Current Biology25 citations Open access
Semantic Scholar
Current status and impending progress for cassava structural genomics
J. Lyons, J. Bredeson, B. Mansfeld, G. Bauchet +5 more
2021Plant Molecular Biology25 citations Open access
Semantic Scholar

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