研究業績
論文（査読有、英文）
Watanabe T, Kure A, Horiike T. OrthoPhy: A Program to Construct Ortholog Data Sets Using Taxonomic Information, Genome Biol Evol. 15(3), 1-16, 2023.
Watanabe T, Horiike T. The Evolution of Molybdenum Dependent Nitrogenase in Cyanobacteria. Biology, 10(4), 329 2021.
Ito G, Koya Y, Kitanishi S, Horiike T, Mukai T. Genetic population structure of the eight-barbel loach Lefua echigonia in the Ise Bay region, a single paleo-river basin in central Honshu, Japan. Ichthyological Research. 66:411-416 2019.
Shimoyama Y, Horiike T. Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes. IPSJ Transactions on Bioinformatics. 12:17-20 2019.
Kurilung A, Keeratipusana C, Horiike T, Suriyaphol P, Hampson DJ, Prapasarakul N. Chronology of emergence of the genus Leptospira and over-representation of gene families enriched by vitamin B2, B12 biosynthesis, cell adhesion and external encapsulating structure in L. interrogans isolates from asymptomatic dogs. Infect Genet Evol. 73:7-12 2019.
Soffan A, Subandiyah S, Makino H, Watanabe T, Horiike T. Evolutionary Analysis of the Highly Conserved Insect Odorant Coreceptor (Orco) Revealed a Positive Selection Mode, Implying Functional Flexibility. J Insect Sci. 18(6): 2018.
Horiike T, Minai R, Miyata D, Nakamura Y, Tateno Y. Ortholog-Finder: A Tool for Constructing an Ortholog Data Set. Genome Biol Evol. 8(2):446-457 2016.
Horiike T. An Introduction to molecular phylogenetic analysis. Reviews in Agricultural Science. 4:36-45 2016.
Hirata H, Kashihara M, Horiike T, Suzuki T, Dohra H, Netsu O, Tsuyumu S. Genome Sequence of Pectobacterium carotovorum Phage PPWS1, Isolated from Japanese Horseradish [Eutrema japonicum (Miq.) Koidz] Showing Soft-Rot Symptoms. Genome Announc. 4(2): 2016.
Horiike T, Miyata D, Tateno Y, Minai R, HGT-Gen: a tool for generating a phylogenetic tree with horizontal gene transfer. Bioinformation. 7(5):211-213 2011.
Hara M, Shinoda Y, Kubo M, Kashima D, Takahashi I, Kato T, Horiike T, Kuboi T, Biochemical characterization of the Arabidopsis KS-type dehydrin protein, whose gene expression is constitutively abundant rather than stress dependent. Acta Physiologiae Plantarum, 33(6):2103-2116 2011.
Hara M, Kashima D, Horiike T, Kuboi T, Metal-binding characteristics of the protein which shows the highest histidine content in the Arabidopsis genome. Plant Biotechnology 27(5):475-480 2010.
Hiura H, Sugawara A, Ogawa H, John RM, Miyauchi N, Miyanari Y, Horiike T, Li Y, Yaegashi N, Sasaki H, Kono T, Arima T. A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip. Nucleic Acids Res. 38(15):4929-4945 2010.
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. 441:187-191, 2009.
Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T and Tateno Y, Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene. 429:59-64, 2009.
Saruhashi S, Hamada K, Miyata D, Horiike T, Shinozawa T, Comprehensive analysis of the origin of eukaryotic genomes. Genes & Genetic Systems, 83, 285-291, 2008.
Saruhashi S, Hamada K, Horiike T, Shinozawa T., Determination of whole prokaryotic phylogeny by the development of a random extraction method. Gene. 392, 1-2, 157-163, 2007
Horiike T, Hamada K, Miyata D, Shinozawa T, The origin of eukaryotes is suggested as the symbiosis of pyrococcus into γ-proteobacteria by phylogenetic tree based on gene content. Journal of Molecular Evolution, 59, 5, 606-619, 2004
Watanabe M, Kobayashi N, Shin-i T, Horiike 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: Identity of EST sequences between Haplochromis chilotes and Haplochromis sp. "Redtailsheller". Gene, 343;263-269, 2004
Sghaier H, Ai TL, Horiike T, Shinozawa T, Molecular chaperones: proposal of a systematic computer-oriented nomenclature and construction of a centralized database. In Silico Biology, 4, 3, 0025, 2004
Hamada K, Horiike T, Ota H, Mizuno K, and Shinozawa T, Presence of isochore structures in reptile genomes suggested by the relationship between GC contents of intron regions and those of coding regions. Genes & Genetic Systems, 78, 2, 195-198, 2003
Horiike T, Hamada K, Shinozawa T, Origin of Eukaryotic Cell Nuclei by Symbiosis of Archaea in Bacteria supported by the newly clarified origin of functional genes. Genes & Genetic Systems, 77, 5, 369-376, 2002
Hamada K, Horiike T, Kanaya S, Nakamura H, Ota H, Yatogo T, Okada K, Nakamura H and Shinozawa T, Changes in body temperature pattern in vertebrates do not influence the codon usages of α-globin genes. Genes & Genetic Systems, 77, 3, 197-207, 2002
Horiike T, Hamada K, Kanaya S, Shinozawa T, Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nature Cell Biology, 3, 2, 210-214, 2001
論文（査読有、和文）
渡邊知輝、堀池徳祐 ゲノムデータの分子系統解析への応用と今後の展望 化学と生物 61/6 257-259 （2023年）
伊藤 玄, 古屋 康則, 堀池 徳祐, 向井 貴彦 伊勢湾周辺域におけるアカハライモリの遺伝的集団構造 爬虫両棲類学会報 139-150 (2020).
伊藤 玄, 古屋 康則, 堀池 徳祐, 向井 貴彦 トウカイコガタスジシマドジョウの遺伝的集団構造 魚類学雑誌 67(1):41-50 (2020).
堀池徳祐 土と微生物（67巻1号）大量オーソログを用いた系統解析（2013)
堀池徳祐 土と微生物（66巻1号）メタゲノム解析を読む（2012)
堀池徳祐 土と微生物（65巻2号）コンピュータを用いた分子系統解析法（第2回）(2011)
堀池徳祐 土と微生物（65巻1号）コンピュータを用いた分子系統解析法（第1回）(2011)
篠沢隆雄、堀池徳祐、濱田一男 生体の科学（57巻5号）第三章 生物の起源 真核生物の起源の解明 (2006)
著書
Shinozawa T, Horiike T, Hamada K, NUCLEUS SYMBIOSIS HYPOTHESIS: Formation of Eukaryotic Cell Nuclei by the Symbiosis of Archaea in Bacteria. CELLULAR ORIGIN AND LIFE IN EXTREME HABITATS (Volume 3: Symbiosis): 229-235, 2001
石川昭・奥山真紀子・小林敏孝(編著)、堀池徳祐(共著) サイバネティック・ルネサンス : 205-220, 1998
招待講演
Young Researchers Conference on Evolutionary Genomics. August 2011, Tokyo.
Waseda Universit TSC seminar, August 2008, Yugawara.
NASA Astrobiology Institute and Canadian Institute for Advanced Research workshop: Lateral Gene Transfer and the Origins of Eukaryotes. May, 2004, Canada.
特許
「無根系統樹の同型判定方法をコンピュータ上で実行可能なプログラム，それを記録したコンピュータ読取可能な記録媒体および無根系統樹の同型判定装置」特開2007-140701
「相同性解析システム、相同性解析方法、相同性解析プログラム及び取引成立システム」特開2003-76940