The 20th In Silico Megabank Research Seminar will be held on Tuesday, December 18. This Time, we will be welcoming Dr. Edgar Wingender, University Medical Center Göttingen as our lecturer, and he will be speaking on “Construction and analysis of gene regulatory networks.”

・Date/Time: December 18(Tues.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization    http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Construction and analysis of gene regulatory networks: The continuation of the TRANSFAC concept
・Lecturer: Edgar Wingender（Dept. of Bioinformatics, University Medical Center Göttingen, Göttingen, Germany）
・Language:　English

・Abstract:
The database TRANSFAC, which represents sequence-specific regulatory DNA-protein interactions in their different aspects, became a gold-standard in the field of gene expression analysis during the last twenty years. It has provided the basis for approaches to detect potential transcription factor binding sites in genomic sequences, which have been systematically exploited to generate transcriptional networks. It could be shown that combining this approach of pattern-based TFBS prediction with a multi-genome conservativity analysis enables to identify a set of highly relevant TF-target interactions.

The systematic collection of transcription factors (TFs) also helped establish a comprehensive classification of TFs according to their DNA-binding domains. This classification (TFClass) has been recently updated and profoundly revised (http://tfclass.bioinf.med.uni-goettingen.de/). It proved useful in identifying groups of paralogous TFs among which information about DNA-binding specificities and predicted target genes can be passed on to the paralogs. The networks obtained by such “paralogous expansion” provided a suitable basis for reconstructing tissue-specific transcription networks with interesting features.

The transcriptional networks thus constructed have been extended to gene regulatory networks by including micro-RNAs as another important player, both with regard to their targets (TF- and non-TF genes), as well as their own transcriptional regulation by TFs. Comparing the tissue-specific gene regulatory networks of a number of different tissues exhibited typical properties for individual and groups of tissues.

・Organizer: Takako Takai

The 19th In Silico Megabank Research Seminar will be held on Friday, December 14.

・Date/Time: December 14(Fri.) 17:00‐
・Venue: Seminar Room 303 (3F), Research Building No.3, Electrical Engineering and plied Physics
http://www.megabank.tohoku.ac.jp/english/info/access.html
・Title: Robust Sparse Regression Modeling
・Lecturer: Heewon Park (Chuo University)
・Abstract:
The L1 type of the regularization technique, which has been attracting attention recently, has the advantage in that presumption and the variable selection can be performed simultaneously by adding a L1 type of penalty to the likelihood function, and it is especially effective to analyze high-dimensional data including the genomic data. In this study, I introduce an effective algorithm for the analysis of the genomic data and propose a variety of robust sparse regression modeling techniques based on the L1 type of the regularization technique that is more effective than any existing research. As a result of verifying the proposal technique utilizing a numerical experiment, the effectiveness of it has become clear compared with existing techniques.

・Organizer: Masao Nagasaki

Prof. Masao Nagasaki will give an invited talk at 2012 Bilateral Workshop between Tohoku University and National Tsing Hua University.

・Date/Time:  December 12, 2012
・Place: Akiu Resort Hotel Sakan　http://www.sakan-net.co.jp/en/access/index.html
・Language: English
・Title: Data Management and Bioinformatics of High Throughput Sequencing Data on the Massive Parallel Supercomputer Environment and Future
http://www.smapip.is.tohoku.ac.jp/~dex-smi/2012/BW-Tohoku-TsingHua-201212/

The 18th In Silico Megabank Research Seminar will be held on Friday, November 30.

・Date/Time: November 30(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Lecturer: Yukuto Sato (National Institute of Genetics)
・Title: Evolutionary Conserved Feature of Mitochondrial Genome : a New Insight into  Functional Impairment and Disorder

・Abstract:
Although mitochondrial gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years, the functional nature of such long-term persistence has yet to be defined over the past 20 years. We analyzed mitochondrial genome by sequence comparison, focusing on translation and replication. The result showed that the tRNA genes used more frequently for translation are more likely to be located in high expression regions (r = -0.1260, p = 0.0104, n = 336), and the regions spend in the single-stranded state during replication for a longer time are richer in G and T bases in the anti-codon regions. (r = 0.4281 p = 0.0234, n = 22).
This result indicates that arrangement of genes in mitochondrial genome is rational for both efficiency of translation and prevention of loss of function of tRNA during replication, and also provides a new insight into impairment of genome function caused by de novo mutations.

The 17th In Silico Megabank Research Seminar will be held on Friday, November 16.

・Date/Time: November 16(Fri.) 17:00‐18:30
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization

・Title: Type 2 diabetic patients’ intestinal bacterial flora that is uncovered by the meta-genome-wide related analysis
・Lecturer: Shujiro Okuda (Ritsumeikan University)

・Abstract:
Type 2 diabetes is a kind of endocrine disease which has been rapidly increasing in the number of patients all over the world now.
In this study, I conducted a comparative study of the intestinal bacterial flora of the type 2 diabetic patients and that of the healthy persons using a new technique of meta-genome-wide related analysis. As a result, a number of markers related to type 2 diabetes were successfully identified. In addition, a possibility was suggested that type 2 diabetes could be diagnosed using these markers. From now on, a possibility of diagnosis and medical treatment with an application of the meta-genome-wide related markers to the other diseases is highly expected.
In general, meta-genome analysis generally requires high-speed sequence determination capability such as a next-generation sequencer, but it is still expensive and the process is also complicated.
I will also introduce a virtual meta-genome constructive method which does not need such a meta-genome sequence determination.

Tohoku University Graduate School of Medicine is going to hold an explanatory session of Graduate School as follows. This session will also include a talking session with graduate students, presentation of the past tests, and distribution of the application guidebook. We are really looking forward to your active participation.

Date/Time: December 1(Sat.) 13:30‐15:30
Venue: Lecture Room 1, Building #1, Tohoku University School of Medicine

・The past tests will be presented from 13:00 to 13:30 and after the end of the session until 16:00.
・The time for visiting a laboratory is allocated after the end of the session.
・Please be advised that you should make a direct contact with the field you hope to visit in advance.

・Neither prior application nor participation fee is necessary.
・Since parking lot is not available, visitors are encouraged to use public transportation.

・You can see a video clip of a part of the last session on the website.http://www.med.tohoku.ac.jp/mov/intro/index.html

“The 16th In Silico Megabank Research Seminar” will be held on Friday, November 2. The discussion will focus mainly on disease-related databases. So if you are interested, please don’t hesitate to attend the session.

・Date/Time: November 2(Fri.) 16:00‐18:00
・Venue: Conference Room 1 (2F), Tohoku Medical Megabank Organization
・Lecturer: Asako Koike　(Hitachi CRL)

Title: Title: An approach of sharing information about disease-related polymorphisms/mutation information in the integrated promotion program

Abstract: In order to prevent the dissipation of recently increasing disease-related polymorphisms/mutation information as well as to share the information among the researchers, our group (The University of Tokyo Hospital, National Institute of Genetics, and Hitachi CRL) has established “Human/GWAS DB (https://gwas.biosciencedbc.jp/)” and started deposition and redistribution of GWAS/NGS variation data. In these DBs, not only GWAS data or SNV of both healthy and diseased individuals but also the insertion/deficiency of the long sequence and conformation polymorphism are the targets of collection, which aim systematization of the relation between the variations and the phenotypes (disease, medical response, and virus tolerance) of the Japanese/Asians. The presentation will outline the bias caused by experimental methods/calculation methods and the characteristics of variations of every disease, and will also introduce the originally-developed sequence analysis/genetic statistics technology.

「XiP: a computational environment to create, extend, and share workflows 」
Masao Nagasaki; Andre Fujita; Yayoi Sekiya; Ayumu Saito; Emi Ikeda; Chen Li; Satoru Miyano

Abstract:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts630?
ijkey=DXtNf2vgjT88PNG&keytype=ref

PDF:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/bts630?
ijkey=DXtNf2vgjT88PNG&keytype=ref

“Database Workshop for Drug Development”, the 2nd database workshop in 2012, will be held in November 3, 2012.
For more details, click here.
Please be noted that Prof. Masao Nagasaki of our institution will give a lecture in the workshop.

Date/Time： November 3, 2012 10:00-17:00
Venue：IT Educational Facilities (6F), Building #4, Tohoku University School of Medicine

Prof. Masao Nagasaki will give a special lecture on Network Medicine.
Please don’t hesitate to join the heated discussion regardless of whether you are student or not.

・Date/Time: October 19(Fri.) 17:30‐
・Venue: Room #201 (2F), Building #5, Tohoku University School of Medicine
・Title: Present situation and issues of bioinformatics analysis of high performance sequence data

・Abstract:
10 years after the age when researchers all over the world focused on a target human genome, the big advances in sequencing technique allow us to face a new age when one can easily read a gigantic genome from a blood sample using handy sequencer, namely the age of gigantic genome data.
This lecture presents an overview of the basic single nucleotide polymorphism of the next generation sequence data, the flow of human genome re-sequencing bioinformatics analysis such as structural mutation analysis, and the issues in the current re-sequencing data. Regarding the data computed by the international cancer genome consortium (ICGC) which is the international joint research with which the lecturer has been concerned, the lecture also outlines on what kind of scale and how the data has been processed/managed on the supercomputer and on what kind of time scale the data has been analyzed, sharing the experiences of Mr. Nakagawa, the team leader of the biomarker research and development team of ICGC, and Dr. Seishi Ogawa of University of Tokyo Medical School regarding the calculation resources used in the entire genome analysis and the exome analysis.