updated, 30th, Dec., 2013

What's New!

30, Dec., 2013:A paper "Structural insights of post-translational modification sites in the proteome of Thermus thermophilus" by Ryoji Masui et al is accepted by Journal of Structural and Functional Genomics.

25, Oct., 2013:A paper "Complete genome sequence of the mitochondrial DNA of the river lamprey, Lethenteron japonicum" by Yuri Kawai et al is accepted by Mitochondrial DNA.

10, Sep., 2013:A paper "Molecular and clinical characteristics of MSH6 germline variants detected in colorectal cancer patients" by Hiroko Terui et al is accepted by Oncology Reports.

4, Sep., 2013:A paper "Human Origin Recognition Complex Binds Preferentially to G-Quadruplex-Preferable RNA and Single-Stranded DNA" by Shoko Hoshina et al (Collaborative work with Prof. Shou Waga at JWU) is accepted by The Journal of Biological Chemistry.

6, July, 2013:A paper on RNA editing by Yura and Go is cited by Suzuki, H., et al on Mol. Genet. Genomics.

4, July, 2013:A paper on the relationship between alternative splicing sites and protein 3D structure by Yura, Shionyu, et al. is cited by Buljan, M., et al on Current Opinion in Structural Bioloigy.

28, May, 2013:Ms. Midori Yano in the lab presented a poster on a fast algorithm for extracting protein peculiar structure at ABA2013 at Jeju, South Korea.

28, May, 2013:Prof. Kei Yura presented a computational study on protein-DNA interaction in a workshop at ABA2013 at Jeju, South Korea.

16, Apr., 2013:A paper "CoDP: Predicting the Impact of Unclassified Genetic Variants in MSH6 by the Combination of Different Properties of the Protein" by Hiroko Terui et al is accepted by The Journal of Biomedical Science.

22, Mar., 2013:Graduation ceremonies for undergrads and graduates were taken place. Three undergrad and five graduate students completed the course in this lab. Congratulations.

12, Dec., 2012:A paper "Distinct Conformation of ATP Molecule in Solution and on Protein" by Eri Kobayashi et al is accepted by BIOPHYSICS.

27, Nov., 2012: A paper "A bicyclic 1-deoxygalactonojirimycin derivative as a novel pharmacological chaperone for GM1 gangliosidosis" that Yuki Hirano and Kei Yura are the coauthors is accepted by Molecular Therapy.

1, Oct., 2012: Gopi Kuppuraj joined the lab. as a postdoctral fellow.

21, Aug., 2012: Oda et al., in their manuscript, acknowledged the head of this lab.

6, June, 2012: A postdoctoral position for structural bioinformatics is open (deadline: 6th July, 2012).

10, May, 2012: A paper on DNA photolyase electron transfer by Miyazawa, Nishioka, Yura and Yamato is cited by Hitomi et al. on the Journal of Biological Chemistry.

9, May 2012: A paper "Tuning glycosidase inhibition through aglycone interactions: Pharmacological chaperones for Fabry disease and GM1 gangliosidosis" based on the collaborative research with the medical school of Tottori Univ. is accepted by Chemical Communications.

16, Oct. 2011: A paper of an impact of alternative splicing on protein three-dimensional structures by Kei Yura, Masafumi Shionyu et al. is cited by Satoshi Fukuchi et al. on BMC Structural Biology.

16, Oct. 2011: Prof. Kei Yura will talk in the session "Systems biology, bioinformatics and proteomics" in 17th International Biophysics Congress at Beijing held from 30th Oct. to 3rd Nov.

15, Oct. 2011: The lab. is looking for PhD candidate students interested in computational biology. Anyone who wants to enter the master course or PhD course of computational biology in Ochanomizu Univ., please contact Prof. Kei Yura.

10, Sept. 2011: A paper on RNA editing by Yura K. et al. is cited by Fujii, S. and Small, I.. on New Phytologist.

30, Apr. 2011: The web server will be unstable from May 2 through May 13. The PC cluster of the lab.will be relocated to Kansai area during this period to avoid electric shortage in Tokyo area in this summer.

27, Mar. 2011: A paper on the electron transfer in photolyase by Miyzawa, Y., Nishioka, H., Yura, K. and Yamato, Y. is cited by Lei Yu et al. on Jounal of Nucleic Acids.

16, Mar. 2011: We further reduced the computation power of the lab to less than 20 percent. This may preclude the web server.

9, Mar. 2011: The webserver will be down from 25th through 27th March for system maintenance.

27, Feb. 2011: A paper of an impact of alternative splicing on protein three-dimensional structures by Kei Yura, Masafumi Shionyu et al. is cited by Hedi Hegyi et al. on Nucleic Acds Research.

25, Feb. 2011: A paper of simulation for Integrin structural changes by Atsushi Matsumoto, ..., Kei Yura is cited by Chen et al. on PLoS Computational Biology.

19, Feb. 2011: A paper of Kei Yura related to his PhD thesis is cited by Shiba R. et al., on BIOPHYSICS.

10, Feb. 2011: A paper for improved amino acid sequence alignment by Atsushi Hijikata and Kei Yura et al is accepted by Proteins: Structure, Function, and Bioinformatics.

4, Feb. 2011: A paper for the database of the relationship between RNA editing sites and protein 3D structures by Kei Yura et al is cited by Picardi et al. on Mitochondrion.

23, Jan. 2011: A paper of simulation for Integrin structural changes by Atsushi Matsumoto, ..., Kei Yura is cited by Kamata et al. on JBC.

16, Jan. 2011: A paper of the correlation between RNA editing sites and protein 3D structures by Kei Yura et al is cited by Cuenca et al. on BMC Evolutionary Biology.

12, Jan. 2011: A paper of Takakia chloroplast RNA editing by Kei Yura and Yuki Miyata is cited by Salmans et al. on Current Genetics.

11, Jan. 2011: Kei Yura is invited as a speaker of the third symposium in the 7th Asian Biophysics Association Symposium at New Delhi, India.

22, Dec. 2010: Ms. Emi Kuninaga and Kei Yura participated in Ewha Womans Univ.-Japan Women's Univ.-Ochanomizu Univ. Joint Sympoisum 2010 at Ewha Womans University, Seoul.

10, Nov. 2010: A paper by Kei Yura et al. of the status of structural genomics is cited by a Review paper of Chruszcz et al. on Current Opinion on Structural Biology.

17, Oct. 2010: A paper by Kei Yura and Steven Hayward of the interwound nature of protein-protein interface is cited by a Review paper of Perkins et al. on Structure.

12, Sept. 2010: A paper of the relationship between RNA editing sites and protein 3D structures from Yura lab is cited by Sloan et al. on Genetics.

01, Aug. 2010: The lab accepts a graduate student from the bioinformatics course in King Mongkutfs University of Technology for two months.

19, June 2010: A paper of RNA binding residue prediction by Prof. Yura is cited by Liu et al. on Bioinformatics.

14, June 2010: A paper of the interwinding nature of protein-protien interface by K. Yura and S. Hayward is cited by Patil et al. on Int. J. Mol. Sci..

14, June 2010: A paper of the relationship between RNA editing sites and protein 3D structures from Yura lab is cited by Sloan et al. on Genetics.

14, June 2010: A paper of the relationship between RNA editing sites and protein 3D structures from Yura lab is cited by Traphagen et al. on RNA.

14, June 2010: A paper of the relationship between RNA editing sites and protein 3D structures from Yura lab is cited by Picardi et al. on Ncleic Acids Res.

05, May, 2010: Prof. Kei Yura is acknowledged in "The Effect of End Constraints on Protein Loop Kinematics" by Steven Hayward and Akio Kitao.

24, Apr., 2010: DNA space-filling plastic model was built in the lab. We felt the structure and improved understanding of DNA.

10, Apr., 2010: Prof. Kei Yura is invited as a lecturer at the 15th Joint Biophyscs Conference at Taipei from 19th to 21st of May, 2010.

12, Mar., 2010: The members of the lab in school year 2010 are determined.

6, Mar., 2010: Prof. Kei Yura is going to have an intensive course on protein comparative modeling at Ewha Womans University, South Korea from 22nd to 24th, March.

5, Mar., 2010: Prof. Kei Yura is going to have an intensive course on protein comparative modeling at University of East Anglia, Britain from 15th to 17th, March.

27, Feb., 2010: Our paper on Genome-wide protein comparative modelling was cited by Hrmova and Fincher. (2009) on Plant Genomics.

17, Jan., 2010: Professor Kei Yura takes a chairperson ship in Beyond-Omics session in JFFoS 2009 at Futuroscope, France. His recent research will also bo presented in the poster session.

27, Dec., 2009: Miyazawa, Y. et al. (2008) on electron pathway of DNA photolyase was cited by Damiani, M.J. et al (2009) on Biochemistry.

13, Dec., 2009: KYG, RNA-binding residue prediction, is updated. A tool to use KYG from Linix command line is described in FAQ.

01, Dec., 2009: Prof Kei Yura will talk about his recent work and eduction system of computational biology in the university in the workshop, Bioinformatics beyond Omics Data Analyses.

18, Nov., 2009: The paper by Kei Yura and Steven Hayward about interwinding nature protein-protien interface is on Bioinformatics (Dec. 1st issue).

14, Nov., 2009: The paper of RESOPS, RNA editing site database, on Plant & Cell Physiology is selected as Editor-in-Chief's choice.

14, Nov., 2009: The web server will be down from 21:00, 22nd, Nov. to 21:00, 24th, Nov. for the system maintenance.

12, Nov., 2009: The manuscript "RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures" by Yura, Sulaiman et al. is pubished on the November issue of Plant and Cell Physiology.

19, Oct., 2009: Our paper on RNA interface prediction for RNA-binding proteins was cited by Pérez-Cano and Fernández-Recio (2009) on PROTEINS.

11, Oct., 2009: The lab has new members.

10, Oct., 2009: A paper by Matsumoto, et al. was cited by Jian-Ping Xiong et al. (2009) "Crystal structure of the complete integrin alphaVbeta3 ectodomain plus an alpha/beta transmembrane fragment" on the Journal of Cell Biology.

25, Sep., 2009: The manuscript "The interwinding nature of protein-protein interfaces and its implication for protein complex formation " by Yura and Hayward is accepted by Bioinformatics.

25, Sep., 2009: The manuscript "RESOPS: A Database for Analyzing the Correspondence of RNA Editing Sites to Protein Three-Dimensional Structures" by Yura, Sulaiman et al. is accepted by Plant and Cell Physiology.

20, Sep., 2009: Prof. Kei Yura gave a talk in Asian workshop for Protein Structure Prediction Methodology at KIAS, Korea from 18th to 19th, Sept.

13, Sep., 2009: A paper by Kei Yura and Mitiko Go was cited by Sung-Ryul Kim et al. (2009) "Rice OGR1 encodes a pentatricopeptide tepeat-DYW protein and is essential for RNA editing in mitochondria" on the Plant Journal.

29, Aug., 2009: RESOPS: the Database for plant organelle RNA editing site is now fully functional. The manuscript explaining the detail of RESPOS is submitted.

6, Aug., 2009: Prof. Chai Lihong from Institute of Nuclear Agricultural Sciences, Zhejiang University visits the lab for collaborative work on DNA repair proteins from 3rd to 7th of August.

20, July, 2009: Database for plant organelle RNA editing site is coming to complete and is now available on the lab server. The manuscript for the database is in preparation.

07, July, 2009: Prof. Kei Yura will give a talk on "The interwinding nature of protein-protien interfaces and its implication for protein complex formation" at International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function on 14th July, 2009.

27, June, 2009: A paper by Kim OTP et al. was cited by Zhou P. et al. (2009) "Geometric similarity between protein-RNA interfaces" on Journal of Computational Chemistry.

20, June, 2009: A paper by Yura K et al. was cited in Chapter 2: The Impact of Structural Proteomics on Macromolecular Structure Databases of "Structural Proteomics and Its Impact on the Life Sciences" published by World Scientific.

23, May, 2009: The lab welcomes internshinp graduate students (up to 90 days) from abroad. A graduate school student who is interested in the computational biology in this lab can conatct prof. Kei Yura and seek the chance. The expenditure for the accommodation in Japan may be covered by the grant of this lab.

8, May, 2009: A paper by Yura, K. Miyata, Y. et al. is cited by Du, P. et al (2009) in BMC Bioinformatics.

5, May, 2009: A paper by Kim OTP et al., a previous collaborator is extensively cited by Fan-Minogue et al (2008) in Molecular Cell.

30, Apr, 2009: A little progress in web tools built by the members. The tools are found here. Anyone interested in building new computational biology tools for protein structures as undergraduate thesis or graduate master course thesis, conatct Prof. Kei Yura.

25, Apr, 2009: Positions for graduate (master/PhD) students are open. Plese contact Prof. Kei Yura. The entracne exams will be held in the summer and the course starts in the coming Oct. or Apr.

16, Apr, 2009: Graduate class "Computational Biology" starts 16th, April (15:00 - 16:30). This is a bookreading class. The book this year is "Gregory A Petsko & Dagmar Ringe: Protein Structure and Function." Class homepage is here (password protected).

03, Apr, 2009: Invited talk by Prof. Kei Yura at the 9th Annual Meeting of the Protein Science Society of Japan (20th May, 2009) .

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