top of page

Published Papers

(* Corresponding author; § Equally contributed)


Iwai H, Kono N* (2023) Cuticular Hydrocarbon Profiling by Fractionation and GC‒MS in Socially Parasitic Ants. bio-protocol, 13(13):e4772.

Nakamura H, Kono N*, Mori M, Masunaga H, Numata K, Arakawa K* (2023) Composition of Minor Ampullate Silk Makes Its Properties Different from Those of Major Ampullate Silk. Biomacromolecules, 24(5): 2042-2051.


Arakawa K§, Kono N§, Malay AD, Tateishi A, Ifuku N, Masunaga H, Sato R, Tsuchiya K, Ohtoshi R, Pedrazzoli D, Shinohara A, Ito Y, Nakamura H, Tanikawa A, Suzuki Y, Ichikawa T, Fujita S, Fujiwara M, Tomita M, Blamires SJ, Chuah JA, Craig H, Foong CP, Greco G, Guan J, Holland C, Kaplan DL, Sudesh K, Mandal BB, Norma-Rashid Y, Oktaviani NA, Preda RC, Pugno NM, Rajkhowa R, Wang X, Yazawa K, Zheng Z, Numata K (2022) 1000 spider silkomes: Linking sequences to silk physical properties. Science Advances, 8(41): eabo6043. Article

Iwai H, Mori M, Tomita M, Kono N*, Arakawa K (2022) Molecular evidence of chemical disguise by the socially parasitic spiny ant Polyrhachis lamellidens (Hymenoptera: Formicidae) when invading a host colony. Front Ecol Evol, 10: 915517. Article

Kurihara Y, Iwai H, Kono N*, Tomita M, Arakawa K (2022) Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment. Biology Open, 11 (3): bio058956. Article


Kono N, Ohtoshi R, Malay AD, Mori M, Masunaga H, Yoshida Y, Nakamura H, Numata K, Arakawa K (2021) Darwin’s bark spider shares a spidroin repertoire with Caerostris extrusa but achieves extraordinary silk toughness through gene expression. Open Biology, 11(12):210242. Article

Kono N, Nakamura H, Ohtoshi R, Arakawa K (2021), Transcriptomic data during development of a two-spotted cricket Gryllus bimaculatus. Data Brief, 38:107388. Article

Kono N*, Nakamura H, Arakawa K (2021), The complete mitochondrial genome of Trichonephila clavipes (Araneae: Araneidae). Mitochondrial DNA Part B, 6(10):2986-2988. Article

Iwai H, Kurihara Y, Kono N*, Tomita M, Arakawa K (2021), The evidence of temporary social parasitism by Polyrhachis lamellidens (Hymenoptera, Formicidae) in a Camponotus obscuripes colony (Hymenoptera, Formicidae). Insectes Sociaux, 68:375-382. Article "Mymecological News Blog"

Kono N, Nakamura H, Mori M, Yoshida Y, Ohtoshi R, Malay AD, Pedrazzoli-Moran AD, Tomita M, Numata K, Arakawa K (2021) Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk. Proc Natl Acad Sci U S A, 118(31):e2107065118. Article - PNAS highlight

Kono N*, Nakamura H, Tateishi A, Numata K, Arakawa K (2021) The balance of crystalline and amorphous regions in the fibroin structure underpins the tensile strength of bagworm silk. Zoological Letters, 7(1):11. Article

Arakawa K, Mori M, Kono N, Suzuki T, Gotoh T, Shimano S (2021) Proteomic evidence for the silk fibroin genes of spider mites (Order Trombidiformes: Family Tetranychidae). Journal of Proteomics, 239:104195. Article

Fujiwara M, Kono N, Hirayama A, Malay AD, Nakamura H, Ohtoshi R, Numata K, Tomita M, Arakawa K (2021) Xanthurenic Acid Is the Main Pigment of Trichonephila clavata Gold Dragline Silk. Biomolecules, 11(4):563. Article

Berger AC, Brewer SM, Kono N, Nakamura H, Arakawa K, Kennedy RS, Wood MH, Adams AS, Gillespie GR (2021) Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders. BMC Ecology and Evolution, 21(1):48. Article


Malay A, Suzuki T, Katashima T, Kono N, Arakawa K, Numata K (2020) Spider silk self-assembly via modular liquid-liquid phase separation and nanofibrillation. Science Advances, 6(45):eabb6030. Article

Kono N*, Nakamura H, Mori M, Tomita M, Arakawa K (2020) Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies. Scientific Reports, 10(1):15721. Article


Masuda T§, Kono N§*, Tomita M, Arakawa K (2019) Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes, Bio-protocol, 9(15): e3329. Article

Kono N, Nakamura H, Ohtoshi R, Pedrazzoli-Moran AD, Shinohara A, Yoshida Y, Fujiwara M, Mori M, Tomita M, Arakawa K (2019) Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue, Scientific Reports, 9(1):8380. Article

Kono N, Nakamura H, Ohtoshi R, Tomita M, Numata K, Arakawa K (2019) The bagworm genome reveals a unique fibroin gene that provides high tensile strength, Communications Biology, 2:148. Article

Kono N, Arakawa K (2019) Nanopore sequencing: review of potential applications in functional genomics, Development Growth and Differentiation, 61(5):316-326. Article

Ii MK, Kono N, Paulino-Lima IG, Tomita M, Rothschild LJ, Arakawa K (2019) Complete genome sequence of Arthrobacter sp. Strain MN05-02, a UV-resistant bacterium from a manganese deposit in the Sonoran Desert, Journal of Genomics, 7:18-25. Article

Ohshima Y§, Kono N§, Yokota Y, Watanabe S, Sasaki I, Ishioka N, Sakashita T, Arakawa K (2019) Anti-tumor Effects and Potential Therapeutic Response Biomarkers in α-Emitting meta-211At-Astato-Benzylguanidine Therapy for Malignant Pheochromocytoma Explored by RNA-sequencing, Theranostics, 9(6):1538-1549. Article


Kono N*, Tomita M, Arakawa K (2018) Accelerated laboratory evolution reveals the influence of replication on the GC skew in Escherichia coli. Genome Biology and Evolution, 10(11):3110-3117. Article

Arakawa K, Kono N, Ohtoshi R, Nakamura H, Tomita M (2018) The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae), Mitochondrial DNA Part B, 3(2):812-813. Article

Itaya M, Sato M, Hasegawa M, Kono N, Tomita M, Kaneko S (2018) Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system. Scientific Reports, 8(1):8792. Article


Kono N*, Tomita M, Arakawa K (2017) eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC Genomics 18(1):784. Article


Kono N, Nakamura H, Ito Y, Tomita M, Arakawa K (2016) Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Molecular Ecology Resources, 16(3):662-672. Article


Kanoh Y, Matsumoto S, Fukatsu R, Kakusho N, Kono N, Renard-Guillet C, Masuda K, Iida K, Nagasawa K, Shirahige K, Masai H (2015) Rif1 binds to G quadruplexes and suppresses replication over long distances. Nature Structural & Molecular Biology, 22(11), 889-897. Article


Kono N*, Arakawa K, Sato M, Yoshikawa H, Tomita M, Itaya M (2014) Undesigned selection for replication termination of bacterial chromosomes. Journal of Molecular Biology, 426(16), 2918-2927. (* Corresponding author) Article


Hisano Y, Ota S, Arakawa K, Muraki M, Kono N, Oshita K, Sakuma T, Tomita M, Yamamoto T, Okada Y, Kawahara A (2013) Quantitative assay for TALEN activity at endogenous genomic loci. Biology Open, 2 (4): 363–367.. Article


Kono N, Arakawa K, Tomita M (2012) Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations. PLoS One, 7(4), e34526. Article

Toya Y, Kono N, Arakawa K, Tomita M (2011) Metabolic flux analysis and visualization. Journal of Proteome Research, 10(8), 3313-3323. Article

Kono N, Arakawa K, Tomita M (2011) Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics, 12(1), 19. Article

Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M (2009) Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API. PLoS One, 4(11), e7710. Article

Arakawa K, Tamaki S, Kono N, Kido N, Ikegami K, Ogawa R, Tomita M (2009) Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics, 10(1), 31. Article

Tamaki S, Arakawa K, Kono N, Tomita M (2007) Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics. Genomics Proteomics Bioinformatics, 5(1), 53-58. Article

Kono N, Arakawa K, Tomita M (2006) MEGU: Pathway mapping web-service based on KEGG and SVG. In Silico Biology, 6(6), 621-655. Article

Arakawa K, Kono N, Yamada Y, Mori H, Tomita M (2005) KEGG-based pathway visualization tool for complex omics data. In Silico Biology, 5, 0039. Article


Kono N (2023) A Guide to Sequencing for Long Repetitive Regions. Methods in Molecular Biology, 2632: 131-146.

河野暢明 (2021) 動物の長鎖リピート解析, 実験医学別冊 最強のステップUPシリーズ ロングリードWET&DRY解析ガイド シークエンスをもっと自由に!, 69, 60-79.

河野暢明 (2020), ウズグモの篩板糸遺伝子から見る円網の進化, 生物の科学 遺伝, 74(6), 684-691.

河野暢明 (2019), 三若手が,三日間,三島で.- 生命科学系フロンティアミーティング2018, 実験医学, 37(6).


河野暢明 (2018), 若手科学者サミット -よい研究とは-, 学術の動向, 23(12), 74-77.


河野暢明, 荒川和晴 (2018), 解析困難な長鎖リピート配列の解析に挑むークモ糸遺伝子を例に, 実験医学,, 36(1), 49-53.


河野暢明, 大上雅史, 黒木健, 堀之内貴明 (2017), [AI・ロボットコミュニティレポート]生命情報科学若手の会, 実験医学別冊, 54.

Invited talk

河野暢明, 動物の道具を人間が借りるには, JT生命誌研究館30周年公開シンポジウム-ゲノムが紡ぐ生きものの個性と関係性, Oct. 1, 2023, Osaka, Japan


Nobuaki Kono, Multiple omics approach reveals the design of protein-based materials -the case of spider silk-, The 5th International Union of Materials Research Societies International Conference of Young Researchers on Advanced Materials (IUMRS-ICYRAM2022), Aug. 5, 2022, Fukuoka

河野暢明, AlphaFold2が変革した常識, 大隅基礎科学創成財団 微生物コンソーシアム, Sep. 7, 2021, オンライン


河野暢明, マルチオミクス解析が解き明かす生命のデザイン(バクテリアゲノムやクモ糸を例に), 東京工業大学化学生命科学研究所講演会, Apr. 9, 2021, Tokyo

河野暢明, 大規模マルチオミクス解析で解き明かす糸遺伝子の系統進化, 日本蚕糸学会第89回 大会, Mar. 22, 2019, Tokyo


河野暢明, シーケンス技術で迫るバクテリアゲノム構造と非モデル生物のデザイン原理, 極域 大気~アイスコア中の微生物に関する研究集会~, Feb. 26, 2019, Tokyo

Nobuaki Kono, Masayuki Fujiwara, Hiroyuki Nakamura, Rintaro Ohtoshi, Masaru Tomita, Kazuharu Arakawa, Large-scale comparative analysis of spider fibroin genes using hybrid sequencing approach, 第88回日本動物学会, Sep. 21-23, 2017, Toyama

河野暢明, Nanoporeによるゲノム解析の実際, Rinkai Hackathon 2017, Jun. 13-15, 2017, Chiba, Japan

河野暢明, ゲノム対称構造からのゲノムデザイン, 第13回微化研オープンセミナー, Aug. 1, 2014, Tokyo

河野暢明, ゲノムから攻める細菌学~新たな合成生物学の挑戦~, 細菌学若手コロッセウム, Aug. 6-8, 2014, Hokkaido

河野暢明, 大規模マルチオミクス解析に向けたパスウェイブラウザ, ゲノム微生物学若手の会, Sep. 28-29, 2014, Shizuoka

bottom of page