Publications List
1976㹼2020239. Iwasaki Y, Ikemura T, Kurokawa k, Okada N.
Implication of a new function of human tDNAs in chromatinorganization.
Scientific Reports 10, 17440 (2020)
238. Vu TD, Iwasaki Y, Oshima K, Nikaido M, Chiu MT, Okada N.
A unique neurogenomic state emerges after aggressive confrontations
in males of the fish Betta splendens.
bioRxiv 10,237586 (2020)
237. Vu TD, Iwasaki Y, Shigenobu S, Maruko A, Oshima K, Iioka E, Huang
CL, Abe T, Tamaki S, Lin YW, Chen CK, Lu MY, Hojo M, Wang HV,
Tzeng SF, Huang HJ, Kanai A, Gojobori T, Chiang TY, Sun HS, Li WH,
Okada N.
Behavioral and brain- transcriptomic synchronization between the two
opponents of a fighting pair of the fish Betta splendens.
PLOS Genetics 16(6), June (2020)236. Okada N, Oshima K, Iwasaki Y, Maruko A, Iioka E, Vu T, Fujitsuka N,
Nishi A, Sugiyama A, Nishiyama M, Kaneko A, Yamamoto M,
Nishimura S.
Intron retention as a new marker of the pre-disease state and its
recovery to the normal state by a traditional Japanese multi-herbal
medicine.
bioRxiv 2020.02.10.941435 (2020)
235. Takuno S, Miyagi R,Onami J, Takahashi-kariyazono S, Sato A, Tichy H,
Nikaido M, Aibara M, Mizoiri S, Mrosso D.J.H, Mzighani S.I, Okada N, Terai Y.
Patterns of genomic differentiation between two Lake Victoria cichlid species,
Haplochromis pyrrhocephalus and H. sp. ‘macula’.
BMC Evolutionary Biology 19(68), March (2019)234. Sagai T, Amano T, Maeno A㸪Kimura T,Nakamoto M, Takehana Y㸪
Naruse K 㸪Okada N㸪Kiyonari H㸪Shiroishi T.
Evolution of Shh endoderm enhancers during morphological transition
from ventral lungs to dorsal gas bladder.
Nature Communications 8 (14300), Feb 㸦2017㸧
233. Terai Y㸪Miyagi R㸪Aibara M, Mizoiri S㸪Imai H㸪Okitsu T,
Wada A㸪Takahashi-Kariyazono S㸪Sato A㸪Herbert T, Hillary D.J.,
Semvua I.M, Okada N.
Visual adaptation in Lake Victoria cichlid fishes: depth-relatedvariation of color and scotopic opsins in species from sand/mud
bottoms.
BMC Evolutionary Biology 17, Article number:200㸦2017㸧
232. Hori M, Nakajima M, Hata H㸪Yasugi M, Takahashi S㸪Nakae M,
Yamaoka K, Kohada M, Kitamura J, Maehata M, Tanaka H㸪
Okada N㸪Takeuchi Y.
Laterality is Universal Among Fishes but Increasingly Cryptic Among
Derived Groups.
Zoological Science 2017 Aug㸹34(4):267-274㸦2017㸧
231. Otsu M, Kajikawa M, Okada N, Kawai G.
Solution structure of a reverse transcriptase recognition site of a LINE
RNA from zebrafish.
The Journal of Biochemistry, Volume 162, Issue 4, October 2017,
Pages 279-285 (2017)230. Nishihara H (12 coauthors) and Okada N.
Coordinately Co-opted Multiple Transposable Elements Constitute an
Enhancer for wnt5a Expression in the Mammalian Secondary Palate.
PLOS Genetics journal pgen.1006380. (2016)229. Nishihara H, Plazzi F, Passamonti M, Okada N.
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in
Animals.
Genome Biology and Evolution, Volume 8, Issue 3, Pages 528-539 (2016)
228. Tatsumi N, Kobayashi R, Yano T, Noda M, Fujimura K, Okada N,
Okabe M.
Molecular developmental mechanism in polypterid fish provides insight
into the origin of vertebrate lungs.
Scientific Reports 6, Artcle Number: 30580㸦2016)
227. Kuramoto T, Nishihara H㸪Watanabe M, Okada N.
Determining the Position of Storks on the Phylogenetic Tree of
Waterbirds by Retroposon Insertion Analysis.
Genome Biology and Evolution. Pages 3180–3189(2015)
226. Yamaguchi K, Kajikawa M, Okada N.
LINE retrotransposition and host DNA repair machinery.
Mobile Genetic Elements Volume 5 2015, Issue 6 Pages 92-97. Nov.2015(2015)
225. Kudo Y, Nikaido M, Kondo A, Suzuki H, Yoshida K, Kikuchi K,

Okada N.
A microsatellite-based genetic linkage map and putative sexdetermining genomic regions in Lake Victoria cichlids.
Gene Volume 560, Issue 2, Pages 156-164㸦2015㸧
224. Suzuki H, Nikaido M, Hagino-Yamagishi K, Okada N.
Distinct functions of two olfactory marker protein genes derived fromteleost-specific whole genome duplication.
BMC Evolutionary Biology 15, Article number:245 (2015)
223. Yamaguchi K, Kajikawa M, Okada N.
Integrated mechanism for the generation of the 5͛ junctions of LINE
inserts
Nucleic Acids Research 42(21) 13269 -13279㸦2014㸧
222. Shirai K, Inomata N, Mizoiri S, Aibara M, Terai Y, Okada N,
Tachida H.
High prevalence of non-synonymous substitutions in mtDNA of cichlid
fishes from Lake Victoria.
Gene Voluma 552, Issue 2, 1 December 2014, Pages 239-245 (2014)
221. Brawand D, (45 coauthors), Nikaido M, Nishihara H, (18 coauthers),
Okada N, (10coauthers) and Palma F.
The genomic substrate for adaptive radiation in African cichlid fish.
Nature (article) 513:375-381. (2014)
220. Hayashi Y, Kajikawa M, Matsumoto T, Okada N.
Mechanism by which a LINE protein recognizes its 3 tail RNA.
Nucleic Acids Research, Volume 42, Issue 16, 15 September 2014, Pages
10605–10617(2014)
219. Nikaido M, Ota T, Hirata T, Suzuki H, Satta Y, Aibara M, Mzighani
SI, Sturmbauer C, Hagino-Yamagishi K, Okada N.
Multiple episodic evolution events in V1R receptor genes of EastAfrican cichlids.
Genome Biology and Evolution Advance Access published May 6, 2014
doi:10.1093/gbe/evu086 (2014)
218. Matsumoto T, Terai Y, Okada N, Tachida.
Sensory drive speciation and patterns of variation at selectively
neutral genes.
Evolutionary Ecology 28, 591-609 (2014)
217. Iwasaki Y, Abe T, Okada N, Wada K, Wada Y, Ikemura T.
Evolutionary Changes in Vertebrate Genome Signatures with Special

Focus on Coelacanth.
DNA Research, Volume 21, Issue 5, October 2014,
Pages 459-467(2014)
216. Kuroiwa AɾTerai YɾKobayashi NɾYoshida K, Suzuki M, Nakanishi
AɾMatsuda YɾWatanabe M, Okada N.
Construction of Chromosome Markers from the Lake Victoria Cichlid
Paralabidochromis chilotes and Their Application to Comparative
Mapping.
Cytogenetic and Genome Research 2014; 142:112-120 (2014)
215. Kawashima Y, Nishihara H, Akasaki T, Nikaido M, Tsuchiya K, Sagawa S,
Okada N.
The complete mitochondrial genomes of deep-sea squid (Bathyteuthis
abyssicola), bob-tail squid (Semirossia patagonica) and four giant
cuttlefish (Sepia apama, S. latimanus, S. lycidas and S. pharaonis), andtheir application to the phylogenetic analysis of Decapodiformes.
Molecular Phylogenetics and Evolution Volume 69, Issue 3, December
2013, Pages 980-993(2013)
214. Takeda M, Kusumi J, Mizoiri S, Aibara M, Mzighani SI, Sato T, Terai
Y, Okada N, Tachida H.
Genetic Structure of Pelagic and Littoral Cichlid Fishes from Lake
Victoria.
PLOS ONE| Volume 8 | Issue 9 | e74088 (2013)
213. Terasaki N, Goodier JL, Cheung LE, Wang YJ, Kajikawa M, Kazazian
Jr. H, Okada N.
In Vitro Screening for Compounds That Enhance Human L1
Mobilization.
PLOS ONE| Volume 8 | Issue 9 | e74629 (2013)212. Nikaido M, Suzuki H, Toyoda A, Fujiyama A, Hagino-Yamagishi K,
Kocher TD, Carleton K, Okada N.
Lineage-Specific Expansion of Vomeronasal Type 2 Receptor-like(OlfC) Genes in Cichlids May Contribute to Diversification of Amino
Acid Detection Systems.
Genome Biology and Evolution Advance Access published March 15,
2013 doi:10.1093/gbe/evt041(2013)211. Nikaido M (27 coauthors) Okada,N.
Coelacanth genomes reveal signatures for evolutionary transition
from water to land.
Genome Res. 1, October (2013)
210. Yoshioka YɾTakahashi YɾMatsumoto SɾKojima Sɾ
Matsuoka K, Nakamura K, Ohoshima K, Okada NɾMachida Y.

Mechanisms of T-DNA transfer and integration into plantchoromosomes : role of vir B,vir D4 and vir E2 and a shortinterspersed repetitive element (SINE) from tobacco.
Molecular Mechanisms of Bacterial Virulence(2012)
209. Kajikawa M, Yamaguchi K, Okada N.
A new mechanism to ensure integration during LINE
retrotransposition: A suggestion from analyses of the 5’ extra
nucleotides.
Gene. Mar 1 Epub ahead of print (2012)
208. Kajikawa M, Sugano T, Sakurai R, Okada N.
Low dependency of retrotransposition on the ORF1 protein of thezebrafish LINE, ZfL2-1.
Gene. May 10;499(1):41-7 (2012)
207. Ota T, Nikaido M, Suzuki H, Hagino-Yamaguchi K, Okada N.
Characterization of V1R receptor (ora) genes in Lake Victoria cichlids.
Gene May 15;499(2):273-9 (2012)206. Nakamura M, Kajikawa M, Okada N.
Self-interaction, nucleic acid binding, and nucleic acid chaperone
activities are unexpectedly retained in the unique ORF1p of zebrafish.
LINE. Mol. Cell Biol. Jan 32 (2): 458-69 (2012)
205. Nakanishi A, Kobayashi N, Suzuki-Hirano A, Nishihara H, Sasaki T,
Hirakawa M, Sumiyama K, Shimogori T, Okada N.
A SINE-derived element constitutes a unique modular enhancer for
mammalian diencephalic Fgf8.
PLOS One 2012; 7(8)e43785 (2012)
204. Higasa K, Nikaido M, Saito TL, Yoshimura J, Suzuki Y, Suzuki H,
Nishihara H, Aibara M, Ngatunga BP, Kalombo HW, Sugano S,
Morishita S, Okada N.
Extremely slow rate of evolution in the HOX cluster revealed bycomparison between Tanzanian and Indonesian coelacanths.
Gene. Jun 12. Epub ahead of print (2012)
203. Miyagi R, Terai Y, Aibara M, Sugawara T, Imai H, Tachida H,
Mzighani SI, Okitsu T, Wada A, Okada N.
Correlation between nuptial colors and visual sensitivities tuned byopsins leads to species richness in sympatric Lake Victoria cichlid
fishes.
Molecular Biology and Evolution, Volume 29, Issue 11, November
2012, Pages 3281–3296(2012)202. Yuzawa Y, Nishihara H, Haraguchi T, Masuda S, Shimojima M,
Shimoyama A, Yuasa H, Okada N, Ohta H.
Phylogeny of Galactolipid Synthase Homologs Together with their
Enzymatic Analyses Revealed a Possible Origin and Divergence Timefor Photosynthetic Membrane Biogenesis.
Author Notes DNA Research. Volume 19, Issue 1, February (2012)201. Nikaido M, Sasaki T, Emerson J.J, Aibara M, Mzighani S.I, Budeba
Y.L, Ngatunga B.P, Iwata M, Abe Y, Li W.H, Okada N.
Genetically distinct coelacanth population off the northern Tanzaniancoast.
Proceedings of the National Academy of Sciences of the United States ofAmerica.108ʤ44ʥ18009-18013 Nov.2011(2011)200. Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M,
Kuroiwa A, Hirai H, Hirai Y, Matsuda Y, Okada N.
B chromosomes have a functional effect on female sex determination inlake victoria cichlid fishes.
PLOS Genet. 2011 ug;7(8): e1002203. (2011)199. Tashiro K, Teissier A, Kobayashi N, Nakanishi A, Sasaki T, Yan K,
Tarabykin V, Vigier L, Sumiyama K, Hirakawa M, Nishihara H,
Pierani A, Okada N.
A mammalian conserved element derived from SINE displays
enhancer properties recapitulating Satb2 expression in early-born
callosal projection neurons.
PLOS One. 6 e28497 (2011)
198.Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, Okada N.
Reverse evolution in RH1 for adaptation of cichlids to water depth inLake Tanganyika.
Mol Biol Evol. Dec 20. (2010) [Epub ahead of print]
197.Okada N, Sasaki T, Shimogori T, Nishihara H.
Emergence of mammals by emergency: exaptation.
Genes Cells. Aug;15(8):801-12. Epub Jul 14. (2010)
196.Murata Y, Tamura M, Aita Y, Fujimura K, Murakami Y, Okabe M,
Okada N, Tanaka M.
Allometric growth of the trunk leads to the rostral shift of the pelvic fin
in teleost fishes.
Dev Biol. Nov 1;347(1):236-45. Epub Aug 6. (2010)
195.Akasaki T, Nikaido M, Nishihara H, Tsuchiya K, Segawa S, Okada N.
Characterization of a novel SINE superfamily from invertebrates:

"Ceph-SINEs" from the genomes of squids and cuttlefish.
Gene. Apr 1;454(1-2):8-19. (2010)
194.Sugawara T, Imai H, Nikaido M, Imamoto Y, OkadaN
Vertebrate Rhodopsin Adaptation to Dim Light via Rapid Meta-II
Intermediate Formation. Mol Biol Evol. Mar;27(3):506-19. (2010)
193.Mzighani SI, Nikaido M, Takeda M, Seehausen O, Budeba YL,
Ngatunga BP, Katunzi EFB, Aibara M, Mizoiri S, Sato T, Tachida H,
Okada N.
Genetic Variation and Demographic History of the Laparogramma
Cichlid Species Group of Lake Victoria-An Analysis Based on SINEs
and Mitochondrial DNA. Gene. Jan 15;450(1-2):39-47. (2010)
192.Suzuki J, Yamaguchi K, Kajikawa M, Ichiyanagi K, Adachi N, Koyama
H, Takeda S, Okada N.
Genetic evidence that the non-homologous end-joining repair pathway
is involved in LINE retrotransposition.
PLoS Genet. Apr;5(4):e1000461.(2009)
191.Ohara H, Nikaido M, Date-Ito A, Mogi K, Okamura H, Okada N,
Takeuchi Y, Mori Y, Hagino-Yamagishi K.
Conserved repertoire of orthologous vomeronasal type 1 receptor genes
in ruminant species.
BMC Evol. Biol. 9(1):233. (2009)190. Okada N.
Special issue on phylogenomics and its future
Gene Jul 15;441(1-2):1-2 (2009) [Editorial]
189.Kojima K.K, and Okada N.
mRNA retrotransposition coupled with 5' inversion as a possible sourceof new genes.
Mol Biol Evol. 26 (6): 1405-20 (2009)
188.Nishihara H, Maruyama S, Okada N.
Retroposon analysis and recent geological data suggest nearsimultaneous divergence of the three superorders of mammals.
Proc Natl Acad Sci USA. Mar 31;106(13):5235-40 (2009) [Abstract][OPEN ACCESS]
187.Kobayashi N, Watanabe M, Horiike T, Kohara Y, Okada N.
Extensive analysis of EST sequences reveals that all cichlid species in
Lake Victoria share almost identical transcript sets.
Gene. Jul 15;441(1-2):187-91 (2009)186.Hirakawa M, Nishihara H, Kanehisa M, Okada N.
Characterization and evolutionary landscape of AmnSINE1 in Amniota
genomes.
Gene Jul 15;441(1-2):100-10 (2009)
185. Maeda K, Takeda M, Kamiya K, Aibara M, Mzighani S.I, Nishida M,
Mizoiri S, Sato T, Terai Y, Okada N, Tachida H.
Population structure of two closely related pelagic cichlids in Lake
Victoria, Haplochromis pyrrhocephalus and H. laparogramma.
Gene Jul 15;441(1-2):67-73 (2009)
184.Murata Y, Yonezawa T, Kihara I, Kashiwamura T, Sugihara Y, Nikaido
M, Okada N, Endo H, Hasegawa M.
Chronology of the extant African elephant species and case study of thespecies identification of the small African elephant with the molecularphylogenetic method.
Gene Jul 15;441(1-2):176-86 (2009)
183.Piskurek O, Nishihara H, Okada N.
The evolution of two partner LINE/SINE families and a full-length
chromodomain-containing Ty3/Gypsy LTR element in the first reptilian
genome of Anolis carolinensis.
Gene Jul 15;441(1-2):111-8 (2009)
182.Matveev V, Okada N.
Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and theirevolution.
Gene. 434(1-2):16-28 (2009)
181.Seehausen O, Terai Y, Magalhaes I. S, Carleton K. L., Mrosso H. D. J,
Miyagi R, van der Sluijs I, Schneider M. V, Maan M, Tachida H, Imai
H, Okada N.
Speciation through sensory drive in cichlid fish.
Nature. Oct 2;455(7213) 620-6 (2008)
180.Fujimura K, Okada N
Shaping of the lower jaw bone during growth of Nile tilapia
Oreochromis niloticus and a Lake Victoria cichlid Haplochromis
chilotes: A geometric morphometric approach.
Develop. Growth Differ. Oct;50(8):653-63. (2008)
179.Nishihara H, Okada N.
Retroposons: Genetic Footprints on the Evolutionary Paths of Life.
Phylogenomics (Methods in Molecular Biology, vol. 422)
Chapter 13, Pages 201-225, Ed. Murphy, W. J., Humana Press. (2008)178.Matsuura M, Nishihara H, Onimaru K, Kokubo N, Kuraku S, Kusakabe
R, Okada N, Kuratani S, Tanaka M.
Identification of Four Engrailed Genes in the Japanese Lamprey,
Lethenteron japonicum.
Dev. Dyn. Jun;237(6):1581-9. (2008)
177.Ichiyanagi K, Okada N.
Mobility Pathways for Vertebrate L1-, L2-, CR1-, and RTE-CladeRetrotransposons.
Mol Biol Evol. Jun;25(6):1148-57 (2008)
176.Fujimura K, Okada N
Bone development in the jaw of Nile tilapia Oreochromis niloticus(Pisces: Cichlidae)
Develop. Growth Differ. 50(5): 339-55 (2008)
175.Fujimura K, Terai Y, Ishiguro N, Miya M, Nishida M, Okada N
Heterotypy in the N-terminal region of Growth/Differentiation Factor 5(GDF5) mature protein during teleost evolution
Mol Biol Evol 25(5): 797-800 (2008)
174.Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo
N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, Shimogori T,
Okada N.
Possible involvement of SINEs in mammalian-specific brain formation.
Proc Natl Acad Sci USA. v105(11), 4220-5 (2008) [OPEN ACCESS]
173. Maeda K, Takeshima H, Mizoiri S, Okada N, Nishida M, Tachida H.
Isolation and characterization of microsatellite loci in the cichlid fish in
Lake Victoria, Haplochromis chilotes.
Molecular Ecology Resources 8(2) 428 - 430 (2008)
172.Munemasa M, Nikaido M, Nishihara H, Donnellan S, Austin CC,
Okada N.
Newly discovered young CORE-SINEs in marsupial genomes.
Gene. Jan 15;407(1-2):176-85. (2008)
171.Nishihara H, Okada N, Hasegawa M.
Rooting the eutherian tree: the power and pitfalls of phylogenomics.
Genome Biol. Sep 21;8(9) R199 (2007)
170.Nishihara H, Kuno S, Nikaido M, Okada N.
MyrSINEs: a novel SINE family in the anteater genomes.
Gene. Oct 1;400(1-2):98-103. (2007)169.Ichiyanagi K, Nishihara H, Duvernell D.D, Okada N.
Acquisition of Endonuclease Specificity During Evolution of L1
Retrotransposon.
Mol Biol Evol. Sep;24(9):2009-15 (2007)
168. Watanabe M, Hiraide K, Okada N.
Functional diversification of kir7.1 in cichlids accelerated by gene
duplication.
Gene Sep;399(1):46-52 (2007)
167. Piskurek O, Okada N.
Poxviruses as possible vectors for horizontal transfer of retroposons
from reptiles to mammals.
Proc Natl Acad Sci U S A. Jul 17;104(29):12046-51 (2007) [OPEN
ACCESS]
166. Matveev V, Nishihara H, Okada N.
Novel SINE Families from Salmons Validate Parahucho (Salmonidae)
as a Distinct Genus and Evidence that SINEs Can Incorporate LINErelated 3'-Tails of Other SINEs.
Mol Biol Evol. Aug;24(8):1656-66 (2007)
165. Onami J, Nikaido M, Mannen H, Okada N.
Genomic expansion of the Bov-A2 retroposon relating to phylogeny andbreed management.
Mamm Genome. Mar;18(3):187-96. (2007)
164.Yonezawa T, Nikaido M, Kohno N, Fukumoto Y, Okada N,
Hasegawa M.
Molecular phylogenetic study on the origin and evolution of Mustelidae.
Gene. Jul 1;396(1):1-12 (2007)
163.Xue B, Rooney AP, Kajikawa M, Okada N, Roelofs WL.
Novel sex pheromone desaturases in the genomes of corn borers
generated through gene duplication and retroposon fusion.
Proc Natl Acad Sci U S A. Mar 13;104(11):4467-72 (2007) [OPEN
ACCESS]
162.Fujimura K, Okada N.
Development of the embryo, larva and early juvenile of Nile tilapia
Oreochromis niloticus (Pisces: Cichlidae).
Developmental staging system
Develop. Growth Differ. 49 (4), 301-324 (2007)161.Nikaido M, Piskurek O, Okada N.
Toothed whale monophyly reassessed by SINE insertion analysis: The
absence of lineage sorting effects suggests a small population of acommon ancestral species.
Mol. Phylogenet. Evol. 43:216-224 (2007)
160.Honda H, Ichiyanagi K, Suzuki J, Ono T, Koyama H, Kajikawa M,
Okada N.
A new system for analyzing LINE retrotransposition in the chicken
DT40 cell line widely used for reverse genetics.
GENE, Jun 15;395(1-2):116-24 (2007)
159.Sasaki T, Sato T, Miura S, Bwathondi PO, Ngatunga BP, Okada N.
Mitogenomic analysis for coelacanths (Latimeria chalumnae) caught inTanzania.
Gene. 389 73-79 (2007)
158. Babushok D.V, Ohshima K, Ostertag E.M, Chen X, Wang,
Mandal P.K, Okada N, Abrams C.S, Kazazian Jr.H.H.
A novel testis ubiquitin-binding protein gene arose by exon shuffling in
hominoids.
Genome Research 17(8) 1129 – 1138 (2007)
157.Ichiyanagi K, Nakajima R, Kajikawa M, Okada N.
Novel retrotransposon analysis reveals multiple mobility pathways
dictated by hosts.
Genome Res. Jan;17(1):33-41 (2007)
156.Sasaki T, Yasukawa Y, Takahashi K, Miura S, Shedlock AM, Okada N.
Extensive morphological convergence and rapid radiation in theevolutionary history of the family Geoemydidae (old world pond turtles)
revealed by SINE insertion analysis.
Syst Biol. 55(6),912-27 (2006)
155.Tamura M, Kajikawa M, Okada N.
Functional splice sites in a zebrafish LINE and their influence on
zebrafish gene expression.
Gene. Apr 1;390(1-2):221-31 (2006)
154.Terai Y, Seehausen O, Sasaki T, Takahashi K, Mizoiri S, Sugawara T,
Sato T, Watanabe M, Konijnendijk N, Mrosso HD, Tachida H, Imai H,
Shichida Y, Okada N.
Divergent Selection on Opsins Drives Incipient Speciation in Lake
Victoria Cichlids.
PLoS Biol. 4(12):e433 (2006)153.Iwashita M, Watanabe M, Ishii M, Chen T, Johnson SL, Kurachi Y,
Okada N, Kondo S.
Pigment Pattern in jaguar/obelix Zebrafish Is Caused by a Kir7.1
Mutation: Implications for the Regulation of Melanosome Movement.
PLoS Genet. Nov.24;2(11): e197 (2006)
152.Ichiyanagi K, Okada N.
Genomic alterations upon integration of zebrafish L1 elements revealedby the TANT method.
Gene. 15;383: 108-16. (2006)
151.Watanabe M, Iwashita M, Ishii M, Kurachi Y, Kawakami A, Kondo S,
Okada N.
Spot pattern of leopard Danio is caused by mutation in the zebrafish
connexin41.8 gene.
EMBO Rep. 7(9):893-7. (2006)
150.Nomura Y, Kajikawa M, Baba S, Nakazato S, Imai T, Sakamoto T,
Okada N, Kawai G.
Solution structure and functional importance of a conserved RNA
hairpin of eel LINE UnaL2.
Nucleic Acids Res. 34;18: 5184-93 (2006)
149.Sasaki T, Nikaido M, Wada S, Yamada T K, Cao Y, Hasegawa M,
Okada N.
Balaenoptera omurai is a newly discovered baleen whale that
represents an ancient evolutionary lineage.
Mol Phylogenet Evol. 41;40 :40-52 (2006)
148.Munemasa M, Nikaido M, Donnellan S, Austin C C, Okada N,
Hasegawa M.
Phylogenetic analysis of diprotodontian marsupials based on complete
mitochondrial genomes.
Genes Genet Syst. 81:181-91 (2006)
147.Piskurek O, Okada N.
Simple and complex SINEs: A brief critical comment.
Gene 375, 110 (2006)
146.Watanabe M, Nikaido M, Tsuda T T, Kobayashi T, Mindell D, Cao Y,
Okada N, Hasegawa M.
New candidate species most closely related to penguins.
Gene 378, 65-73 (2006)

145.Nishihara H, Hasegawa M, Okada N.
Pegasoferae, an unexpected mammalian clade revealed by tracking
ancient retroposon insertions.
Proc Natl Acad Sci USA. 103(26),9929-34 (2006) [OPEN ACCESS]
144.Nishihara H, Smit AF, Okada N.
Functional noncoding sequences derived from SINEs in the mammalian
genome.
Genome Res. Jul;16(7):864-74 (2006)
143.Piskurek O, Austin CC, Okada N.
Sauria SINEs: Novel Short Interspersed Retroposable Elements That
Are Widespread in Reptile Genomes.
J Mol Evol. 62(5), 630-44. (2006)
142.Nikaido M, Hamilton H, Makino H, Sasaki T, Takahashi K, Goto M,
Kanda N, Pastene LA, Okada N.
Baleen Whale Phylogeny and a Past Extensive Radiation Event
Revealed by SINE Insertion Analysis.
Mol Biol Evol. 23, :866-73 (2006)
141.Kobayashi N, Watanabe M, Kijimoto T, Fujimura K, Nakazawa M, Ikeo
K, Kohara Y, Gojobori T, Okada N.
magp4 gene may contribute to the diversification of cichlid morphs andtheir speciation.
Gene 373, 126-33 (2006)
140.Akasaki T, Nikaido M, Tsuchiya K, Segawa S, Hasegawa M, Okada N.
Extensive mitochondrial gene arrangements in coleoid Cephalopoda
and their phylogenetic implications.
Mol Phylogenet Evol. 38, 648-58 (2006)
139.Sugano T, Kajikawa M, Okada N.
Isolation and characterization of retrotransposition-competent LINEs
from zebrafish.
Gene 365, 74-82. (2006)
138.Kawagoe-Takaki H, Nameki N, Kajikawa M, Okada N.
Probing the secondary structure of salmon SmaI SINE RNA.
Gene 365, 67-73. (2006)
137.Watanabe M, Nikaido M, Tsuda TT, Inoko H, Mindell DP, Murata K,
Okada N.
The rise and fall of the CR1 subfamily in the lineage leading topenguins.
Gene 365, 57-66. (2006)
136.Ohshima K, and Okada N.
SINEs and LINEs: symbionts of eukaryotic genomes with a common
tail.
Cytogenet Genome Res. 110, 475-90. (2005)
135.Nishihara H, Satta Y, Nikaido M, Thewissen J G, Stanhope M J, andOkada N.
A Retroposon Analysis of Afrotherian Phylogeny.
Mol Biol Evol. 22(9), 1823-33. (2005)
134.Kijimoto T, Watanabe M, Fujimura K, Nakazawa M, Murakami Y,
Kuratani S, Kohara Y, Gojobori T, and Okada N.
cimp1, A Novel Astacin Family Metalloproteinase Gene from East
African Cichlids, Is Differentially Expressed Between Species During
Growth.
Mol Biol Evol. 22(8), 1649-60. (2005)
133.Sugawara T, Terai Y, Imai H, Turner G F, Koblmuller S, Sturmbauer C,
Shichida Y, and Okada N.
Parallelism of amino acid changes at the RH1 affecting spectral
sensitivity among deep-water cichlids from Lakes Tanganyika andMalawi.
Proc. Natl. Acad. Sci. USA 102(15), 5448-53 (2005) [OPEN ACCESS]
132.Sasaki T, Nikaido M, Hamilton H, Goto M, Kato H, Kanda N, Pastene L
A, Cao A, Fordyce R E, Hasegawa M, and Okada N.
Mitochondrial phylogenetics and evolution of mysticete whales.
Syst Biol. 54, 77-90 (2005)
131.Kajikawa M, Ichiyanagi K, Tanaka N, and Okada N.
Isolation and characterization of active LINE and SINEs from the eel.
Mol. Biol. Evol. 22, 673-82 (2005)
130.Segawa T, Miyamoto K, Ushida K, Agata K, Okada N, and Kohshima S.
Seasonal Change in Bacterial Flora and Biomass in Mountain Snowfrom the Tateyama Mountains, Japan, Analyzed by 16S rRNA GeneSequencing and Real-Time PCR.
Applied and Environmental Microbiology 71(1), 123-30 (2005)
129.Sugie A, Terai Y, Ota R, and Okada N.
The evolution of genes for pigmentation in African cichlid fishes.
GENE 343(2), 337-46 (2004)

128.Watanabe M, Kobayashi N, Shin-i T, Tateno Y, Kohara Y, and Okada
N.
Extensive analysis of ORF sequences from two different cichlid species
in Lake Victoria provides molecular evidence for a recent radiation
event of the Victoria species flock.
GENE 343(2), 263-9 (2004)
127.Baba S, Kajikawa M, Okada N, and Kawa G.
Solution structure of an RNA stem-loop derived from the 3' conserved
region of eel LINE UnaL2.
RNA 10(9), 1380-7 (2004)
126.Shedlock A M, Takahashi K, and Okada N.
SINEs of speciation: tracking lineages with retroposons.
Trends in Ecology & Evolution 19(10), 545-53 (2004)
125.Imanishi T, et al.
Integrative Annotation of 21,037 Human Genes Validated by FullLength cDNA Clones.
Plos Biology 2(6), 856-75 (2004)
124.Okada N, Shedlock A M, and Nikaido M.
Retroposon mapping in molecular systematics.
Methods. Mol. Biol. 260, 189-226 (2004)
123.Sasaki T, Takahashi K, Nikaido M, Miura S, Yasukawa Y, and Okada
N.
First Application of the SINE (Short Interspersed Repetitive Element)
Method to Infer Phylogenetic Relationships in Reptiles: An Example
from the Turtle Superfamily Testudinoidea.
Mol. Biol. Evol. 21, 705-15 (2004)
122.Terai Y, Takezaki N, Mayer W E, Tichy H, Takahata N, Klein J, andOkada N.
Plylogenetic relationships among East African haplochromine fishes asrevealed by short interspersed elements (SINEs).
J. Mol. Evol. 58, 64-78 (2004)
121. Kawai K, Nikaido M, Harada M, Matsumura S, Lin L.K, Yi Wu,
Hasegawa M, Okada N.
Erratum: The status of the Japanese and East Asian bats of the genus
Myotis (Vespertilionidae) based on mitochondrial sequences (MolecularPhylogenetics and Evolution (2003) 28 (297-307))
Molecular Phylogenetics and Evolution. 30(1)259(2004)

120.Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, and Okada N.
Whole-genome screening indicates a possible burst of formation ofprocessed pseudogenes and Alu repeats by particular L1 subfamilies inancestral primates.
Genome Biol. 4(11)R74, Epub 2003 Oct 28. (2003)
119.Terai Y, Morikawa N, Kawakami K, and Okada N.
The complexity of alternative splicing of hagoromo mRNA is increased
in an explosively speciated lineage in East African cichlids.
Proc. Natl. Acad. Sci. U S A. Oct.28,100(22), 12798-803 (2003) [OPEN
ACCESS]
118.Terai Y, Takahashi K, Nishida M, Sato T, and Okada N.
Using SINEs to Probe Ancient Explosive Speciation: "Hidden"
Radiation of African Cichlids?
Mol. Biol. Evol. 20, 924-30 (2003)
117.Piskurek O, Nikaido M, Boeadi Baba M, and Okada N.
Unique mammalian tRNA-derived repetitive elements in
Dermopterans: The t-SINEfamily and its retrotransposition throughmultiple sources.
Mol. Biol. Evol. 20, 1659-68 (2003)
116.Murata Y, Nikaido M, Sasaki T, Cao Y, Fukumoto Y, Hasegawa M, andOkada N.
Afrotherian phylogeny as inferred from complete mitochondrial
genomes.
Mol. Phylogenet. Evol. 28, 253-60 (2003)
115.Nikaido M, Cao Y, Harada M, Okada N, and Hasegawa M.
Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla.
Mol. Phylogenet. Evol. 28, 276-84 (2003)
114.Kawai K, Nikaido M, Harada M, Matsumura S, Lin L K, Wu Y.,
Hasegawa M and Okada N.
The status of the Japanese and East Asian bats of the genus Myotis(Vespertilionidae) based on mitochondrial sequences.
Mol. Phylogenet. Evol. 28, 297-307 (2003)
113.Nikaido M, Nishihara H, Fukumoto Y, and Okada N.
Ancient SINEs from African Endemic Mammals
Mol. Biol. Evol. 20, 522-7 (2003)

112.Watanabe M, Kobayashi N, Fujiyama A, and Okada N.
Construction of a BAC library for Haplochromis chilotes, a cichlid fishfrom Lake Victoria.
Genes. Genet. Syst. 78, 103-5 (2003)
111.Nikaido M, Cao Y, Okada N, and Hasegawa M.
The phylogenetic relationships of insectivores with special reference tothe lesser hedgehog tenrec as inferred from the complete sequence of
their mitochondrial genome.
Genes. Genet. Syst. 78, 107-12 (2003)
110.Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, andYokoyama S.
Alternative Tertiary Structure of tRNA for Recognition by a
Posttranscriptional Modification Enzyme.
Cell 113, 383-94 (2003)
109. D Huchon, Nikaido M, Okada N.
Use of SINE retroposon in phylogeny.
M S-MEDECINE SCIENCES 18(12) 1276-1281(2002)
108. Pupko T, Huchon D, Cao Y, Okada N, and Hasegawa M.
Combining multiple data sets in a likelihood analysis: which models
are the best?
Mol Biol Evol. 19(12), 2294-307 (2002)
107. Terai Y, Mayer W E, Klein J, Tichy H, and Okada N.
The effect of selection on a long wavelength-sensitive (LWS) opsin geneof Lake Victoria cichlid fishes.
Proc. Natl. Acad. Sci. USA
99, 15501-6 (2002) [OPEN ACCESS]
106. Kajikawa M, and Okada N.
LINEs Mobilize SINEs in the Eel through a Shared 3' Sequence.
Cell 111, 433-44 (2002)
105. Nishihara H, Terai Y, and Okada N.
Characterization of Novel Alu- and tRNA-Related SINEs from the Tree
Shrew and Evolutionary Implications of Their Origins.
Mol. Biol. Evol. 19, 1964-72 (2002)
104. Sugawara T, Terai Y, and Okada N.
Natural selection of the rhodopsin gene during the adaptive radiationof East african great lakes cichlid fishes.
Mol. Biol. Evol. 19, 1807-11 (2002)

103. Terai Y, Morikawa N, and Okada N.
The evolution of the pro-domain of bone morphogenetic protein 4(bmp4) in an explosively speciated lineage of East african cichlid fishes.
Mol. Biol. Evol. 19(9), 1628-32 (2002)
102. Kawai K, Nikaido M, Harada M, Matsumura S, Lin L K, Wu Y,
Hasegawa M, and Okada N.
Intra- and Interfamily Relationships of Vespertilionidae Inferred by
Various Molecular Markers Including SINE Insertion Data.
J. Mol. Evol. 55(3), 284-301 (2002)
101. Takahashi K, and Okada N.
Mosaic structure and retropositional dynamics during evolution of
subfamilies of short interspersed elements in african cichlids.
Mol. Biol. Evol. 19(8), 1303-12 (2002)
100. Terai Y, Morikawa N, Kawakami K, and Okada N.
Accelerated Evolution of the Surface Amino Acids in the WD-Repeat
Domain Encoded by the hagoromo Gene in an Explosively SpeciatedLineage of East African Cichlid Fishes.
Mol. Biol. Evol. 19(4), 574-8 (2002)
99. Ishitani R, Nureki O, Fukai S, Kijimoto T, Nameki N, Watanabe M,
Kondo H, Sekine M, Okada N, Nishimura S, and Yokoyama S.
Crystal structure of archaeosine tRNA-guanine transglycosylase.
J. Mol. Biol. 318(3), 665-77 (2002)
98. Ogiwara I, Miya M, Ohshima K, and Okada N.
V-SINEs: a new superfamily of vertebrate SINEs that are widespread invertebrate genomes and retain a strongly conserved segment withineach repetitive unit.
Genome Res. 12, 316-24 (2002)
97. Ishitani R, Nureki O, Kijimoto T, Watanabe M, Kondo H, Nameki N,
Okada N, Nishimura S, and Yokoyama S.
Crystallization and preliminary X-ray analysis of the archaeosine tRNAguanine transglycosylase from Pyrococcus horikoshii.
Acta. Crystallogr. 57, 1659-62 (2001)
96. Nikaido M, Matsuno F, Abe H, Shimamura M, Hamilton H,
Matsubayashi H, and Okada N.
Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence
for the monophyletic origin of toothed whales.
Mamm. Genome. 12, 909-15 (2001)

95. Takahashi K, Terai Y, Nishida M, and Okada N.
Phylogenetic relationships and ancient incomplete lineage sorting
among cichlid fishes in Lake Tanganyika as revealed by analysis of theinsertion of retroposons.
Mol. Biol. Evol. 18, 2057-66 (2001)
94. Nikaido M, Kawai K, Cao Y, Harada M, Tomita S, Okada N, andHasegawa M.
Maximum likelihood analysis of the complete mitochondrial genomes of
eutherians and a reevaluation of the phylogeny of bats and insectivores.
J. Mol. Evol. 53, 508-16 (2001)
93. Takahashi K, Nishida M, Yuma M, and Okada N.
Retroposition of the AFC family of SINEs (short interspersed repetitiveelements) before and during the adaptive radiation of cichlid fishes in
Lake Malawi and related inferences about phylogeny.
J. Mol. Evol. 53, 496-507 (2001)
92. Nikaido M, Matsuno F, Hamilton H, Brownell R L Jr., Cao Y, Ding W,
Zuoyan Z, Shedlock A M, Fordyce R E, Hasegawa M, and Okada N.
Retroposon analysis of major cetacean lineages: the monophyly of
toothed whales and the paraphyly of river dolphins.
Proc. Natl. Acad. Sci. USA. 98(13), 7384-9 (2001) [OPEN ACCESS]
91. Watanabe M, Nameki N, Matsuo-Takasaki M, Nishimura S, and Okada
N.
tRNA recognition of tRNA-guanine transglycosylase from a
hyperthermophilic archaeon, Pyrococcus horikoshii.
J. Biol. Chem. 276(4), 2387-94 (2001)
90. Cao Y, Fujiwara M, Nikaido M, Okada N, and Hasegawa M.
Interordinal relationships and timescale of eutherian evolution as
inferred from mitochondrial genome data.
GENE 259, 149-58 (2000)
89. Nikaido M, and Okada N.
CetSINEs and AREs are not SINEs but are parts of cetartiodactyl L1.
Mamm. Genome. 11ʤ12ʥ, 1123-6 (2000)
88. Nikaido M, Harada M, Cao Y, Hasegawa M, and Okada N.
Monophyletic origin of the order chiroptera and its phylogenetic position
among mammalia, as inferred from the complete sequence of themitochondrial DNA of a Japanese megabat, the Ryukyu flying fox(Pteropus dasymallus).
J. Mol. Evol. 51(4), 318-28 (2000)

87. Lum J K, Nikaido M, Shimamura M, Shimodaira H, Shedlock A M,
Okada N, and Hasegawa M.
Consistency of SINE insertion topology and flanking sequence tree:
quantifying relationships among cetartiodactyls.
Mol. Biol. Evol. 17ʤ10ʥ, 1417-24 (2000)
86. Shedlock A M, and Okada N.
SINE Insertions : Powerful Tools for Molecular Systematics.
BioEssays. 22(2), 148-60 (2000)
85. Shedlock A M, Milinkovitch M C, and Okada N.
SINE evolution, missing data, and the origin of whales.
Syst. Bio. 49(4), 808-17 (2000)
84. Waddell P J, Okada N, and Hasegawa M.
Towards resolving the interordinal relationships of placental mammals.
Syst. Biol. 48, 1-5 (1999)
83. Nikaido M, Rooney A P, and Okada N
Phylogenetic relationships among cetartiodactyls based on insertions ofshort and long interspersed elements: Hippopomamuses are the closest
extant relatives of whales.
Proc. Natl. Acad. Sci. USA. 96, 10261-6 (1999) [OPEN ACCESS ]82. Shimamura M, Abe H, Nikaido M, Ohshima K, and Okada N.
Genealogy of families of SINEs in cetaceans and artiodactyls: The
presenxe of a huge superfamily of tRNA Glu-derived families of SINEs.
Mol. Bio. Evol. 16(8), 1046-60 (1999)
81. Ogiwara I, Miya M, Ohshima K, and Okada N.
Retropositional parasitism of SINEs on LINEs: Identification of SINEs
and LINEs in elasmobranchs.
Mol. Bio. Evol. Sep.16(9), 1238-50 (1999)
80. Murata S, Takasaki N, Okazaki T, Kobayasi T, Numachi K, Chang K H,
and Okada N.
Molecular evidence from short interspersed elements (SINEs) that
Oncorhynchus masou (cherry salmon) is monophyletic.
Can. J. Fish. Aquat. Sci. 55(8): 1864-70 (1998)
79. Terai Y, Takahashi K, and Okada N.
SINE cousins: The 3'-end tails of the two oldest and distantly relatedfamilies of SINEs are descended from the 3' ends of LINEs with thesame genealogical origin.
Mol. Biol. Evol. 15, 1460-71 (1998)
78. Shimamura M, Nikaido M, Ohshima K, and Okada N.
A SINE that acquired a role in signal transduction during evolution.
Mol. Biol. Evol. 15, 923-5 (1998)
77. Hamada M, Takasaki N, Reist J D, DeCicco A L, Goto A, and Okada N.
Detection of the on-going sorting of ancestrally polymorphic SINEs
towards fixation or loss in populations of two species of charr during
speciation.
Genetics 150(1), 301-11 (1998)
76. Takahasi I, Nobukuni T, Ohmori H, Kobayashi M, Tanaka S, Ohshima
K, Okada N, Masui T, Hashimoto K, and Iwashita S.
Existence of a bovine LINE repetitive insert that appears in the cDNA ofbovine protein BCNT in ruminant, but not in human, genomes.
GENE 211, 387-94 (1998).
75. Takahashi K, Terai Y, Nishida M, and Okada N.
A novel family of short interspersed repetitive elements (SINEs) fromcichlids: the patterns of insertion of SINEs at orthologous loci support
the proposed monophyly of four major groups of cichlid fishes in Lake
Tanganyika.
Mol. Biol. Evol. 15(4), 391-407 (1998)
74. Hamada M, Himberg M, Bodalu R A, Reist J D, and Okada N.
Monophyletic origin of the genera stenodus and coregonus as inferredfrom an analysis of the insertion of SINEs (short interspersed repetitiveelements).
Biology and Management of Coregonid Fishes. 50, 383-9 (1998)
73. Cao Y, Waddell P J, Okada N, and Hasegawa M.
The complete mitochondrial DNA sequence of the shark Mustelus
manazo: evaluating rooting contradictions to living bony vertebrates .
Mol. Biol. Evol. 15, 1637-46 (1998)
72. Cao Y, Janke A., Waddell P J., Westerman M, Takenaka O, Murata S,
Okada N, Paabo S, and Hasegawa M.
Conflict among individual mitochondral proteins in resolving thephylogeny of eutherian orders.
J. Mol. Evol. 47, 307-22 (1998)
71. Watanabe M, Matsuo M, Tanaka S, Akimoto H, Asahi S, Nishimura S,
Katze J R, Hashizume T, Crain P F, McCloskey J A, and Okada N.

Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine
specific to archaeal tRNA, proceeds via a pathway involving basereplacement on the tRNA polynucleotide chain.
J. Biol. Chem. 272, 20146-51 (1997)
70. Okada N, Hamada M, Ogiwara I, and Ohshima K.
SINEs and LINEs share common 3' sequences: a review.
GENE 205(1-2), 229-43 (1997)
69. Shimamura M, Yasue H, Ohshima K, Abe H, Kato H, Kishiro T, Goto M,
Munechika I, and Okada N.
Molecular evidence that whales form a clade within even-toed ungulates.
Nature 388ʤ6643ʥ, 666-70 (1997)
68. Ishida K, Cao Y, Hasegawa M, Okada N, and Hara Y.
The origin of chlorarachniophyte plastids, as inferred from phylogenetic
comparisons of amino acid sequences of EF-Tu.
J. Mol. Evol. 45, 682-7 (1997)
67. Hamada M, Kido Y, Himberg M, Hasegawa M, and Okada N.
A newly isolated family of short interspersed repetitive elements(SINEs) in coregonid fishes (whitefishes) with sequences that are almost
identical to those of the Sma I family of repeats: possible evidence for thehorizontal transfer of SINEs.
Genetics 146(1), 355-67 (1997)
66. Takasaki N, Yamaki T, Hamada M, Park L, and Okada N.
The salmon Sma I family of SINEs: interspecific and intraspecificpolymorphism of the insertion of SINEs in the genomes of chum andpink salmon.
Genetics 146(1), 369-80 (1997)
65. Kajikawa M, Ohshima K, and Okada N.
Determination of the entire sequence of turtle CR1: the first open
reading frame of the turtle CR1 element encodes a protein with a novel
zinc finger motif.
Mol. Biol. Evol. 14, 1206-17 (1997)
64. Okada N, and Hamada M.
The 3' ends of tRNA-derived SINEs originated from the 3" ends ofLINEs: A new example from the bovine genome.
J. Mol. Evol. 44, Supplementally 52-6 (1997)
63. Ohshima K, Hamada M, Terai Y, and Okada N.
The 3' ends of tRNA-deriverd short interspersed repetitive elements arederiverd from the 3' ends of long interspersed repetitive elements.
Mol. Cell. Biol. 16, 3756-64 (1996)
62. Kamaishi T, Hashimoto T, Nakamura Y, Nakamura F, Murata S, Okada
N, Okamoto K, Shimizu M, and Hasegawa M.
Protein phylogeny of translation elongation factor EF-1a suggests
microsporidians are extremely eukaryotes.
J. Mol. Evol. 42, 257-63 (1996)
61. Murata S, Takasaki N, Saitoh M, Tachida H, and Okada N.
Details of retropositional genome dynamics that provide a rational for ageneric division: The distinct branching of all the Pacific salmon andtrout (Oncorhynchus) from the Atlantic salmon and trout (Salmo).
Genetics 142(3), 915-26 (1996)
60. Takasaki N, Park L, Kaeriyama M, Gharrett A J, and Okada N.
Characterization of species-specifically amplified SINEs in threesalmonid species, chum salmon, pink salmon and kokanee: the local
environment of the genome might be important for the generation of adominant source gene at a newly retroposed locus.
J. Mol. Evol. 42(2), 103-16 (1996)
59. Kido Y Saito M, Murata S, and Okada N.
Evolution of the source sequence of Hpa I short interspersed elements.
J. Mol. Evol. 41(6), 986-95 (1995)
58. Okada N, and Ohshima K.
Evolution of tRNA-derived SINEs. The Impact of short interspersed
elements (SINEs) on the host genome.
Ed. Richard J. Maraia, Springer RG. Landes Company. (1995)
57. Matsuo M, Yokogawa T, Nishikawa K, Watanabe K, and Okada N.
Highly specific and efficient cleavage of squid tRNA(Lys) catalyzed bymagnesium ions.
J. Biol. Chem. 270, 10097-104 (1995)
56. Matsuo M, Abe Y, Saruta Y, and Okada N.
Mollusk genes encoding lysine tRNA(UUU) contain introns.
GENE 165, 249-53 (1995)
55. Nameki N, Asahara H, Shimizu M, Okada N, and Himeno H.
Identity elements of Saccharomyces cerevisiae tRNAHis.
Nucleic. Acids. Res. 23, 389-94 (1995)

54. Nakanishi S, Ueda T, Hori H, Yamazaki N, Okada N, and Watanabe K.
A UGU sequence in the anticodon loop is a minimum requirement forrecognition by Escherichia coli tRNA-guanine transglycosylase.
J. Biol. Chem. 269(51), 32221-5 (1994)
53. Ohshima K, and Okada N.
Generality of the tRNA origin of short interspersed repetitive elements(SINEs); Characterization of three different tRNA-derived retroposons
in the octopus.
J. Mol. Biol. 243, 25-37 (1994).
52. Yokobori S, Hasegawa M, Ueda T, Okada N, Nishikawa K, and
Watanabe K.
Relationship among Coelacanths, Lungfishes, and Tetrapods:
A phylogenetic analysis based on mitochondrial cytochrome oxidase I
gene sequences.
J. Mol. Evol. 38(6), 602-9 (1994)
51. Takasaki N, Murata S, Saitoh M, Kobayashi T, Park L, and Okada N.
Species-specific amplification of tRNA-derived SINEs via retroposition; aprocess of parasitization of entire genomes during the evolution of
salmonids.
Proc. Natl. Acad. Sci. USA. 91(21), 10153-7 (1994) [OPEN ACCESS]
50. Kido Y, Himberg M, Takasaki N, and Okada N.
Amplification of distinct subfamilies of short interspersed elements(SINEs) during evolution of the Salmonidae.
J. Mol. Biol. 241(5), 633-44 (1994)
49. Sakagami M, Ohshima K, Mukoyama H, Yasue H, and Okada N.
A novel tRNA species as an origin of short interspersed repetitiveelements (SINEs); Equine SINEs may have originated from tRNA(Ser).
J. Mol. Biol. 239(5), 731-5 (1994)
48. Yoshioka Y, Takahashi Y, Matsumoto S, Kojima S, Matsuoka K,
Nakamura K, Ohshima K, Okada N, and Machida Y.
Mechanisms of T-DNA transfer and integration into plant chromosomes:role of virB, virD4 and virE2 and a short interspersed repetitive element(SINE) from tobacco.
Molecular Mechanisms of Bacterial Virulence, Kluwer Academic
Publishers.
(eds. C. Kado & J. Crosa) 231-48 (1994)
47. Ozawa Y, Uchida K, Uchida M, Ami Y, Kushida S, Okada N, and Miwa
M.

Isolation of cDNAs encoding the catalytic domain of poly(ADP-ribose)polymerase from Xenopus laevis and cherry salmon using heterologous
oligonucleotide consensus sequences.
Biochem. Biophys. Res. Commun. 193, 119-25 (1993)
46. Murata S, Takasaki N, Saitoh M, and Okada N.
Determination of the phylogenetic relationships among Pacificsalmonids using short interspersed elements (SINEs) as temporal
landmarks of evolution.
Proc. Natl. Acad. Sci. USA .90(15), 6995-9 (1993) [OPEN ACCESS]
45. Yoshioka Y, Matsumoto S, Kojima S, Ohshima K, Okada N, andMachida Y.
Molecular characterization of a short interspersed repetitive elementfrom tobacco that exhibits sequence homology to specific tRNAs.
Proc. Natl. Acad. Sci. USA. 90(14), 6562-6 (1993) [OPEN ACCESS]
44. Ohshima K, Koishi R, Matsuo M, and Okada N.
Several short interspersed repetitive elements (SINEs) in distant species
may have originated from a common ancestral retrovirus:
characterization of a squid SINE and a possible mechanism forgeneration of tRNA-derived retroposons.
Proc. Natl. Acad. Sci. USA .90(13), 6260-4 (1993) [OPEN ACCESS]
43. Kojima S, Hashimoto T, Hasegawa M, Murata S, Ohta S, Seki F, andOkada N.
Close phylogenetic relationship between Vestimentifera (tube worms)
and Annelida revealed by the amino acid sequence of elongation factor1a.
J. Mol. Evol. 37(1), 66-70 (1993)
42. Okada N, and Ohshima K.
A model for the mechanism of initial generation of short interspersed
elements (SINEs).
J. Mol. Evol. 37(2), 167-70 (1993)
41. Kido Y, Aono M, Matsumoto K, Yamaki T, Saneyoshi M, and Okada N.
Shaping and reshaping of salmonid genomes by amplification of tRNAderived retroposons during evolution.
Proc. Natl. Acad. Sci. USA.88(6), 2326-30 (1991) [OPEN ACCESS]
40. Okada N.
Transfer RNA-derived retroposons.
New Aspect of the Genetics of Molecular Evolution

(eds. M.Kimura and N.Takahata)
Japan Scientific Societies Press pp.227-41 (1991)
39. Okada N, Aono M, Endoh H, Kido Y, Koishi R, Matsumoto K, Matsuo M,
Murata S, Nagahashi S, and Yamaki T.
Evolution of repetitive sequences. Evolution of Life.
(eds. S.Osawa and T.Honjo)
JSpringer-Verlag pp.175-86(1991)
38. Okada N.
SINEs: Short interspersed repeated elements of the eukaryotic genome.
Trends in Ecology & Evolution. 6(11), 358-61 (1991)
37. Okada N.
SINEs.
Current Opinion in Genetics & Development 1, pp.498-504 (1991)
36. Koishi R, and Okada N.
Distribution of the salmonid HPA-1 family in the salmonid species
demonstrated by In vitro run-off transcription assay of total genomic
DNA : A procedure to estimate repetitive frequency and sequence
divergence of a certain repetitive family with a few known sequences.
J. Mol. Evol. 32(1), 43-52 (1991)
35. Nagahashi S, Endoh H, Suzuki Y, and Okada N.
Characterization of a tandemly repeated DNA sequence family
originally derived by retroposition of tRNAGlu in the newt.
J. Mol. Biol. 222, 391-404 (1991)
34. Endoh H, Nagahashi S, and Okada N.
Highly repetitive and transcribable sequence in the tortoise genome isprobably a retroposon.
Eur. J. Biochem. 189(1), 25-31 (1990)
33. Okada N.
Transfer RNA-like structure of the human Alu family: Implications of its
generation mechanism and possible functions.
J. Mol. Evol. 31(6), 500-10 (1990)
32. Matsumoto K, Takii T, and Okada N.
Characterization of a new termination signal for RNA polymerase III
responsible for generation of a discrete-sized RNA transcribed from
salmon genomic total DNA in a HeLa cell extract.
J. Biol. Chem. 264(2),1124-31 (1989)

31. Endoh H, Nagahashi S, and Okada N.
Tetrahymena pyriformis DNA fragment with a gene cluster for 3
putative serine tRNAs and an asparagine tRNA.
Nucleic Acids Res. 17, 10122 (1989)
30. Okada N, Aono M, Matsumoto K, Kido Y, Koishi R, and Saneyoshi M.
Shaping and reshaping of the genomes of salmonid species during
evolution. Biology of Charrs and Masu Salmon .
(eds. Kawanabe, Yamazaki and Noakes)
Special Vol. 1, Physiology and Ecology Japan, pp.451-4 (1989)
29. Okada N, Aono M, Matsumoto K, Endoh H, Koishi R, Takii T, andSuzuki Y.
Several aspects of total genomic DNA transcription in a HeLa cell
extract.
Nucleic Acids Res. Sympo. Ser. No. 19, 181-4 (1988)
28. Hirono M, Endoh H, Okada N, Numata O, and Watanabe Y.
Tetrahymena actin, cloning and sequencing of the Tetrahymena actin
gene and identification of its gene product.
J. Mol. Biol. 194, 181-92 (1987)
27. Okada N, Mimori T, Mukai R, Kashiwagi H, and Hardin J A.
Characterization of human autoantibodies that selectively precipitate
the 7SL RNA component of the signal recognition particle.
J. Immunology 138, 3219-23 (1987)
26. Endoh H , and Okada N.
Total DNA transcription in vitro: A procedure to detect highly repetitive
and transcribable sequences with tRNA-like structures.
Proc. Natl. Acad. Sci. USA 83, 251-5 (1986)
25. Matsumoto K, Murakami K, and Okada N.
Gene for lysine tRNA1 as a progenitor of the highly repetitive andtranscribable sequences present in the salmon genome.
Proc. Natl. Acad. Sci. USA 83, 3156-60 (1986)
24. Sakamoto K, and Okada N.
Rodent type 2 Alu family, rat identifier sequence, rabbit C family, andbovine or goat 73-bp repeat may have evolved from tRNA genes.
J. Mol. Evol. 22, 134-40 (1985)
23. Okada N, Endoh H, Sakamoto K, and Matsumoto K.
Many highly repetitive and transcribable sequences are derived from

tRNA genes.
Proc. Jpn. Acad. 61, Ser. B, 363-7 (1985)
22. Sakamoto K, and Okada N.
5-Methylcytidylic modification of in vitro transcript from the rat
identifier sequence; evidence that the transcript forms a tRNA-likestructure.
Nucleic Acids Res. 13, 7195-206 (1985)
21. Hoshino H, Tanaka H, Shimotono K, Miwa M, Okada N, and Sugimura
T.
Nucleotide sequences homologous to human T-cell leukemia virus arepresent in pig and wild bore cells.
Gann. 75, 849-52 (1984)
20. Okada N, Mukai R, Harada F, Kabashima T, Nakao Y, Yamane K,
Ohshima Y, Sakamoto K, Itoh M, Kashiwagi H, and Hamaguchi H.
Isolation of a novel antibody which precipitates ribonucleoprotein
complex containing threonine tRNA from a patient with polymyositis.
Eur. J. Biochem. 139, 425-9 (1984)
19. Sakamoto K, Komimani R, Mishima Y, and Okada N.
The 6S RNA transcribed from rodent total DNA in vitro is the transcriptof the type 2 Alu family.
Mol. Gen. Genet. 194, 1-6 (1984)
18. Matsumoto K, Murakami K, and Okada N.
Pseudouridylic modification of a 6S RNA transcribed in vitro from highly
repetitive and transcribable (Hirt) sequences of salmon total DNA.
Biochem. Biophys. Res. Commun. 124, 514-22 (1984)
17. Okada N, Sakamoto K. and Kondo A.
Total DNA transcription reveals the existence of highly repetitivetranscribable sequences in higher animals.
J. Biochem. 93, 723-31 (1983)
16. Watanabe-Nagasu N., Itoh Y., Tani T., Okano K., Koga N., Okada N.
and Ohshima Y.
Structural analysis of gene loci for rat U1 small nuclear RNA.
Nucleic Acids Research. 11, 1791-801 (1983)
15. Tani T., Watanabe-Nagasu N., Okada N. and Ohshima Y.
Molecular cloning and characterization of a gene for rat U2 small
nuclear RNA.
J. Mol. Biol. 168, 579-94 (1983)

14. Okada N., Sakamoto K., Itoh Y. and Ohshima Y.
Sequence determination of rat U5 RNA using a chemical modification
procedure for counteracting sequence compression.
J. Biochem. 91, 1281-91 (1982)
13. Nakao Y., Mukai R., Kabashima T., Ohshima Y., Hamaguchi H.,
Kashiwagi H. and Okada N.
A novel antibody which precipitates 7.5S RNA is isolated from a patientwith autoimmune disease.
Biochem. Biophys. Res. Commun. 109, 1332-8 (1982)
12. Shindo-Okada N., Kuchino Y., Harada F., Okada N. and Nishimura S.
Biological and structural differences between tRNAVal species isolated
from rat ascites hepatoma cells and nomal rat liver.
J. Biochem. 90, 535-44 (1981)
11. Ohshima Y., Itoh M., Okada N. and Miyata T.
Novel models for RNA splicing that involve a small nuclear RNA.
Proc. Natl. Acad. Sci. USA. 78, 4471-4 (1981)
10. Ohshima Y., Okada N., Tani T., Itoh Y. and Itoh M.
Nucleotide sequences of mouse genomic loci including a gene or
pseudogene for U6(4.8S) nuclear RNA.
Nucleis Acids Res. 9, 5145-58 (1981)
9. Shindo-Okada N., Okada N., Ohgi T., Goto T. and Nishimura S.
Transfer ribonucleic acid guanine transglycosylase isolated from rat liver.
Biochemistry 19, 395-400 (1980)
8. Okada N. and Nishimura S.
Isolation and characterization of a guanine insertion enzyme, a specifictRNA transglycosylase, from Escherichia coli.
J. Biol. Chem. 254, 3061-6 (1979)
7. Okada N., Noguchi S., Kasai H., Shindo-Okada N., Ohgi T., Goto T. andNishimura S.
Novel mechanism of posttranscriptional modification of tRNA. - insertionof bases of Q-precursors into transfer-RNA by a specific transfer-RNA
transglycosylase reaction.
J. Biol. Chem. 254, 3067-73 (1979)
6. Okada N., Noguchi S., Nishimura S., Ohgi T., Goto T., Crain P.F. and
MacCloskey J.A.
Structure determination of a nucleoside Q precursor isolated from E. coli

tRNA: 7-(aminomethyl)-7-deazaguanosine.
Nucleic Acids Res. 5, 2289-96 (1978)
5. Okada N., Shindo-Okada N., Sato S., Itoh Y.H., Oda K-I. and NishimuraS.
Detection of unique tRNA species in tumor tissues by Escherichia coli
guanine insertion enzyme.
Proc. Natl. Acad. Sci. USA 75, 4247-51 (1978)
4. Okada N. Shindo-Okada N. and Nishimura S.
Isolation of mammalian tRNAAsp and tRNATyr by lectin-Sepharoseaffinity column chromatography.
Nucleic Acids Res. 4, 415-23 (1977)
3. Okada N. and Nishimura S.
Enzymatic synthesis of Q* nucleoside containing mannose in the
anticodon of tRNA: Isolation of a novel mannosyltransferase from a cellfree extract of rat liver.
Nucleic Acids Res. 4, 2931-7 (1977)
2. Okada N., Yasuda T. and Nishimura S.
Detection of nucleoside Q precursor in methyl-deficient E. coli tRNA.
Nucleic Acids Res. 4, 4063-75 (1977)
1. Okada N., Harada F. and Nishimura S.
Specific replacement of Q base in the anticodon of tRNA by guanine
catalyzed by a cell-free extract of rabbit reticulocytes.
Nucleic Acids Res. 3, 2593-603 (1976)