Publications

Schultz DT*, Heath-Heckman EAC*, Winchell CJ*, Kuo DH, Yu YS, Oberauer F, Kocot KM, Cho SJ†, Simakov O†, Weisblat DA†. (2024). “Acceleration of genome rearrangement in clitellate annelids.” bioRxiv.

Ahuja N†, Schultz DT, Destanović D, Church SH, Picciani N, Munro C, Kon-Nanjo K, Kon T, Mańko MK, Shi W, Haddock SHD, Simakov O, Dunn CW. (2025). “A chromosome-scale genome of Nanomia septata reveals extensive rearrangement but no clear driver of the unique colony-level organization of siphonophores.” bioRxiv.

Rogers TF†, Stock J, Schulz NG, Yalçin G, Rencken S, Weissenbacher A, Clarence T, Schultz DT, Ragsdale CW, Albertin CB, Simakov O†. (2025). “Genome reorganisation and expansion shape 3D genome architecture and define a distinct regulatory landscape in coleoid cephalopods.” bioRxiv.

Schultz DT†, Blümel A, Destanović D, Sarigol F, Simakov O†. (2026). “Topological mixing and irreversibility in animal chromosome evolution.” Science Advances, 12(34), eadz5561.

(Review) Schultz DT†, Simakov O†. (2026). “Topological Approaches in Animal Comparative Genomics.” Annual Review of Animal Biosciences, 14, 17–48.

Han B*, Connolly SM*, Schultz DT, Wilson LFL, Gulsevin A, Meiler J, Karakas E, Ohi MD†, Kenworthy AK†. (2025). “Evolutionarily diverse caveolins share a common structural framework built around amphipathic disks.” Journal of Cell Biology, 224(9), e202411175.

Liu H, Steenwyk JL, Zhou X, Schultz DT, Kocot KM, Shen X, Rokas A†, Li Y†. (2024). “A taxon-rich and genome-scale phylogeny of Opisthokonta.” PLOS Biology, doi: 10.1371/journal.pbio.3002794.

Ahuja N†*, Cao X*, Schultz DT*, Picciani N, Lord A, Shao S, Jia K, Burdick DR, Haddock SHD, Li Y, Dunn CW. (2024). “Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores.” Genome Biology and Evolution, 16, 3.

(Book Chapter) Schultz DT. (2024). “The story of bioluminescent jellyfish” (in Japanese, trans. Y. Oba). In The Story of Bioluminescent Organisms — Y. Oba. Asakura Publishing Co., Ltd. Tokyo. ISBN: 978-4254171921.

Schultz DT†, Haddock SHD, Bredeson JV, Green RE, Simakov O†, Rokhsar DS†. (2023). “Ancient gene linkages support ctenophores as sister to other animals.” Nature, 618, 110–117.

Zimmermann B*, Montenegro JD*, Robb SMC, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Chen CY, Ragkousi K, Praher D, Fredman D, Schultz DT, Moran Y, Simakov O, Genikhovich G, Gibson MC†, Technau U†. (2023). “Topological structures and syntenic conservation in sea anemone genomes.” Nature Communications, 14, 8270.

Destanović D*, Schultz DT*, Styfhals R, Cruz F, Gómez-Garrido J, Gut M, Gut I, Fiorito G, Simakov O†, Alioto TS, Ponte G†, Seuntjens E†. (2023). “A chromosome-level reference genome for the common octopus, Octopus vulgaris (Cuvier, 1797).” G3: Genes | Genomes | Genetics, 13, 12, jkad220.

Roberts MB, Schultz DT†, Gatins R, Escalona M, Bernardi G†. (2023). “Chromosome-level genome of the three-spot damselfish, Dascyllus trimaculatus.” G3: Genes | Genomes | Genetics, 13(4), jkac339.

Limón J, Roberts M, Schultz DT, Bernardi G†. (2023). “The complete mitochondrial genome of Dascyllus trimaculatus (Rüppell, 1829).” Mitochondrial DNA Part B, 8:1, 105–106.

(Review) Baden T, Briseño J, Coffing G, Cohen-Bodénès S, Courtney A, Dickerson D, Dölen G, Fiorito G, Gestal C, Gustafson T, Heath-Heckman E, Hua Q, Imperadore P, Kimbara R, Król M, Lajbner Z, Lichilín N, Macchi F, McCoy MJ, Nishiguchi MK, Nyholm SV, Otjacques E, Pérez-Ferrer PA, Ponte G, Pungor JR, Rogers TF, Rosenthal JJC, Rouressol L, Rubas N, Sanchez G, Pereira Santos C, Schultz DT, Seuntjens E, Songco-Casey JO, Stewart IE, Styfhals R, Tuanapaya S, Vijayan N, Weissenbacher A, Zifcakova L, Schulz G, Weertman W, Simakov O†, Albertin CB†. (2023). “Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology.” Integrative and Comparative Biology, 63(6), 1226–1239.

Simakov O†, Bredeson J, Berkoff K, Marletaz F, Mitros T, Schultz DT, O’Connell BL, Dear P, Martinez DE, Steele RE, Green RE, David CN, Rokhsar DS†. (2022). “Deeply conserved synteny and the evolution of metazoan chromosomes.” Science Advances, 8, 5.

Johnson SB†, Winnikoff JR, Schultz DT, Christianson LM, Patry WL, Mills CE, Haddock SHD†. (2022). “Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores.” Frontiers in Genetics, 13:970314.

(Review) Oba Y†, Schultz DT. (2022). “Firefly genomes illuminate the evolution of beetle bioluminescent systems.” Current Opinion in Insect Science, 100879.

Christianson LM†, Johnson S†, Schultz DT, Haddock SHD†. (2022). “Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.” Molecular Ecology Resources, 22(1), 283–294.

Schultz DT†*, Francis WR*, McBroome JD, Christianson LM, Haddock SHD, Green RE. (2021). “A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.” G3: Genes | Genomes | Genetics, 11, 11.

Martini S†*, Schultz DT*, Lundsten L, Haddock SHD. (2020). “Bioluminescence in an Undescribed Species of Carnivorous Sponge (Cladorhizidae) From the Deep Sea.” Frontiers in Marine Science, 7, 1041.

Lambert GG, Depernet H, Gotthard G, Schultz DT, Navizet I, Lambert T, Adams SR, Torreblanca-Zanca A, Chu M, Bindels DS, Levesque V, Moffatt JN, Salih A, Royant A, Shaner NC†. (2020). “Aequorea’s secrets revealed: New fluorescent proteins with unique properties for bioimaging and biosensing.” PLOS Biology, 18(11), e3000936.

Breusing C†, Schultz DT, Sudek S, Worden AZ, Young CR. (2020). “High-contiguity genome assembly of the chemosynthetic gammaproteobacterial endosymbiont of the cold seep tubeworm Lamellibrachia barhami.” Molecular Ecology Resources, 20, 5.

Goodheart JA, Minsky G, Brynjegard-Bialik MN, Drummond MS, Munoz JD, Fallon TR, Schultz DT, Weng JK, Torres E, Oakley TH†. (2020). “Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence.” Scientific Reports, 10, 10443.

Schultz DT†, Eizenga JM, Corbett-Detig RB, Francis WR, Christianson LM, Haddock SHD. (2020). “Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii.” PeerJ, 8, e8356.

De Coster W†, D’Hert S, Schultz DT, Cruts M, Broeckhoven CV. (2018). “NanoPack: visualizing and processing long-read sequencing data.” Bioinformatics, 34(15), 2666–2669.

Schultz DT†*, Kotlobay A*, Ziganshin R, Bannikov A, Markina NM, Chepurnyh TV, Shakova ES, Palkina K, Haddock SHD, Yampolsky IV†, Oba Y†. (2018). “Luciferase of the Japanese syllid polychaete Odontosyllis undecimdonta.” Biochemical and Biophysical Research Communications, 502(3), 318–323.

Haddock SHD†, Christianson LM, Francis WR, Martini S, Dunn CW, Pugh PR, Mills CE, Osborn KJ, Seibel BA, Choy CA, Schnitzler CE, Matsumoto GI, Messié M, Schultz DT, Winnikoff JR, Powers ML, Gasca R, Browne WE, Johnsen S, Schlining KL, von Thun S, Erwin BE, Ryan JF, Thuesen EV. (2017). “Insights into the Biodiversity, Behavior, and Bioluminescence of Deep-Sea Organisms: Using Molecular and Maritime Technology.” Oceanography, 30(4), 38–47.

Leung W, Shaffer CD, Chen EJ, et al., Schultz DT (author 156 of 1,014), ..., Elgin SCR. (2017). “Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.” G3: Genes | Genomes | Genetics, 7(8), 2439–2460.

Leung W, Elgin SCR, et al., Schultz DT (author ~550 of ~940), et al. (2015). “Drosophila Muller F elements maintain a distinct set of genomic properties over 40 million years of evolution.” G3: Genes | Genomes | Genetics, 5(5), 719–740.

(Review) Oba Y, Schultz DT. (2014). “Eco-Evo bioluminescence on land and in the sea.” In Bioluminescence: Fundamentals and Applications in Biotechnology. Adv Biochem Eng Biotechnol, 144, 3–36.

Schultz DT. (2018). “A review of Michel Anctil’s book, Luminous Creatures.” Science, 360, 6393.