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Author Details

Takuji Yamada
Tokyo Institute of Technology
2004
68
35
PMIDPaper TitleJournal TitlePublished Year
34969979Variation and transmission of the human gut microbiota across multiple familial generations.Nat Microbiol2022
33469050The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds.Sci Rep2021
33868815The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites.PeerJ2021
34912870Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis.Front Cardiovasc Med2021
34789871Reporting guidelines for human microbiome research: the STORMS checklist.Nat Med2021
34622235Identification of <i>Faecalibacterium prausnitzii</i> strains for gut microbiome-based intervention in Alzheimer's-type dementia.Cell Rep Med2021
34102245Metagenomic analysis of gut microbiota reveals its role in trimethylamine metabolism in heart failure.Int J Cardiol2021
34224861Analysis of genomic characteristics and their influence on metabolism in Aspergillus luchuensis albino mutants using genome sequencing.Fungal Genet Biol2021
32257635Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication.PeerJ2020
31910311Significance of the gut microbiome in multistep colorectal carcinogenesis.Cancer Sci2020
31953253Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles.Gut2020
32747669A possible beneficial effect of Bacteroides on faecal lipopolysaccharide activity and cardiovascular diseases.Sci Rep2020
32581149Metabolomic LC-MS/MS analyses and meta 16S rRNA gene analyses on cecal feces of Japanese rock ptarmigans reveal fundamental differences between semi-wild and captive raised individuals.J Vet Med Sci2020
32821539<i>Gluconobacter</i> dominates the gut microbiome of the Asian palm civet <i>Paradoxurus hermaphroditus</i> that produces kopi luwak.PeerJ2020
31171880Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer.Nat Med2019
31755931Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis.DNA Res2019
31695050Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water.Sci Rep2019
31720217Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites.Metab Eng Commun2019
31664237Author Correction: Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.Nat Med2019
31406033Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan.J Vet Med Sci2019
31004476FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization.Bioinformatics2019
30936548Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.Nat Med2019
30936547Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.Nat Med2019
29560821VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.BMC Syst Biol2018
30044822Minor taxa in human skin microbiome contribute to the personal identification.PLoS One2018
30060588Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans (<i>Lagopus muta japonica</i>) Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria.Microorganisms2018
30487369Gut Microbiome and Plasma Microbiome-Related Metabolites in Patients With Decompensated and Compensated Heart Failure.Circ J2018
30571343Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis.Circulation2018
29718427iPath3.0: interactive pathways explorer v3.Nucleic Acids Res2018
27683270Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy.Nephrol Dial Transplant2017
26822930Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.J Chem Inf Model2016
27562257High-affinity monoclonal IgA regulates gut microbiota and prevents colitis in mice.Nat Microbiol2016
27340192High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy.Gut2016
27340092A key genetic factor for fucosyllactose utilization affects infant gut microbiota development.Nat Commun2016
25974630FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.PLoS One2015
25888481DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.BMC Bioinformatics2015
24621522Classification and quantification of bacteriophage taxa in human gut metagenomes.ISME J2014
25495907CLAST: CUDA implemented large-scale alignment search tool.BMC Bioinformatics2014
25432777Potential of fecal microbiota for early-stage detection of colorectal cancer.Mol Syst Biol2014
24997787Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes.Nat Biotechnol2014
24865297Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.Nat Commun2014
23222723Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.J Bacteriol2013
23929476Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4.Genome Announc2013
22569339Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.Mol Syst Biol2012
21508958Enterotypes of the human gut microbiome.Nature2011
21546551iPath2.0: interactive pathway explorer.Nucleic Acids Res2011
21292972The ecoresponsive genome of Daphnia pulex.Science2011
21407210Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.Mol Syst Biol2011
20075255Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.Science2010
30532817Development of a tennis ball-sized tumor at the site of an implanted pacemaker.J Cardiol Cases2010
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Collaborators

Peer Bork
University of Wurzburg
Co-authored papers 22
Minoru Kanehisa
Co-authored papers 13
Jeroen Raes
KU Leuven - University of Leuven
Co-authored papers 8
Manimozhiyan Arumugam
Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen
Co-authored papers 8
Ivica Letunic
Co-authored papers 6
Georg Zeller
Max Planck Institute for Developmental Biology
Co-authored papers 6
Tatsuhiro Shibata
Kurume University School of Medicine
Co-authored papers 5
Nicola Segata
University of Trento
Co-authored papers 5
Levi Waldron
City University of New York School of Public Health
Co-authored papers 4
S??ren Brunak
Novo Nordisk Foundation Center for Protein Research, University of Copenhagen
Co-authored papers 3
Marc G??ell
Universitat Pompeu Fabra
Co-authored papers 3
Torben Hansen
Co-authored papers 3
Jean Muller
INSERM, Universite de Strasbourg
Co-authored papers 3
Oluf Pedersen
Co-authored papers 3
Francesco Beghini
University of Trento
Co-authored papers 3
Anne-Claude Gavin
Co-authored papers 3
Edoardo Pasolli
University of Naples Federico II
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Vera van Noort
Leiden University, Institute of Biology Leiden
Co-authored papers 3
Jean Weissenbach
Institut Francois Jacob, CNRS, Universite Paris-Saclay
Co-authored papers 3
Emmanuel Dias-Neto
A.C. Camargo Cancer Center
Co-authored papers 2
Jeong-Hyeon Choi
National Marine Biodiversity Institute of Korea
Co-authored papers 2
Alexandre Souvorov
Co-authored papers 2
Andreas Rechtsteiner
University of California
Co-authored papers 2
Shuichi Kawashima
Database Center for Life Science, Joint Support-Center for Data Science Research
Co-authored papers 2
Zhenjun Hu
Co-authored papers 2
Don Gilbert
Indiana University
Co-authored papers 2
Zachary D Smith
University of Maryland Baltimore County
Co-authored papers 2
Jo??o C Setubal
Chemistry Institute, Universidade de Sao Paulo - USP
Co-authored papers 2
Jacqueline A Lopez
University of Notre Dame
Co-authored papers 2
Evgenia V Kriventseva
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