List of publications
Jiaqi Wu, Kirill Kryukov, Junko S. Takeuchi, So Nakagawa (2024) “Sgv-Caller: Sars-Cov-2
Genome Variation Caller” SSRN preprint:
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4881790
Alexey P. Kryukov, Kirill A. Kryukov, Bohao Fang, Katherene Collier, Scott Edwards (2024)“Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica
nuttalli) within the Holarctic magpie radiation” Current Zoology, in press, epub: 1 Nov 2023
(accepted on October 27, 2023), doi: 10.1093/cz/zoad048.
Kosuke Takada, So Nakagawa, Kirill Kryukov, Makoto Ozawa, Tokiko Watanabe (2024)“Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on theIzumi plain in Japan” FEBS Open Bio, in press (accepted on August 1, 2024).
Kirill Kryukov, Naoyuki Nakahama, Shigehiro Kuraku (2024) “Genome assembly catalog forspecies in the Japanese Red List: unlocking endangered biodiversity through genomicinventory” [version 2; peer review: 2 approved] F1000Research, 13, 583, 22 July 2024
(accepted on July 23, 2024), doi: 10.12688/f1000research.149793.2, PMID: 39050029.
Kentaro Harakawa, Shinpei Kawarai, Kirill Kryukov, So Nakagawa, Shigeharu Moriya, andKazuhiko Imakawa (2024) “Buccal Swab Samples from Japanese Brown Cattle Fed with
Limonite Reveal Altered Rumen Microbiome” Animals, 14(13), 1968, July 3, 2024 (acceptedon July 1, 2024), doi: 10.3390/ani14131968, PMID: 38998081.
Jakaria Al-Mujahidy, Kirill Kryukov, Kei Saito, Kazuho Ikeo (2024) “Functional GenomicAnalysis of the Isolated Potential Probiotic Lactobacillus delbrueckii subsp. indicus TY11, and its Comparison with other Lactobacillus delbrueckii Strains” Microbiology
Spectrum, 12(7), e03470-23, July 2, 2024, published online on May 21, 2024 (accepted on April11, 2024), doi: 10.1128/spectrum.03470-23, PMID: 38771133.
Kirill Kryukov, So Nakagawa, Tadashi Imanishi (2024) “GenomeSync: a synchronizable
database of genome sequences” iDarwin, vol. 4, 4-23, 13 March 2024.
So Nakagawa, Toshiaki Katayama, Lihua Jin, Jiaqi Wu, Kirill Kryukov, Rise Oyachi, Junko S.
Takeuchi, Takatomo Fujisawa, Satomi Asano, Momoka Komatsu, Jun-ichi Onami, Takashi Abe,
Masanori Arita (2023) “SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2
haplotypes spread in Japan” Genes & Genetic Systems, 2023, 23-00085, October 14, 2023
(accepted on June 10, 2023), doi: 10.1266/ggs.23-00085, PMID: 37839865, Jxiv preprint:
https://jxiv.jst.go.jp/index.php/jxiv/preprint/view/338.
Ricky Indra Alfaray, Batsaikhan Saruuljavkhlan, Kartika Afrida Fauzia, Roberto C. Torres, Kaisa
Thorell, Selva Rosyta Dewi, Kirill A. Kryukov, Takashi Matsumoto, Junko Akada, Ratha-korn
Vilaichone, Muhammad Miftahussurur, Yoshio Yamaoka (2023) “Global AntimicrobialResistance Gene Study of Helicobacter pylori: Comparison of Detection Tools, ARG andEfflux Pump Gene Analysis, Worldwide Epidemiological Distribution, and Information
Related to the Antimicrobial-Resistant Phenotype” Antibiotics, 12(7), 1118, June 28, 2023
(accepted on June 25, 2023), doi: 10.3390/antibiotics12071118, PMID: 37508214.
Kirill Kryukov, Tadashi Imanishi, So Nakagawa (2023) “Nanopore sequencing data analysis of16S rRNA genes using GenomeSync-GSTK system” Methods in Molecular Biology, Vol.
2632, 215-226, 14 February 2023, Kazuharu Arakawa (Eds): Nanopore Sequencing, doi:
10.1007/978-1-0716-2996-3_15, PMID: 36781731, book ISBN: 978-1-0716-2995-6.
Jianshi Jin, Taisaku Ogawa, Nozomi Hojo, Kirill Kryukov, Kenji Shimizu, Tomokatsu Ikawa,
Tadashi Imanishi, Taku Okazaki, Katsuyuki Shiroguchi (2023) “Robotic data acquisition withdeep learning enables cell image-based prediction of transcriptomic states” PNAS, 120(1),e2210283120, 3 Jan 2023, epub: 28 Dec 2022 (accepted on November 30, 2022), doi:
10.1073/pnas.2210283120, PMID: 36577074.
Alexey P. Kryukov, Oleg A. Goroshko, Vladimir Y. Arkhipov, Yaroslav A. Red’kin, Sang-im Lee,Beatriz A. Dorda, Kirill A. Kryukov, Martin Kapun, Elisabeth Haring (2022) “Introgression at
the emerging secondary contact zone of magpie Pica pica subspecies: integrating data on
nuclear and mitochondrial markers, vocalizations and field observations” Organisms
Diversity & Evolution, 22(4), 1037-1064, Dec 2022, epub: 29 July 2022 (accepted: 23 May2022), doi: 10.1007/s13127-022-00568-6.
Guangwei Cui, Akihiro Shimba, Taisaku Ogawa, Jianshi Jin, Hitoshi Miyachi, Shinya Abe, Takuma
Asahi, Shizue Tani-ichi, Johannes M. Dijkstra, Kirill Kryukov, Daichi Takami, Yuanbo Zhu,
Takahiro Hara, Satsuki Kitano, Yan Xu, Keishi Miyata, Takashi Kanaya, Yuichi Oike, Tadashi
Imanishi, Hiroshi Ohno, Toshiaki Ohteki, Nagahiro Minato, Masato Kubo, Georg A. Hollander,Katsuyuki Shiroguchi, Koichi Ikuta (2022) “A circulating subset of iNKT cells mediates
antitumor and antiviral immunity” Science Immunology, 7(26), eabj8760, 28 Oct 2022,
epub: 21 Oct 2022, doi: 10.1126/sciimmunol.abj8760, PMID: 36269840.
Kirill Kryukov, Lihua Jin, So Nakagawa (2022) “Efficient compression of SARS-CoV-2 genome
data using Nucleotide Archival Format (NAF)” Patterns, 3(9), 100562, 9 September 2022,
epub: 6 July 2022 (accepted: 1 July 2022), doi: 10.1016/j.patter.2022.100562, PMID:35818472.
Rumiko Suzuki, Naruya Saitou, Osamu Matsuari, Seiji Shiota, Takashi Matsumoto, Junko Akada,Nagisa Kinjo, Fukunori Kinjo, Kuniko Teruya, Makiko Shimoji, Akino Shiroma, Mototsugu
Kato, Kazuhito Satou, Takashi Hirano, Masahiro Asaka, Kirill Kryukov, Yoshan Moodley,
Yoshio Yamaoka (2022) “Helicobacter pylori genomes reveal Paleolithic human migration
to the east end of Asia” iScience, 25, 7, 104477, 15 July 2022, epub: 30 May 2022 (accepted:27 May 2022), doi: 10.1016/j.isci.2022.104477, PMID: 35720267.
Shinnosuke Komiya, Yoshiyuki Matsuo, So Nakagawa, Yoshiharu Morimoto, Kirill Kryukov,Hidetaka Okada, Kiichi Hirota (2022) “MinION™, a portable long-read sequencer, enables
rapid vaginal microbiota analysis in a clinical setting” BMC Medical Genomics, 15, 68, 25
March 2022, doi: 10.1186/s12920-022-01218-8, PMID: 35337329.
Yoshiki Shiraishi, Kirill Kryukov, Katsuyoshi Tomomatsu, Fumio Sakamaki, Shigeaki Inoue, SoNakagawa, Tadashi Imanishi, Koichiro Asano (2021) “Diagnosis of pleuralempyema/parapneumonic effusion by next-generation sequencing” Infectious Diseases,
53(6), 450-459, epub: 9 March 2021, doi: 10.1080/23744235.2021.1892178, PMID: 33689538.
Ayumu Ohno, Kazuo Umezawa, Satomi Asai, Kirill Kryukov, So Nakagawa, Hayato Miyachi,
Tadashi Imanishi (2021) “Rapid profiling of drug-resistant bacteria using DNA-bindingdyes and a nanopore-based DNA sequencer” Scientific Reports, 11, 3436, 9 February 2021,
doi: 10.1038/s41598-021-82903-z, PMID: 33564026.
Yoshiyuki Matsuo, Shinnosuke Komiya, Yoshiaki Yasumizu, Yuki Yasuoka, Katsura Mizushima,
Tomohisa Takagi, Kirill Kryukov, Tadashi Imanishi, Aisaku Fukuda, Yoshiharu Morimoto, Yuji
Naito, Hidetaka Okada, Hidemasa Bono, So Nakagawa, Kiichi Hirota (2021) “Full-length 16S
rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore
sequencing confers species-level resolution” BMC Microbiology, 21(1), 35, 26 January 2021,
doi: 10.1186/s12866-021-02094-5, PMID: 33499799.
Yasuko Orba, Keita Matsuno, Ryo Nakao, Kirill Kryukov, Yumi Saito, Fumihiko Kawamori, ArielLoza Vega, Tokiko Watanabe, Tadashi Maemura, Michihito Sasaki, William W. Hall, Roy A.
Hall, Juan Antonio Pereira, So Nakagawa, Hirofumi Sawa (2021) “Diverse Mosquito Specific
Flaviviruses in the Bolivian Amazon basin” Journal of General Virology, 102(3), 001518,

epub: 8 Jan 2021, doi: 10.1099/jgv.0.001518, PMID: 33416463.
Alexey P. Kryukov, Liudmila N. Spiridonova, Alexey P. Tyunin, Kirill A. Kryukov, Beatriz A.
Dorda (2020) “Complete mitochondrial genomes of five subspecies of the Eurasian magpie
Pica pica, obtained with Oxford Nanopore MinION, and their interpretation regarding
intraspecific taxonomy” Mitochondrial DNA part B, 5(3), 3792-3793, 20 November 2020,
doi: 10.1080/23802359.2020.1838354, PMID: 33367109.
Mahoko Takahashi Ueda, Kirill Kryukov, Satomi Mitsuhashi, Hiroaki Mitsuhashi, Tadashi
Imanishi, So Nakagawa (2020) “Comprehensive genomic analysis reveals dynamic
evolution of endogenous retroviruses that code for retroviral-like protein domains” MobileDNA, 11, 29, 17 September 2020, doi: 10.1186/s13100-020-00224-w, PMID: 32963593.
Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi (2020) “Sequence
Compression Benchmark (SCB) database — a comprehensive evaluation of reference-freecompressors for FASTA-formatted sequences” GigaScience, 9(7), giaa072, 6 July 2020, doi:
10.1093/gigascience/giaa072, PMID: 32627830.
Toru Ishihara, Nobuo Watanabe, Shigeaki Inoue, Hiromichi Aoki, Tomoatsu Tsuji, Bunsei
Yamamoto, Hidetaka Yanagi, Masayuki Oki, Kirill Kryukov, So Nakagawa, Sadaki Inokuchi,Hideki Ozawa, Tadashi Imanishi (2020) “Usefulness of next-generation DNA sequencing forthe diagnosis of urinary tract infection” Drug Discoveries & Therapeutics, 14(1), 42-49,
2020, doi: 10.5582/ddt.2020.01000, PMID: 32101813.
Yahiro Mukai, Yuriko Tomita, Kirill Kryukov, So Nakagawa, Makoto Ozawa, Tsutomu Matsui,Keizo Tomonaga, Tadashi Imanishi, Yoshihiro Kawaoka, Tokiko Watanabe, Masayuki Horie(2019) “Identification of a distinct lineage of aviadenovirus from crane feces” Virus Genes,55(6), 815-824, December 2019 (epub: 23 September 2019), doi: 10.1007/s11262-019-01703w, PMID: 31549291.
So Nakagawa, Shigeaki Inoue, Kirill Kryukov, Junya Yamagishi, Ayumu Ohno, Kyoko Hayashida,Ruth Nakazwe, Mox Kalumbi, Darlington Mwenya, Nana Asami, Chihiro Sugimoto, Mable M.
Mutengo, Tadashi Imanishi (2019) “Rapid sequencing-based diagnosis of infectious
bacterial species from meningitis patients in Zambia” Clinical & Translational Immunology,
8(11), e01087, 5 November 2019, doi: 10.1002/cti2.1087, PMID: 31709051.
Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi (2019) “Nucleotide
Archival Format (NAF) enables efficient lossless reference-free compression of DNA
sequences” Bioinformatics, 35(19), 3826-3828, 1 October 2019, doi:
10.1093/bioinformatics/btz144, PMID: 30799504.
Hideaki Kanzawa-Kiriyama, Timothy A. Jinam, Yosuke Kawai, Takehiro Sato, Kazuyoshi
Hosomichi, Atsushi Tajima, Noboru Adachi, Hirofumi Matsumura, Kirill Kryukov, Naruya
Saitou, Ken-ichi Shinoda (2019) “Late Jomon male and female genome sequences from theFunadomari site in Hokkaido, Japan” Anthropological Science, 127(2), 83-108, 29 May
2019, doi: 10.1537/ase.190415.
Hiromasa Tanaka, Yoshiyuki Matsuo, So Nakagawa, Kenichiro Nishi, Akihisa Okamoto, Shinichi
Kai, Teppei Iwai, Yoshiteru Tabata, Takeshi Tajima, Yuji Komatsu, Motohiko Satoh, Kirill
Kryukov, Tadashi Imanishi, Kiichi Hirota (2019) “Application of the MinION™ portable
DNA sequencer in clinical microbiology evaluation: a case report” JA Clinical Reports, 5,24, 19 March 2019, doi: 10.1186/s40981-019-0244-z.
Shinichi Kai, Yoshiyuki Matsuo, So Nakagawa, Kirill Kryukov, Shino Matsukawa, HiromasaTanaka, Teppei Iwai, Tadashi Imanishi, Kiichi Hirota (2019) “Rapid bacterial identification
by direct PCR amplification of 16S rRNA genes using the MinION™ nanoporesequencer” FEBS Open Bio, 9(3), 548-557, March 2019 (epub: 29 January 2019), doi:
10.1002/2211-5463.12590, PMID: 30868063.

Kirill Kryukov, Mahoko Takahashi Ueda, Tadashi Imanishi, So Nakagawa (2019) “Systematicsurvey of non-retroviral virus-like elements in eukaryotic genomes” Virus Research, 262,30-36, March 2019 (epub: 6 February 2018), doi: 10.1016/j.virusres.2018.02.002, PMID:29425804.
Nobuo Watanabe, Kirill Kryukov, So Nakagawa, Junko S. Takeuchi, Meiko Takeshita, Yukiko
Kirimura, Satomi Mitsuhashi, Toru Ishihara, Hiromichi Aoki, Sadaki Inokuchi, Tadashi
Imanishi, Shigeaki Inoue (2018) “Detection of pathogenic bacteria in the blood from sepsis
patients using 16S rRNA gene amplicon sequencing analysis” PLoS One, 13(8), e0202049,
15 August 2018, doi: 10.1371/journal.pone.0202049, PMID: 30110400.
Taisaku Ogawa, Kirill Kryukov, Tadashi Imanishi, Katsuyuki Shiroguchi (2017) “The efficacy andfurther functional advantages of random-base molecular barcodes for absolute and digitalquantification of nucleic acid molecules” Scientific Reports, 7(1), 13576, 19 October 2017,
doi: 10.1038/s41598-017-13529-3, PMID: 29051542.
Mari Tenno, Katsuyuki Shiroguchi, Sawako Muroi, Eiryo Kawakami, Keita Koseki, Kirill Kryukov,Tadashi Imanishi, Florent Ginhoux, Ichiro Taniuchi (2017) “Cbfβ2 deficiency preserves
Langerhans cell precursors by lack of selective TGFβ receptor signaling” Journal ofExperimental Medicine, 214(10), 2933-2946, 2 October 2017, doi: 10.1084/jem.20170729,
PMID: 28814567.
Satomi Mitsuhashi, Kirill Kryukov, So Nakagawa, Junko S. Takeuchi, Yoshiki Shiraishi, Koichiro
Asano, Tadashi Imanishi (2017) “A portable system for rapid bacterial composition analysis
using a nanopore-based sequencer and laptop computer” Scientific Reports, 7(1), 5657, 18July 2017, doi: 10.1038/s41598-017-05772-5, PMID: 28720805.
Hideaki Kanzawa-Kiriyama, Kirill Kryukov, Timothy A. Jinam, Kazuyoshi Hosomichi, Aiko Saso,Gen Suwa, Shintaroh Ueda, Minoru Yoneda, Atsushi Tajima, Ken-ichi Shinoda, Ituro Inoue,Naruya Saitou (2017) “A partial nuclear genome of the Jomons who lived 3000 years ago inFukushima, Japan” Journal of Human Genetics, 62(2), 213–221, February 2017, doi:
10.1038/jhg.2016.110, PMID: 27581845.
Kirill Kryukov, Tadashi Imanishi (2016) “Human Contamination in Public Genome Assemblies”
PLoS One, 11(9), e0162424, 9 September 2016, doi: 10.1371/journal.pone.0162424, PMID:27611326.
Nilmini Hettiarachchi, Kirill Kryukov, Kenta Sumiyama, Naruya Saitou (2014) “Lineage specificconserved noncoding sequences of plant genomes: their possible role in nucleosomepositioning” Genome Biol. Evol., 6(9), 2527-2542, 5 September 2014, doi:
10.1093/gbe/evu188, PMID: 25364802.
Kirill Kryukov, Kenta Sumiyama, Kazuho Ikeo, Takashi Gojobori, Naruya Saitou (2012) “A newdatabase (GCD) on genome composition for eukaryote and prokaryote genome sequences
and their initial analyses” Genome Biol. Evol., 4(4), 501-512, 14 March 2012, doi:
10.1093/gbe/evs026, PMID: 22417913.
Kirill Kryukov, Naruya Saitou (2010) “MISHIMA - a new method for high speed multiplealignment of nucleotide sequences of bacterial genome scale data” BMC Bioinformatics, 11,142, 18 March 2010, doi: 10.1186/1471-2105-11-142, PMID: 20298584.
Mahoko Takahashi, Kirill Kryukov, Naruya Saitou (2009) “Estimation of bacterial species
phylogeny through oligonucleotide frequency distances” Genomics, 93(6), 525-533, June
2009, doi: 10.1016/j.ygeno.2009.01.009, PMID: 19442633.
Lihua Jin, Kirill Kryukov, Yoshiyuki Suzuki, Tadashi Imanishi, Kazuho Ikeo, Takashi Gojobori(2009) “The evolutionary study of small RNA-directed gene silencing pathways byinvestigating RNase III enzymes” Gene, 435(1-2), 1-8, 15 April 2009, doi:10.1016/j.gene.2008.12.022, PMID: 19393176.

Lihua Jin, Kirill Kryukov, Jose C. Clemente, Tomoyoshi Komiyama, Yoshiyuki Suzuki, TadashiImanishi, Kazuho Ikeo, Takashi Gojobori (2008) “The evolutionary relashionship between
gene duplication and alternative splicing” Gene, 427(1-2), 19-31, 31 December 2008, doi:
10.1016/j.gene.2008.09.002, PMID: 18835337.
Kirill Kryukov, Naruya Saitou (2003) “Netview: application software for constructing andvisually exploring phylogenetic networks” Genome Informatics, 14, 280-281, journal
website: http://www.jsbi.org/pdfs/journal1/GI14.html, published in: M. Gribskov, M. Kanehisa,
S. Miyano, and T. Takagi (eds.) "Genome Informatics 2003" Universal Academy Press, Tokyo,
2003.