DR
Daniel S. Rokhsar
Evolution, MolecularGenomeGenome, PlantPhylogenyBiological EvolutionGenomicsSequence Analysis, DNAgenomicsPolyploidycond-mat
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
212 papers in the corpus · 1986–2026Distinct cell states define larval and adult body plans in a hemichordate.42711331 · Bump, Paul, Brewster, Carolyn, Formery, Laurent et al.2026 · 0 citationsNature communications. 2026;17(1)
Citrus Vein Enation Virus Acts as the Dominant Contributor to Host Transcriptional Reprogramming During Synergistic Mixed Infection with Citrus Yellow-Vein Associated Virus in 'Mexican' Lime.42535905 · Comstock, Stacey, Mitra, Arunabha, Bodaghi, Sohrab et al.2026 · 0 citationsPhytopathology. 2026
Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches.41912859 · Sanchez, Gustavo, Fernández-Álvarez, Fernando Ángel, Bernal, Ainhoa et al.2026 · 5 citationsNature ecology & evolution. 2026;10(4):662-676
Major cell type differences between larval and adult hemichordate body plans10.1101/2025.10.31.685866v2 · Bump, P., Brewster, C., Formery, L. et al.2025 · 1 citationbioRxiv
The genomic origin of the unique chaetognath body plan.40804517 · Piovani, Laura, Gavriouchkina, Daria, Parey, Elise et al.2025 · 13 citationsNature. 2025;645(8082):964-973
A single-cell atlas of the bobtail squid visual and nervous system highlights molecular principles of convergent evolution.40481147 · Gavriouchkina, Daria, Tan, Yongkai, Parey, Elise et al.2025 · 44 citationsNature ecology & evolution. 2025;9(7):1245-1262
Antero-posterior patterning in the brittle star Amphipholis squamata and the evolution of echinoderm body plans.40450286 · Formery, L, Peluso, P, Rank, D R et al.2025 · 3 citationsEvoDevo. 2025;16(1):7
Antero-posterior patterning in the brittle star Amphipholis squamata and the evolution of body plans across echinoderms10.1101/2025.02.13.638179v1 · Formery, L., Peluso, P., Rank, D. R. et al.2025 · 3 citationsbioRxiv
Population Genomics Reveals Local Adaptation Related to Temperature Variation in Two Stream Frog Species: Implications for Vulnerability to Climate Warming.39825598 · Forester, Brenna R, Cicchino, Amanda S, Shah, Alisha A et al.2025 · 6 citationsMolecular ecology. 2025;34(23):e17651
Chromosome-level genome assemblies of 2 hemichordates provide new insights into deuterostome origin and chromosome evolution.38829909 · Lin, Che-Yi, Marlétaz, Ferdinand, Pérez-Posada, Alberto et al.2024 · 17 citationsPLoS biology. 2024;22(6):e3002661
Pluripotency of a founding field: rebranding developmental biology.38345109 · Rogers, Crystal D, Amemiya, Chris, Arur, Swathi et al.2024 · 7 citationsDevelopment (Cambridge, England). 2024;151(3)
Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs.38233380 · Bredeson, Jessen V, Mudd, Austin B, Medina-Ruiz, Sofia et al.2024 · 49 citationsNature communications. 2024;15(1):579
Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources.38023930 · Ferguson, Morag E, Eyles, Rodney P, Garcia-Oliveira, Ana Luísa et al.2024 · 6 citationsFrontiers in plant science. 2023;14:1270963
Molecular evidence of anteroposterior patterning in adult echinoderms.37914929 · Formery, L, Peluso, P, Kohnle, I et al.2023 · 67 citationsNature. 2023;623(7987):555-561
Cephalopod behaviour.37875088 · Gutnick, Tamar, Rokhsar, Daniel S, Kuba, Michael J2023 · 8 citationsCurrent biology : CB. 2023;33(20):R1083-R1086
Creation of an albino squid line by CRISPR-Cas9 and its application for in vivo functional imaging of neural activity.37343558 · Ahuja, Namrata, Hwaun, Ernie, Pungor, Judit R et al.2023 · 29 citationsCurrent biology : CB. 2023;33(13):2774-2783.e5
Transposon signatures of allopolyploid genome evolution.37263993 · Session, Adam M, Rokhsar, Daniel S2023 · 37 citationsNature communications. 2023;14(1):3180
Ancient gene linkages support ctenophores as sister to other animals.37198475 · Schultz, Darrin T, Haddock, Steven H D, Bredeson, Jessen V et al.2023 · 361 citationsNature. 2023;618(7963):110-117
The hagfish genome and the evolution of vertebrates.37131617 · Marlétaz, Ferdinand, Timoshevskaya, Nataliya, Timoshevskiy, Vladimir et al.2026 · 128 citationsbioRxiv : the preprint server for biology. 2023
The little skate genome and the evolutionary emergence of wing-like fins.37046085 · Marlétaz, Ferdinand, de la Calle-Mustienes, Elisa, Acemel, Rafael D et al.2023 · 72 citationsNature. 2023;616(7957):495-503
CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production.37007603 · Gomez, Michael A, Berkoff, Kodiak C, Gill, Baljeet K et al.2026 · 65 citationsFrontiers in plant science. 2022;13:1079254
Tracing cancer evolution and heterogeneity using Hi-C10.1101/2023.02.20.529175v1 · Erdmann-Pham, D. D., Batra, S. S., Turkalo, T. K. et al.2023 · 16 citationsbioRxiv
New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog X. borealis.36054077 · Evans, Ben J, Mudd, Austin B, Bredeson, Jessen V et al.2022 · 15 citationsJournal of evolutionary biology. 2022;35(12):1777-1790
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly2207.04350v1 · Giulia Guidi, Gabriel Raulet, Daniel Rokhsar et al.2022 · 4 citationsICPP22, August 29-September 1, 2022, Bordeaux, France
Correction to: Current status and impending progress for cassava structural genomics.33847871 · Lyons, Jessica B, Bredeson, Jessen V, Mansfeld, Ben N et al.2022 · 3 citationsPlant molecular biology. 2022;109(3):193
Genome and transcriptome mechanisms driving cephalopod evolution.35508532 · Albertin, Caroline B, Medina-Ruiz, Sofia, Mitros, Therese et al.2022 · 120 citationsNature communications. 2022;13(1):2427
Chromosome evolution and the genetic basis of agronomically important traits in greater yam.35422045 · Bredeson, Jessen V, Lyons, Jessica B, Oniyinde, Ibukun O et al.2022 · 104 citationsNature communications. 2022;13(1):2001
The little skate genome and the evolutionary emergence of wing-like fin appendages10.1101/2022.03.21.485123v1 · Marletaz, F., de la Calle-Mustienes, E., Acemel, R. D. et al.2022 · 7 citationsbioRxiv
Deeply conserved synteny and the evolution of metazoan chromosomes.35108053 · Simakov, Oleg, Bredeson, Jessen, Berkoff, Kodiak et al.2025 · 197 citationsScience advances. 2022;8(5):eabi5884
Beyond "living fossils": Can comparative genomics finally reveal novelty?34407301 · Sanchez, Gustavo, Simakov, Oleg, S Rokhsar, Daniel2021 · 2 citationsMolecular ecology resources. 2022;22(1):9-11
Analysis of meiosis in Pristionchus pacificus reveals plasticity in homolog pairing and synapsis in the nematode lineage.34427184 · Rillo-Bohn, Regina, Adilardi, Renzo, Mitros, Therese et al.2021 · 35 citationseLife. 2021;10
Diversification of mandarin citrus by hybrid speciation and apomixis.34312382 · Wu, Guohong Albert, Sugimoto, Chikatoshi, Kinjo, Hideyasu et al.2021 · 78 citationsNature communications. 2021;12(1):4377
Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida).34188187 · Sanchez, Gustavo, Fernández-Álvarez, Fernando Á, Taite, Morag et al.2021 · 35 citationsCommunications biology. 2021;4(1):819
Plant Pan-Genomics Comes of Age.33848428 · Lei, Li, Goltsman, Eugene, Goodstein, David et al.2021 · 102 citationsAnnual review of plant biology. 2021;72:411-435
Current status and impending progress for cassava structural genomics.33604743 · Lyons, Jessica B, Bredeson, Jessen V, Mansfeld, Ben N et al.2022 · 30 citationsPlant molecular biology. 2022;109(3):177-191
Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.33505029 · Lovell, John T, MacQueen, Alice H, Mamidi, Sujan et al.2021 · 246 citationsNature. 2021;590(7846):438-444
Discovering subgenomes of octoploid strawberry with repetitive sequences10.1101/2020.11.04.330431v1 · Session, A. M., Rokhsar, D. S.2020 · 6 citationsbioRxiv
Genome biology of the paleotetraploid perennial biomass crop Miscanthus.33116128 · Mitros, Therese, Session, Adam M, James, Brandon T et al.2020 · 125 citationsNature communications. 2020;11(1):5442
A chromosome-scale reference genome of trifoliate orange (Poncirus trifoliata) provides insights into disease resistance, cold tolerance and genome evolution in Citrus.32985030 · Peng, Ze, Bredeson, Jessen V, Wu, Guohong A et al.2021 · 113 citationsThe Plant journal : for cell and molecular biology. 2020;104(5):1215-1232
Analysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution.32873878 · Mudd, Austin B, Bredeson, Jessen V, Baum, Rachel et al.2021 · 60 citationsCommunications biology. 2020;3(1):480
Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors.32728126 · Gordon, Sean P, Contreras-Moreira, Bruno, Levy, Joshua J et al.2020 · 110 citationsNature communications. 2020;11(1):3670
Terabase-scale metagenome coassembly with MetaHipMer.32612216 · Hofmeyr, Steven, Egan, Rob, Georganas, Evangelos et al.2020 · 73 citationsScientific reports. 2020;10(1):10689
Deeply conserved synteny resolves early events in vertebrate evolution.32313176 · Simakov, Oleg, Marlétaz, Ferdinand, Yue, Jia-Xing et al.2020 · 363 citationsNature ecology & evolution. 2020;4(6):820-830
New bobtail squid (Sepiolidae: Sepiolinae) from the Ryukyu islands revealed by molecular and morphological analysis.31840110 · Sanchez, Gustavo, Jolly, Jeffrey, Reid, Amanda et al.2020 · 17 citationsCommunications biology. 2019;2:465
Correction to: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.31399118 · Wang, Baosheng, Mojica, Julius P, Perera, Nadeesha et al.2020 · 3 citationsGenome biology. 2019;20(1):161
Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta.31227026 · Wang, Baosheng, Mojica, Julius P, Perera, Nadeesha et al.2019 · 63 citationsGenome biology. 2019;20(1):126
A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.30980799 · Mitros, Therese, Lyons, Jessica B, Session, Adam M et al.2020 · 68 citationsDevelopmental biology. 2019;452(1):8-20
Acoel genome reveals the regulatory landscape of whole-body regeneration.30872491 · Gehrke, Andrew R, Neverett, Emily, Luo, Yi-Jyun et al.2019 · 172 citationsScience (New York, N.Y.). 2019;363(6432)
A large CRISPR-induced bystander mutation causes immune dysregulation.30793048 · Simeonov, Dimitre R, Brandt, Alexander J, Chan, Alice Y et al.2020 · 23 citationsCommunications biology. 2019;2:70
Symbiotic organs shaped by distinct modes of genome evolution in cephalopods.30635418 · Belcaid, Mahdi, Casaburi, Giorgio, McAnulty, Sarah J et al.2019 · 162 citationsProceedings of the National Academy of Sciences of the United States of America. 2019;116(8):3030-3035
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