Kazutaka Katoh

Kazutaka Katoh Associate Professor katoh [at] biken.osaka-u.ac.jp

Education

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Research & Career

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Awards

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Publications

Year Authors Title Publication Cites
2013 K Katoh, DM Standley MAFFT multiple sequence alignment software version 7: improvements in performance and usability MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30, 772-780 15216
2002 K Katoh, K Misawa, K Kuma, T Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform NUCLEIC ACIDS RESEARCH, 2002, 30, 3059-3066 8680
2005 K Katoh, K Kuma, H Toh, T Miyata MAFFT version 5: improvement in accuracy of multiple sequence alignment NUCLEIC ACIDS RESEARCH, 2005, 33, 511-518 4058
2008 K Katoh, H Toh Recent developments in the MAFFT multiple sequence alignment program BRIEFINGS IN BIOINFORMATICS, 2008, 9, 286-298 3150
2019 K Katoh, J Rozewicki, KD Yamada MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization BRIEFINGS IN BIOINFORMATICS, 2019, 20, 1160-1166 1262
2009 K Katoh, G Asimenos, H Toh Multiple alignment of DNA sequences with MAFFT BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS, 2009, 39-64 1064
2010 K Katoh, H Toh Parallelization of the MAFFT multiple sequence alignment program BIOINFORMATICS, 2010, 26, 1899-1900 605
2008 K Katoh, H Toh Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework BMC BIOINFORMATICS, 2008, 9, 212-212 527
2015 I Sela, H Ashkenazy, K Katoh, T Pupko GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters NUCLEIC ACIDS RESEARCH 43 (W1), W7-W, 2015, 14 359
2014 K Katoh, DM Standley MAFFT: iterative refinement and additional methods MULTIPLE SEQUENCE ALIGNMENT METHODS, 2014, 131-146 265
2013 S Kuraku, CM Zmasek, O Nishimura, K Katoh aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity NUCLEIC ACIDS RESEARCH 41 (W1), W22-W, 2013, 28 224
2016 K Katoh, DM Standley A simple method to control over-alignment in the MAFFT multiple sequence alignment program BIOINFORMATICS, 2016, 32, 1933-1942 213
2005 N Iwabe, Y Hara, Y Kumazawa, K Shibamoto, Y Saito, T Miyata, K Katoh Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA–coded proteins MOLECULAR BIOLOGY AND EVOLUTION, 2005, 22, 810-813 192
2018 T Nakamura, KD Yamada, K Tomii, K Katoh Parallelization of MAFFT for large-scale multiple sequence alignments BIOINFORMATICS, 2018, 1, 3-3 176
2016 KD Yamada, K Tomii, K Katoh Application of the MAFFT sequence alignment program to large data—reexamination of the usefulness of chained guide trees BIOINFORMATICS, 2016, 32, 3246-3251 145
2012 K Katoh, MC Frith Adding unaligned sequences into an existing alignment using MAFFT and LAST BIOINFORMATICS, 2012, 28, 3144-3146 144
2005 K Katoh, K Kuma, T Miyata, H Toh Improvement in the accuracy of multiple sequence alignment program MAFFT GENOME INFORMATICS, 2005, 16, 22-33 143
1999 S Kuraku, D Hoshiyama, K Katoh, H Suga, T Miyata Monophyly of lampreys and hagfishes supported by nuclear DNA–coded genes JOURNAL OF MOLECULAR EVOLUTION, 1999, 49, 729-735 131
2004 K Kikugawa, K Katoh, S Kuraku, H Sakurai, O Ishida, N Iwabe, T Miyata Basal jawed vertebrate phylogeny inferred from multiple nuclear DNA-coded genes BMC BIOLOGY, 2004, 2, 3-3 114
2007 K Katoh, H Toh PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences BIOINFORMATICS, 2007, 23, 372-374 90
2001 K Katoh, K Kuma, T Miyata Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny JOURNAL OF MOLECULAR EVOLUTION 53 (4-5), 2001, 477-484 87
2009 CB Do, K Katoh Protein multiple sequence alignment FUNCTIONAL PROTEOMICS, 2009, 379-413 84
1999 H Suga, D Hoshiyama, S Kuraku, K Katoh, K Kubokawa, T Miyata Protein tyrosine kinase cDNAs from amphioxus, hagfish, and lamprey: isoform duplications around the divergence of cyclostomes and gnathostomes JOURNAL OF MOLECULAR EVOLUTION, 1999, 49, 601-608 70
2003 B Werding, A Hiller, R Lemaitre Geographic and depth distributional patterns of western Atlantic Porcellanidae (Crustacea: Decapoda: Anomura), with an updated list of species MEMOIRS OF MUSEUM VICTORIA, 2003 63
2008 M Koyanagi, T Nagata, K Katoh, S Yamashita, F Tokunaga Molecular evolution of arthropod color vision deduced from multiple opsin genes of jumping spiders JOURNAL OF MOLECULAR EVOLUTION, 2008, 66, 130-137 59
2019 J Rozewicki, S Li, KM Amada, DM Standley, K Katoh MAFFT-DASH: integrated protein sequence and structural alignment NUCLEIC ACIDS RESEARCH 47 (W1), W5-W, 2019, 10 52
2001 RK Koduri, JT Miller, P Thammana An efficient homologous recombination vector pTV (I) contains a hot spot for increased recombinant protein expression in Chinese hamster ovary cells GENE 280 (1-2), 2001, 87-95 51
2019 J Sone, S Mitsuhashi, A Fujita, T Mizuguchi, K Hamanaka, K Mori, H Koike, ... Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease NATURE GENETICS, 2019, 51, 1215-1221 49
2001 H Suga, K Katoh, T Miyata Sponge homologs of vertebrate protein tyrosine kinases and frequent domain shufflings in the early evolution of animals before the parazoan–eumetazoan split GENE 280 (1-2), 2001, 195-201 46
1996 M Majima, K Nishiyama, Y Iguchi, K Yao, M Ogino, T Ohno, N Sunahara, ... Determination of bradykinin-(1–5) in inflammatory exudate by a new ELISA as a reliable indicator of bradykinin generation INFLAMMATION RESEARCH, 1996, 45, 416-423 45
2007 G Sasaki, K Katoh, N Hirose, H Suga, K Kuma, T Miyata, ZH Su Multiple receptor-like kinase cDNAs from liverwort Marchantia polymorpha and two charophycean green algae, Closterium ehrenbergii and Nitella axillaris: extensive gene … GENE 401 (1-2), 2007, 135-144 42
2005 JD Thompson, SR Holbrook, K Katoh, P Koehl, D Moras, E Westhof, ... MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences NUCLEIC ACIDS RESEARCH, 2005, 33, 4164-4171 38
1999 K Katoh, T Miyata A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalian SOX-3 origin of the testis-determining gene SRY FEBS LETTERS 463 (1-2), 1999, 129-132 34
2000 K Ono-Koyanagi, H Suga, K Katoh, T Miyata Protein tyrosine phosphatases from amphioxus, hagfish, and ray: divergence of tissue-specific isoform genes in the early evolution of vertebrates JOURNAL OF MOLECULAR EVOLUTION, 2000, 50, 302-311 31
2015 N Fukushima, S Ishii, T Tsujiuchi, N Kagawa, K Katoh Comparative analyses of lysophosphatidic acid receptor-mediated signaling CELLULAR AND MOLECULAR LIFE SCIENCES, 2015, 72, 2377-2394 27
2002 K Katoh, K Misawa ichi Kuma K, Miyata T MAFFT: A NOVEL METHOD FOR RAPID MULTIPLE SEQUENCE ALIGNMENT BASED ON FAST …, 2002 16
2019 D Schritt, S Li, J Rozewicki, K Katoh, K Yamashita, W Volkmuth, G Cavet, ... Repertoire builder: high-throughput structural modeling of B and T cell receptors MOLECULAR SYSTEMS DESIGN & ENGINEERING, 2019, 4, 761-768 10
2002 K Katoh, T Miyata Cyclostome hemoglobins are possibly paralogous to gnathostome hemoglobins JOURNAL OF MOLECULAR EVOLUTION, 2002, 55, 246-249 9
1995 K Masuhara, T Ohno, K Hamaguchi, K Katoh, K Kashiwada, S Takahashi, ... Relationship between the therapeutic effects or side-effects and the serum disopyramide or mono-N-dealkylated disopyramide concentration after repeated oral administration of … INTERNATIONAL JOURNAL OF CLINICAL PHARMACOLOGY RESEARCH, 1995, 15, 103-113 6
2020 H Nakamura, H Doi, S Mitsuhashi, S Miyatake, K Katoh, MC Frith, T Asano, ... Long-read sequencing identifies the pathogenic nucleotide repeat expansion in RFC1 in a Japanese case of CANVAS JOURNAL OF HUMAN GENETICS, 2020, 65, 475-480 3
2014 Y Morimoto, S Ishii, J Ishibashi, K Katoh, T Tsujiuchi, N Kagawa, ... Functional lysophosphatidic acid receptors expressed in Oryzias latipes GENE, 2014, 551, 189-200 3
2020 M Lei, D Liang, Y Yang, S Mitsuhashi, K Katoh, N Miyake, MC Frith, L Wu, ... Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer–Giedion syndrome and Cornelia de Lange syndrome-4 JOURNAL OF HUMAN GENETICS, 2020, 1-8 2
2019 S Li, J Wilamowski, S Teraguchi, FJ van Eerden, J Rozewicki, A Davila, ... Structural modeling of lymphocyte receptors and their antigens IN VITRO DIFFERENTIATION OF T-CELLS, 2019, 207-229 2
2014 K Yamada, K Katoh, K Tomii 1P267 application of novel amino acid substitution matrix, MIQS, to the mafft multiple sequence aligner (22c. Bioinformatics: Comparative genomics, poster, the 52nd annual … SEIBUTSU BUTSURI 54 (SUPPLEMENT1-2), S, 2014, 185 1
1994 K Katoh, Y Ohkaru, H Kimura, H Ishii, N Sunahara, Y Ikeda, A Takagi, ... Sandwich-EIA for determination of human lipoprotein lipase (LPL): a combination of the same monoclonal antibody (MAb) cannot sandwich LPL, but that of two distinct MAbs can ATHEROSCLEROSIS, 1994, 109, 69-69 1
2020 S Mitsuhashi, S Ohori, K Katoh, MC Frith, N Matsumoto A pipeline for complete characterization of complex germline rearrangements from long DNA reads GENOME MEDICINE, 2020, 12, 1-17 0
2020 DS Saputri, S Li, FJ Van Eerden, J Rozewicki, Z Xu, HS Ismanto, A Davila, ... Flexible, functional and familiar: characteristics of SARS-CoV-2 spike protein evolution FRONTIERS IN MICROBIOLOGY, 2020, 11, 2112-2112 0
2019 S Mitsuhashi, S Ohori, K Katoh, MC Frith, N Matsumoto A method for complete characterization of complex germline rearrangements from long DNA reads MEDRXIV, 2019, 19006379 0
2017 D Schritt, K Katoh, S Li, DM Standley Modeling Biocatalysts FUTURE DIRECTIONS IN BIOCATALYSIS, 2017, 385-398 0
2015 K Takahashi, K Katoh, N Iwabe Phylogenetic position of ctenophores and early evolution of metazoans GENES & GENETIC SYSTEMS, 2015, 90, 394-394 0
2014 K Takahashi, K Katoh, N Iwabe Molecular phylogenetic analyses of deuterostomes: evolutionary position of cephalochordates GENES & GENETIC SYSTEMS, 2014, 89, 312-312 0
2011 N Iwabe, K Katoh, H Toh, G Sasaki, H Suga, H Nishiyori, N Hirose, ... A study of the evolution of metazoan multicellularity based on comparative genomic analysis: II. Diversification of gene family members GENES & GENETIC SYSTEMS, 2011, 86, 418-418 0
2011 K Kuma, K Katoh, H Toh, G Sasaki, A Fujiyama, T Miyata, N Iwabe A study of the evolution of metazoan multicellularity based on comparative genomic analysis: I. Comprehensive genome comparison of metazoans, choanoflagellates, and other organisms GENES & GENETIC SYSTEMS, 2011, 86, 418-418 0
2009 K Kuma, N Iwabe, K Katoh, H Toh, N Hirose, G Sasaki, H Suga, T Miyata, ... Genome sequencing project of a choanoflagellate, Monosiga ovata: I. Genome structure GENES & GENETIC SYSTEMS, 2009, 84, 449-449 0
2009 N Iwabe, K Kuma, K Katoh, H Toh, N Hirose, G Sasaki, Y Murata, H Suga, ... Genome sequencing project of a choanoflagellate, Monosiga ovata: II. Divergence patterns of gene family members in the early evolution of animals GENES & GENETIC SYSTEMS, 2009, 84, 450-450 0
2006 H Oda, H Toh, K Katoh 2P073 Quantitative analysis of conservation of amino acid residues critical for protein-protein interaction (30. Protein function (II), Poster Session, Abstract, Meeting … SEIBUTSU BUTSURI 46 (SUPPLEMENT2), S, 2006, 314 0
2006 H ICHIHARA, TD SATO, D HOSHIYAMA, K KOJIMA, W NEMOTO, ... Bioinformatics Center ICR ANNUAL REPORT, 2006, 12, 66-67 0
2004 W OBARA, K KATOH, Y SUZUKI, S TANJI, R KONDA, T FUJIOKA Genetic polymorphisms of the vitamin D receptor gene are associated with an increasing risk and a poor prognosis of renal cell carcinoma in a Japanese population BJU INTERNATIONAL-SUPPLEMENT, 2004, 94, 104-105 0
2001 M Koyanagi, K Katoh, N Iwabe, A Terakita, Y Shichida, K Kubokawa, ... CHARACTERIZATION OF CDNA CLONES ENCODING PHOTORECEPTOR PROTEIN (OPSIN) FROM CEPHALOCHORDATE LANCELET (Physiology)(Proceeding of the Seventy-Third Annual Meeting of the … ZOOLOGICAL SCIENCE, 2001, 18, 110-110 0
1994 H Kimura, K Katoh, T Iwanaga, Y Ohkaru, H Ishii, N Sunahara, Y Ikeda, ... New ELISA method for determination of LPL using two distinct monoclonal antibodies ATHEROSCLEROSIS, 1994, 109, 69-69 0
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