Publications by authors named "Takuji Yamada"

90Publications

Intrahepatic cholangiocarcinoma with gastric infiltration misdiagnosed as gastric submucosal tumor.

J Surg Case Rep 2020 Nov 10;2020(11):rjaa359. Epub 2020 Nov 10.

Department of Surgery, Tama-Hokubu Medical Center, Tokyo, Japan.

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http://dx.doi.org/10.1093/jscr/rjaa359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7655014PMC
November 2020

dominates the gut microbiome of the Asian palm civet that produces kopi luwak.

PeerJ 2020 30;8:e9579. Epub 2020 Jul 30.

School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan.

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http://dx.doi.org/10.7717/peerj.9579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7396140PMC
July 2020

Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication.

PeerJ 2020 27;8:e8722. Epub 2020 Mar 27.

School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan.

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http://dx.doi.org/10.7717/peerj.8722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7104724PMC
March 2020

Significance of the gut microbiome in multistep colorectal carcinogenesis.

Cancer Sci 2020 Mar 3;111(3):766-773. Epub 2020 Feb 3.

Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.

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http://dx.doi.org/10.1111/cas.14298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7060472PMC
March 2020

Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis.

DNA Res 2019 Dec;26(6):465-472

Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.1093/dnares/dsz024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6993814PMC
December 2019

Targeted enzyme gene re-positioning: A computational approach for discovering alternative bacterial enzymes for the synthesis of plant-specific secondary metabolites.

Metab Eng Commun 2019 Dec 9;9:e00102. Epub 2019 Sep 9.

School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo, 152-8550, Japan.

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http://dx.doi.org/10.1016/j.mec.2019.e00102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838473PMC
December 2019

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan.

J Vet Med Sci 2019 Oct 12;81(9):1389-1399. Epub 2019 Aug 12.

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.

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http://dx.doi.org/10.1292/jvms.19-0014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6785603PMC
October 2019

FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization.

Bioinformatics 2019 11;35(21):4519-4521

Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btz245DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821421PMC
November 2019

Staging of gastric cancer with the Clinical Stage Prediction score.

World J Surg Oncol 2019 Mar 8;17(1):47. Epub 2019 Mar 8.

Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan.

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http://dx.doi.org/10.1186/s12957-019-1589-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408856PMC
March 2019

Cecal Microbiome Analyses on Wild Japanese Rock Ptarmigans () Reveals High Level of Coexistence of Lactic Acid Bacteria and Lactate-Utilizing Bacteria.

Microorganisms 2018 Jul 28;6(3). Epub 2018 Jul 28.

Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Kyoto Prefecture 606-8522, Japan.

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http://dx.doi.org/10.3390/microorganisms6030077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164970PMC
July 2018

Minor taxa in human skin microbiome contribute to the personal identification.

PLoS One 2018 25;13(7):e0199947. Epub 2018 Jul 25.

School of Life Science and Technology, Tokyo Institute of Technology, Ookayama, Meguro-ku, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199947PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059399PMC
January 2019

iPath3.0: interactive pathways explorer v3.

Nucleic Acids Res 2018 07;46(W1):W510-W513

Department of Biological Information, Tokyo Institute of Technology, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.1093/nar/gky299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031023PMC
July 2018

VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.

BMC Syst Biol 2018 03 19;12(Suppl 2):30. Epub 2018 Mar 19.

Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan.

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http://dx.doi.org/10.1186/s12918-018-0545-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861490PMC
March 2018

A primary tumor of mixed histological type is a novel poor prognostic factor for patients undergoing resection of liver metastasis from gastric cancer.

J Hepatobiliary Pancreat Sci 2017 May 10;24(5):281-288. Epub 2017 Apr 10.

Department of Gastroenterological Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan.

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http://dx.doi.org/10.1002/jhbp.445DOI Listing
May 2017

Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy.

Nephrol Dial Transplant 2017 Dec;32(12):2072-2079

Division of Clinical Nephrology and Rheumatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.

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http://ndt.oxfordjournals.org/content/early/2016/09/27/ndt.g
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http://dx.doi.org/10.1093/ndt/gfw343DOI Listing
December 2017

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development.

Nat Commun 2016 06 24;7:11939. Epub 2016 Jun 24.

Department of Biological Information, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.

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http://dx.doi.org/10.1038/ncomms11939DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4931012PMC
June 2016

Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

J Chem Inf Model 2016 Mar 17;56(3):510-6. Epub 2016 Feb 17.

Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1021/acs.jcim.5b00216DOI Listing
March 2016

Population pharmacokinetics of mizoribine in pediatric patients with kidney disease.

Clin Exp Nephrol 2016 Oct 9;20(5):757-763. Epub 2015 Dec 9.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, 1-2 Osakada, Morioka-cho, Obu, 474-8710, Japan.

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http://dx.doi.org/10.1007/s10157-015-1209-9DOI Listing
October 2016

The transcription factor ATF7 mediates lipopolysaccharide-induced epigenetic changes in macrophages involved in innate immunological memory.

Nat Immunol 2015 Oct 31;16(10):1034-43. Epub 2015 Aug 31.

Laboratory of Molecular Genetics, CREST Research Project of the Japan Science and Technology Agency, RIKEN Tsukuba Institute, Tsukuba, Japan.

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http://dx.doi.org/10.1038/ni.3257DOI Listing
October 2015

Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals.

PLoS One 2015 29;10(6):e0131607. Epub 2015 Jun 29.

Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131607PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487993PMC
April 2016

FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data.

PLoS One 2015 14;10(5):e0126967. Epub 2015 May 14.

Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126967PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4431737PMC
February 2016

A hospital-acquired outbreak of catheter-related nontuberculous mycobacterial infection in children on peritoneal dialysis.

CEN Case Rep 2015 May 20;4(1):43-47. Epub 2014 Jul 20.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, 1-2 Osakata, Morioka-cho, Obu, Aichi, Japan.

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http://dx.doi.org/10.1007/s13730-014-0137-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411622PMC
May 2015

DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.

BMC Bioinformatics 2015 Mar 21;16:96. Epub 2015 Mar 21.

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.

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http://dx.doi.org/10.1186/s12859-015-0499-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389672PMC
March 2015

CLAST: CUDA implemented large-scale alignment search tool.

BMC Bioinformatics 2014 Dec 11;15:406. Epub 2014 Dec 11.

Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.

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http://dx.doi.org/10.1186/s12859-014-0406-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271471PMC
December 2014

Potential of fecal microbiota for early-stage detection of colorectal cancer.

Mol Syst Biol 2014 Nov 28;10:766. Epub 2014 Nov 28.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299606PMC
http://dx.doi.org/10.15252/msb.20145645DOI Listing
November 2014

Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation.

Nat Commun 2014 May 28;5:3978. Epub 2014 May 28.

1] Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan [2] CREST, Japan Science and Technology Agency, Yokohama City, Kanagawa 226-8501, Japan [3] Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan [4] Department of Biological Sciences, Tokyo Institute of Technology, Yokohama City, Kanagawa 226-8501, Japan.

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http://dx.doi.org/10.1038/ncomms4978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052687PMC
May 2014

Classification and quantification of bacteriophage taxa in human gut metagenomes.

ISME J 2014 Jul 13;8(7):1391-402. Epub 2014 Mar 13.

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/ismej.2014.30DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4069399PMC
July 2014

HER2-positive gastric cancer with paraaortic nodal metastasis successfully resected after chemotherapy with trastuzumab: a case report.

Anticancer Res 2014 Feb;34(2):867-72

Department of Chemotherapy and Palliative Care, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan

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February 2014

Orthologous gene clusters and taxon signature genes for viruses of prokaryotes.

J Bacteriol 2013 Mar 7;195(5):941-50. Epub 2012 Dec 7.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1128/JB.01801-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571318PMC
March 2013

Weight-based high- and low-dose ribavirin in combination with peginterferon α-2b therapy for genotype 2 chronic hepatitis C: A randomized trial.

Hepatol Res 2012 Apr 16;42(4):351-8. Epub 2011 Dec 16.

Division of Gastroenterology, Department of Internal Medicine, Tokai University School of Medicine, Isehara Division of Gastroenterology, Department of Internal Medicine, Tokai University Hachioji Hospital, Hachioji Ikegami General Hospital Division of Gastroenterology, Department of Internal Medicine, Tokai University Tokyo Hospital, Tokyo Division of Gastroenterology, Department of Internal Medicine, Tokai University Oiso Hospital, Nakagun Hadano Red Cross Hospital, Hadano Japan Medical Alliance Ebina General Hospital, Ebina Hiratsuka City Hospital, Hiratsuka Tomei-Atsugi Hospital, Atsugi Chigasaki Municipal Hospital, Chigasaki Kanagawa Dental College, Yokosuka, Japan.

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http://doi.wiley.com/10.1111/j.1872-034X.2011.00944.x
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http://dx.doi.org/10.1111/j.1872-034X.2011.00944.xDOI Listing
April 2012

Age effect on whole blood cyclosporine concentrations following oral administration in children with nephrotic syndrome.

Eur J Pediatr 2012 Apr 26;171(4):663-8. Epub 2011 Nov 26.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, 1-2 Osakada Morioka-cho, Obu, Aichi, 474-8710, Japan.

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http://link.springer.com/10.1007/s00431-011-1633-0
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http://dx.doi.org/10.1007/s00431-011-1633-0DOI Listing
April 2012

iPath2.0: interactive pathway explorer.

Nucleic Acids Res 2011 Jul 5;39(Web Server issue):W412-5. Epub 2011 May 5.

EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1093/nar/gkr313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125749PMC
July 2011

Measurements of serum cystatin C concentrations underestimate renal dysfunction in pediatric patients with chronic kidney disease.

Clin Exp Nephrol 2011 Aug 21;15(4):535-8. Epub 2011 Apr 21.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, 1-2 Osakada, Morioka-cho, Obu, Aichi 474-8710, Japan.

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http://dx.doi.org/10.1007/s10157-011-0446-9DOI Listing
August 2011

Enterotypes of the human gut microbiome.

Nature 2011 May 20;473(7346):174-80. Epub 2011 Apr 20.

European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

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http://www-huber.embl.de/pub/pdf/Arumugam_Nature_2011.pdf
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http://www.nature.com/doifinder/10.1038/nature09944
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http://dx.doi.org/10.1038/nature09944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728647PMC
May 2011

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data.

Mol Syst Biol 2011 Mar;7:473

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

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http://dx.doi.org/10.1038/msb.2011.6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094067PMC
March 2011

The ecoresponsive genome of Daphnia pulex.

Science 2011 Feb;331(6017):555-61

Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.

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http://www3.nd.edu/~mpfrende/PDFs/Science-2011-Colbourne-555
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http://www.sciencemag.org/cgi/doi/10.1126/science.1197761
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http://dx.doi.org/10.1126/science.1197761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199PMC
February 2011

Development of a tennis ball-sized tumor at the site of an implanted pacemaker.

J Cardiol Cases 2010 Dec 16;2(3):e151-e153. Epub 2010 Jul 16.

Department of Cardiovascular Medicine, Uji Tokushukai Hospital, 86 Kasugamori, Ogura-cho, Uji-shi, Kyoto 611-0042, Japan.

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http://dx.doi.org/10.1016/j.jccase.2010.06.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265228PMC
December 2010

Reference serum cystatin C levels in Japanese children.

Clin Exp Nephrol 2010 Oct 6;14(5):453-6. Epub 2010 Jul 6.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, 1-2 Osakada, Morioka-cho, Obu, Aichi, 474-8710, Japan.

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http://dx.doi.org/10.1007/s10157-010-0314-zDOI Listing
October 2010

Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.

Authors:
John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne John H Werren Stephen Richards Christopher A Desjardins Oliver Niehuis Jürgen Gadau John K Colbourne Leo W Beukeboom Claude Desplan Christine G Elsik Cornelis J P Grimmelikhuijzen Paul Kitts Jeremy A Lynch Terence Murphy Deodoro C S G Oliveira Christopher D Smith Louis van de Zande Kim C Worley Evgeny M Zdobnov Maarten Aerts Stefan Albert Victor H Anaya Juan M Anzola Angel R Barchuk Susanta K Behura Agata N Bera May R Berenbaum Rinaldo C Bertossa Márcia M G Bitondi Seth R Bordenstein Peer Bork Erich Bornberg-Bauer Marleen Brunain Giuseppe Cazzamali Lesley Chaboub Joseph Chacko Dean Chavez Christopher P Childers Jeong-Hyeon Choi Michael E Clark Charles Claudianos Rochelle A Clinton Andrew G Cree Alexandre S Cristino Phat M Dang Alistair C Darby Dirk C de Graaf Bart Devreese Huyen H Dinh Rachel Edwards Navin Elango Eran Elhaik Olga Ermolaeva Jay D Evans Sylvain Foret Gerald R Fowler Daniel Gerlach Joshua D Gibson Donald G Gilbert Dan Graur Stefan Gründer Darren E Hagen Yi Han Frank Hauser Da Hultmark Henry C Hunter Gregory D D Hurst Shalini N Jhangian Huaiyang Jiang Reed M Johnson Andrew K Jones Thomas Junier Tatsuhiko Kadowaki Albert Kamping Yuri Kapustin Bobak Kechavarzi Jaebum Kim Jay Kim Boris Kiryutin Tosca Koevoets Christie L Kovar Evgenia V Kriventseva Robert Kucharski Heewook Lee Sandra L Lee Kristin Lees Lora R Lewis David W Loehlin John M Logsdon Jacqueline A Lopez Ryan J Lozado Donna Maglott Ryszard Maleszka Anoop Mayampurath Danielle J Mazur Marcella A McClure Andrew D Moore Margaret B Morgan Jean Muller Monica C Munoz-Torres Donna M Muzny Lynne V Nazareth Susanne Neupert Ngoc B Nguyen Francis M F Nunes John G Oakeshott Geoffrey O Okwuonu Bart A Pannebakker Vikas R Pejaver Zuogang Peng Stephen C Pratt Reinhard Predel Ling-Ling Pu Hilary Ranson Rhitoban Raychoudhury Andreas Rechtsteiner Justin T Reese Jeffrey G Reid Megan Riddle Hugh M Robertson Jeanne Romero-Severson Miriam Rosenberg Timothy B Sackton David B Sattelle Helge Schlüns Thomas Schmitt Martina Schneider Andreas Schüler Andrew M Schurko David M Shuker Zilá L P Simões Saurabh Sinha Zachary Smith Victor Solovyev Alexandre Souvorov Andreas Springauf Elisabeth Stafflinger Deborah E Stage Mario Stanke Yoshiaki Tanaka Arndt Telschow Carol Trent Selina Vattathil Eveline C Verhulst Lumi Viljakainen Kevin W Wanner Robert M Waterhouse James B Whitfield Timothy E Wilkes Michael Williamson Judith H Willis Florian Wolschin Stefan Wyder Takuji Yamada Soojin V Yi Courtney N Zecher Lan Zhang Richard A Gibbs

Evolution of biomolecular networks: lessons from metabolic and protein interactions.

Nat Rev Mol Cell Biol 2009 Nov;10(11):791-803

European Molecular Biology Laboratory, Heidelberg, Germany.

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http://www.nature.com/articles/nrm2787
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http://dx.doi.org/10.1038/nrm2787DOI Listing
November 2009

Reference serum creatinine levels determined by an enzymatic method in Japanese children: relationship to body length.

Clin Exp Nephrol 2009 Dec 24;13(6):585-8. Epub 2009 Jul 24.

Department of Pediatric Nephrology, Aichi Children's Health and Medical Center, Obu, Aichi, Japan.

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http://link.springer.com/content/pdf/10.1007/s10157-009-0211
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http://link.springer.com/10.1007/s10157-009-0211-5
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http://dx.doi.org/10.1007/s10157-009-0211-5DOI Listing
December 2009

Quantifying environmental adaptation of metabolic pathways in metagenomics.

Proc Natl Acad Sci U S A 2009 Feb 22;106(5):1374-9. Epub 2009 Jan 22.

Program in Computational Biology and Bioinformatics, Departments of Molecular Biophysics and Biochemistry, Computer Science, and Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1073/pnas.0808022106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2629784PMC
February 2009

[Chronic kidney disease in children].

Nihon Rinsho 2008 Sep;66(9):1814-20

Department of Pediatric Nephrology, Aichi Children' s Health and Medical Center.

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September 2008

Effects of pegylated interferon alpha-2a on hepatitis-C-virus-associated glomerulonephritis.

Pediatr Nephrol 2009 Jan 12;24(1):199-202. Epub 2008 Aug 12.

Department of Pediatrics, Toyohashi Municipal Hospital, 50 Hachiken-nishi, Aotake, Toyohashi, Aichi, 441-8570, Japan.

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http://dx.doi.org/10.1007/s00467-008-0948-1DOI Listing
January 2009

KEGG Atlas mapping for global analysis of metabolic pathways.

Nucleic Acids Res 2008 Jul 13;36(Web Server issue):W423-6. Epub 2008 May 13.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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https://nar.oxfordjournals.org/content/36/suppl_2/W423.full-
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkn282
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http://dx.doi.org/10.1093/nar/gkn282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447737PMC
July 2008

iPath: interactive exploration of biochemical pathways and networks.

Trends Biochem Sci 2008 Mar 13;33(3):101-3. Epub 2008 Feb 13.

EMBL, Meyerhofstrasse 1, Heidelberg, Germany.

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http://dx.doi.org/10.1016/j.tibs.2008.01.001DOI Listing
March 2008

Association of microRNA-34a overexpression with proliferation is cell type-dependent.

Cancer Sci 2007 Dec 19;98(12):1845-52. Epub 2007 Sep 19.

Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.

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http://dx.doi.org/10.1111/j.1349-7006.2007.00619.xDOI Listing
December 2007

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W625-32. Epub 2007 Jun 22.

Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gkm295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933155PMC
July 2007

Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways.

J Chem Inf Model 2007 Jul-Aug;47(4):1702-12. Epub 2007 May 22.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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http://dx.doi.org/10.1021/ci700006fDOI Listing
October 2007

Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes.

Genome Inform 2006 ;17(1):230-9

Bioinformatics center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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July 2007

The repertoire of desaturases for unsaturated fatty acid synthesis in 397 genomes.

Genome Inform 2006 ;17(1):173-83

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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July 2007

Extraction of phylogenetic network modules from the metabolic network.

BMC Bioinformatics 2006 Mar 13;7:130. Epub 2006 Mar 13.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.

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http://dx.doi.org/10.1186/1471-2105-7-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1501048PMC
March 2006

Comprehensive analysis and prediction of synthetic lethality using subcellular locations.

Genome Inform 2005 ;16(1):150-8

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

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January 2006

An odorant-binding protein facilitates odorant transfer from air to hydrophilic surroundings in the blowfly.

Chem Senses 2005 Sep 17;30(7):559-64. Epub 2005 Aug 17.

Human Information Systems, Kanazawa Institute of Technology, 3-1 Yakkaho, Hakusan, Ishikawa 924-0834, Japan.

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http://dx.doi.org/10.1093/chemse/bji049DOI Listing
September 2005

VisANT: data-integrating visual framework for biological networks and modules.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W352-7

Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA.

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http://dx.doi.org/10.1093/nar/gki431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160192PMC
July 2005

Extraction of phylogenetic network modules from prokayrote metabolic pathways.

Genome Inform 2004 ;15(1):249-58

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.

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May 2005

Clustering under the line graph transformation: application to reaction network.

BMC Bioinformatics 2004 Dec 24;5:207. Epub 2004 Dec 24.

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, 611-0011, Japan.

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http://dx.doi.org/10.1186/1471-2105-5-207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC545960PMC
December 2004

Feasibility and effect on blood pressure of 6-week trial of low sodium soy sauce and miso (fermented soybean paste).

Circ J 2003 Jun;67(6):530-4

Department of Hygiene, Hamamatsu University School of Medicine, Japan.

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http://dx.doi.org/10.1253/circj.67.530DOI Listing
June 2003

Essential role of NF-kappa B-inducing kinase in T cell activation through the TCR/CD3 pathway.

J Immunol 2002 Aug;169(3):1151-8

Division of Molecular Immunology, Institute for Enzyme Research, University of Tokushima, Tokushima, Japan.

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http://dx.doi.org/10.4049/jimmunol.169.3.1151DOI Listing
August 2002