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A new paper about human genome contamination

September 12th, 2016 | Posted by Nobuo Obi in Paper - (Comments Off on A new paper about human genome contamination)

We published a new paper about human contamination in assembled genome sequences of various organisms that have been registered in public databases.
Kryukov K, and Imanishi T (2016) Human contamination in public genome assemblies. PLoS One 11(9): e0162424. Web PDF

Our new paper about VaDE database published

November 7th, 2014 | Posted by Tadashi Imanishi in Database | Paper - (Comments Off on Our new paper about VaDE database published)

Our new paper about VaDE database was published in Nucleic Acids Research.

Nagai Y†, Takahashi Y†, and Imanishi T* (2014) VaDE: a manually-curated database of reproducible associations between various traits and human genomic polymorphisms. Nucleic Acids Research, Database Issue 2014;43(Database issue):D868-72. doi: 10.1093/nar/gku1037.

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Medical School Students Visited Our Laboratory

September 6th, 2014 | Posted by Tadashi Imanishi in News - (Comments Off on Medical School Students Visited Our Laboratory)

Four students of Tokai University School of Medicine visited our laboratory for a week to experience basic research activities. They joined the journal club, and analyzed personal genome sequences using computers.

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VaDE version 1.3 was released.

August 26th, 2014 | Posted by Tadashi Imanishi in Database - (Comments Off on VaDE version 1.3 was released.)

A new version of VaDE database was released.

  • Added association data for type 2 diabetes based on manual curation
  • Counted the correct number of statistically significant studies in each paper
  • Altered the way of reproducibility assessment based on significant studies

URL: http://bmi-tokai.jp/VaDE

VarySysDB Disease Edition (VaDE) version 1.2 was released.

June 26th, 2014 | Posted by Yoko Nagai in Uncategorized - (Comments Off on VarySysDB Disease Edition (VaDE) version 1.2 was released.)

We released VarySysDB Disease Edition (VaDE) version 1.2.

  • New URL is http://bmi-tokai.jp/VaDE/.
  • Released genome browser and supported Japanese language.
  • Data update: Add association data of hypertention and rheumatoid arthritis that is manually curated by our team.
  • Enhancements: Enhanced record click function to show detail information, search system, categorized trait search system, and inner-links.
  • Bug fixes: Fixed outer-link URL.

A New Database of “Reproducible” Disease-Associated Genomic Polymorphisms Launched

April 24th, 2014 | Posted by Yoko Nagai in News - (Comments Off on A New Database of “Reproducible” Disease-Associated Genomic Polymorphisms Launched)

We developed a new database of genomic polymorphisms that are “reproducibly” associated with disease risks, drug responses and other traits by comprehensively extracting information from many scientific papers, and released it as “VarySysDB Disease Edition (VaDE)”. The VaDE database contains detailed information of disease-associated genomic polymorphisms that have been confirmed by multiple, independent studies for each human population. For example, users can search, show and download all the disease-associated genomic polymorphisms that are reproduced in the East Asian population. VaDE also provides functional information and linkage disequilibria of the polymorphic genomic sites. While genomic polymorphisms are being widely used in researches for predicting disease risks, our database can provide reliable sets of disease-associated genomic polymorphisms with the firm evidence.

The VaDE database is accessible temporarily from here. Your feedback is highly appreciated and will help us to improve our database in the future.

This database project is partially supported by JSPS KAKENHI, Grant-in-Aid for Publication of Scientific Research Results (Grant Numbers 258055 and 268046) in 2013-2014.

October 4th, 2013 | Posted by Kirill Kryukov in Uncategorized - (Comments Off on )

Biomedical Informatics Laboratory
(Imanishi Laboratory)

Department of Molecular Life Science
Division of Basic Medical Science and Molecular Medicine
Tokai University School of Medicine

Towards genome-based medicine

In our laboratory starting on October 2012, we aimed to study on bioinformatics and comparative genomics including human genomes towards the genome-based medicine. For this purposes, we are working on various projects including endogenous hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC), retrovirus databases, evolution of multigene families (Fox, IFNL, IFNT, etc).

Last modified on October 4, 2013.
Created on October 3, 2013.